bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole Blood Cardiac Troponin “Triaging” to Improve Early Detection of Myocardial Injury at a Pediatric Hospital
Authors: de Koning Lawrence , Seiden-Long Isolde , Anker Katherine , Myers Kimberley , Stang Antonia 
Published: February 2024

Abstract

Background
The importance of offering on-site cardiac troponin (cTn) testing at pediatric hospitals may be underappreciated. We developed a rapid rule-in process for myocardial injury at a pediatric hospital experiencing delays in off-site high-sensitivity cardiac troponin T (hs-cTnT) testing.

Methods
Collect-to-verify turnaround times (TATs) for off-site testing were reviewed. Pre-analytic changes to improve TATs were devised, implemented and evaluated, after which a new analyzer was selected and evaluated for on-site cTn testing. Performance of the new analyzer's assay was compared to the off-site hs-cTnT assay, and post go-live TATs for on-site testing were assessed.

Results
Median collect-to-verify TAT for short turnaround-time (STAT) priority off-site plasma hs-cTnT testing was 104 min, with 35% of orders having a TAT &gt;120 min. Eliminating serum separator tubes and requiring a separate plasma separator tube did not significantly reduce TATs. A QuidelOrtho Triage® MeterPro whole blood cardiac troponin I (cTnI) assay was implemented to “triage” time-critical and STAT priority specimens collected for off-site hs-cTnT testing. Elevated cTnI (≥0.02 µg/L) had a sensitivity of 91% for clear elevations in hs-cTnT (≥53 ng/L) but a 0% sensitivity for modest elevations (5 to 13 ng/L, 14 to 52 ng/L). An interpretive comment was auto-appended to cTnI results indicating that clinicians should wait for the hs-cTnT result if cTnI was normal. Median collect-to-verify TAT for on-site cTnI testing was &lt;50% the TAT for off-site hs-cTnT testing.

Conclusions
On-site point-of-care whole blood cTn testing can rapidly confirm significant or late-presenting myocardial injury. Combined with simultaneous off-site high-sensitivity cardiac troponin (hs-cTn) testing, this workflow is a viable interim solution for pediatric hospitals without on-site hs-cTn testing.
Effects of burn severity and postfire salvage logging on carnivore communities in montane forests
Authors: Volkmann Logan A , Hodges Karen E 
Published: February 2024

Abstract
Wildfire and postfire salvage logging are major drivers of forest succession in western North America. Although postfire landscapes support a variety of carnivore species, it is unclear how these animals respond to differing patterns and severities of burning, or to additional landscape change from postfire salvage logging. Open, early-seral habitats created by these disturbances are predicted to benefit generalists such as coyotes (Canis latrans) and weasels (Mustela spp.), but restrict the activity of forest specialists such as Canadaian Lynx (Lynx canadensis) and Pacific Marten (Martes caurina). We used winter track surveys, supplemented with remote cameras, to examine carnivore habitat use in and around large, mixed-severity burns in north-central Washington, United States (burned in 2006), and central British Columbia, Canada (burned in 2010, then partially salvage-logged; some areas reburned in 2017). At 10 to 13 years postfire, marten had similar detection rates across lightly and severely burned areas of the 2006 burn, as did coyotes. Marten selected lightly burned areas of the 2010 burn (6 to 9 years postfire) over higher burn severities, and selected burns over adjacent unburned forests. Weasels selected areas of higher burn severity on both landscapes, while Lynx selected lower burn severities. Weasels and coyotes selected areas with a greater proportion of salvage-logged habitat in the 2010 burn, while marten, lynx, and wolves (Canis lupus) avoided areas with salvage logging. Fishers (Pekania pennanti) showed no clear patterns of selection or avoidance in relation to burn severity or salvage logging. Burn severity strongly influences wildlife activity postfire; lightly burned residual habitats are critical for forest specialists. Postfire salvage logging alters carnivore communities and may hinder species that require structurally complex landscapes.
Parasitic leiomyoma of the greater omentum: a case report and literature review
Authors: Huang Zhiman , Wang Yongzhou , Lei Hongyan 
Published: February 2024

