bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acute colonic pseudo-obstruction in polytrauma patients
Authors: Johnny Cecil S. , Schlegel Richard N. , Balachandran Mayurathan , Casey Laura , Mathew Joseph , Carne Peter , Varma Dinesh , Ban Ee-Jun , Fitzgerald Mark C. 
Published: May 2024

BACKGROUND
Acute colonic pseudo-obstruction (ACPO) is characterized by severe colonic distension without mechanical obstruction. It has an uncertain pathogenesis and poses diagnostic challenges. This study aimed to explore risk factors and clinical outcomes of ACPO in polytrauma patients and contribute information to the limited literature on this condition.

METHODS
This retrospective study, conducted at a Level 1 trauma center, analyzed data from trauma patients with ACPO admitted between July 2009 and June 2018. A control cohort of major trauma patients was used. Data review encompassed patient demographics, abdominal imaging, injury characteristics, analgesic usage, interventions, complications, and mortality. Statistical analyses, including logistic regression and correlation coefficients, were employed to identify risk factors.

RESULTS
There were 57 cases of ACPO, with an incidence of 1.7 per 1,000 patients, rising to 4.86 in major trauma. Predominantly affecting those older than 50 years (75%) and males (75%), with motor vehicle accidents (50.8%) and falls from height (36.8%) being the commonest mechanisms. Noteworthy associated injuries included retroperitoneal bleeds (RPBs) (37%), spinal fractures (37%), and pelvic fractures (37%). Analysis revealed significant associations between ACPO and shock index >0.9, Injury Severity Score >18, opioid use, RPBs, and pelvic fractures. A cecal diameter of ≥12 cm had a significant association with cecal ischemia or perforation.

CONCLUSION
This study underscores the significance of ACPO in polytrauma patients, demonstrating associations with risk factors and clinical outcomes. Clinicians should maintain a high index of suspicion, particularly in older patients with RPBs, pelvic fractures, and opioid use. Early supportive therapy, vigilant monitoring, and timely interventions are crucial for a favorable outcome. Further research and prospective trials are warranted to validate these findings and enhance understanding of ACPO in trauma patients.

LEVEL OF EVIDENCE
Prognostic and Epidemiological; Level IV.
Differences in Racial and Ethnic Disparities Between First and Repeat Kidney Transplantation
Authors: Sandal Shaifali , Ahn JiYoon , Chen Yusi , Thompson Valerie , Purnell Tanjala S. , Cantarovich Marcelo , Clark-Cutaia Maya N. , Wu Wenbo , Suri Rita , Segev Dorry L. , McAdams-DeMarco Mara 
Published: May 2024

Background.
Recent data suggest patients with graft failure had better access to repeat kidney transplantation (re-KT) than transplant-naive dialysis accessing first KT. This was postulated to be because of better familiarity with the transplant process and healthcare system; whether this advantage is equitably distributed is not known. We compared the magnitude of racial/ethnic disparities in access to re-KT versus first KT.

Methods.
Using United States Renal Data System, we identified 104 454 White, Black, and Hispanic patients with a history of graft failure from 1995 to 2018, and 2 357 753 transplant-naive dialysis patients. We used adjusted Cox regression to estimate disparities in access to first and re-KT and whether the magnitude of these disparities differed between first and re-KT using a Wald test.

Results.
Black patients had inferior access to both waitlisting and receiving first KT and re-KT. However, the racial/ethnic disparities in waitlisting for (adjusted hazard ratio [aHR] = 0.77; 95% confidence interval [CI], 0.74-0.80) and receiving re-KT (aHR = 0.61; 95% CI, 0.58-0.64) was greater than the racial/ethnic disparities in first KT (waitlisting: aHR = 0.91; 95% CI, 0.90-0.93; P
interaction = 0.001; KT: aHR = 0.68; 95% CI, 0.64-0.72; P
interaction < 0.001). For Hispanic patients, ethnic disparities in waitlisting for re-KT (aHR = 0.83; 95% CI, 0.79-0.88) were greater than for first KT (aHR = 1.14; 95% CI, 1.11-1.16; P
interaction < 0.001). However, the disparity in receiving re-KT (aHR = 0.76; 95% CI, 0.72-0.80) was similar to that for first KT (aHR = 0.73; 95% CI, 0.68-0.79; P
interaction = 0.55). Inferences were similar when restricting the cohorts to the Kidney Allocation System era.

