bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying Incarceration Status in the Electronic Health Record Using Natural Language Processing in Emergency Department Settings
Authors: Huang Thomas , Socrates Vimig , Gilson Aidan , Safranek Conrad , Chi Ling , Wang Emily A. , Puglisi Lisa B. , Brandt Cynthia , Taylor R. Andrew , Wang Karen 
Published: October 2023

ABSTRACTBackgroundIncarceration is a highly prevalent social determinant of health associated with high rates of morbidity and mortality and racialized health inequities. Despite this, incarceration status is largely invisible to health services research due to poor electronic health record capture within clinical settings. Our primary objective is to develop and assess natural language processing (NLP) techniques for identifying incarceration status from clinical notes to improve clinical sciences and delivery of care for millions of individuals impacted by incarceration.MethodsWe annotated 1,000 unstructured clinical notes randomly selected from the emergency department for incarceration history. Of these annotated notes, 80% were used to train the Longformer-based and RoBERTa NLP models. The remaining 20% served as the test set. Model performance was evaluated using accuracy, sensitivity, specificity, precision, F1 score and Shapley values.ResultsOf annotated notes, 55.9% contained evidence for incarceration history by manual annotation. ICD-10 code identification demonstrated accuracy of 46.1%, sensitivity of 4.8%, specificity of 99.1%, precision of 87.1%, and F1 score of 0.09. RoBERTa NLP demonstrated an accuracy of 77.0%, sensitivity of 78.6%, specificity of 73.3%, precision of 80.0%, and F1 score of 0.79. Longformer NLP demonstrated an accuracy of 91.5%, sensitivity of 94.6%, specificity of 87.5%, precision of 90.6%, and F1 score of 0.93.ConclusionThe Longformer-based NLP model was effective in identifying patients’ exposure to incarceration and has potential to help address health disparities by enabling use of electronic health records to study quality of care for this patient population and identify potential areas for improvement.
Health Systems Reforms in Bangladesh: An Analysis of the Last Three Decades
Authors: Udechukwu Treasure , Fofana Thierno Oumar , Carnapete Louise , Haider Shams Shabab , Hanif Suhi , Clech Lucie , Ridde Valéry 
Published: October 2023

ABSTRACTObjectiveWe reviewed the evidence regarding the health sector reforms implemented in Bangladesh within the past 30 years to understand their impact on the health system and healthcare outcomes.MethodWe completed a scoping review of the most recent and relevant publications on health system reforms in Bangladesh from 1990 through 2023. Studies were included if they identified health sector reforms implemented in the last 30 years in Bangladesh, if they focused on health sector reforms impacting health system dimensions, if they were published between 1991 and 2023 in English or French and were full-text peer-reviewed articles, literature reviews, book chapters, grey literature, or reports.ResultsTwenty-four studies met the inclusion criteria. The primary health sector reform shifted from a project-based approach to financing the health sector to a sector-wide approach. Studies found that implementing reform initiatives such as expanding community clinics and a voucher scheme improved healthcare access, especially for rural districts. Despite government efforts, there is a significant shortage of formally qualified health professionals, especially nurses and technologists, low public financing, a relatively high percentage of out-of-pocket payments, and significant barriers to healthcare access.ConclusionEvidence suggests that health sector reforms implemented within the last 30 years had a limited impact on health systems. More emphasis should be placed on addressing critical issues such as human resources management and health financing, which may contribute to capacity building to cope with emerging threats, such as climate change.
The neurostructural consequences of glaucoma and their overlap with disorders exhibiting emotional dysregulations: a voxel-based meta-analysis and tripartite system model
Authors: Klugah-Brown Benjamin , Bore Mercy C. , Liu Xiqin , Gan Xianyang , Biswal Bharat B. , Kendrick Keith M. , Chang Dorita , Zhou Bo , Becker Benjamin 
Published: October 2023

