bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short-term Outcome of Peroral Endoscopic Myotomy Performed by the Same Endoscopist on Achalasia and Nonachalasia Esophageal Motility Disorders
Authors: Mubashir Maryam , Andrus Victoria , Okuampa David , Neice Michelle , Armstrong Elizabeth , Canezaro Hailey , Dies Ross , Deville Ashely , Kawji Lena , Rashid Shazia , Raza Syed Musa , Hafiz Nazar , Faisal Abu Saleh Mosa , Bhuiyan Mohammad Alfrad Nobel , Cai Qiang 
Published: October 2023

Background:
Peroral endoscopic myotomy (POEM) is a relatively new but increasingly therapeutic option for achalasia. In recent years, POEM has been used for nonachalasia esophageal motility disorders (NAEMDs), such as diffuse esophageal spasm, esophagogastric junction outlet obstruction, and hypercontractile disorder, with some clinical success. No studies thus far compare the outcomes of these two groups. We perform the first head-to-head comparison of outcomes after POEM in patients with achalasia and NAEMD.

Patients and Methods:
A retrospective analysis of all patients undergoing POEM at one university hospital by a single expert endoscopist from July 2021 to December 2022 was performed. All patients were symptomatic, and the presence of esophageal motility disorders was confirmed using multiple diagnostic modalities. These patients were then divided into 2 groups, achalasia and NAEMD, based on the underlying diagnosis. Statistical analysis of different clinical outcomes, including effectiveness and safety, was performed.

Results:
Thirty-seven patients (mean age: 59.55, females: 22) underwent POEM in the study period. Twenty patients had achalasia and 17 patients had NAEMD. The median myotomy length was 5.5 cm for the achalasia group and 10 cm for the NAEMD group. This excluded patients with esophagogastric junction outlet obstruction in which the median myotomy length was 3 cm. The procedure time, the duration of hospital stays, the rates of same-day discharge, and complications were similar between the two. Short-term outcomes of POEM for the two groups were similar with improvement in 94% of patients in the achalasia group and 93.75% in the NAEMD group.

Conclusion:
Contrary to prior observations, our study highlights that POEM is equally effective in achieving clinical improvement in patients with NAEMD as achalasia over 6 months of follow-up. In addition, POEM has a comparable safety profile in both patient groups making it a feasible therapeutic option for these debilitating and challenging disorders.
Consciousness Recovery in Traumatic Brain Injury: A Systematic Review Comparing Modafinil and Amantadine
Authors: Seifi Ali , Hassannezhad Sina , Mosaddeghi-Heris Reza , Haji Kamanaj Olia Arash , Adib Ali , Hafeez Shaheryar , Barthol Colleen 
Published: October 2023

ObjectivesAcute traumatic brain injury is one of the most common causes of death and disability. Reduction in the level of consciousness is a significant complication that can impact morbidity. Glasgow Coma Scale (GCS) is the most widely used method of assessing the level of consciousness. Neurostimulants such as amantadine and modafinil are common pharmacologic agents that increase GCS in patients with brain trauma. This study aimed to compare the effectiveness of these 2 drugs.MethodsThis systematic review obtained articles from Google Scholar, PubMed, Scopus, Embase, and MEDLINE databases. Extensive searches were conducted separately by 4 individuals in 3 stages. Ultimately, 16 clinical trials, cohort studies, case reports, and case series articles were obtained after reading the title, abstract, and full text and considering the exclusion criteria. The data of the final article were entered into the analysis table. This study was registered with PROSPERO (registration number CRD42022334409) and conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines.ResultsAmantadine seems to be associated with a higher overall response rate. In contrast, modafinil is associated with the most remarkable change in GCS score during treatment. However, the number of clinical trials with high quality and sample size has not been satisfactory to compare the effectiveness of these 2 drugs and their potential side effects.ConclusionsThe authors recommend additional double-blind clinical trials are needed to be conducted with a larger sample size, comparing amantadine with modafinil to delineate the efficacy and adverse effects, both short and long term.
Probabilistic Graphical Modeling under Heterogeneity
Authors: Chen Liying , Acharyya Satwik , Luo Chunyu , Ni Yang , Baladandayuthapani Veerabhadran 
Published: October 2023