Conclusions.
Unlike White patients, Black and Hispanic patients with graft failure do not experience improved access to re-KT. This suggests that structural and systemic barriers likely persist for racialized patients accessing re-KT, and systemic changes are needed to achieve transplant equity.
Time matters for mental health: a systematic review of quantitative studies on time perspective in psychiatric populations
Authors: Stolarski Maciej , Czajkowska-Łukasiewicz Katarzyna , Styła Rafał , Zajenkowska Anna 
Published: May 2024

Purpose of review
The ability to perform mental time travels and to develop representations of the past, the present, and the future is one of the distinctive capacities of the human mind. Despite its pronounced consequences for motivation, cognition, affect, and subjective well being, time perspective (TP) has been outside mainstream psychiatry and clinical psychology. We highlight the role of psychological-temporal phenomena in various disorders and summarize the current research on TP and psychopathology.

Recent findings
Our review ultimately comprised 21 articles, including 18 unique datasets. It revealed that persons with different psychiatric diagnoses (attention defict hyperactivity disorder (ADHD), alcohol dependence, anxiety disorders, depression, bipolar disorder, personality disorders, posttraumatic stress disorder, schizophrenia) display different temporal profiles than control groups. We also found marked associations between temporal features and psychiatric symptom severity. The effects of specific TPs vary across different psychiatric diagnoses and to some extent between various age groups, with a consistent, widespread, and nonspecific effect of past-negative and less balanced, inflexible TP profile.

Summary
Based on the review, TP biases are crucial factors in symptom development, while adaptive temporal profiles can serve as protective features against mental disorders. Understanding cognitive-temporal processes can enhance comprehension of psychopathological conditions and facilitate the development of temporality-focused clinical interventions.
Analyzing RNA-Seq Data fromChlamydiawith Super Broad Transcriptomic Activation: Challenges, Solutions, and Implications for Other Systems
Authors: Wan Danny , Cheng Andrew , Wang Yuxuan , Zhong Guangming , Li Wei Vivian , Fan Huizhou 
Published: May 2024

AbstractMotivationRNA sequencing (RNA-Seq) offers profound insights into the complex transcriptomes of diverse biological systems. However, standard differential expression analysis pipelines based on DESeq2 and edgeR encounter challenges when applied to the immediate early transcriptomes ofChlamydiaspp., obligate intracellular bacteria. These challenges arise from their reliance on assumptions that do not hold in scenarios characterized by extensive transcriptomic activation and limited repression. Standard analyses using unique chlamydial RNA-Seq reads alone identify nearly 300 upregulated and about 300 downregulated genes, significantly deviating from actual RNA-Seq read trends.ResultsBy incorporating both chlamydial and host reads or adjusting for total sequencing depth, the revised normalization methods each detected over 700 upregulated genes and 30 or fewer downregulated genes, closely aligned with observed RNA-Seq data. Further validation through qRT-PCR analysis confirmed the effectiveness of these adjusted approaches in capturing the true extent of transcriptomic activation during the immediate early phase of chlamydial infection. While the strategies employed are developed in the context ofChlamydia, the principles of flexible and context-aware normalization may inform adjustments in other systems with unbalanced gene expression dynamics, such as bacterial spore germination.Availability and implementationThe code for reproducing the presented bioinformatic analysis is available athttps://zenodo.org/records/11201379.
π-PrimeNovo: An Accurate and Efficient Non-Autoregressive Deep Learning Model for De Novo Peptide Sequencing
Authors: Zhang Xiang , Ling Tianze , Jin Zhi , Xu Sheng , Gao Zhiqiang , Sun Boyan , Qiu Zijie , Dong Nanqing , Wang Guangshuai , Wang Guibin , Li Leyuan , Abdul-Mageed Muhammad , Lakshmanan Laks V.S. , Ouyang Wanli , Chang Cheng , Sun Siqi 
Published: May 2024

