bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical outcomes and quality of life after contemporary isolated coronary bypass grafting: a prospective cohort study
Authors: Sandner Sigrid , Misfeld Martin , Caliskan Etem , Böning Andreas , Aramendi Jose , Salzberg Sacha P. , Choi Yeong-Hoon , Perrault Louis P. , Tekin Ilker , Cuerpo Gregorio P. , Lopez-Menendez Jose , Weltert Luca P. , Böhm Johannes , Krane Markus , González-Santos José M. , Tellez Juan-Carlos , Holubec Tomas , Ferrari Enrico , Doros Gheorghe , Vitarello Clara J. , Emmert Maximilian Y. ,   on behalf of the Registry Investigators; European DuraGraft Registry investigators’
Published: March 2023

Objectives:
The objective of the European Multicenter Registry to Assess Outcomes in coronary artery bypass grafting (CABG) patients (DuraGraft Registry) was to determine clinical outcomes and quality of life (QoL) after contemporary CABG that included isolated CABG and combined CABG/valve procedures, using an endothelial damage inhibitor (DuraGraft) intraoperatively for conduit preservation. Here, we report outcomes in the patient cohort undergoing isolated CABG.

Methods:
The primary outcome was the composite of all-cause death, myocardial infarction (MI), or repeat revascularization (RR) [major adverse cardiac events (MACE)] at 1 year. Secondary outcomes included the composite of all-cause death, MI, RR, or stroke [major adverse cardiac and cerebrovascular events (MACCE)], and QoL. QoL was assessed with the EuroQol-5 Dimension questionnaire. Independent risk factors for MACE at 1 year were determined using Cox regression analysis.

Results:
A total of 2532 patients (mean age, 67.4±9.2 years; 82.5% male) underwent isolated CABG. The median EuroScore II was 1.4 [interquartile range (IQR), 0.9–2.3]. MACE and MACCE rates at 1 year were 6.6% and 7.8%, respectively. The rates of all-cause death, MI, RR, and stroke were 4.4, 2.0, 2.2, and 1.9%, respectively. The 30-day mortality rate was 2.3%. Age, extracardiac arteriopathy, left ventricular ejection fraction less than 50%, critical operative state, and left main disease were independent risk factors for MACE. QoL index values improved from 0.84 [IQR, 0.72–0.92] at baseline to 0.92 [IQR, 0.82–1.00] at 1 year (P<0.0001).

Conclusion:
Contemporary European patients undergoing isolated CABG have a low 1-year clinical event rate and an improved QoL.
Can prophylactic tamsulosin reduce the risk of urinary retention after surgery? A systematic review and meta-analysis of randomized control trials
Authors: Zhou Zhaohui , Gan Wenyi , Li Zhiyong , Li Zhen , Zhou Fangjian , Li Hua , Liu Zhuowei 
Published: March 2023

Objective:
The meta-analysis aimed to integrate the evidence of randomized control trials to estimate the efficacy of prophylactic tamsulosin on postoperative urinary retention (POUR).

Methods:
The PubMed, Embase, Web of Science, and Cochrane Library databases were searched through 1 March 2022 using predetermined keywords. Randomized control trials reporting the preventive efficacy of prophylactic tamsulosin against POUR were identified according to the PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) guideline. Pooled risk ratios (RRs) were calculated using a random-effects model or a fixed-effects model based on the results of heterogeneity assessment. A meta-regression analysis was performed to explore the potential sources of heterogeneity.

Results:
There were 14 studies with 1102 patients in the Tamsulosin group and 1119 patients in the Control group. The risk of POUR was significantly lower in the Tamsulosin group (156/1102 [14.2%] vs. 238/1119 [21.3%]; RR=0.65; 95% CI: 0.50–0.86; P=0.002; Heterogeneity: I
2=51%; P=0.01). Tamsulosin administration was associated with a higher risk of adverse events (65/614 [10.6%] vs. 39/626 [6.2%]; RR=1.72; 95% CI: 1.19–2.48; P=0.004; Heterogeneity: I
2=0%; P=0.70). The meta-regression identified the mean age of patients as the only potential source of heterogeneity. Subgroup analysis showed that the younger patients (age <50 years) might benefit more from tamsulosin intake (RR=0.36; 95% CI: 0.19–0.70; P=0.003; Heterogeneity: I
2=49%; P=0.14).