Abstract
Parasitic leiomyomas (PL), also known as free leiomyomas, which occur outside the uterus and rarely happen in clinical practice. They are usually reported in women of reproductive age who underwent hysterectomy or myomectomy and frequently present with symptoms such as abdominal pain and distention. In fact, it is hard to determine the nature of the mass according to the imaging examination and clinical manifestation. At present, the most common treatment involves an abdominal or laparoscopic surgery in order to remove the mass and perform the next step of treatment based on the histological diagnosis. In this case report, we describe a 35-year-old woman with a 12.4 × 9.3 × 9.8 cm3 PL with blood supply from the greater omentum. Considering the prolonged menstruation of the patient, she underwent the hysteroscopic and laparotomy exploration. The mass was confirmed as smooth leiomyoma with necrosis by the immunohistochemical examination. The patient had a good recovery and being discharged seven days after the surgery. The patient is still in the follow-up.
First report of a post-pneumonectomy nocardia empyema
Authors: Nakata Jonathan A , Arif Azzan , Chai Louis F , Su Stacey 
Published: February 2024

Abstract
Post-pneumonectomy empyema (PPE) is an uncommon but serious complication that carries significant therapeutic challenges. We present a late-onset PPE due to Nocardia nova in an immunocompetent individual. Nine years after a right pneumonectomy for non-small cell lung cancer, surveillance scans revealed new right pleural thickening and FDG avidity concerning for recurrence. Thoracoscopic pleural biopsies were negative for malignancy, but tissue cultures grew N. nova. Nocardia empyema is rare with few reported cases. Most occur in immunocompromised hosts, and all were associated with pulmonary or disseminated nocardiosis. Our case describes the first report of a PPE secondary to Nocardia.
Small bowel volvulus with chylous ascites: a case report
Authors: Nakamura Shun , Tajima Masaaki , Yokoyama Naoki , Kikuchi Nobuyuki 
Published: February 2024

Abstract
Here, we report a rare case of small bowel volvulus with chylous ascites. A 93-year-old man with a medical history of angina pectoris presented to the emergency department with abdominal pain. Computed tomography revealed a whirl sign of the mesenteric vessels with the axis of the superior mesenteric artery. A diagnosis of small bowel volvulus was made, and emergency surgery was performed. Laparoscopic examination revealed chylous ascites. Due to severe intestinal edema and difficulty in manipulating the forceps, surgery was transferred to a laparotomy. The entire small bowel was twisted 360° counterclockwise, requiring manual untwisting. Examination of the intestinal tract after untwisting revealed no evidence of ischemia or necrosis. However, because a diverticulum was observed on the mesenteric side of the upper jejunum and considering the influence of secondary small bowel volvulus, partial small bowel resection was performed. The patient had a favorable postoperative course.
Promoting the consumption of insect-based foods: The role of information, protein-based nutrition claims, and dietary styles
Authors: Gassler Birgit , Koetzsche Maike , Koemle Dieter , Teuber Ramona 
Published: February 2024

Abstract
Although insects have been approved as novel foods since 2021, European consumers’ willingness to purchase insect-based (IB) foods remains low. The aim of this study was to evaluate the effectiveness of (i) information treatments highlighting either the safety or environmental benefits of IB ingredients, and (ii) protein-based nutrition claims in promoting the consumption of IB foods. Additionally, we investigated how vegans, vegetarians, flexitarians, and omnivores differ in their entomophagy attitudes and choice behavior. We collected data from 844 German consumers via an online questionnaire that included a choice experiment featuring bread made with insect flour. Our findings highlight differences in entomophagy attitudes by diet, with vegetarians, and vegans showing a stronger aversion to insect consumption compared with omnivores and flexitarians. Results from random parameters logit models indicate that the information treatments had no effect and that the majority of consumers, regardless of their diet, would require a discount to buy bread made with insect flour. Protein-based nutrition claims only promoted the purchase of IB bread by vegetarians.
A Dynamic Model of Input–Output Networks
Authors: Liu Ernest , Tsyvinski Aleh 
Published: February 2024

Abstract
We develop a dynamic model of input–output networks that incorporates adjustment costs of changing inputs. Our closed-form solution for the dynamics of the economy shows that temporary shocks to upstream sectors, whose output travels through long supply chains, have disproportionately significant welfare impact compared to affected sectors’ Domar weights. We conduct a spectral analysis of the U.S. production network and reveal that the welfare impact of temporary sectoral shocks can be represented by a low-dimensional, 3-factor structure.
scCensus: Off-target scRNA-seq reads reveal meaningful biology
Authors: He Dongze , Mount Stephen M. , Patro Rob 
Published: February 2024

