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Items 1 to 10 of about 105
1. Zhou W, Smalheiser NR, Yu C: A tutorial on information retrieval: basic terms and concepts. J Biomed Discov Collab; 2006;1:2
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] A tutorial on information retrieval: basic terms and concepts.
  • This informal tutorial is intended for investigators and students who would like to understand the workings of information retrieval systems, including the most frequently used search engines: PubMed and Google.
  • Having a basic knowledge of the terms and concepts of information retrieval should improve the efficiency and productivity of searches.
  • As well, this knowledge is needed in order to follow current research efforts in biomedical information retrieval and text mining that are developing new systems not only for finding documents on a given topic, but extracting and integrating knowledge across documents.

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  • (PMID = 16722601.001).
  • [ISSN] 1747-5333
  • [Journal-full-title] Journal of biomedical discovery and collaboration
  • [ISO-abbreviation] J Biomed Discov Collab
  • [Language] eng
  • [Publication-type] Journal Article
  • [Publication-country] England
  • [Other-IDs] NLM/ PMC1459215
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2. Landis CA, Collins BJ, Cribbs LL, Sukhatme VP, Bergmann BM, Rechtschaffen A, Smalheiser NR: Expression of Egr-1 in the brain of sleep deprived rats. Brain Res Mol Brain Res; 1993 Mar;17(3-4):300-6
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  • [Title] Expression of Egr-1 in the brain of sleep deprived rats.
  • In previous research, rats subjected to prolonged sleep deprivation have shown disturbances of thermoregulation, hormonal and metabolic changes in apparent response to the thermoregulatory problems, lesions on the tail and paws, and eventual death.
  • To search for alterations of functional activity in brain, the expression of the immediate early gene Egr-1 was examined by immunocytochemistry and Northern blotting in rats subjected to total sleep deprivation (TSD) for 10 days.
  • Controls included yoked stimulus-control (TSC) rats, surgically implanted but otherwise undisturbed control rats, and unoperated control rats.
  • Photographs of immunoreacted coronal sections from four sets of rats were ranked blindly for 25 brain regions.
  • TSD rats showed tendencies for regionally specific increases in Egr-1-like immunoreactivity in dorsal raphe, lateral habenula, superior colliculus, and ventral periaqueductal grey.
  • However, most regions showed no differences in Egr-1-like immunoreactivity between TSD and control rats.
  • Neither was there a difference in whole brain Egr-1 mRNA by Northern blot in two additional sets of rats.
  • Thus, this study, like previous studies of brain histology, amines, adrenoceptors, and glucose utilization, does not provide positive support for the hypothesis that sleep protects the central nervous system against massive global damage, fatigue, or dysfunction.
  • [MeSH-major] Brain / physiology. DNA-Binding Proteins / analysis. Gene Expression. Immediate-Early Proteins. Sleep Deprivation / physiology. Transcription Factors / analysis. Zinc Fingers
  • [MeSH-minor] Animals. Brain Chemistry / physiology. Cell Count. Early Growth Response Protein 1. Immunohistochemistry. Male. Rats. Rats, Sprague-Dawley