AbstractGlaucoma is a neurodegenerative disorder characterized by progressive optic nerve damage and the most common cause for irreversible blindness. Emotional dysregulations are common in glaucoma patients, with high rates of generalized anxiety and depression. Glaucoma leads to pathological changes in the visual pathways of the brain, yet accumulating evidence suggests that the brain changes may reach beyond the visual system. To robustly determine brain morphological alterations in glaucoma and determine a potential overlap with changes observed in anxiety and depression we performed a pre-registered comparative meta-analysis of case control studies examining brain structural integrity in patients with glaucoma, and further determined whether the identified regions are nodes of distinct overarching large-scale networks and overlap with meta-analytic brain structural maps of generalized anxiety disorder (GAD) and major depressive disorder (MDD). Glaucoma patients exhibited robust reductions in gray matter volume in regions contributing to visual processing (lingual gyrus, thalamus), but volumetric reductions extended beyond systems involved in visual processing and also affected the left putamen and insula. Behavioral and functional network level decoding demonstrated distinct large-scale networks and involvement in visual, motivational or affective domains, respectively. Reductions in the insular region involved in pain and affective processes overlapped with alterations previously observed in GAD. Our findings may suggest a tripartite brain model of glaucoma, with changes in visual processing regions such as the lingual gyrus as well as additional alterations in putamen and insular regions meta-analytically associated with motivational or emotional functions, respectively. Together the findings indicate broad neuroanatomical alterations in glaucoma that extend beyond the visual system and may gate further pathological developments.
Delay in Clearance of Labeled Protons Post-Acute Head Trauma Utilizing 3D ASL MRI (Arterial Spin Labeling) a Pilot Study
Authors: Joseph Charles R , Kang Jubin , Grohol Bryce N , Zivcevska Marija , Lenke Joshua , Rich Ethan Dean , Arrasmith Connor James , Dorman Ian Shepherd , Clark Bradley Waman , Love Kim , Ferry Ben , Rolfs Mark E 
Published: October 2023

BackgroundThe study aims were to correlate acute head injury cognitive changes with ASL-MRI reduced glymphatic clearance rate (GCRs) and determine GC improvement with recovery. Concussive-brain injury disrupts the blood brain barrier (BBB) and reduces cMTT (capillary mean transit time) and GCRs. Concussion is clinically diagnosed utilizing history and exam findings. ASL-MRI assesses brain perfusion ingress and outflow.Methods3D TGSE (turbo-gradient and spin echo) PASL (pulsed arterial spin labeling) 3T MRI with 7 long TI’s (time to inversion) assessed the GCRs (slope of the linear decay of signal vs. time) of labeled protons 2800-4000 ms post-labeling in bifrontal, bitemporal, and biparietal regions within 7 days of mild acute traumatic brain injury and after clinically cleared to return to usual activities. The Sport Concussion Assessment Tool Version 5 (SKAT5) and Brief Oculomotor/Vestibular Assessment (administered by sports physicians) evaluated injured student athletes’ cognitive function prior to ASL MRIs.ResultsPilot study demonstrated significant GCRs improvement (95% [CI] -0.06 to -0.03 acute phase; to [CI] - recovery [CI] 0.0772 to -0.0497 ; P <0.001 in Frontal lobes; and Parietal lobes (95% [CI] -0.0584 to -0.0251 acute; [CI] -0.0727 to - 0.0392 recovery; P = 0.024) in 9 head injured athletes (8 female 1 male mean age 20). 6 age/activity matched normal controls (4 female 2 male mean age 22) were also compared.ConclusionAcute head trauma disrupts the BBB reducing GCR measured using this 3D ASL MRI technique. ASL MRI is a potential noninvasive biomarker of acute brain injury and subsequent recovery.Key MessageObjective measure of post mild TBI recovery has remained elusive as conventional anatomic imaging techniques and biomarkers are not sensitive. This pilot study demonstrates the potential of leveraging alterations in brain perfusion in the late phase capturing both delayed capillary perfusion and retained free fluid clearance from the brain, both the result of blood brain barrier leak from the acute trauma. Our noninvasive ASL MRI technique identified both anatomic site-specific delay in clearance acutely as well as restoration of normal flow post recovery. This time and cost-efficient noninvasive technique may, with additional validation, provide a needed objective measure for identifying physiologic changes post-acute injury and upon clinical recovery.
Perceptual formant discrimination during speech movement planning
Authors: Wang Hantao , Ali Yusuf , Max Ludo 
Published: October 2023