AbstractSingle-cell RNA-sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity. Although scRNA-seq reads from most prevalent and popular tagged-end protocols are expected to arise from the 3′ end of polyadenylated RNAs, recent studies have shown that “off-target” reads can constitute a substantial portion of the read population. in this work, we introducedscCensus, a comprehensive analysis workflow for systematically evaluating and categorizing off-target reads in scRNA-seq. We appliedscCensusto seven scRNA-seq datasets. Our analysis of intergenic reads shows that these off-target reads contain information about chromatin structure and can be used to identify similar cells across modalities. Our analysis of antisense reads suggests that these reads can be used to improve gene detection and capture interesting transcriptional activities like antisense transcription. Furthermore, using splice-aware quantification, we find that spliced and unspliced reads provide distinct information about cell clusters and biomarkers, suggesting the utility of integrating signals from reads with different splicing statuses.Overall, our results suggest that off-target scRNA-seq reads contain underappreciated information about various transcriptional activities. These observations about yet-unexploited information in existing scRNA-seq data will help guide and motivate the community to improve current algorithms and analysis methods, and to develop novel approaches that utilize off-target reads to extend the reach and accuracy of single-cell data analysis pipelines.Data AvailabilityThe scripts for reproducing the results are available athttps://github.com/COMBINE-lab/sc-census. Supplementary files can be found athttps://doi.org/10.5281/zenodo.10520670.
Puzzle Hi-C: an accurate scaffolding software
Authors: Lin Guoliang , Huang Zhiru , Yue Tingsong , Chai Jing , Li Yan , Yang Huimin , Qin Wanting , Yang Guobing , Murphy Robert W. , Zhang Ya-ping , Zhang Zijie , Zhou Wei , Luo Jing 
Published: February 2024

AbstractHigh-quality, chromosome-scale genomes are essential for genomic analyses. Analyses, including 3D genomics, epigenetics, and comparative genomics rely on a high-quality genome assembly, which is often accomplished with the assistance of Hi-C data. Current Hi-C-assisted assembling algorithms either generate ordering and orientation errors or fail to assemble high-quality chromosome-level scaffolds. Here, we offer the software Puzzle Hi-C, which uses Hi-C reads to accurately assign contigs or scaffolds to chromosomes. Puzzle Hi-C uses the triangle region instead of the square region to count interactions in a Hi-C heatmap. This strategy dramatically diminishes scaffolding interference caused by long-range interactions. This software also introduces a dynamic, triangle window strategy during assembly. Initially small, the window expands with interactions to produce more effective clustering. Puzzle Hi-C outperforms available scaffolding tools.
Real-World Effectiveness of a Third Dose of mRNA-1273 versus BNT162b2 on Inpatient and Medically Attended COVID-19 among Immunocompromised Adults in the United States
Authors: Sun Tianyu , Li Linwei , Mues Katherine , Georgieva Mihaela , Kirk Brenna , Mansi James , Van de Velde Nicolas , Beck Ekkehard 
Published: February 2024

ABSTRACTRecent data have shown elevated infection rates in several subpopulations at risk of SARS-CoV-2 infection and COVID-19, including immunocompromised (IC) individuals. Previous research suggests that IC persons have reduced risks of hospitalization and medically-attended COVID-19 with 2 doses of mRNA-1273 (SpikeVax; Moderna) compared to two doses of BNT162b2 (Comirnaty; Pfizer/BioNTech). The main objective of this retrospective cohort study was to compare real-world effectiveness of third doses of mRNA-1273 versus BNT162b2 at multiple time points on occurrence of COVID-19 hospitalization and medically-attended COVID-19 among IC adults in the US. The HealthVerity (HV) medical and pharmacy claims database, which contains data from >330 million patients, was the data source. Both subgroup and sensitivity analyses were conducted in addition to the core comparisons noted. In propensity score-adjusted analyses, receiving mRNA-1273 vs BNT162b2 as third dose was associated with 32% (relative risk [RR] 0.68; 95% confidence interval [CI] 0.51-0.89), 29% (0.71; 0.57-0.86), and 23% (0.77; 0.62-0.93) lower risk of COVID-19 hospitalization after 90, 180, and 270 days, respectively. Corresponding reductions in medically-attended COVID-19 were 8% (0.92; 0.86-0.98), 6% (0.94; 0.90-0.98), and 2% (0.98; 0.94-1.02), respectively. Our findings suggest a third dose of mRNA-1273 is more effective than a third dose of BNT162b2 in preventing COVID-19 hospitalization and breakthrough medically-attended COVID-19 among IC adults in the US.
Brain white matter pathways of resilience to chronic back pain: a multisite validation
Authors: Mišić Mina , Lee Noah , Zidda Francesca , Sohn Kyungjin , Usai Katrin , Löffler Martin , Uddin Md Nasir , Farooqi Arsalan , Schifitto Giovanni , Zhang Zhengwu , Nees Frauke , Geha Paul , Flor Herta 
Published: February 2024