Conclusions:
The current meta-analysis suggested that prophylactic tamsulosin contributed to the prevention of POUR, and younger patients (<50 years) might benefit more from this preventive regimen. Tamsulosin was also associated with a higher risk of adverse events.
Uromodulin: more than a marker for chronic kidney disease progression
Authors: LaFavers Kaice , Garimella Pranav S. 
Published: March 2023

Purpose of review
Uromodulin, a protein that is highly conserved across several species through evolution, functions to maintain homeostasis and prevent disease development and progression. Historically, the role of uromodulin has been thought to be limited to the kidney and genitourinary tract. This review highlights developments indicating a broader role of uromodulin in human health.

Recent findings
Although initially discovered in the urine and found to have immunomodulatory properties, recent findings indicate that serum uromodulin (sUMOD) is distinct from urine uromodulin (uUMOD) in its structure, function, and regulation. uUMOD binds pathogenic bacteria in the urine preventing infection and is also upregulated in kidneys undergoing repair after injury. Uromodulin knockout mice exhibit higher mortality in the setting of sepsis which is also associated with upregulation of sUMOD. sUMOD lowers calcification risk but this may be influenced by presence of kidney disease.

Summary
Uromodulin is an evolutionarily conserved protein produced exclusively in the kidney tubule cells with evolving roles being reported both in the kidney and systemically. Further research should be focused at harnessing its use as a potential therapeutic.
Beyond donation to organ utilization in the USA
Authors: Stewart Darren , Hasz Richard , Lonze Bonnie 
Published: March 2023

Purpose of review
The deceased donor organ pool has broadened beyond young, otherwise healthy head trauma victims. But an abundance of donated organs only benefits patients if they are accepted, expeditiously transported and actually transplanted. This review focuses on postdonation challenges and opportunities to increase the number of transplants through improved organ utilization.

Recent findings
We build upon recently proposed changes in terminology for measuring organ utilization. Among organs recovered for transplant, the nonuse rate (NURREC) has risen above 25% for kidneys and pancreata. Among donors, the nonuse rate (NURDON) has risen to 40% for livers and exceeds 70% for thoracic organs. Programme-level variation in offer acceptance rates vastly exceeds variation in the traditional, 1-year survival benchmark. Key opportunities to boost utilization include donation after circulatory death and hepatitis C virus (HCV)+ organs; acute kidney injury and suboptimal biopsy kidneys; older and steatotic livers.

Summary
Underutilization of less-than-ideal, yet transplant-worthy organs remains an obstacle to maximizing the impact of the U.S. transplant system. The increased risk of inferior posttransplant outcomes must always be weighed against the risks of remaining on the waitlist. Advanced perfusion technologies; tuning allocation systems for placement efficiency; and data-driven clinical decision support have the potential to increase utilization of medically complex organs.
The genetic architecture of pain intensity in a sample of 598,339 U.S. veterans
Authors: Toikumo Sylvanus , Vickers-Smith Rachel , Jinwala Zeal , Xu Heng , Saini Divya , Hartwell Emily , Venegas Mirko P. , Sullivan Kyle A. , Xu Ke , Jacobson Daniel A. , Gelernter Joel , Rentsch Christopher T. ,   Million Veteran Program, Stahl Eli , Cheatle Martin , Zhou Hang , Waxman Stephen G. , Justice Amy C. , Kember Rachel L. , Kranzler Henry R. 
Published: March 2023

AbstractChronic pain is a common problem, with more than one-fifth of adult Americans reporting pain daily or on most days. It adversely affects quality of life and imposes substantial personal and economic costs. Efforts to treat chronic pain using opioids played a central role in precipitating the opioid crisis. Despite an estimated heritability of 25-50%, the genetic architecture of chronic pain is not well characterized, in part because studies have largely been limited to samples of European ancestry. To help address this knowledge gap, we conducted a cross-ancestry meta-analysis of pain intensity in 598,339 participants in the Million Veteran Program, which identified 125 independent genetic loci, 82 of which are novel. Pain intensity was genetically correlated with other pain phenotypes, level of substance use and substance use disorders, other psychiatric traits, education level, and cognitive traits. Integration of the GWAS findings with functional genomics data shows enrichment for putatively causal genes (n = 142) and proteins (n = 14) expressed in brain tissues, specifically in GABAergic neurons. Drug repurposing analysis identified anticonvulsants, beta-blockers, and calcium-channel blockers, among other drug groups, as having potential analgesic effects. Our results provide insights into key molecular contributors to the experience of pain and highlight attractive drug targets.
Molecular diversity of bivalve transmissible neoplasia of blue mussels in the Kola Bay (Barents Sea) indicates a recent migration of the cancer lineages between the North Pacific and Northern Europe
Authors: Skazina M. , Ponomartsev N. , Maiorova M. , Dolganova I. , Khaitov V. , Marchenko J. , Lentsman N. , Odintsova N. , Strelkov P. 
Published: March 2023