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  • (PMID = 8510502.001).
  • [ISSN] 0169-328X
  • [Journal-full-title] Brain research. Molecular brain research
  • [ISO-abbreviation] Brain Res. Mol. Brain Res.
  • [Language] eng
  • [Grant] United States / NICHD NIH HHS / HD / HD 09402; United States / NIMH NIH HHS / MH / MH04151; United States / NINDS NIH HHS / NS / NS 26055
  • [Publication-type] Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.
  • [Publication-country] NETHERLANDS
  • [Chemical-registry-number] 0 / DNA-Binding Proteins; 0 / Early Growth Response Protein 1; 0 / Egr1 protein, rat; 0 / Immediate-Early Proteins; 0 / Transcription Factors
  • [Gene-symbol] Egr-1
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3. Lugli G, Krueger JM, Davis JM, Persico AM, Keller F, Smalheiser NR: Methodological factors influencing measurement and processing of plasma reelin in humans. BMC Biochem; 2003 Sep 07;4:9
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  • [Title] Methodological factors influencing measurement and processing of plasma reelin in humans.
  • BACKGROUND: Reelin, intensively studied as an extracellular protein that regulates brain development, is also expressed in a variety of tissues and a circulating pool of reelin exists in adult mammals.
  • Here we describe the methodological and biological foundation for carrying out and interpreting clinical studies of plasma reelin.
  • RESULTS: Reelin in human plasma was sensitive to proteolysis, freeze-thawing and heating during long-term storage, sample preparation and electrophoresis.
  • Reelin in plasma was a dimer under denaturing conditions.
  • Boiling of samples resulted in laddering, suggesting that each of the 8 repeats expressed in reelin contains a heat-labile covalent bond susceptible to breakage.
  • Urinary-type and tissue-type plasminogen activator converted reelin to a discrete 310 kDa fragment co-migrating with the major immunoreactive reelin fragment seen in plasma and also detected in brain. (In contrast, plasmin produced a spectrum of smaller unstable reelin fragments.
  • ) We examined archival plasma of 10 pairs of age-matched male individuals differing in repeat length of a CGG repeat polymorphism of the 5'-untranslated region of the reelin gene (both alleles < 11 repeats vs. one allele having >11 repeats).
  • Reelin 310 kDa band content was lower in subjects having the long repeats in all 10 pairs, by 25% on average (p < 0.001).
  • In contrast, no difference was noted for amyloid precursor protein.
  • CONCLUSIONS: Our studies indicate the need for caution in measuring reelin in archival blood samples, and suggest that assays of plasma reelin should take into account three dimensions that might vary independently: a) the total amount of reelin protein;.
  • b) the relative amounts of reelin vs. its proteolytic processing products; and c) the aggregation state of the native protein.
  • Reelin-plasminogen activator interactions may affect their roles in synaptic plasticity.
  • Our results also suggest that the human CGG repeat polymorphism affects reelin gene expression, and may affect susceptibility to human disease.

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  • (PMID = 12959647.001).
  • [ISSN] 1471-2091
  • [Journal-full-title] BMC biochemistry
  • [ISO-abbreviation] BMC Biochem.
  • [Language] ENG
  • [Grant] United States / NIMH NIH HHS / MH / MH60778
  • [Publication-type] Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.
  • [Publication-country] England
  • [Chemical-registry-number] 0 / Cell Adhesion Molecules, Neuronal; 0 / Extracellular Matrix Proteins; 0 / Nerve Tissue Proteins; EC 3.4.21.- / Plasminogen Activators; EC 3.4.21.- / Serine Endopeptidases; EC 3.4.21.- / reelin protein; EC 3.4.21.7 / Fibrinolysin
  • [Other-IDs] NLM/ PMC200967
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4. Wallace BC, Noel-Storr A, Marshall IJ, Cohen AM, Smalheiser NR, Thomas J: Identifying reports of randomized controlled trials (RCTs) via a hybrid machine learning and crowdsourcing approach. J Am Med Inform Assoc; 2017 Nov 01;24(6):1165-1168
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Identifying reports of randomized controlled trials (RCTs) via a hybrid machine learning and crowdsourcing approach.
  • Objectives: Identifying all published reports of randomized controlled trials (RCTs) is an important aim, but it requires extensive manual effort to separate RCTs from non-RCTs, even using current machine learning (ML) approaches.
  • We aimed to make this process more efficient via a hybrid approach using both crowdsourcing and ML.
  • Methods: We trained a classifier to discriminate between citations that describe RCTs and those that do not.
  • We then adopted a simple strategy of automatically excluding citations deemed very unlikely to be RCTs by the classifier and deferring to crowdworkers otherwise.
  • Results: Combining ML and crowdsourcing provides a highly sensitive RCT identification strategy (our estimates suggest 95%-99% recall) with substantially less effort (we observed a reduction of around 60%-80%) than relying on manual screening alone.
  • Conclusions: Hybrid crowd-ML strategies warrant further exploration for biomedical curation/annotation tasks.

