Readme.md

Table of Contents

• pmid-neuroscien-set.txt : Contains the pmid of 20 articles.
• main.py: Python code for extracting abstract, title from the XML files.
• abstract.txt : Contains the pmid(UI), title(TI) and abstract(AB) of 20 articles which was extracted from the XML file.
• mesh_terms.txt: Contains the mesh terms which was obtained after running the Web API.

1. PMID: 28303019

Mesh Terms	Mesh Terms(Web API)
Animals
Electrophysiology
Neuroanatomy
Neuroimaging
Optogenetics/ trends
Neurosciences/ trends
Neurosciences/ methods*	*Neuroscience
Optogenetics/ methods*	*Optogenetics
	Rod Opsins
	Opsin
	Brain

2. PMID: 29096079

Mesh Terms	Mesh Terms(Web API)
Neurons / physiology*	*Neurons
Signal Transduction / physiology*	*Signal Transduction
Neurosciences / trends*	*Neuroscience
Cytoskeleton / physiology*
Neurosciences / methods
Humans
Animals
Cell Biology / trends*
	Organelle
	*Biological Processes
	Protein Transport

3. PMID: 29432512

Mesh Terms	Mesh Terms(Web API)
Psychoanalysis / history*	Psychoanalysis
Psychoanalytic Theory	Psychoanalytic Theory
Emotions	*Emotions
Psychoanalytic Therapy / trends	Psychoanalytic Therapy
Neurosciences / trends	Neuroscience
Humans
History, 19th Century
History, 21st Century
History, 20th Century
Psychology / history
Psychoanalysis / trends
Neurosciences / history*
Interdisciplinary Communication*
	Neurobiology
	Memory
	Empathy
	Motivations

4. PMID: 29460160

Mesh Terms	Mesh Terms(Web API)
Humans	Humans
Human Experimentation / history*	Human Experimentation
Neurosciences / history*	*Neuroscience
History, 20th Century
Neurosciences / ethics
Human Experimentation / ethics
	Informed Consent
	Nazi
	Ethics, Medical
	Morals

5. PMID: 29924477

Mesh Terms	Mesh Terms(Web API)
Humans	Humans
Animals	Animals
Neurosciences / trends*	*Neuroscience
Brain Mapping*	Brain Mapping
Brain / anatomy & histology	Brain
Brain / diagnostic imaging
Brain / physiology*
Electroencephalography
Neurosciences / history*
Magnetic Resonance Imaging
History, 20th Century
History, 21st Century
	Functions, Cognitive
	Cerebral Cortex
	Electrical Stimulation

6. PMID: 29766913

Mesh Terms	Mesh Terms(Web API)
Humans	Humans
Telemedicine / methods*	*Telemedicine
Neurosciences / methods*	*Neurosciences
Telemedicine / trends*
Neurosciences / trends*
	India
	Videoconferencing
	Delivery, Healthcare

7. PMID: 29110344

Mesh Terms	Mesh Terms(Web API)
Brain / metabolism*	*Brain
Energy Metabolism*	*Energy Metabolism
Neurosciences / methods*	Neuroscience
Neurosciences / methods*	*Neurochemistry
Humans
Animals
	Neurology
	Molecular Biology
	Neurons
	Cells, Glial

8. PMID: 29096071

Mesh Terms	Mesh Terms(Web API)
Neurosciences / trends*	*Neuroscience
Brain / cytologyh	Brain
Neuronal Plasticity / physiology*	Neuronal Plasticity
Neurobiology / trends*
Humans
Brain / physiology*
Animals

9. PMID: 29121942

Mesh Terms	Mesh Terms(Web API)
Humans	Humans
Brain-Computer Interfaces / ethics*	*Brain-Computer Interfaces
Communication Aids for Disabled / ethics*	Communication Aids for Disabled
Electroencephalography	Electroencephalography
User-Computer Interface	User-Computer Interface
Brain Diseases / rehabilitation
Brain-Computer Interfaces / trends
Biomedical Research / ethics*
Communication Aids for Disabled / trends
Ethics, Research
Neurosciences / ethics*
Neurosciences / trends*
Personhood
	Brain
	Amyotrophic Lateral Sclerosis

10. PMID: 27634721

Mesh Terms	Mesh Terms(Web API)
Reproducibility of Results	Reproducibility of Results
Neurosciences / ethics*	Neurosciences
Neuroimaging / ethics*	Neuroimaging
Morals*	Morals
Brain / diagnostic imaging*	Brain
Intention*	Intentions
Social Responsibility*	Social Responsibility
Trust
Humans
Neuroimaging / methods
Neurosciences / legislation & jurisprudence*
Criminal Behavior*
	Criminal Law
	*Social Behavior
	Crime

11. PMID: 30980031

Mesh Terms	Mesh Terms(Web API)
Animals	Animals
Mice	Mice
Humans	Humans
Silicon / chemistry*	*Silicon
Neurosciences / instrumentation*	Neurosciences
Neurons / cytology	Neurons
Nanotechnology / instrumentation*	Nanotechnology
Brain / cytology	Brain
Cells, Cultured
Equipment Design
Neurons / physiology
Neurosciences / methods*
Photic Stimulation / instrumentation*
Rats
	Action Potentials

12. PMID: 30731065

Mesh Terms	Mesh Terms(Web API)
Neurosciences / ethics*	*Neuroscience
Bioethics
Humans
National Institutes of Health (U.S.) / ethics*
National Institutes of Health (U.S.) / standards
Neurosciences / methods
Neurosciences / organization & administration
Practice Guidelines as Topic
United States
	*Brain
	*Drive
	Electric Power Supplies

13. PMID: 31260438

Mesh Terms	Mesh Terms(Web API)
Brain / anatomy & histology*	*Brain
Brain / diagnostic imaging	Brain Mapping
Humans	Humans
Image Processing, Computer-Assisted / methods	Image Processing, Computer-Assisted
Medical Informatics / methods*	Medical Informatics
Neurosciences / methods*	*Neuroscience
Technology / methods*	*Technology
Medical Informatics / trends
Neurosciences / trends
Reproducibility of Results
Technology / trends
Diagnostic Imaging / methods