AbstractBivalve transmissible neoplasia (BTN) is a leukemia-like cancer “metastasizing” by transmission of living cancer cells between molluscs. Blue mussels harbor two evolutionary lineages of BTN,MtrBTN1 andMtrBTN2, both derived fromMytilus trossulus. WhileMtrBTN1 has been found only inM. trossulusin North Pacific,MtrBTN2 parasitizes differentMytilusspecies worldwide, particularly in Western Europe. No targeted studies of BTN in Northern European mussels (M. edulis,M. trossulus) have been made. We searched for BTN in mussels from the Kola Bay (Barents Sea) with the help of flow cytometry of the hemolymph, qPCR with primers specific to cancer-associated alleles and sequencing of mitochondrial and nuclear loci. The species of the mussel hosts was ascertained genetically. BothMtrBTN1 andMtrBTN2 were present in our material, though their prevalence was low (∼0.4%). The only instance ofMtrBTN2 was found inM. trossulus.MtrBTN1 occurred inM. trossulusand in a hybrid betweenM. trossulusandM. edulis. This finding indicates thatMtrBTN1 may potentially infect the latter species. The mtDNA haplotypes found in both lineages were nearly identical to those known from the North Pacific, but not from elsewhere. Our results suggest that they arrived in the Kola Bay fairly recently, probably with the maritime transport along the Northern Sea Route, and that the invasion was independent of that in Western Europe. A relatively young evolutionary age ofMtrBTN1 seems to suggest that it is an emerging disease in the process of niche expansion.
Nondestructive Spatial Lipidomics for Glioma Classification
Authors: Martella Davide Alessandro , Rose Leor Ariel , Rouatbi Nadia , Gu Chenlei , Caprettini Valeria , Jensen Magnus , Hagemann Cathleen , Serio Andrea , Al-Jamal Khuloud , Parsons Maddy , Bergholt Mads , Brennan Paul , Zaritsky Assaf , Chiappini Ciro 
Published: March 2023

AbstractMapping the molecular composition of tissues using spatial biology provides high-content information for molecular diagnostics. However, spatial biology approaches require invasive procedures to collect samples and destroy the investigated tissue, limiting the extent of analysis, particularly for highly functional tissues such as those of the brain. To address these limitations, we developed a workflow to harvest biomolecules from brain tissues using nanoneedles and characterise the distribution of lipids using desorption electrospray ionization mass spectrometry imaging. The nanoneedles preserved the original tissue while harvesting a reliable molecular profile and retaining the original lipid distribution for mouse and human brain samples, accurately outlining the morphology of key regions within the brain and tumour lesions. The deep neural network analysis of a cohort containing 23 human glioma biopsies showed that nanoneedle samples maintain the molecular signatures required to accurately classify disease state. Thus, nanoneedles provide a route for tissue-preserving spatial lipidomic and molecular diagnostics.
The GlycoPaSER prototype as a real-time N-glycopeptide identification tool based on the PaSER parallel computing platform
Authors: Armony Gad , Brehmer Sven , Srikumar Tharan , Pfennig Lennard , Zijlstra Fokje , Trede Dennis , Kruppa Gary , Lefeber Dirk J. , van Gool Alain J. , Wessels Hans J.C.T. 
Published: March 2023