AbstractProbabilistic graphical models are powerful and widely used tools to quantify, visualize and interpret dependencies in complex biological systems such as highthroughput genomics and proteomics. However, most existing graphical modeling methods assume homogeneity within and across samples which restricts their broad applicability to cases where sample-specific heterogeneity exists e.g. tumor heterogeneity. We propose a flexible Bayesian approach calledGraphicalRegression (GraphR) which (a) allows direct incorporation of intrinsic factors of sample heterogeneity at different scales through a regression-based formulation, (b) enables sparse network estimation at a sample-specific level, (c) allows identification and uncertainty quantification of potential effects of heterogeneity on network structures, and (d) is computationally efficient through the use of variational Bayes algorithms. We illustrate the comparative efficiency of GraphR against existing methods in terms of graph structure recovery and computational cost across multiple realistic simulation settings. We use GraphR to analyze four diverse multi-omics and spatial transcriptomics datasets to study inter- and intra-sample molecular networks and delineate biological discoveries that otherwise cannot be revealed by existing approaches. We have developed aGraphR R-packagealong with an accompanyingShiny Appthat provides comprehensive analysis and dynamic visualization functions.
Cortical circuits for cross-modal generalization
Authors: Guyoton Maëlle , Matteucci Giulio , Foucher Charlie G. , Getz Matthew P. , Gjorgjieva Julijana , El-Boustani Sami 
Published: October 2023

SummaryAdapting goal-directed behaviors to changing sensory conditions is a fundamental aspect of intelligence. The brain uses abstract representations of the environment to generalize learned associations across sensory modalities. The circuit organization that mediates such cross-modal generalizations remains, however, unknown. Here, we demonstrate that mice can bidirectionally generalize sensorimotor task rules between touch and vision by using abstract representations of peri-personal space within the cortex. Using large-scale mapping in the dorsal cortex at single-cell resolution, we discovered multimodal neurons with congruent spatial representations within multiple associative areas of the dorsal and ventral streams. Optogenetic sensory substitution and systematic silencing of these associative areas revealed that a single area in the dorsal stream is necessary and sufficient for cross-modal generalization. Our results identify and comprehensively describe a cortical circuit organization that underlies an essential cognitive function, providing a structural and functional basis for abstract reasoning in the mammalian brain.
BioKG: a comprehensive, large-scale biomedical knowledge graph for AI-powered, data-driven biomedical research
Authors: Zhang Yuan , Sui Xin , Pan Feng , Yu Kaixian , Li Keqiao , Tian Shubo , Erdengasileng Arslan , Han Qing , Wang Wanjing , Wang Jianan , Wang Jian , Sun Donghu , Chung Henry , Zhou Jun , Zhou Eric , Lee Ben , Zhang Peili , Qiu Xing , Zhao Tingting , Zhang Jinfeng 
Published: October 2023

AbstractTo cope with the rapid growth of scientific publications and data in biomedical research, knowledge graphs (KGs) have emerged as a powerful data structure for integrating large volumes of heterogeneous data to facilitate accurate and efficient information retrieval and automated knowledge discovery (AKD). However, transforming unstructured content from scientific literature into KGs has remained a significant challenge, with previous methods unable to achieve human-level accuracy. In this study, we utilized an information extraction pipeline that won first place in the LitCoin NLP Challenge to construct a large-scale KG using all PubMed abstracts. The quality of the large-scale information extraction rivals that of human expert annotations, signaling a new era of automatic, high-quality database construction from literature. Our extracted information markedly surpasses the amount of content in manually curated public databases. To enhance the KG’s comprehensiveness, we integrated relation data from 40 public databases and relation information inferred from high-throughput genomics data. The comprehensive KG enabled rigorous performance evaluation of AKD, which was infeasible in previous studies. We designed an interpretable, probabilistic-based inference method to identify indirect causal relations and achieved unprecedented results for drug target identification and drug repurposing. Taking lung cancer as an example, we found that 40% of drug targets reported in literature could have been predicted by our algorithm about 15 years ago in a retrospective study, demonstrating that substantial acceleration in scientific discovery could be achieved through automated hypotheses generation and timely dissemination. A cloud-based platform (https://www.biokde.com) was developed for academic users to freely access this rich structured data and associated tools.
Developmental pyrethroid exposure in mouse leads to disrupted brain metabolism in adulthood
Authors: Curtis Melissa A. , Saferin Nilanjana , Nguyen Jennifer H. , Imami Ali S. , Ryan William G. , Neifer Kari L. , Miller Gary W. , Burkett James P. 
Published: October 2023