14. PMID: 27637950

Mesh Terms	Mesh Terms(Web API)
Brain*	Brain
Humans	Humans
Neurosciences / methods*	*Neuroscience
Population Dynamics*
Gene-Environment Interaction*

15. PMID: 28250055

Mesh Terms	Mesh Terms(Web API)
Humans	HCRT protein, human
Neurons / metabolism*	*Neurons
Orexins / physiology*	*Orexins
Neurosciences / history
Neurosciences / trends*
Orexins / history
Periodicals as Topic* / history
Periodicals as Topic* / trends
Animals
Brain / metabolism*
History, 20th Century
History, 21st Century
	Neuropeptides
	Wakefulness
	Intracellular Signaling Peptides and Proteins
	Hypothalamus

16. PMID: 29547172

Mesh Terms	Mesh Terms(Web API)
Academies and Institutes	Academies and Institutes
Humans	Humans
India	India
Nervous System Diseases* / history	Nervous System Diseases
Neurology / history*	*Neurology
Neurosciences / history*	Neurosciences
Neurosciences / methods
Photography
Neurology / methods*
Nervous System Diseases* / therapy
Nervous System Diseases* / diagnosis
History, 19th Century
History, 20th Century
History, 21st Century
	United States
	Societies, Medical
	National Institute of Mental Health
	Faculty
	Government

17. PMID: 30720413

Mesh Terms	Mesh Terms(Web API)
Bioethical Issues	Bioethical Issues
Humans	Humans
Neurosciences / ethics*	Neuroscience
Bioethics
Jurisprudence*
Neurosciences / legislation & jurisprudence
	Technology
	Brain
	Confusion
	Recognition, Psychology
	Sister
	Organizations
	Charges
	Reconstructive Surgical Procedures
	Rubiaceae

18. PMID: 28552516

Mesh Terms	Mesh Terms(Web API)
Animals	Animals
Behavior, Animal / physiology*	Behavior, Animal
Behavioral Research / standards	Behavioral Research
Neurosciences / methods*	*Neuroscience
Biological Assay / methods*
Biological Assay / standards
Neurosciences / standards
Behavioral Research / methods*
Reproducibility of Results
	*Bioassays

19. PMID: 29316506

Mesh Terms	Mesh Terms(Web API)
Animals	Animals
Humans	Humans
Microscopy*	Microscopy, Fluorescence
Neurons / cytology*	Neurons
Neurosciences / methods*	Neuroscience
Synapses / physiology*	Synapses
Neurosciences / instrumentation*
	Mice
	Microscopy, Confocal
	Specimen Handling
	Brain
	Polymer

20. PMID: 29733893

Mesh Terms	Mesh Terms(Web API)
Animal Testing Alternatives	Animal Testing Alternatives
Animal Welfare* / organization & administration	Animal Welfare
Animals	Animals
Humans	Humans
Biomedical Research / methods*	Biomedical Research
Neurosciences / methods*	*Neuroscience
Primates*	Primates
Research Design*	Research Methodology
Biomedical Research / organization & administration
Models, Animal
Bibliometrics
Neurosciences / organization & administration
United Kingdom
	Animal Experimentation
	Researchers

abstract.txt

UI  -  28303019
TI  -  Integration of optogenetics with complementary methodologies in systems neuroscience.
AB  -  Modern optogenetics can be tuned to evoke activity that corresponds to naturally occurring local or global activity in timing, magnitude or individual-cell patterning. This outcome has been facilitated not only by the development of core features of optogenetics over the past 10 years (microbial-opsin variants, opsin-targeting strategies and light-targeting devices) but also by the recent integration of optogenetics with complementary technologies, spanning electrophysiology, activity imaging and anatomical methods for structural and molecular analysis. This integrated approach now supports optogenetic identification of the native, necessary and sufficient causal underpinnings of physiology and behaviour on acute or chronic timescales and across cellular, circuit-level or brain-wide spatial scales.


UI  -  29096079
TI  -  Compartmentalized Signaling in Neurons: From Cell Biology to Neuroscience.
AB  -  Neurons are the largest known cells, with complex and highly polarized morphologies. As such, neuronal signaling is highly compartmentalized, requiring sophisticated transfer mechanisms to convey and integrate information within and between sub-neuronal compartments. Here, we survey different modes of compartmentalized signaling in neurons, highlighting examples wherein the fundamental cell biological processes of protein synthesis and degradation, membrane trafficking, and organelle transport are employed to enable the encoding and integration of information, locally and globally within a neuron. Comparisons to other cell types indicate that neurons accentuate widely shared mechanisms, providing invaluable models for the compartmentalization and transfer mechanisms required and used by most eukaryotic cells.


UI  -  29432512
TI  -  Theory of drives and emotions - from Sigmund Freud to Jaak Panksepp.
AB  -  The article discusses the development of psychoanalytic theory in the direction of broadening the reflection on their own based on data derived from empirical studies other than clinical case study. Particularly noteworthy is the convergence that followed between neuroscience and psychoanalysis and the rise of the so-called neuropsychoanalysis. Consequently, this led to eject empirical hypotheses and begin research on defense mechanisms, self, memory, dreams, empathy, dynamic unconscious and emotional-motivational processes (theory of drives). Currently neuropsychoanalysis constituted itself as a discipline contained in itself three separate areas: the psychodynamic neuroscience, clinical neuropsychoanalysis and theory building. The article introduces the theory of Jaak Panksepp emotional systems as an example of anintegrated neurobiology of affect, behavioral biology, evolutionary psychology and psychoanalysis. The theory of emotional systems includes the description of the SEEKING system representing basic motivational system of the organism. Apart from a new perspective on the theory of drives described by Sigmund Freud, it offers the possibility to take into account the emotional and motivational systems within the understanding of mental disorders such as depression, addiction and psychosis, which is the core of psychoanalytic thinking.