AbstractPeptide sequencing via tandem mass spectrometry (MS/MS) is fundamental in proteomics data analysis, playing a pivotal role in unraveling the complex world of proteins within biological systems. In contrast to conventional database searching methods, deep learning models excel in de novo sequencing peptides absent from existing databases, thereby facilitating the identification and analysis of novel peptide sequences. Current deep learning models for peptide sequencing predominantly use an autoregressive generation approach, where early errors can cascade, largely affecting overall sequence accuracy. And the usage of sequential decoding algorithms such as beam search suffers from the low inference speed. To address this, we introduceπ-PrimeNovo, a non-autoregressive Transformer-based deep learning model designed to perform accurate and efficient de novo peptide sequencing. With the proposed novel architecture,π-PrimeNovo achieves significantly higher accuracy and up to 69x faster sequencing compared to the state-of-the-art methods. This remarkable speed makes it highly suitable for computation-extensive peptide sequencing tasks such as metaproteomic research, whereπ-PrimeNovo efficiently identifies the microbial species-specific peptides. Moreover,π-PrimeNovo has been demonstrated to have a powerful capability in accurately mining phosphopeptides in a non-enriched phosphoproteomic dataset, showing an alternative solution to detect low-abundance post-translational modifications (PTMs). We suggest that this work not only advances the development of peptide sequencing techniques but also introduces a transformative computational model with wide-range implications for biological research.
The Novel Chimeric Multi-Agonist Peptide (GEP44) Reduces Energy Intake and Body Weight in Male and Female Diet-Induced Obese Mice in a Glucagon-Like Peptide-1 Receptor-Dependent Manner
Authors: Blevins James E. , Honeycutt Mackenzie K. , Slattery Jared D. , Goldberg Matvey , Rambousek June R. , Tsui Edison , Dodson Andrew D. , Shelton Kyra A. , Salemeh Therese S. , Elfers Clinton T. , Chichura Kylie S. , Ashlaw Emily F. , Zraika Sakeneh , Doyle Robert P. , Roth Christian L. 
Published: May 2024

AbstractWe recently reported that a novel chimeric peptide (GEP44) targeting both the glucagon-like peptide-1 receptor (GLP-1R) and neuropeptide Y1- and Y2 receptor (Y1R and Y2R) reduced energy intake and body weight (BW) in diet-induced obese (DIO) rats. We hypothesized that GEP44 reduces energy intake and BW primarily through a GLP-1R dependent mechanism. To test this hypothesis, GLP-1R+/+mice and GLP-1R null (GLP-1R-/-) mice were fed a high fat diet for 4 months to elicit diet-induced obesity prior to undergoing a sequential 3-day vehicle period, 3-day drug treatment (5, 10, 20 or 50 nmol/kg; GEP44 vs the selective GLP-1R agonist, exendin-4) and a 3-day washout. Energy intake, BW, core temperature and activity were measured daily. GEP44 (10, 20 and 50 nmol/kg) reduced BW after 3-day treatment in DIO male GLP-1R+/+mice by - 1.5±0.6, -1.3±0.4 and -1.9±0.4 grams, respectively (P<0.05), with similar effects being observed in female GLP-1R+/+mice. These effects were absent in male and female DIO GLP-1R-/-mice suggesting that GLP-1R signaling contributes to GEP44-elicited reduction of BW. Further, GEP44 decreased energy intake in both male and female DIO GLP-1R+/+mice, but GEP44 appeared to produce more consistent effects across multiple doses in males. In GLP-1R-/-mice, the effects of GEP44 on energy intake were only observed in males and not females, suggesting that GEP44 may reduce energy intake, in part, through a GLP-1R independent mechanism in males. In addition, GEP44 reduced core temperature and activity in both male and female GLP-1R+/+mice suggesting that it may also reduce energy expenditure. Lastly, we show that GEP44 reduced fasting blood glucose in DIO male and female mice through GLP-1R. Together, these findings support the hypothesis that the chimeric peptide, GEP44, reduces energy intake, BW, core temperature, and glucose levels in male and female DIO mice primarily through a GLP-1R dependent mechanism.
Accuracy of dipole source reconstruction in the 3-layer BEM model against the 5-layer BEM-FMM model
Authors: Nuñez Ponasso Guillermo , McSweeney Ryan C. , Wartman William A. , Lai Peiyao , Haueisen Jens , Maess Burkhard , Knösche Thomas R. , Weise Konstantin , Noetscher Gregory M. , Raij Tommi , Makaroff Sergey N. 
Published: May 2024