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  • (PMID = 28541493.001).
  • [ISSN] 1527-974X
  • [Journal-full-title] Journal of the American Medical Informatics Association : JAMIA
  • [ISO-abbreviation] J Am Med Inform Assoc
  • [Language] eng
  • [Publication-type] Journal Article
  • [Publication-country] England
  • [Keywords] NOTNLM ; crowdsourcing / evidence-based medicine / human computation / machine learning / natural language processing
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5. Cohen AM, Smalheiser NR, McDonagh MS, Yu C, Adams CE, Davis JM, Yu PS: Automated confidence ranked classification of randomized controlled trial articles: an aid to evidence-based medicine. J Am Med Inform Assoc; 2015 May;22(3):707-17
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  • [Title] Automated confidence ranked classification of randomized controlled trial articles: an aid to evidence-based medicine.
  • OBJECTIVE: For many literature review tasks, including systematic review (SR) and other aspects of evidence-based medicine, it is important to know whether an article describes a randomized controlled trial (RCT).
  • Current manual annotation is not complete or flexible enough for the SR process.
  • In this work, highly accurate machine learning predictive models were built that include confidence predictions of whether an article is an RCT.
  • MATERIALS AND METHODS: The LibSVM classifier was used with forward selection of potential feature sets on a large human-related subset of MEDLINE to create a classification model requiring only the citation, abstract, and MeSH terms for each article.
  • RESULTS: The model achieved an area under the receiver operating characteristic curve of 0.973 and mean squared error of 0.013 on the held out year 2011 data.
  • Accurate confidence estimates were confirmed on a manually reviewed set of test articles.
  • A second model not requiring MeSH terms was also created, and performs almost as well.
  • DISCUSSION: Both models accurately rank and predict article RCT confidence.
  • Using the model and the manually reviewed samples, it is estimated that about 8000 (3%) additional RCTs can be identified in MEDLINE, and that 5% of articles tagged as RCTs in Medline may not be identified.
  • CONCLUSION: Retagging human-related studies with a continuously valued RCT confidence is potentially more useful for article ranking and review than a simple yes/no prediction.
  • The automated RCT tagging tool should offer significant savings of time and effort during the process of writing SRs, and is a key component of a multistep text mining pipeline that we are building to streamline SR workflow.
  • In addition, the model may be useful for identifying errors in MEDLINE publication types.
  • The RCT confidence predictions described here have been made available to users as a web service with a user query form front end at: http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/RCT_Tagger.cgi.

  • NCI CPTC Antibody Characterization Program. NCI CPTC Antibody Characterization Program .
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  • [Copyright] © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.
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  • (PMID = 25656516.001).
  • [ISSN] 1527-974X
  • [Journal-full-title] Journal of the American Medical Informatics Association : JAMIA
  • [ISO-abbreviation] J Am Med Inform Assoc
  • [Language] ENG
  • [Grant] United States / NIA NIH HHS / AG / P01 AG039347; United States / NLM NIH HHS / LM / R01 LM010817; United States / NLM NIH HHS / LM / R01LM010817
  • [Publication-type] Journal Article; Research Support, N.I.H., Extramural
  • [Publication-country] England
  • [Other-IDs] NLM/ PMC4457112
  • [Keywords] NOTNLM ; Evidence-Based Medicine / Information Retrieval / Natural Language Processing / Randomized Controlled Trials as Topic / Support Vector Machines / Systematic Reviews
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6. Dwivedi Y, Roy B, Lugli G, Rizavi H, Zhang H, Smalheiser NR: Chronic corticosterone-mediated dysregulation of microRNA network in prefrontal cortex of rats: relevance to depression pathophysiology. Transl Psychiatry; 2015 Nov 17;5:e682
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  • [Title] Chronic corticosterone-mediated dysregulation of microRNA network in prefrontal cortex of rats: relevance to depression pathophysiology.
  • Stress plays a major role in inducing depression, which may arise from interplay between complex cascades of molecular and cellular events that influence gene expression leading to altered connectivity and neural plasticity.
  • In recent years, microRNAs (miRNAs) have carved their own niche owing to their innate ability to induce disease phenotype by regulating expression of a large number of genes in a cohesive and coordinated manner.
  • In this study, we examined whether miRNAs and associated gene networks have a role in chronic corticosterone (CORT; 50 mg  kg(-1) × 21 days)-mediated depression in rats.
  • Rats given chronic CORT showed key behavioral features that resembled depression phenotype.
  • Expression analysis revealed differential regulation of 26 miRNAs (19 upregulated, 7 downregulated) in prefrontal cortex of CORT-treated rats.
  • Interaction between altered miRNAs and target genes showed dense interconnected molecular network, in which multiple genes were predicated to be targeted by the same miRNA.
  • A majority of altered miRNAs showed binding sites for glucocorticoid receptor element, suggesting that there may be a common regulatory mechanism of miRNA regulation by CORT.
  • Functional clustering of predicated target genes yielded disorders such as developmental, inflammatory and psychological that could be relevant to depression.
  • Prediction analysis of the two most prominently affected miRNAs miR-124 and miR-218 resulted into target genes that have been shown to be associated with depression and stress-related disorders.
  • Altogether, our study suggests miRNA-mediated novel mechanism by which chronic CORT may be involved in depression pathophysiology.
  • [MeSH-major] Corticosterone / administration & dosage. Depressive Disorder / physiopathology. Gene Regulatory Networks / genetics. MicroRNAs / genetics. Prefrontal Cortex / physiopathology
  • [MeSH-minor] Animals. Behavior, Animal. Disease Models, Animal. Male. Rats. Rats, Sprague-Dawley. Signal Transduction / genetics