UI  -  29460160
TI  -  Unethical human research in the field of neuroscience: a historical review.
AB  -  Understanding the historical foundations of ethics in human research are key to illuminating future human research and clinical trials. This paper gives an overview of the most remarkable unethical human research and how past misconducts helped develop ethical guidelines on human experimentation such as The Nuremberg Code 1947 following WWII. Unethical research in the field of neuroscience also proved to be incredibly distressing. Participants were often left with life-long cognitive disabilities. This emphasizes the importance of implicating strict rules and ethical guidelines in neuroscience research that protect participants and respects their dignity. The experiments conducted by German Nazi in the concentration camps during WWII are probably the most inhumane and brutal ever conducted. The Nuremberg Code of 1947, one of the few positive outcomes of the Nazi experiments, is often considered the first document to set out ethical regulations of human research. It consists of numerous necessary criteria, to highlight a few, the subject must give informed consent, there must be a concrete scientific basis for the experiment, and the experiment should yield positive results that cannot be obtained in any other way. In the end, we must remember, the interest of the patient must always prevail over the interest of science or society.


UI  -  29924477
TI  -  System neuroscience: Past, present, and future.
AB  -  In this review, we discuss first the anatomical and lesion studies that allowed the localization of fundamental functions in the cerebral cortex of primates including humans. Subsequently, we argue that the years from the end of the Second World War until the end of the last century represented the "golden age" of system neuroscience. In this period, the mechanisms-not only the localization-underlying sensory, and in particular visual functions were described, followed by those underlying cognitive functions and housed in temporal, parietal, and premotor areas. At the end of the last century, brain imaging techniques were developed that allowed the assessment of the functions of different cortical areas in a more precise and sophisticated way. However, brain imaging tells little about the neural mechanisms underlying functions. Furthermore, the brain imaging suffers from 3 major problems: time is absent, the data are merely correlative and the testing is often not ecological. We conclude our review discussing the possibility that these pitfalls might be overcome by using intracortical recordings (eg stereo-EEG), which have millisecond time resolution, allow direct electrical stimulation of specific sites, and finally enable to study patients while freely moving.


UI  -  29766913
TI  -  Telemedicine and neurosciences.
AB  -  It is well documented that there is an acute shortage of neurologists and neurosurgeons in India and globally. Despite all efforts, it will be impossible to make available neurospecialists in all suburban and rural areas. Simultaneously, there has been an exponential increase in the growth and development of Information and Communication Technology (ICT). Plummeting costs and unbelievable sophistication in the availability of user-friendly mobile video conferencing devices is making distance meaningless. Geography has become History! Worldwide, the ultraconservative health care industry, in particular, the medical community, has been uniformly slow to adopt and embrace the use of ICT to extend their clinical reach. In the last decade, however, specialists in all branches of neurosciences are slowly accepting the inevitable that telemedicine must and will have to be incorporated into the core of the healthcare delivery system. This literature review summarizes the current use of telemedicine in different subspecialties of neurosciences. The author defines the growth and development of clinical telemedicine in India with special reference to Neurosciences and attempts to show the stellar role telemedicine has to play in enhancing the services provided by doctors. As clinicians regularly using technology, it should not be difficult for us to convince our patients that today a virtual remote consult and management can indeed effectively substitute for a physical face-to-face encounter.


UI  -  29110344
TI  -  Current technical approaches to brain energy metabolism.
AB  -  Neuroscience is a technology-driven discipline and brain energy metabolism is no exception. Once satisfied with mapping metabolic pathways at organ level, we are now looking to learn what it is exactly that metabolic enzymes and transporters do and when, where do they reside, how are they regulated, and how do they relate to the specific functions of neurons, glial cells, and their subcellular domains and organelles, in different areas of the brain. Moreover, we aim to quantify the fluxes of metabolites within and between cells. Energy metabolism is not just a necessity for proper cell function and viability but plays specific roles in higher brain functions such as memory processing and behavior, whose mechanisms need to be understood at all hierarchical levels, from isolated proteins to whole subjects, in both health and disease. To this aim, the field takes advantage of diverse disciplines including anatomy, histology, physiology, biochemistry, bioenergetics, cellular biology, molecular biology, developmental biology, neurology, and mathematical modeling. This article presents a well-referenced synopsis of the technical side of brain energy metabolism research. Detail and jargon are avoided whenever possible and emphasis is given to comparative strengths, limitations, and weaknesses, information that is often not available in regular articles.


UI  -  29096071
TI  -  Molecular Neuroscience in the 21
AB  -  Neuroscience is inherently interdisciplinary in its quest to explain the brain. Like all biological structures, the brain operates at multiple levels, from nano-scale molecules to meter-scale systems. Here, I argue that understanding the nano-scale organization of the brain is not only helpful for insight into its function, but is a requisite for such insight. I propose that one impediment to a better understanding of the brain is that most of its molecular processes are incompletely understood, and suggest a number of key questions that require our attention so that progress can be achieved in neuroscience beyond a description of the activity of neural circuits.


UI  -  29121942
TI  -  Ethical aspects of brain computer interfaces: a scoping review.
AB  -  Brain-Computer Interface (BCI) is a set of technologies that are of increasing interest to researchers. BCI has been proposed as assistive technology for individuals who are non-communicative or paralyzed, such as those with amyotrophic lateral sclerosis or spinal cord injury. The technology has also been suggested for enhancement and entertainment uses, and there are companies currently marketing BCI devices for those purposes (e.g., gaming) as well as health-related purposes (e.g., communication). The unprecedented direct connection created by BCI between human brains and computer hardware raises various ethical, social, and legal challenges that merit further examination and discussion.


UI  -  27634721
TI  -  Naturalizing Responsibility.
AB  -  In the contemporary debate on the use of the neurosciences in ethics and law, numerous arguments have been bandied about among scientists and philosophers looking to uphold or reject the reliability and validity of scientific findings obtained by brain imaging technologies. Among the most vexing questions is, Can we trust that technology? One point of disagreement is whether brain scans offer a window through which to observe the functioning of the mind, in such a way as to enable lawyers, judges, physicians, and lawmakers to detect anomalies in brain function that may account for criminal unconscious behavior. Those who stand behind brain imaging believe that this can indeed be achieved, whereas those in opposition stress that brain scans are highly open to interpretation and that the data they provide is insufficient to establish causal connections. The question essentially comes down to whether technology can reliably be used to determine the intentions of the individual, thus establishing mens rea, for example, and hence responsibility. This article focuses on the latter notion and explores whether we can rely on the neurosciences to shed light on a complex form of moral and legal reasoning, as well as the role of the neurosciences in reawakening a philosophical and legal interest in trying to set responsibility on an empirical basis. 