ObjectiveTo compare cortical dipole fitting spatial accuracy between the widely used yet highly simplified 3-layer and modern more realistic 5-layer BEM-FMM models with and withoutadaptive mesh refinement(AMR) methods.MethodsWe generate simulated noiseless 256-channel EEG data from 5-layer (7-compartment) meshes of 15 subjects from the Connectome Young Adult dataset. For each subject, we test four dipole positions, three sets of conductivity values, and two types of head segmentation. We use theboundary element method(BEM) withfast multipole method(FMM) acceleration, with or without (AMR), for forward modeling. Dipole fitting is carried out with the FieldTrip MATLAB toolbox.ResultsThe average position error (across all tested dipoles, subjects, and models) is ∼4 mm, with a standard deviation of ∼2 mm. The orientation error is ∼20° on average, with a standard deviation of ∼15°. Without AMR, the numerical inaccuracies produce a larger disagreement between the 3- and 5-layer models, with an average position error of ∼8 mm (6 mm standard deviation), and an orientation error of 28° (28° standard deviation).ConclusionsThe low-resolution 3-layer models provide excellent accuracy in dipole localization. On the other hand, dipole orientation is retrieved less accurately. Therefore, certain applications may require more realistic models for practical source reconstruction. AMR is a critical component for improving the accuracy of forward EEG computations using a high-resolution 5-layer volume conduction model.SignificanceImproving EEG source reconstruction accuracy is important for several clinical applications, including epilepsy and other seizure-inducing conditions.
Millennial-scale societal shifts drive the widespread loss of a marine ecosystem
Authors: Lau Sally C. Y. , Thomas Marine , Williams Jessica M. , Thurstan Ruth H. , Hancock Boze , Russell Bayden D. 
Published: May 2024

AbstractDegradation of marine ecosystems by human activities is a global problem, with only recent recognition that exploitation of ecosystems over millennia can result in their functional extinction and loss from human memory. To reconstruct the historical distribution of oyster reefs in China, and the context behind loss, we extracted information from archaeological records and historical documents (pre-modern Chinese literature, administration reports, art, maps, newspapers) spanning ∼7600 years, then constrained records with past coastlines and habitable environmental conditions. Oyster reefs were extensively distributed along >750 km of coastline in the Pearl River Delta, and their exploitation underpinned the region’s development into China’s first economic hub in the 6thcentury. Millennial-scale overexploitation alongside societal shifts were central in their regional extirpation by the 19thcentury, but the enduring cultural importance of oysters is maintained by aquaculture expansion. Informed conservation practices can be developed from reconstructing the temporal interplay between human societies and the natural environment.
ZBTB11 Depletion Targets Metabolic Vulnerabilities in K-Ras Inhibitor Resistant PDAC
Authors: Tran Nathan L. , Jiang Jiewei , Ma Min , Gadbois Gillian E. , Gulay Kevin C. M. , Verano Alyssa , Zhou Haowen , Huang Chun-Teng , Scott David A. , Bang Anne G. , Tiriac Herve , Lowy Andrew M. , Wang Eric S. , Ferguson Fleur M. 
Published: May 2024