AbstractEnvironmental and genetic risk factors, and their interactions, contribute significantly to the etiology of neurodevelopmental disorders (NDDs). Recent epidemiology studies have implicated pyrethroid pesticides as an environmental risk factor for autism and developmental delay. Our previous research showed that low-dose developmental exposure to the pyrethroid pesticide deltamethrin in mice caused male-biased changes in the brain and in NDD-relevant behaviors in adulthood. Here, we used a metabolomics approach to determine the broadest possible set of metabolic changes in the adult male mouse brain caused by low-dose pyrethroid exposure during development. Using a litter-based design, we exposed mouse dams during pregnancy and lactation to deltamethrin (3 mg/kg or vehicle every 3 days) at a concentration well below the EPA-determined benchmark dose used for regulatory guidance. We raised male offspring to adulthood and collected whole brain samples for untargeted high-resolution metabolomics analysis. Developmentally exposed mice had disruptions in 116 metabolites which clustered into pathways for folate biosynthesis, retinol metabolism, and tryptophan metabolism. As a cross-validation, we integrated metabolomics and transcriptomics data from the same samples, which confirmed previous findings of altered dopamine signaling. These results suggest that pyrethroid exposure during development leads to disruptions in metabolism in the adult brain, which may inform both prevention and therapeutic strategies.HighlightsDevelopmental pyrethroid exposure disrupts brain metabolism in adulthoodExposure disrupts metabolic pathways for folate, retinol, and tryptophanExposure disrupts genetic and metabolic pathways for dopamine signaling
Interspecific Aggression Of Two Wrens Along An Environmental Gradient In Western Ecuador
Authors: Montalvo Luis Daniel , Kimball Rebecca T. , Robinson Scott K. 
Published: October 2023

ABSTRACTInterspecific territoriality is a prevalent form of interference competition among animals. However, the connections between hybridization, climate, and interspecies territorial aggression in tropical regions remain largely unexplored. Here, we investigated territorial aggression in two hybridizing tropical bird species,C. z. brevirostrisandC. f. pallescens, in western Ecuador using playback experiments. We tested three hypotheses: 1) hybridizing species exhibit comparable intra- and inter-specific territorial aggression; 2) asymmetrical aggression driven byC. z. brevirostrisdominance determines gene flow patterns; and 3) precipitation influences territorial aggression. Supporting hypothesis 1, the admixedC. f. pallescensNorth showed no difference in intra-vs inter-specific aggression. However, the non-admixedC. f. pallescensSouth exhibited greater inter-specific aggression, providing partial support for hypothesis 1. Contrary to hypothesis 2,C. f. pallescensSouth displayed significantly higher aggression thanC. z. brevirostrisandC. f. pallescens North. Furthermore, precipitation models outperformed null models, supporting hypothesis 3 that precipitation influencesCampylorhynchusterritorial aggression. Collectively, these findings suggest hybridization can stabilize coexistence via territoriality, and precipitation strongly affects aggression, potentially through resource availability. Unexpectedly,C. z. brevirostrisdominance did not appear to drive asymmetric introgression between species, warranting further investigation into the underlying mechanisms. Complex factors shape territorial aggression in tropical birds, including genetic admixture, group size, latitude, and climate. This study highlights the need for additional research elucidating the relationships between hybridization, territoriality, and environmental stressors in tropical avian communities. We discuss possible mechanisms explaining the detected effects of precipitation on aggression and the lack ofC. z. brevirostrisdominance in determining introgression patterns.
Zebrafish model oftcn2deletion reveals new molecular insights into the role of vitamin B12 in embryonic development
Authors: Verma Ajay Deepak , Nongmaithem Suraj S , Mounika Challapalli , Ramachandran Swetha , Umesh Anushri , Chandak Giriraj Ratan 
Published: October 2023