UI  -  30980031
TI  -  Nongenetic optical neuromodulation with silicon-based materials.
AB  -  Optically controlled nongenetic neuromodulation represents a promising approach for the fundamental study of neural circuits and the clinical treatment of neurological disorders. Among the existing material candidates that can transduce light energy into biologically relevant cues, silicon (Si) is particularly advantageous due to its highly tunable electrical and optical properties, ease of fabrication into multiple forms, ability to absorb a broad spectrum of light, and biocompatibility. This protocol describes a rational design principle for Si-based structures, general procedures for material synthesis and device fabrication, a universal method for evaluating material photoresponses, detailed illustrations of all instrumentation used, and demonstrations of optically controlled nongenetic modulation of cellular calcium dynamics, neuronal excitability, neurotransmitter release from mouse brain slices, and brain activity in the mouse brain in vivo using the aforementioned Si materials. The entire procedure takes ~4-8 d in the hands of an experienced graduate student, depending on the specific biological targets. We anticipate that our approach can also be adapted in the future to study other systems, such as cardiovascular tissues and microbial communities.


UI  -  30731065
TI  -  The NIH BRAIN Initiative: Integrating Neuroethics and Neuroscience.
AB  -  The NIH Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative is focused on developing new tools and neurotechnologies to transform our understanding of the brain, and neuroethics is an essential component of this research effort. Coordination with other brain projects around the world will help maximize success.


UI  -  31260438
TI  -  The Human Brain Project-Synergy between neuroscience, computing, informatics, and brain-inspired technologies.
AB  -  The Human Brain Project (HBP) is a European flagship project with a 10-year horizon aiming to understand the human brain and to translate neuroscience knowledge into medicine and technology. To achieve such aims, the HBP explores the multilevel complexity of the brain in space and time; transfers the acquired knowledge to brain-derived applications in health, computing, and technology; and provides shared and open computing tools and data through the HBP European brain research infrastructure. We discuss how the HBP creates a transdisciplinary community of researchers united by the quest to understand the brain, with fascinating perspectives on societal benefits.


UI  -  27637950
TI  -  Population neuroscience.
AB  -  Population neuroscience endeavors to identify influences shaping the human brain from conception onwards, thus generating knowledge relevant for building and maintaining brain health throughout the life span. This can be achieved by studying large samples of participants drawn from the general population and evaluated with state-of-the-art tools for assessing (a) genes and their regulation; (b) external and internal environments; and (c) brain properties. This chapter reviews the three elements of population neuroscience (principles, tools, innovations, limitations), and discusses future directions in this field. 


UI  -  28250055
TI  -  Mapping the Hypocretin/Orexin Neuronal System: An Unexpectedly Productive Journey.
AB  -  Early in 1998, we (de Lecea et al., 1998) and others (Sakurai et al., 1998) described the same hypothalamic neuropeptides, respectively called the hypocretins or orexins, which were discovered using two different approaches. In December of that year, we published the subject of this commentary in the 


UI  -  29547172
TI  -  Six decades of Neurology at NIMHANS: A historical perspective.
AB  -  The Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka has a long tradition of excellence in education, teaching, research, and patient care. Its exceptional alumni, as well as current and past faculty members, have made considerable contributions to the development of neurological services throughout the world. The six decades of its existence have seen a momentous growth in clinical, investigative, and community Neurology. As a result of the immense scientific individual as well as collaborative contributions of the faculty members in various departments, the Institute has had the honour of attaining the status of an autonomous 'Institute of National Importance' under the Ministry of Health, Government of India, through a novel concept of collaboration and partnership of central and state governments. This article traces the dedicated pursuit of members of the Department of Neurology, NIMHANS, in managing neurologic diseases through compassionate patient-centred care, transformative research and education.


UI  -  30720413
TI  -  Neurolaw and Neuroethics.
AB  -  This short article proposes a conceptual structure for "neurolaw," modeled loosely on the bipartite division of the sister field of neuroethics by Adina Roskies into the "ethics of neuroscience" and the "neuroscience of ethics." As normative fields addressing the implications of scientific discoveries and expanding technological capacities affecting the brain, "neurolaw" and neuroethics have followed parallel paths. Similar foundational questions arise for both about the validity and utility of recognizing them as distinct subfields of law and ethics, respectively. In both, a useful distinction can be drawn between a self-reflexive inquiry (the neuroscience of ethics and law) and an inquiry into the development and use of brain science and technologies (the ethics and law of neuroscience). In both fields, these two forms of inquiry interact in interesting ways. In addition to a proposed conceptual structure for neurolaw, the article also addresses the neurolegal versions of the critiques made against neuroethics, including charges of reductionism, fact/value confusion, and biological essentialism.


UI  -  28552516
TI  -  The importance of behavioural bioassays in neuroscience.
AB  -  The behavioural bioassay is fundamental to research in behavioural neuroscience. A described by Tinbergen, behaviour is measured to answer questions about development, mechanisms, adaptation and evolution.


UI  -  29316506
TI  -  Expansion microscopy: development and neuroscience applications.
AB  -  Many neuroscience questions center around understanding how the molecules and wiring in neural circuits mechanistically yield behavioral functions, or go awry in disease states. However, mapping the molecules and wiring of neurons across the large scales of neural circuits has posed a great challenge. We recently developed expansion microscopy (ExM), a process in which we physically magnify biological specimens such as brain circuits. We synthesize throughout preserved brain specimens a dense, even mesh of a swellable polymer such as sodium polyacrylate, anchoring key biomolecules such as proteins and nucleic acids to the polymer. After mechanical homogenization of the specimen-polymer composite, we add water, and the polymer swells, pulling biomolecules apart. Due to the larger separation between molecules, ordinary microscopes can then perform nanoscale resolution imaging. We here review the ExM technology as well as applications to the mapping of synapses, cells, and circuits, including deployment in species such as Drosophila, mouse, non-human primate, and human.