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  • (PMID = 26575223.001).
  • [ISSN] 2158-3188
  • [Journal-full-title] Translational psychiatry
  • [ISO-abbreviation] Transl Psychiatry
  • [Language] eng
  • [Grant] United States / NIMH NIH HHS / MH / R21MH081099; United States / NIMH NIH HHS / MH / R01MH100616; United States / NIMH NIH HHS / MH / R01MH082802; United States / NIMH NIH HHS / MH / 1R01MH101890; United States / NIMH NIH HHS / MH / 1R01MH107183-01
  • [Publication-type] Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
  • [Publication-country] United States
  • [Chemical-registry-number] 0 / MicroRNAs; W980KJ009P / Corticosterone
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7. Smalheiser NR, Shao W, Yu PS: Nuggets: findings shared in multiple clinical case reports. J Med Libr Assoc; 2015 Oct;103(4):171-6
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Nuggets: findings shared in multiple clinical case reports.
  • OBJECTIVE: The researchers assessed prevalence in the clinical case report literature of multiple reports independently reporting the same (or nearly the same) main finding.
  • METHODS: Results from forty-five PubMed queries were examined for incidence and features of main findings ("nuggets") shared in at least four case reports.
  • RESULTS: The authors found that nuggets are surprisingly prevalent and large in the case report literature, the largest found so far was reported in seventeen articles.
  • In most cases, the main findings of case reports were evident from examining titles alone.
  • CONCLUSIONS: Our curated examples should serve as gold standards for developing specific automated methods for finding nuggets.
  • Nuggets potentially enable finding-based (instead of topic-based) information retrieval.
  • [MeSH-major] Evidence-Based Medicine. Information Storage and Retrieval
  • [MeSH-minor] Medical Informatics. PubMed

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  • (PMID = 26512214.001).
  • [ISSN] 1558-9439
  • [Journal-full-title] Journal of the Medical Library Association : JMLA
  • [ISO-abbreviation] J Med Libr Assoc
  • [Language] eng
  • [Grant] United States / NIA NIH HHS / AG / P01 AG039347; United States / NIA NIH HHS / AG / P01 AG039347; United States / NLM NIH HHS / LM / R01 LM010817; United States / NLM NIH HHS / LM / R01 LM010817
  • [Publication-type] Journal Article; Research Support, N.I.H., Extramural
  • [Publication-country] United States
  • [Other-IDs] NLM/ PMC4613375
  • [Keywords] NOTNLM ; Case Reports / Evidence-Based Medicine / Information Storage and Retrieval / Medical Informatics
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8. Palmblad M, Torvik VI: Spatiotemporal analysis of tropical disease research combining Europe PMC and affiliation mapping web services. Trop Med Health; 2017;45:33
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Spatiotemporal analysis of tropical disease research combining Europe PMC and affiliation mapping web services.
  • Background: Tropical medicine appeared as a distinct sub-discipline in the late nineteenth century, during a period of rapid European colonial expansion in Africa and Asia.
  • After a dramatic drop after World War II, research on tropical diseases have received more attention and research funding in the twenty-first century.
  • Methods: We used Apache Taverna to integrate Europe PMC and MapAffil web services, containing the spatiotemporal analysis workflow from a list of PubMed queries to a list of publication years and author affiliations geoparsed to latitudes and longitudes.
  • The results could then be visualized in the Quantum Geographic Information System (QGIS).
  • Results: Our workflows automatically matched 253,277 affiliations to geographical coordinates for the first authors of 379,728 papers on tropical diseases in a single execution.
  • The bibliometric analyses show how research output in tropical diseases follow major historical shifts in the twentieth century and renewed interest in and funding for tropical disease research in the twenty-first century.
  • They show the effects of disease outbreaks, WHO eradication programs, vaccine developments, wars, refugee migrations, and peace treaties.
  • Conclusions: Literature search and geoparsing web services can be combined in scientific workflows performing a complete spatiotemporal bibliometric analyses of research in tropical medicine.
  • The workflows and datasets are freely available and can be used to reproduce or refine the analyses and test specific hypotheses or look into particular diseases or geographic regions.
  • This work exceeds all previously published bibliometric analyses on tropical diseases in both scale and spatiotemporal range.