AbstractChronic back pain (CBP) is a global health concern with significant societal and economic burden. While various predictors of back pain chronicity have been proposed, including demographic and psychosocial factors, neuroimaging studies have pointed to brain characteristics as predictors of CBP. However, large-scale, multisite validation of these predictors is currently lacking. In two independent longitudinal studies, we examined white matter diffusion imaging data and pain characteristics in patients with subacute back pain (SBP) over six- and 12-month periods. Diffusion data from individuals with CBP and healthy controls (HC) were analyzed for comparison. Whole-brain tract-based spatial statistics analyses revealed that a cluster in the right superior longitudinal fasciculus (SLF) tract had larger fractional anisotropy (FA) values in patients who recovered (SBPr) compared to those with persistent pain (SBPp), and predicted changes in pain severity. The SLF FA values accurately classified patients at baseline and follow-up in a third publicly available dataset (Area under the Receiver Operating Curve ∼ 0.70). Notably, patients who recovered had FA values larger than those of HC suggesting a potential role of SLF integrity in resilience to CBP. Structural connectivity-based models also classified SBPp and SBPr patients from the three data sets (validation accuracy 67%). Our results validate the right SLF as a robust predictor of CBP development, with potential for clinical translation. Cognitive and behavioral processes dependent on the right SLF, such as proprioception and visuospatial attention, should be analyzed in subacute stages as they could prove important for back pain chronicity.
Heritability and polygenic load for combined anxiety and depression
Authors: Tabrizi Fara , Rosén Jörgen , Grönvall Hampus , William-Olsson Victor Rahimzadeh , Arner Erik , Magnusson Patrik KE , Palm Camilla , Larsson Henrik , Viktorin Alexander , Bernhardsson Jens , Björkdahl Johanna , Jansson Billy , Sundin Örjan , Zhou Xuan , Speed Doug , Åhs Fredrik 
Published: February 2024

AbstractAnxiety and depression commonly occur together resulting in worse health outcomes than when they occur in isolation. We aimed to determine whether the genetic liability for combined anxiety and depression was greater than when anxiety or depression occurred alone. Data from 12,558 genotyped twins (ages 38-85) were analysed, including 1,986 complete monozygotic and 1,809 complete dizygotic pairs. Outcomes were prescription of antidepressant and anxiolytic drugs, as demined by the World Health Organization Anatomical Therapeutic Chemical Classimication System (ATC) convention, for combined anxiety and depression (n= 1054), anxiety only (n= 744), and depression only (n= 511). Heritability of each outcome was estimated using twin modelling, and the inmluence of common genetic variation was assessed from polygenic scores (PGS) for depressive symptoms, anxiety, and 40 other traits. Heritability of combined anxiety and depression was 79% compared with 41% for anxiety and 50% for depression alone. The PGS for depressive symptoms likewise predicted more variation in combined anxiety and depression (adjusted odds ratio perSDPGS = 1.53, 95% CI = 1.43-1.63; ΔR2= .031, ΔAUC = .044) than the other outcomes, with nearly identical results when combined anxiety and depression was demined by International Classimication of Diseases (ICD) diagnoses (adjusted odds ratio perSDPGS = 1.70, 95% CI = 1.53-1.90; ΔR2= .036, ΔAUC = .051). Individuals in the highest decile of PGS for depressive symptoms had over 5 times higher odds of being prescribed medication for combined anxiety and depression compared to those in the lowest decile. We conclude that genetic factors explain substantially more variation in combined anxiety and depression than anxiety or depression alone.
Exploring distinct and joint contributions of the Locus Coeruleus and the Substantia Nigra/Ventral Tegmental Area complex to reward and valence processing using high-resolution fMRI
Authors: Hall J. M. , Shahnazian D. , Krebs R. M. 
Published: February 2024