UI  -  29733893
TI  -  Applying the 3Rs to neuroscience research involving nonhuman primates.
AB  -  This Feature focuses on UK neuroscience research using nonhuman primates (NHPs), and the application of the 3Rs, in the light of the recent EU SCHEER report and subsequent article by Prescott et al. (2017). The challenge of understanding the human brain and its disorders means that NHP research is still very much needed, although it is essential that this research is complemented by studies using other approaches, such as human volunteers and patients, and other alternatives to NHP use. Analysis of recent publications shows that these complementary approaches are already being actively exploited by NHP researchers in the UK. Application of the 3Rs has been led by the UK National Centre for the 3Rs (NC3Rs), with active participation of UK NHP researchers, who are constantly refining research methodology. However, not all refinements work, and those that do succeed need to be fully validated before they can be introduced more widely into current practice. More generally, the 3Rs have helped to ameliorate harm experienced by NHPs in procedures, although there is still more to do. Accumulating evidence from recent UK Home Office statistics suggests that most monkeys used in scientific procedures experience a moderate rather than a severe level of harm.

main.py

import requests
from urllib.request import urlopen
from xml.etree.ElementTree import parse

f = open("pmid-neuroscien-set.txt", "r")
with open('abstract.txt','w') as o:
    for i in f:
        var_url = urlopen('https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&id={}'.format(i))
        xmldoc = parse(var_url)
        for item in xmldoc.iterfind('PubmedArticle'):
            abstract_text = item.findtext('MedlineCitation/Article/Abstract/AbstractText')
            article_title = item.findtext('MedlineCitation/Article/ArticleTitle')
            pmid = int(i)
            print('UI  - ', pmid, file=o)
            print('TI  - ', article_title, file=o)
            print('AB  - ', abstract_text, file=o)
            print("\n", file=o)
    o.close()
f.close()

mesh_terms.txt

28303019|*Optogenetics|C3494301|613216|MH|RtM via: Optogenetics;Forced Leaf Node Lookup:optogenetics|TI;AB|MM;RC|711^11^0;363^12^0;120^12^0;36^12^0;520^12^0
28303019|*Neuroscience|C0027910|291822|ET|Entry Term Replacement for "Neurosciences";RtM via: Neuroscience discipline|TI|MM;RC|93^12^0
28303019|Opsin|C2355587|41470|ET|Entry Term Replacement for "Opsins";RtM via: Opsins|AB|MM;RC|410^5^0
28303019|Brain|C0006104|5439|MH|RtM via: Brain|AB|MM;RC|896^5^0
28303019|Rod Opsins|C0069580|990|MH|RtM via: Rod Opsins|AB|MM|410^5^0

29096079|*Neurons|C0027882|418224|MH|RtM via: Neurons;RtM via: neuronal;Forced Non-Leaf Node Lookup:neurons|TI;AB|MM;RC|753^7^0;699^6^0;436^7^0;102^7^0;52^7^0;347^8^0
29096079|*Signal Transduction|C0037083|182733|MH|RtM via: Signal Transduction;RtM via: neuronal signal transduction|TI;AB|MM;RC|423^9^0;39^9^0;196^18^0
29096079|*Neuroscience|C0027910|162132|ET|Entry Term Replacement for "Neurosciences";RtM via: Neuroscience discipline|TI|MM;RC|82^12^0
29096079|Organelle|C0029219|16364|ET|Entry Term Replacement for "Organelles";RtM via: Organelles;RtM via: Cytoplasmic organelle|AB|MM;RC|581^9^0
29096079|Protein Transport|C0599895|7641|MH|RtM via: trafficking|AB|MM;RC|564^11^0
29096079|*Biological Processes|C3714634|1833|ET|Entry Term Replacement for "Biological Phenomena";RtM via: biological signaling;RtM via: Biological Processes;Forced Non-Leaf Node Lookup:biological processes|TI;AB|MM|423^9^0;39^9^0;496^20^0

29432512|Psychoanalysis|C0033884|245516|MH|RtM via: Psychoanalytic psychiatry|AB|MM;RC|1435^14^0;1006^14^0;377^14^0
29432512|Psychoanalytic Theory|C0033886|228135|MH|RtM via: Psychoanalytic Theory|AB|MM;RC|137^21^0
29432512|*Emotions|C0013987|56655|MH|RtM via: Emotions;Forced Non-Leaf Node Lookup:emotions|TI;AB|MM;RC|1289^9^0;1036^9^0;886^9^0;593^9^0;42^8^0
29432512|Psychoanalytic Therapy|C0033887|54194|MH|||RC
29432512|Neuroscience|C0027910|53216|ET|Entry Term Replacement for "Neurosciences";RtM via: Neuroscience discipline|AB|MM;RC|771^12^0;360^12^0
29432512|Neurobiology|C0027817|9054|MH|RtM via: Neurobiology|AB|MM;RC|934^12^0
29432512|Memory|C0025260|5721|MH|RtM via: Memory;RtM via: Memory observations|AB|MM;RC|544^6^0
29432512|Empathy|C0013989|5282|MH|RtM via: Empathy|AB|MM;RC|560^7^0
29432512|Motivations|C0026605|4197|ET|Entry Term Replacement for "Motivation";RtM via: Motivation|AB|MM;RC|1303^12^0;1120^12^0;603^12^0

29460160|Humans|C0086418|366576|CT|Forced Leaf Node Lookup:humans;CT Text Lookup: human;CT Text Lookup: patient|TI;AB|MM;RC|31^5^0;157^5^0;203^5^0;301^5^0;1064^5^0;1387^7^0
29460160|Human Experimentation|C0020123|365576|MH|RtM via: Human Experimentation|AB|MM;RC|378^21^0
29460160|Nazi|C0949876|93461|ET|Entry Term Replacement for "National Socialism";RtM via: Nazis|AB|MM;RC|973^4^0;803^4^0
29460160|Informed Consent|C0021430|91683|MH|RtM via: Informed Consent|AB|MM;RC|1166^16^0
29460160|Ethics, Medical|C0015004|48289|MH|||RC
29460160|*Neuroscience|C0027910|31440|ET|Entry Term Replacement for "Neurosciences";RtM via: Neuroscience discipline|TI;AB|MM;RC|691^12^0;483^12^0;62^12^0
29460160|Morals|C0026532|7434|MH|RtM via: Morality|AB|MM;RC|1041^7^0;669^7^0;356^7^0