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  • (PMID = 29093641.001).
  • [ISSN] 1348-8945
  • [Journal-full-title] Tropical medicine and health
  • [ISO-abbreviation] Trop Med Health
  • [Language] eng
  • [Publication-type] Journal Article
  • [Publication-country] Japan
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9. Mishra S, Torvik VI: Quantifying Conceptual Novelty in the Biomedical Literature. Dlib Mag; 2016 Sep-Oct;22(9-10)
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Quantifying Conceptual Novelty in the Biomedical Literature.
  • We introduce several measures of novelty for a scientific article in MEDLINE based on the temporal profiles of its assigned Medical Subject Headings (MeSH).
  • First, temporal profiles for all MeSH terms (and pairs of MeSH terms) were characterized empirically and modelled as logistic growth curves.
  • Second, a paper's novelty is captured by its youngest MeSH (and pairs of MeSH) as measured in years and volume of prior work.
  • Across all papers in MEDLINE published since 1985, we find that individual concept novelty is rare (2.7% of papers have a MeSH ≤ 3 years old; 1.0% have a MeSH ≤ 20 papers old), while combinatorial novelty is the norm (68% have a pair of MeSH ≤ 3 years old; 90% have a pair of MeSH ≤ 10 papers old).
  • Furthermore, these novelty measures exhibit complex correlations with article impact (as measured by citations received) and authors' professional age.

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  • (PMID = 27942200.001).
  • [ISSN] 1082-9873
  • [Journal-full-title] D-Lib magazine : the magazine of the Digital Library Forum
  • [ISO-abbreviation] Dlib Mag
  • [Language] eng
  • [Grant] United States / NIA NIH HHS / AG / P01 AG039347
  • [Publication-type] Journal Article
  • [Publication-country] United States
  • [Keywords] NOTNLM ; Bibliometrics / MEDLINE / Novelty
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10. Smalheiser NR, Zhang H, Dwivedi Y: Enoxacin Elevates MicroRNA Levels in Rat Frontal Cortex and Prevents Learned Helplessness. Front Psychiatry; 2014;5:6
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Enoxacin Elevates MicroRNA Levels in Rat Frontal Cortex and Prevents Learned Helplessness.
  • Major depressive disorder (MDD) is a major public health concern.
  • Despite tremendous advancement, the pathogenic mechanisms associated with MDD are still unclear.
  • Moreover, a significant number of MDD subjects do not respond to the currently available medication.
  • MicroRNAs (miRNAs) are a class of small non-coding RNAs that control gene expression by modulating translation, mRNA degradation or stability of mRNA targets.
  • The role of miRNAs in disease pathophysiology is emerging rapidly.
  • Recently, we reported that miRNA expression is down-regulated in frontal cortex of depressed suicide subjects, and that rats exposed to repeated inescapable shock show differential miRNA changes depending on whether they exhibited normal adaptive responses or learned helpless (LH) behavior.
  • Enoxacin, a fluoroquinolone used clinically as an anti-bacterial compound, enhances the production of miRNAs in vitro and in peripheral tissues in vivo, but has not yet been tested as an experimental tool to study the relation of miRNA expression to neural functions or behavior.
  • Treatment of rats with 10 or 25 mg/kg enoxacin for 1 week increased the expression of miRNAs in frontal cortex and decreased the proportion of rats exhibiting LH behavior following inescapable shock.
  • Further studies are warranted to learn whether enoxacin may ameliorate depressive behavior in other rodent paradigms and in human clinical situations, and if so whether its mechanism is due to upregulation of miRNAs.

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  • (PMID = 24575053.001).
  • [ISSN] 1664-0640
  • [Journal-full-title] Frontiers in psychiatry
  • [ISO-abbreviation] Front Psychiatry
  • [Language] eng
  • [Grant] United States / NIMH NIH HHS / MH / R01 MH101890
  • [Publication-type] Journal Article
  • [Publication-country] Switzerland
  • [Other-IDs] NLM/ PMC3918929
  • [Keywords] NOTNLM ; behavior / depression / enoxacin / miRNAs / rat
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