AbstractVitamin B12 (B12) is one of the key co-factors in One-Carbon Metabolism pathway, and its dysregulation is associated with various clinical conditions including congenital malformations, neural tube defects, and low birthweight, etc. However, the underlying molecular mechanism is scarcely studied. This study investigated the role of B12 in early embryonic development by generating a knockout of transcobalamin 2 (tcn2), a B12 transporter in zebrafish.We generatedtcn2-/-zebrafish by creating premature stop codons in exon 7 and confirmed by qRT-PCR and immunoblotting. Phenotypic changes were captured, growth and survival assays were conducted at different developmental stages. B12 supplementation assay was conducted by rearingtcn2-/-embryos in embryo-medium containing 10 µM cyanocobalamin. RNA-sequencing data was generated in triplicates in embryos at 1-cell and 24 hpf stages, with and without B12 supplementation. Genes with log2FC ≥ 0.6 and adjusted p-value ≤ 0.01 were considered differentially expressed genes (DEGs) and proceeded for functional annotation and enrichment analysis.The F1tcn2-/-embryos grew normally. However, the F2tcn2-/-embryos remained unhatched, showed delayed somitogenesis, curved or deformed tails, abnormal yolk extension, pericardial and yolk sac edema, etc. and ∼70% were dead by 4 dpf. The abnormalities were partially ameliorated by B12 supplementation throughout developmental stages. Transcriptome analysis identified DEGs enriched in pathways including spliceosome, ribosome biogenesis, branched-chain amino acid degradation, lysosome, iron homeostasis, metabolic and immune response pathways, etc. We observed dysregulated expression of many genes with epigenetic functions includingsfswap,ctcf,mettl3,alkbh5, andhdac,etc.,in the 1-celltcn2-/-embryos. Notably, B12 supplementation restored expression of many DEGs indicating a potential role of B12 in transcriptional regulation during embryonic development.Our study delineates the importance of B12 during embryonic development and provides interesting insights into the molecular mechanisms underlying the observed phenotypic changes.
White Matter Correlates of Impulsive Behavior in Healthy Individuals: A Diffusion MRI Study
Authors: Rashidi Fatemeh , Parsaei Mohammadamin , Kiani Iman , Sadri Arash , Aarabi Mohammad Hadi , Darijani Seyed Reza , Lee Yune Sang , Moghaddam Hossein Sanjari 
Published: October 2023

AbstractBackgroundImpulsivity is closely related to the tendency to engage in risky behaviors. Previous research identified macrostructural brain alterations in individuals exhibiting impulsive behaviors. Understanding the microstructural brain changes linked to impulsivity can elucidate its underlying mechanisms and guide effective treatment strategies. In this study, we employed diffusion magnetic resonance imaging (DMRI) connectometry to investigate white matter tracts associated with impulsivity while considering potential sex differences.MethodsWe enrolled 218 healthy participants from the Leipzig Study for Mind-Body-Emotion Interactions (LEMON) database. Correlations between DMRI-derived white matter changes and impulsivity were assessed using scores from the UPPS Impulsive Behavior Scale’s four subscales (lack of perseverance (PE), lack of premeditation (PM), sensation seeking (SS), and negative urgency (NU)).ResultsOur findings revealed negative correlations between quantitative anisotropy (QA) values in bilateral cerebellum, middle cerebellar peduncle (MCP), and the severity of PE and PM across the cohort. Additionally, QA values within MCP, corpus callosum (CC) body, and forceps major exhibited negative correlations with SS. Conversely, QA values in forceps minor were positively correlated with PM, and QA values in both the forceps minor and bilateral cingulum showed positive correlations with SS. Remarkably, the observed correlations between UPPS subscale scores and QA value alterations within white matter tracts varied between males and females.ConclusionsImpulsivity is correlated with discernible alterations in white matter integrity across diverse tracts, including CC, cerebellum, and cingulum. Moreover, males and females show distinct patterns of correlations between white matter integrity and impulsivity.HighlightsImpulsivity is associated with QA changes and white matter alterations in various brain tracts.Lower white matter integrity in the cerebellum is negatively correlated with impulsivity.QA values in the CC parts showed divergent correlations with impulsive behavior.The patterns of correlations across various tracts varied between males and females.
TALEN-induced contraction of CTG trinucleotide repeats in myotonic dystrophy type 1 cells
Authors: Bétemps Laureline , Descorps-Declère Stéphane , Frenoy Olivia , Poggi Lucie , Mosbach Valentine , Tomé Stéphanie , Viterbo David , Klein Arnaud , Ma Laurence , Lameiras Sonia , Cokelaer Thomas , Monot Marc , Dumas Bruno , Gourdon Geneviève , Furling Denis , Richard Guy-Franck 
Published: October 2023