29924477|Humans|C0086418|577612|CT|CT Text Lookup: human;CT Text Lookup: humans;CT Text Lookup: patient;CT Text Lookup: patients|AB|MM;RC|242^6^0;1328^8^0
29924477|Animals|C0003062|577612|CT|CT Text Lookup: primate|AB|MM;RC|223^8^0
29924477|*Neuroscience|C0027910|576612|ET|Entry Term Replacement for "Neurosciences";RtM via: Neuroscience discipline|TI;AB|MM;RC|398^12^0;28^12^0
29924477|Brain Mapping|C0006117|125476|MH|||RC
29924477|Brain|C0006104|103817|MH|RtM via: Brain|AB|MM;RC|932^5^0;838^5^0
29924477|Functions, Cognitive|C0009240|26986|ET|Entry Term Replacement for "Cognition";RtM via: Cognition;RtM via: Cognitive functions|AB|MM;RC|569^19^0
29924477|Cerebral Cortex|C0007776|14199|MH|RtM via: Cerebral cortex|AB|MM;RC|773^8^0;204^15^0
29924477|Electrical Stimulation|C0013786|8859|ET|Entry Term Replacement for "Electric Stimulation";RtM via: Electric stimulation technique|AB|MM;RC|1258^22^0

29766913|Humans|C0086418|173338|CT|CT Text Lookup: patient;CT Text Lookup: patients|AB|MM;RC|1433^8^0
29766913|*Telemedicine|C0162648|172338|MH|RtM via: Telemedicine;Forced Non-Leaf Node Lookup:telemedicine|TI;AB|MM;RC|1169^12^0;1052^12^0;899^12^0;21^12^0;1269^12^0
29766913|*Neurosciences|C0027910|61356|MH|RtM via: Neuroscience discipline;Forced Non-Leaf Node Lookup:neurosciences|TI;AB|MM;RC|1217^13^0;1096^13^0;844^13^0;38^13^0
29766913|Videoconferencing|C1450048|21748|MH|RtM via: videoconferencing communications|AB|MM;RC|510^18^0
29766913|Delivery, Healthcare|C0011211|10824|ET|Entry Term Replacement for "Delivery of Health Care";RtM via: Delivery of Health Care;RtM via: Health Care Systems|AB|MM;RC|971^19^0;991^6^1
29766913|India|C0021201|5|MH|RtM via: India|AB|MM|1185^5^0;150^5^0

29110344|*Brain|C0006104|290142|MH|RtM via: Brain;Forced Non-Leaf Node Lookup:brain|TI;AB|MM;RC|1233^5^0;531^5^0;135^5^0;53^5^0;735^5^0
29110344|*Energy Metabolism|C0014272|171273|MH|RtM via: Energy Metabolism;RtM via: Bioenergetics;Forced Non-Leaf Node Lookup:energy metabolisms|TI;AB|MM;RC|1239^17^0;619^17^0;141^17^0;59^17^0;1046^13^0
29110344|Neuroscience|C0027910|151661|ET|Entry Term Replacement for "Neurosciences";RtM via: Neuroscience discipline|AB|MM;RC|84^12^0
29110344|*Neurochemistry|C0027820|47295|MH|RtM via: brain metabolism|TI;AB|MM|1233^5^1;1246^10^1;135^5^1;148^10^1;53^5^1;66^10^1
29110344|Neurons|C0027882|23440|MH|RtM via: Neurons|AB|MM;RC|437^7^0
29110344|Cells, Glial|C0027836|20203|ET|Entry Term Replacement for "Neuroglia";RtM via: Neuroglia|AB|MM;RC|446^11^0
29110344|Neurology|C0027855|12328|MH|RtM via: Neurology speciality|AB|MM;RC|1121^9^0
29110344|Molecular Biology|C0026376|6866|MH|RtM via: Molecular Biology|AB|MM;RC|1079^17^0

29096071|*Neuroscience|C0027910|904926|ET|Entry Term Replacement for "Neurosciences";RtM via: Neuroscience discipline|TI;AB|MM;RC|662^12^0;60^12^0;31^12^0
29096071|Brain|C0006104|75939|MH|RtM via: Brain|AB|MM;RC|486^5^0;329^5^0;176^5^0;133^5^0
29096071|Neuronal Plasticity|C0027880|71548|MH|||RC

29121942|Humans|C0086418|131256|CT|CT Text Lookup: human;CT Text Lookup: individuals|AB|MM;RC|655^5^0;245^11^0
29121942|*Brain-Computer Interfaces|C3494288|130256|MH|Forced Leaf Node Lookup:brain computer interfaces;Forced Leaf Node Lookup:brain-computer interfaces;Forced Leaf Node Lookup:bci|TI;AB|MM;RC|40^25^0;91^24^0;117^3^0;195^3^0;492^3^0;643^3^0
29121942|Communication Aids for Disabled|C0009453|79876|MH|||RC
29121942|Electroencephalography|C0013819|32631|MH|||RC
29121942|User-Computer Interface|C0042117|21306|MH|||RC
29121942|Brain|C0006104|7288|MH|RtM via: Brain|AB|MM;RC|661^6^0
29121942|Amyotrophic Lateral Sclerosis|C0002736|3336|MH|RtM via: Amyotrophic Lateral Sclerosis|AB|MM;RC|316^29^0