ABSTRACTOver 95% of pancreatic ductal adenocarcinomas (PDAC) harbor oncogenic mutations in K-Ras. Upon treatment with K-Ras inhibitors, PDAC cancer cells undergo metabolic reprogramming towards an oxidative phosphorylation-dependent, drug-resistant state. However, direct inhibition of complex I is poorly tolerated in patients due to on-target induction of peripheral neuropathy. In this work, we develop molecular glue degraders against ZBTB11, a C2H2zinc finger transcription factor that regulates the nuclear transcription of components of the mitoribosome and electron transport chain. Our ZBTB11 degraders leverage the differences in demand for biogenesis of mitochondrial components between human neurons and rapidly-dividing pancreatic cancer cells, to selectively target the K-Ras inhibitor resistant state in PDAC. Combination treatment of both K-Ras inhibitor-resistant cell lines and multidrug resistant patient-derived organoids resulted in superior anti-cancer activity compared to single agent treatment, while sparing hiPSC-derived neurons. Proteomic and stable isotope tracing studies revealed mitoribosome depletion and impairment of the TCA cycle as key events that mediate this response. Together, this work validates ZBTB11 as a vulnerability in K-Ras inhibitor-resistant PDAC and provides a suite of molecular glue degrader tool compounds to investigate its function.
Cell surface RNA expression modulates alveolar epithelial function
Authors: Abledu Jubilant Kwame , Herbst Christopher J. , Brandt Raphael , Kocak Alen , Ghosh Pritam , Gorenflos López Jacob L. , Diestelhorst Kevin , Block Stephan , Hackenberger Christian , Seitz Oliver , Lopez-Rodriguez Elena , Ochs Matthias , Kuebler Wolfgang M. 
Published: May 2024

AbstractGlycosylated RNA (glycoRNA) has recently emerged as a novel constituent of the glycocalyx on cell surfaces, yet its biological functions remain largely unexplored. In this report, we present the first analysis of glycoRNA expression and functionality in alveolar epithelial cells.To this end, we optimized new techniques for the detection of glycoRNA on living cell surfaces and in cell membrane-associated RNA samples through in-gel imaging after labeling with fluorescent dye conjugates. Specifically, we used conjugation of Cy5-hydrazide following mild oxidation with sodium periodate for detection of the entire cell surface sialoglycoRNA pool. Conjugation of dibenzocyclooctyne-sulfo-Cy5 (DBCO-Sulfo-Cy5) in cells fed with tetraacetylatedN-azidoacetyl-mannosamine (Ac4ManNAz) or 6-azido-L-fucose (FucAz) detectedde novoformed sialoglycoRNA or fucoglycoRNA. Finally, biotinylated lectins in combination with infrared dye-conjugated streptavidin was used to differentiate between specific glycosidic linkages.Comparisons across primary alveolar epithelial cells and different alveolar-epithelial like cell lines revealed a cell-type specific variation in glycoRNA abundance. Treatment of primary alveolar epithelial cells with an RNAse cocktail reduced epithelial surface glycoRNA and was associated with a reduction in trans-epithelial electrical resistance and influenza A viral particle abundance.As such, the present work identifies glycoRNA as a novel component of the alveolar epithelial glycocalyx, suggesting its potential relevance in epithelial barrier regulation and viral infection.
Human birth tissue products as a non-opioid medicine to inhibit post-surgical pain
Authors: Zhang Chi , Huang Qian , Ford Neil C. , Limjunyawong Nathachit , Lin Qing , Yang Fei , Cui Xiang , Uniyal Ankit , Liu Jing , Mahabole Megha , He Hua , Wang Xue-Wei , Duff Irina , Wang Yiru , Wan Jieru , Zhu Guangwu , Raja Srinivasa N , Jia Hongpeng , Yang Dazhi , Dong Xinzhong , Cao Xu , Tseng Scheffer C. , He Shao-Qiu , Guan Yun 
Published: May 2024