AbstractTrinucleotide repeat expansions are the cause of two dozen neurodegenerative and developmental disorders. One of these, myotonic dystrophy type 1 (Steinert disease, or DM1) is due to the expansion of a CTG triplet in the 3’ UTR of theDMPKgene. We used highly specific DNA endonucleases to induce a double-strand break in the repeat tract to contract it below pathological length. Expression of a TALE Nuclease (TALEN) in human DM1 cells induced moderate CTG repeat contractions in 27% of the clones analyzed. These clones exhibited large internal deletions within the TALEN, occurring by homologous recombination between internal TALE repeats, inactivating the nuclease, and explaining its reduced efficacy. Taking advantage of the degeneracy of the genetic code, we recoded the TALEN sequence, to decrease internal redundancy and optimize codon usage. The new recoded TALEN showed increased efficacy in DM1 cells, with 68% of clones exhibiting a moderate to large contraction of the CTG repeat tract. In contrast,Staphylococcus aureusCas9 (SaCas9) was unable to contract the CTG repeat tract. In parallel, we completely sequenced to very high coverage the DM1 genome using the PacBio technology. Several clones in which the TALEN was induced were also totally sequenced. In some of them, length changes of other long CTG repeats were detected, possibly corresponding to off-target effects, all of them in introns or intergenic regions. Repeat contractions were never associated with recombination of flanking markers, suggesting that contractions most probably occur by an intra-allelic mechanism such as single-strand annealing. TALENs should now be considered as a promising gene therapy approach, not only for DM1 but also for many other microsatellite expansion disorders.
Myofascial Trigger Point (MTrP) Size and Elasticity Properties Can Be Used to Differentiate Active and Latent MTrPs in Lower Back Skeletal Muscle
Authors: Tsai P. , Edison J. , Wang C. , Sefton J. , Manning K. , Gramlich M.W. 
Published: October 2023

AbstractMyofascial Trigger Points (MTrPs) are localized contraction knots that develop after muscle overuse or an acute trauma. Significant work has been done to understand, diagnose, and treat MTrPs in order to improve patients suffering from their effects. However, effective non-invasive diagnostic tools are still a missing gap in both understanding and treating MTrPs. Effective treatments for patients suffering from MTrP mediated pain require a means to measure MTrP properties quantitatively and diagnostically both prior to and during intervention. Further, quantitative measurements of MTrPs are often limited by the availability of equipment and training. Here we develop ultrasound (US) based diagnostic metrics that clinicians can use during patient diagnosis and treatment. We highlight the advantages and limitations of previous US-based approaches that utilize elasticity theory. We show how US-based measurements can distinguishActivefromLatentMTrPs. We demonstrate that Active MTrPs tend to be smaller, stiffer, and deeper in the muscle tissue. We provide evidence that more than one MTrP within a single US-image field increases the stiffness of neighboring MTrPs. Finally, we highlight a combination of metrics (depth, thickness, and stiffness) that can be used to assess individual MTrPs in combination with standard clinical assessments.