27634721|Reproducibility of Results|C0035149|25072|MH|Forced Lookup:reliability|AB|MM;RC|243^11^0
27634721|Neurosciences|C0027910|158787|MH|RtM via: Neuroscience discipline|AB|MM;RC|1195^13^0;101^13^0
27634721|Neuroimaging|C0679575|103256|MH|RtM via: Brain scan;RtM via: Imaging of brain|AB|MM;RC|794^11^0;434^11^0;303^13^0
27634721|Morals|C0026532|49652|MH|RtM via: Morality;RtM via: Morals|AB|MM;RC|1244^5^0
27634721|Brain|C0006104|36507|MH|RtM via: Brain|AB|MM;RC|698^5^0;303^5^0
27634721|Criminal Law|C0010328|31585|MH|||RC
27634721|Crime|C0010325|16556|MH|||RC
27634721|Intentions|C0162425|13527|ET|Entry Term Replacement for "Intention";RtM via: Intention - mental process|AB|MM;RC|1016^10^0
27634721|*Social Behavior|C0037397|11133|MH|RtM via: Responsibility|TI;AB|MM|1379^14^0;1097^14^0;34^14^0
27634721|Social Responsibility|C0037433|10973|MH|||RC

30980031|Animals|C0003062|352967|CT|CT Text Lookup: mouse|AB|MM;RC|988^5^0
30980031|Mice|C0026809|352967|CT|CT Text Lookup: mouse|AB|MM;RC|988^5^0
30980031|Humans|C0086418|352967|CT|CT Text Lookup: student|AB|MM;RC|1167^7^0
30980031|*Silicon|C0037107|351967|MH|RtM via: Silicon;Forced Leaf Node Lookup:silicon;checkForceMH Boosted|TI;AB|MM;RC|642^2^0;375^7^0;61^7^0
30980031|Action Potentials|C0001272|49465|MH|||RC
30980031|Neurosciences|C0027910|29950|MH|||RC
30980031|Neurons|C0027882|29207|MH|||RC
30980031|Nanotechnology|C0872323|24906|MH|||RC
30980031|Brain|C0006104|9935|MH|||RC

30731065|*Neuroscience|C0027910|412815|ET|Entry Term Replacement for "Neurosciences";RtM via: Neuroscience discipline;Forced Non-Leaf Node Lookup:neuroethics|TI|MM;RC|75^12^0;59^11^0;290^11^0
30731065|*Brain|C0006104|56082|MH|RtM via: Brain;Forced Non-Leaf Node Lookup:brain|TI;AB|MM;RC|377^5^0;166^5^0;103^5^0;279^5^0;29^5^0
30731065|*Drive|C0013126|1200|MH|RtM via: Initiative|TI;AB|MM|173^10^0;35^10^0
30731065|Electric Power Supplies|C0032865|0|MH|RtM via: Transformers|AB|MM|244^9^0

31260438|Humans|C0086418|549193|CT|Forced Leaf Node Lookup:humans;CT Text Lookup: human|TI;AB|MM;RC|25^5^0;142^5^0;247^5^0
31260438|*Neuroscience|C0027910|548193|ET|Entry Term Replacement for "Neurosciences";RtM via: Neuroscience discipline|TI;AB|MM;RC|276^12^0;61^12^0
31260438|*Brain|C0006104|207318|MH|RtM via: Brain;Forced Non-Leaf Node Lookup:brain|TI;AB|MM;RC|656^3^0;751^5^0;355^3^0;401^5^0;148^5^0;253^5^0;31^5^0;103^5^0;462^5^0;606^5^0
31260438|Brain Mapping|C0006117|98201|MH|||RC
31260438|Image Processing, Computer-Assisted|C0020911|42470|MH|||RC
31260438|Medical Informatics|C0025088|12651|MH|||RC
31260438|*Technology|C0039421|2646|MH|RtM via: Technology|TI;AB|MM|515^10^0;317^10^0;118^12^0

27637950|Humans|C0086418|900826|CT|Forced Lookup:general population;CT Text Lookup: human|AB|MM;RC|339^18^0;121^5^0
27637950|*Neuroscience|C0027910|899826|ET|Entry Term Replacement for "Neurosciences";RtM via: Neuroscience discipline|TI;AB|MM;RC|566^12^0;63^12^0;32^12^0
27637950|Brain|C0006104|66054|MH|RtM via: Brain|AB|MM;RC|494^5^0;127^5^0

28250055|HCRT protein, human|C1527908|1862604|NM|RtM via: HCRT protein, human|TI|MM|33^10^0;44^6^0
28250055|*Orexins|C1113688|1862603|MH|RtM via: orexins;RtM via: HCRT protein, human;Forced Leaf Node Lookup:hypocretins;Forced Leaf Node Lookup:orexins|TI;AB|MM;RC|257^11^0;272^7^0;33^10^0;44^6^0
28250055|Neuropeptides|C0027895|382518|MH|RtM via: Neuropeptides|AB|MM;RC|218^13^0
28250055|*Neurons|C0027882|153840|MH|RtM via: neuronal|TI|MM;RC|51^8^0
28250055|Wakefulness|C0043012|75747|MH|||RC
28250055|Intracellular Signaling Peptides and Proteins|C1449791|65190|MH|||RC
28250055|Hypothalamus|C0020663|26980|MH|RtM via: Hypothalamic structure|AB|MM;RC|205^12^0

29547172|Humans|C0086418|1307923|CT|CT Text Lookup: patient|AB|MM;RC|278^7^0
29547172|United States|C0041703|1307923|CT|USA Lookup:National Institute of Mental Health;National Institute of Mental Health;CT Treecode Lookup: I01.409.418.750 (National Institute of Mental Health);National Institute of Mental Health;CT Treecode Lookup: N03.540.348.500.500 (National Institute of Mental Health)||MM;RC
29547172|India|C0021201|0|MH|RtM via: India;Geo Lookup:karnatakas|TI;AB|MM|867^5^0
29547172|*Neurology|C0027855|1306923|MH|RtM via: Neurology speciality;Forced Non-Leaf Node Lookup:neurology|TI;AB|MM;RC|1039^9^0;568^9^0;108^9^0;36^9^0
29547172|Neurosciences|C0027910|233014|MH|RtM via: Neuroscience discipline|AB|MM;RC|159^13^0
29547172|Nervous System Diseases|C0027765|142834|MH|RtM via: nervous system disorder|AB|MM;RC|1071^19^0
29547172|Academies and Institutes|C0000877|42300|MH|RtM via: Institutes|AB|MM;RC|718^9^0
29547172|Societies, Medical|C0037459|12324|MH|||RC
29547172|National Institute of Mental Health|C0027466|1048|ET|Entry Term Replacement for "National Institute of Mental Health (U.S.)";RtM via: National Institute of Mental Health (U.S.)|AB|MM|119^35^0
29547172|Faculty|C0015535|171|MH|RtM via: Faculty|AB|MM|674^7^0;344^7^0
29547172|Government|C0018104|113|MH|RtM via: Government|AB|MM|853^10^0