AbstractDopaminergic neurons in the substantia nigra and the ventral tegmental area (SN/VTA) are classically viewed as key mediators in reward processing, while noradrenergic cells in the locus coeruleus (LC) are thought to modulate (negative) saliency processing. However, this conventional distinction is being revised by more recent research in animals. To explore the respective contributions of both the LC and SN/VTA in reward and valence processing in humans, we assessed fMRI data during stimulus encoding and response phase of a rewarded emotion-discrimination task (n=38). Participants responded significantly faster to reward-predicting and negative valence stimuli compared to their non-salient counterparts. LC activity was overall higher during trials involving reward prospect, and in particular for reward trials featuring positive valence, demonstrating an additive effect of reward and positive valence in LC. Moreover, LC activity was differentially increased for negative compared to positive valence in the response phase, indexing its role in invigorating responses to negative events. The SN/VTA showed increased activity in the response phase of reward trials (neutral valence) and negative valence trials (no-reward), which aligns with coding relative saliency of these events in their respective contexts. LC modulations were accompanied by covariations in occipital cortex, suggesting noradrenergic contributions to visual prioritization of salient events. The findings underscore the sensitivity of both LC and SN/VTA to reward prospects and negative valence, challenging the dominant view of SN/VTA’s involvement in merely positive events and emphasizing their essential role in action invigoration above and beyond mere stimulus encoding. The intricate roles of the DA and NA system in reward and emotional valence processing in humans warrant further exploration and validation, given the limitations inherent to neuroimaging of deep brain structures.
OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide
Authors: Sepulveda Hugo , Li Xiang , Yue Xiaojing , Carlos Angel J. , Arteaga-Vazquez Leo J. , Brown Caitlin , Brunelli Melina , Jansz Natasha , Puddu Fabio , Scotcher Jamie , Creed Páidí , Kennedy Patrick , Manriquez Cindy , Myers Samuel A , Crawford Robert , Faulkner Geoffrey J. , Rao Anjana 
Published: February 2024

ABSTRACTTheO-GlcNAc transferase OGT interacts robustly with all three mammalian TET methylcytosine dioxygenases. We show here that deletion of theOgtgene in mouse embryonic stem cells (mESC) results in a widespread increase in the TET product 5-hydroxymethylcytosine (5hmC) in both euchromatic and heterochromatic compartments, with concomitant reduction of the TET substrate 5-methylcytosine (5mC) at the same genomic regions. mESC engineered to abolish the TET1-OGT interaction likewise displayed a genome-wide decrease of 5mC. DNA hypomethylation in OGT-deficient cells was accompanied by de-repression of transposable elements (TEs) predominantly located in heterochromatin, and this increase in TE expression was sometimes accompanied by increasedcis-expression of genes and exons located 3’ of the expressed TE. Thus, the TET-OGT interaction prevents DNA demethylation and TE expression in heterochromatin by restraining TET activity genome-wide. We suggest that OGT protects the genome against DNA hypomethylation and impaired heterochromatin integrity, preventing the aberrant increase in TE expression observed in cancer, autoimmune-inflammatory diseases, cellular senescence and ageing.
Intermembrane space-localized twin Cx9C motif-containing TbTim15 is an essential subunit of the single mitochondrial inner membrane protein translocase of trypanosomes
Authors: von Känel Corinne , Oeljeklaus Silke , Wenger Christoph , Stettler Philip , Harsman Anke , Warscheid Bettina , Schneider André 
Published: February 2024

AbstractAll mitochondria import >95% of their proteins from the cytosol. This process is mediated by protein translocases in the mitochondrial membranes, whose subunits are generally highly conserved. Most eukaryotes have two inner membrane protein translocases (TIMs) that are specialized to import either presequence-containing or mitochondrial carrier pro-teins. In contrast, the parasitic protozoanTrypanosoma bruceihas a single TIM complex consisting of one conserved and five unique subunits. Here, we show that the trypanoso-mal TIM complex contains an additional trypanosomatid-specific subunit, designated TbTim15. TbTim15 is associated with the TIM complex, lacks transmembrane domains and localizes to the intermembrane space. TbTim15 is essential for procyclic and bloodstream forms of trypanosomes. It contains two twin CX9C motifs and mediates import of both, presequence-containing and mitochondrial carrier proteins. While the precise function of TbTim15 in mitochondrial protein import is unknown, our results are consistent with the notion that it may function as an import receptor for the non-canonical trypanosomal TIM complex.