AbstractReal-time database searching allows for simpler and automated proteomics workflows as it eliminates technical bottlenecks in high throughput experiments. Most importantly, it enables results dependent acquisition (RDA) where search results can be used to guide data acquisition during acquisition. This is especially beneficial for glycoproteomics since the wide range of physicochemical properties of glycopeptides lead to a wide range of optimal acquisition parameters. We established here the GlycoPaSER prototype by extending the Parallel Search Engine in Real-time (PaSER) functionality for real-time glycopeptide identification from fragmentation spectra. Glycopeptide fragmentation spectra were decomposed into peptide- and glycan-moiety spectra using common N-glycan fragments. Each moiety was subsequently identified by a specialized algorithm running in real-time. GlycoPaSER can keep up with the rate of data acquisition for real-time analysis with similar performance to other glycoproteomics software and produces results that are in line with literature reference data. The GlycoPaSER prototype presented here provides the first proof-of-concept for real-time glycopeptide identification that unlocks future development of RDA technology to transcend data acquisition.
A rapid, multiplex digital PCR assay forEGFR,KRAS,BRAF,ERBB2variants andALK,RET,ROS1,NTRK1gene fusions in non-small cell lung cancer
Authors: Leatham Bryan , McNall Katie , Subramanian Hari K. , Jacky Lucien , Alvarado John , Yurk Dominic , Wang Mimi , Green Donald C. , Tsongalis Gregory J. , Rajagopal Aditya , Schwartz Jerrod J. 
Published: March 2023

AbstractDigital PCR (dPCR) is emerging as an ideal platform for the detection and tracking of genomic variants in cancer due to its high sensitivity and simple workflow. The growing number of clinically-actionable cancer biomarkers creates a need for fast, accessible methods that allow for dense information content and high accuracy. Here, we describe a proof-of-concept amplitude modulation based multiplex dPCR assay capable of detecting 12 single nucleotide and indel variants inEGFR,KRAS,BRAF, andERBB2,14 gene fusions inALK, RET, ROS1, NTRK1,andMETexon 14 skipping present in non-small cell lung cancer (NSCLC). We also demonstrate the use of multi-spectral target signal encoding to improve the specificity of variant detection by reducing background noise up to 11-fold. The assay reported an overall 100% PPA and 98.5% NPA compared to a sequencing-based assay in a cohort of 62 human FFPE samples. In addition, the dPCR assay rescued actionable information in 10 samples that failed to sequence, highlighting the utility of a multiplexed digital assay as a potential reflex solution for challenging NSCLC samples.
Multidimensional proteomics identifies molecular trajectories of cellular aging and rejuvenation
Authors: Leutert Mario , Armstrong Joe , Ollodart Anja R. , Hess Kyle , Muir Michael , Rodriguez-Mias Ricard A. , Kaeberlein Matt , Dunham Maitreya , Villén Judit 
Published: March 2023

AbstractThe declining capacity of cells to maintain a functional proteome is a major driver of cellular dysfunction and decreased fitness in aging. Here we assess the impact of aging on multiple proteome dimensions, which are reflective of function, across the replicative lifespan ofSaccharomyces cerevisiae. We quantified protein abundance, protein turnover, protein thermal stability, and protein phosphorylation in mother yeast cells and their derived progeny at different ages. We find progressive and cumulative proteomic alterations that are reflective of dysregulation of complex assemblies, mitochondrial remodeling, post-translational activation of the AMPK/Snf1 energy sensor in mother cells, and an overall shift from biosynthetic to energy-metabolic processes. Our multidimensional proteomic study systematically corroborates previous findings of asymmetric segregation and daughter cell rejuvenation, and extends these concepts to protein complexes, protein phosphorylation, and activation of signaling pathways. Lastly, profiling age-dependent proteome changes in a caloric restriction model of yeast provided mechanistic insights into longevity, revealing minimal remodeling of energy-metabolic pathways, improved mitochondrial maintenance, ameliorated protein biogenesis, and decreased stress responses. Taken together, our study provides thousands of age-dependent molecular events that can be used to gain a holistic understanding of mechanisms of aging.
Hiding in Plain Sight: Phylogenomics Reveals a New Branch on the Noctuoidea Tree of Life
Authors: St Laurent Ryan A. , Goldstein Paul Z. , Miller Scott E. , Robbins Robert K. 
Published: March 2023