AbstractPain after surgery causes significant suffering. Opioid analgesics cause severe side effects and accidental death. Therefore, there is an urgent need to develop non-opioid therapies for managing post-surgical pain. Local application of Clarix Flo (FLO), a human amniotic membrane (AM) product, attenuated established post-surgical pain hypersensitivity without exhibiting known side effects of opioid use in mice. This effect was achieved through direct inhibition of nociceptive dorsal root ganglion (DRG) neurons via CD44-dependent pathways. We further purified the major matrix component, the heavy chain-hyaluronic acid/pentraxin 3 (HC-HA/PTX3) from human AM that has greater purity and water solubility than FLO. HC-HA/PTX3 replicated FLO-induced neuronal and pain inhibition. Mechanistically, HC-HA/PTX3 induced cytoskeleton rearrangements to inhibit sodium current and high-voltage activated calcium current on nociceptive neurons, suggesting it is a key bioactive component mediating pain relief. Collectively, our findings highlight the potential of naturally derived biologics from human birth tissues as an effective non-opioid treatment for post-surgical pain. Moreover, we unravel the underlying mechanisms of pain inhibition induced by FLO and HC-HA/PTX3.
Analyzing Performance of Twist Bioscience Exome Enrichment with Spike-in CNV Backbone Panels at Various Probe Densities Leveraging Golden Helix VS-CNV Analysis Software
Authors: Fortier Nathan , Rudy Gabe , Han Tina , Davassi Alessandro , Scherer Andreas 
Published: May 2024

Clinical Whole Exome Sequencing (WES) offers a high diagnostic yield test by detecting pathogenic variants in all coding genes of the human genome. WES is poised to consolidate multiple genetic tests by accurately identifying Copy Number Variation (CNV) events, typically necessitating microarray analysis. However, standard commercial exome kits are typically limited to targeting exon coding regions, leaving significant gaps in coverage between genes, which could hinder comprehensive CNV detection. To convert microarray CNV calling with NGS, advances in both assay design and computational methods are needed.Addressing the need for comprehensive coverage, Twist Bioscience has developed an enhanced Exome 2.0 Plus Comprehensive Exome Spike-in panel with added CNV “backbone” probes. These probes target common SNPs polymorphic in multiple populations and are evenly distributed in the intergenic and intronic regions, with three varying densities at 25 kb, 50 kb, and 100 kb intervals from highest to lowest resolution respectively. Concurrently, Golden Helix has developed a multi-modal CNV caller designed specifically for target-capture NGS data to detect single-exon to whole-chromosome aneuploidy CNV events. This study evaluates the combined efficacy of the backbone-probe enhanced exome capture kit and VS-CNV 2.6 in identifying known CNVs using the Coriell CNVPANEL01 reference set.The integration of the enhanced capture kit with VS-CNV 2.6 achieved a 100% sensitivity rate for the detection of known CNV events at all three probe densities. The application of best-practice quality metrics, annotations, and filters was shown to have a minimal impact on this high sensitivity. These findings underscore the potential of the augmented Twist Exome in tandem with the VS-CNV caller and VarSeq’s annotation and filtering capabilities. This combination presents a promising alternative to conventional microarray assays, potentially consolidating WES and CNV into a single assay obviating the need for additional testing in clinical CNV detection. The study’s results advocate for the implementation of this integrated approach as a more efficient and equally sensitive method for CNV analysis in a clinical setting.