AbstractEvoked potential studies have shown that speech planning modulates auditory cortical responses. The phenomenon’s functional relevance is unknown. We tested whether, during this time window of cortical auditory modulation, there is an effect on speakers’ perceptual sensitivity for vowel formant discrimination. Participants made same/different judgments for pairs of stimuli consisting of a pre-recorded, self-produced vowel and a formant-shifted version of the same production. Stimuli were presented prior to a “go” signal for speaking, prior to passive listening, and during silent reading. The formant discrimination stimulus /uh/ was tested with a congruent productions list (words with /uh/) and an incongruent productions list (words without /uh/). Logistic curves were fitted to participants’ responses, and the just-noticeable difference (JND) served as a measure of discrimination sensitivity. We found a statistically significant effect of condition (worst discrimination before speaking) without congruency effect. Post-hoc pairwise comparisons revealed that JND was significantly greater before speaking than during silent reading. Thus, formant discrimination sensitivity was reduced during speech planning regardless of the congruence between discrimination stimulus and predicted acoustic consequences of the planned speech movements. This finding may inform ongoing efforts to determine the functional relevance of the previously reported modulation of auditory processing during speech planning.
A Subcortical Feeding Circuit Linking Interoception to Jaw movement
Authors: Kosse Christin , Ivanov Jessica , Knight Zachary , Pellegrino Kyle , Friedman Jeffrey 
Published: October 2023

AbstractThe brain processes an array of stimuli enabling the selection of an appropriate behavioural response but the neural pathways linking interoceptive inputs to outputs for feeding are poorly understood. Here we delineate a subcortical circuit in which brain-derived neurotrophic factor (BDNF) expressing neurons in the ventromedial hypothalamus (VMH) directly connect interoceptive inputs to motor centers controlling food consumption and jaw movements. VMHBDNFneuron inhibition increases food intake by gating motor sequences of feeding through projections to premotor areas of the jaw. When food is unavailable, VMHBDNFinhibition elicits consummatory behaviors directed at inanimate objects such as a wooden block and inhibition of mesencephalic trigeminal area (Me5) projections evokes rhythmic jaw movements. The activity of these neurons is decreased during food consumption and increases when food is in proximity but not consumed. Activity is also increased in obese animals and after leptin treatment. VMHBDNFneurons receive monosynaptic inputs from both agouti-related peptide (AgRP) and proopiomelanocortin (POMC) neurons in the arcuate nucleus (Arc) and constitutive VMHBDNFactivation blocks the orexigenic effect of AgRP activation. These data delineate an Arc→VMHBDNF→Me5 circuit that senses the energy state of an animal and regulates consummatory behaviors in a state dependent manner.
A novel subgroup of light-driven sodium pumps with an additional Schiff base counterion
Authors: Podoliak E. , Lamm G. H. U. , Alekseev A. , Marin E. , Schellbach A. V. , Fedotov D. A. , Stetsenko A. , Maliar N. , Bourenkov G. , Balandin T. , Baeken C. , Astashkin R. , Schneider T. R. , Bateman A. , Wachtveitl J. , Schapiro I. , Busskamp V. , Guskov A. , Gordeliy V. , Kovalev K. 
Published: October 2023