AbstractWe present the results of the first phylogenomic analyses based on anchored hybrid enrichment (AHE) data from densely sampled tribes and subfamilies of Notodontidae (Prominent Moths). Our analyses reveal the family’s polyphyly with respect to an assemblage of genera related toScranciaHolland that has been variously recognized at the tribal or subfamilial rank. We propose and re-describe Scranciidae,stat. nov., and recognize 21 genera and approximately 100 species—distributed in Africa, Asia, and Australia and not represented in previous phylogenomic studies—from the six recognized noctuoid families (Noctuidae, Erebidae, Euteliidae, Nolidae, Notodontidae, and Oenosandridae). We further re-interpret morphological synapomorphies previously proposed for Notodontidae (including Scranciidae) and for the trifid Noctuoidea,viz.the ventral-facing tympanum and trifid forewing venation— characters previously called into question when Doidae were transferred from Noctuoidea to Drepanoidea. Deep-level relationships within Noctuoidea are not firmly established outside the clade comprising the four quadrifid families (Noctuidae, Erebidae, Euteliidae, and Nolidae), and in attempting to establish the phylogenetic position of Scranciidae relative to Notodontidae, Oenosandridae, and the quadrifids, we obtain conflicting results depending on data type (amino acid vs. nucleotide) and analytical framework (maximum likelihood, multi-species coalescent, and parsimony). We also demonstrate that discordant topologies among these ancient lineages yield drastically different divergence time estimates, highlighting the need for caution when interpreting phylogenetic dating of uncertain topologies. Following multiple analyses of several datasets designed around the distribution of missing data, and an evaluation of strict support measures at the deepest nodes of the noctuoid tree, we provisionally conclude that this ambiguity is a function of character conflict amplified by missing data and short branch lengths, and that in the topology best supported by the available data, Scranciidae is placed well outside Notodontidae and sister to the remaining Noctuoidea.
Pathology of natural infection with highly pathogenic avian influenza virus (H5N1) clade 2.3.4.4b in wild terrestrial mammals in the United States in 2022
Authors: Elsmo EJ , Wünschmann A , Beckmen KB , Broughton-Neiswanger LB , Buckles EL , Ellis J , Fitzgerald SD , Gerlach R , Hawkins S , Ip HS , Lankton JS , Lemley EM , Lenoch JB , Killian ML , Lantz K , Long L , Maes R , Mainenti M , Melotti J , Moriarty ME , Nakagun S , Ruden RM , Shearn-Bochsler V , Thompson D , Torchetti MK , Van Wettere AJ , Wise AG , Lim AL 
Published: March 2023

AbstractThis article describes the first detections of disease due to natural infection with highly pathogenic avian influenza virus (HPAIv) H5N1 of the Eurasian lineage goose/Guangdong clade 2.3.4.4b in wild terrestrial mammals throughout the United States during 2021-2022. Affected mammalian species include 50 red foxes (Vulpes vulpes), 6 striped skunks (Mephitis mephitis), 4 raccoons (Procyon lotor), 2 bobcats (Lynx rufus), 2 Virginia opossums (Didelphis virginiana), 1 coyote (Canis latrans), 1 fisher (Pekania pennanti), and 1 gray fox (Urocyon cinereoargenteus). Infected mammals primarily exhibited neurological signs. Necrotizing meningoencephalitis, interstitial pneumonia, and myocardial necrosis were the most common lesions; however, species variations in lesion distribution were observed. Genotype analysis of sequences from 48 animals indicates that these cases represent spillover infections from wild birds.
Impact of Socioeconomic Status on Amygdala and Hippocampus Subdivisions in Children and Adolescents
Authors: Hanson Jamie L , Adkins Dorthea J , Nacewicz Brendon M , Barry Kelly R 
Published: March 2023

ABSTRACTSocioeconomic status (SES) in childhood can impact behavioral and brain development. Past work has consistently focused on the amygdala and hippocampus, two brain areas critical for emotion and behavioral responding. While there are SES differences in amygdala and hippocampal volumes, there are many unanswered questions in this domain connected to neurobiological specificity, and for whom these effects may be more pronounced. We may be able to investigate some anatomical subdivisions of these brain areas, as well as if relations with SES vary by participant age and sex. No work to date has however completed these types of analyses. To overcome these limitations, here, we combined multiple, large neuroimaging datasets of children and adolescents with information about neurobiology and SES (N=2,765). We examined subdivisions of the amygdala and hippocampus and found multiple amygdala subdivisions, as well as the head of the hippocampus, were related to SES. Greater volumes in these areas were seen for higher-SES youth participants. Looking at age- and sex-specific subgroups, we tended to see stronger effects in older participants, for both boys and girls. Paralleling effects for the full sample, we see significant positive associations between SES and volumes for the accessory basal amygdala and head of the hippocampus. We more consistently found associations between SES and volumes of the hippocampus and amygdala in boys (compared to girls). We discuss these results in relation to conceptions of “sex-as-a-biological variable” and broad patterns of neurodevelopment across childhood and adolescence. These results fill in important gaps on the impact of SES on neurobiology critical for emotion, memory, and learning.