30720413|Humans|C0086418|1000|CT|Forced Humans: Sister||MM
30720413|Neuroscience|C0027910|71380|ET|Entry Term Replacement for "Neurosciences";RtM via: Neuroscience discipline;Forced Non-Leaf Node Lookup:neuroethics|AB|MM;RC|706^12^0;234^12^0;34^11^0;185^11^0;431^11^0;1069^11^0
30720413|Bioethical Issues|C0005488|33347|MH|||RC
30720413|Technology|C0039421|1866|MH|RtM via: Technology|AB|MM;RC|803^12^0;370^13^0
30720413|Brain|C0006104|784|MH|RtM via: Brain|AB|MM;RC|785^5^0;409^5^0
30720413|Confusion|C0009676|163|MH|RtM via: Confusion;RtM via: Clouded consciousness|AB|MM|1128^9^0
30720413|Recognition, Psychology|C0524637|51|MH|RtM via: Recognition, Psychology|AB|MM|553^11^0
30720413|Sister|C0337514|32|ET|Entry Term Replacement for "Siblings";RtM via: Sister|AB|MM|169^6^0
30720413|Organizations|C0029246|8|MH|RtM via: Utilities (organization)|AB|MM|542^7^0
30720413|Charges|C0007961|2|ET|Entry Term Replacement for "Fees and Charges";RtM via: charge amounts|AB|MM|1092^7^0
30720413|Reconstructive Surgical Procedures|C0524865|0|MH|RtM via: Surgical reduction|AB|MM|1103^12^0
30720413|Rubiaceae|C0524885|0|MH|RtM via: Adina|AB|MM|200^5^0

28552516|Animals|C0003062|109384|CT|Behavior, Animal;CT Treecode Lookup: F01.145.113 (Behavior, Animal)||RC
28552516|*Neuroscience|C0027910|108384|ET|Entry Term Replacement for "Neurosciences";RtM via: Neuroscience discipline|TI;AB|MM;RC|151^12^0;64^12^0
28552516|Behavioral Research|C0004939|67051|MH|||RC
28552516|Behavior, Animal|C0004935|24380|MH|||RC
28552516|*Bioassays|C0005507|13533|ET|Entry Term Replacement for "Biological Assay";RtM via: Biological Assay;Forced Non-Leaf Node Lookup:bioassays|TI;AB|MM;RC|100^8^0;51^9^0

29316506|Humans|C0086418|310013|CT|CT Text Lookup: human|AB|MM;RC|1150^5^0
29316506|Animals|C0003062|310013|CT|RtM via: Mus;CT Text Lookup: mouse;CT Text Lookup: primate|AB|MM;RC|1139^5^0;1156^7^0
29316506|Mice|C0026809|310013|CT|RtM via: Mus;CT Text Lookup: mouse|AB|MM;RC|1139^5^0
29316506|*Neuroscience|C0027910|121977|ET|Entry Term Replacement for "Neurosciences";RtM via: Neuroscience discipline|TI;AB|MM;RC|97^12^0;59^12^0
29316506|Microscopy, Fluorescence|C0026022|29422|MH|||RC
29316506|Microscopy, Confocal|C0242842|20191|MH|||RC
29316506|Synapses|C0039062|16043|MH|RtM via: Synapses|AB|MM;RC|1056^8^0
29316506|Neurons|C0027882|10614|MH|RtM via: Neurons|AB|MM;RC|315^7^0
29316506|Specimen Handling|C0037793|4380|MH|RtM via: Specimen preservation|AB|MM;RC|556^9^1;572^9^1
29316506|Brain|C0006104|4025|MH|RtM via: Brain|AB|MM;RC|566^5^0
29316506|Polymer|C0032521|3611|ET|Entry Term Replacement for "Polymers";RtM via: Polymers|AB|MM;RC|779^7^0;616^7^0

29733893|Humans|C0086418|164665|CT|CT Text Lookup: human;CT Text Lookup: patient;CT Text Lookup: patients;CT Text Lookup: volunteer;CT Text Lookup: volunteers|AB|MM;RC|340^5^0;545^8^0;530^10^0
29733893|Animals|C0003062|164665|CT|Animal Experimentation;CT Treecode Lookup: E05.017 (Animal Experimentation);Animal Welfare;CT Treecode Lookup: I01.880.604.100 (Animal Welfare);Animal Testing Alternatives;CT Treecode Lookup: E05.017 (Animal Testing Alternatives);Primates;CT Treecode Lookup: B01.050.150.900.649.313.988 (Primates);CT Text Lookup: primate|TI|MM;RC|82^8^0
29733893|*Neuroscience|C0027910|163665|ET|Entry Term Replacement for "Neurosciences";RtM via: Neuroscience discipline|TI;AB|MM;RC|125^12^0;41^12^0
29733893|Animal Experimentation|C0003048|108514|MH|||RC
29733893|Animal Welfare|C0003061|45799|MH|||RC
29733893|Animal Testing Alternatives|C0003059|33076|MH|||RC
29733893|Research Methodology|C0086912|30394|ET|Entry Term Replacement for "Research Design";RtM via: Research Methodology|AB|MM;RC|891^20^0
29733893|Primates|C0033147|28916|MH|Forced Non-Leaf Node Lookup:primates||MM;RC|82^8^0;162^8^0
29733893|Biomedical Research|C0005540|22932|MH|||RC
29733893|Researchers|C0035173|836|ET|Entry Term Replacement for "Research Personnel";RtM via: Research Personnel|AB|MM|850^11^0;708^11^0

pmid-neuroscien-set.txt

28303019
29096079
29432512
29460160
29924477
29766913
29110344
29096071
29121942
27634721
30980031
30731065
31260438
27637950
28250055
29547172
30720413
28552516
29316506
29733893