ABSTRACTLight-driven sodium pumps (NaRs) are unique ion-transporting microbial rhodopsins. The major group of NaRs is characterized by an NDQ motif and has two aspartic acid residues in the central region essential for sodium transport. Here we identified a new subgroup of the NDQ rhodopsins bearing an additional glutamic acid residue in the close vicinity to the retinal Schiff base. We thoroughly characterized a member of this subgroup, namely the proteinErNaR fromErythrobacter sp. HL-111and showed that the additional glutamic acid results in almost complete loss of pH sensitivity for sodium-pumping activity, which is in contrast to previously studied NaRs.ErNaR is capable of transporting sodium efficiently even at acidic pH levels. X-ray crystallography and single particle cryo-electron microscopy reveal that the additional glutamic acid residue mediates the connection between the other two Schiff base counterions and strongly interacts with the aspartic acid of the characteristic NDQ motif. Hence, it reduces its pKa. Our findings shed light on a new subgroup of NaRs and might serve as a basis for their rational optimization for optogenetics.
Association between movement patterns, microbiome diversity, and potential pathogen presence in free-ranging feral pigeons foraging in dairy farms
Authors: Crafton Miranda , Cahani Shai , Lublin Avishai , Rauer Luise , Spiegel Orr 
Published: October 2023

AbstractThe feedback between host behavior and disease transmission is well acknowledged, but empirical studies demonstrating associations between individual’s pathogens or microbiota composition and their movement are rare. We investigated these associations in feral pigeons (Columba livia domestica), a synanthrope species known to host a plethora of zoonotic pathogens. We captured pigeons in three dairy farms along an urbanization gradient in central Israel. We combined GPS-tracking with Next Generation Sequencing to characterize pigeons’ movement and microbiota, respectively. We found that pigeons roosted primarily in human settlements, with frequent visits to dairy farms and other agricultural sites. Microbiota diversity and composition varied between sites and the individuals within them, and several pathogens relevant to poultry, cattle, and human-health were frequently detected. Pigeons in the urban site covered shorter distances and carried a greater diversity of bacteria compared to those in rural sites. Intriguingly, beyond these among-site differences, exploratory individuals (measured by the number of unique locations they visited) had more diverse microbiota. We conclude that pigeons can potentially serve as transmission vectors among wildlife, livestock, and humans . Further, the associations between host behavior and microbiota diversity emphasize the relevance of wildlife movement analyses for disease ecology and One Health.
A methoxylated flavone fromArtemisia afrakillsMycobacterium tuberculosis
Authors: Kellogg Joshua J. , Alonso Maria Natalia , Jordan R. Teal , Xiao Junpei , Cafiero Juan Hilario , Bush Trevor , Towler Melissa , Weathers Pamela , Shell Scarlet S. 
Published: October 2023

AbstractTuberculosis, caused by Mycobacteriumtuberculosis(Mtb), is a deadly and debilitating disease globally affecting millions annually. Emerging drug-resistant Mtb strains endanger the efficacy of the current combination therapies employed to treat tuberculosis; therefore, there is an urgent need to develop novel drugs to combat this disease.Artemisia afrais used traditionally in southern Africa to treat malaria and recently has shown anti tuberculosis activity. This genus synthesizes a prodigious number of phytochemicals, many of which have demonstrated human health effects. Transcriptomic analysis revealed thatA. afraexerts different effects on Mtb compared toA. annuaor the well-known antimalarial artemisinin, suggesting other phytochemicals present inA. afrawith unique modes of action. A biochemometric study ofA. afraresulted in the isolation of a methoxylated flavone (1), which displayed considerable activity against Mtb strain mc26230. Compound1had an MIC of 312.5 μg/mL and yielded no viable colonies after 6 days of treatment. In addition,1was effective in killing hypoxic Mtb cultures, with no viable cultures after 2 days of treatment. This suggested thatA. afrais a source of potentially powerful anti-Mtb phytochemicals with novel mechanisms of action.
Optimising Spectronaut search parameters to improve data quality with minimal proteome coverage reductions in DIA analyses of heterogeneous samples
Authors: Baker Christa P. , Bruderer Roland , Abbott James , Arthur J. Simon C. , Brenes Alejandro J. 
Published: October 2023

AbstractData independent acquisition has seen breakthroughs that enable comprehensive proteome profiling using short gradients. As the proteome coverage continues to increase, the quality of the data generated becomes much more relevant. Using Spectronaut, we show that the default search parameters can be easily optimised to minimise the occurrence of false positives across different samples. Using an immunological infection model system to demonstrate the impact of adjusting search settings we analysed mouse macrophages and compared their proteome to macrophages spiked withCandida albicans. This experimental system enabled the identification of ‘false positives’ sinceCandida albicanspeptides and proteins should not be present in the mouse only samples. We show that adjusting the search parameters reduced ‘false positive’ identifications by 89% at the peptide and protein level, thereby considerably increasing the quality of the data. We also show that these optimised parameters incur a moderate cost, only reducing the overall number of ‘true positive’ identifications across each biological replicate by <6.7% at both the peptide and protein level. We believe the value of our updated search parameters extends beyond a two-organism analysis and would be of great value to any DIA experiment analysing heterogenous populations of cell types or tissues.
Mapping chromatin state and transcriptional response in CIC-DUX4 undifferentiated round cell sarcoma
Authors: Thomas Nicholas J. , Luck Cuyler , Shlimon Nicole , Ponce Rovingaile Kriska , Kosibaty Zeinab , Okimoto Ross A. 
Published: October 2023

AbstractCIC-DUX4 is a rare and understudied transcription factor fusion oncoprotein. CIC-DUX4 co-opts native gene targets to drive a lethal form of human sarcoma. The molecular underpinnings that lead to oncogenic reprograming and CIC-DUX4 sarcomagenesis remain largely undefined. Through an integrative ChIP and RNA-Seq analysis using patient-derived CIC-DUX4 cells, we define CIC-DUX4 mediated chromatin states and function. We show that CIC-DUX4 primarily localizes to proximal and distal cis-regulatory elements where it associates with active histone marks. Our findings nominate key signaling pathways and molecular targets that enable CIC-DUX4 to mediate tumor cell survival. Collectively, our data demonstrate how the CIC-DUX4 fusion oncoprotein impacts chromatin state and transcriptional responses to drive an oncogenic program in undifferentiated sarcoma.SignificanceCIC-DUX4 sarcoma is a rare and lethal sarcoma that affects children, adolescent young adults, and adults. CIC-DUX4 sarcoma is associated with rapid metastatic dissemination and relative insensitivity to chemotherapy. There are no current standard-of-care therapies for CIC-DUX4 sarcoma leading to universally poor outcomes for patients. Through a deep mechanistic understanding of how the CIC-DUX4 fusion oncoprotein reprograms chromatin state and function, we aim to improve outcomes for CIC-DUX4 patients.
Importin-7-dependent nuclear localization of theFlaviviruscore protein is required for infectious virus production
Authors: Itoh Yumi , Tokunaga Makoto , Miyamoto Yoichi , Suzuki Tatsuya , Takada Akira , Ninomiya Akinori , Matsuda Mami , Yoneda Yoshihiro , Oka Masahiro , Suzuki Ryosuke , Matsuura Yoshiharu , Okamoto Toru 
Published: October 2023

AbstractFlaviviridaeis a family of positive-stranded RNA viruses, including human pathogens such as Japanese encephalitis virus (JEV), dengue virus (DENV), zika virus (ZIKV), and West Nile virus (WNV). Nuclear localization of the viral core protein is conserved amongFlaviviridae, and this feature may be targeted for developing broad-ranging anti-flavivirus drugs. However, the mechanism of core protein translocation to the nucleus and the importance of nuclear localization in the viral life cycle remain unknown. We aimed to identify the molecular mechanism underlying core protein nuclear translocation. We identified importin-7 (IPO7), an importin-β family protein, as a nuclear carrier forFlaviviridaecore proteins. Nuclear import assays revealed that core protein was transported into the nucleus via IPO7, whereasIPO7deletion by CRISPR/Cas9 impaired their nuclear localization. To understand the importance of core protein nuclear localization, we evaluated the production of infectious virus or single-round-infectious-particles in wild-type or IPO7-deficient cells; both processes were significantly impaired in IPO7-deficient cells, whereas intracellular infectious virus levels were equivalent in wild-type and IPO7-deficient cells. These data suggested that IPO7-mediated nuclear localization of core proteins plays a role in the release of infectious virus particles of flaviviruses.