bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mesothelioma in situ of the peritoneum: report of three cases and review of the literature
Authors: Symes Emily , Tjota Melissa , Cody Brittany , Kindler Hedy , Mitchell Owen , Witmer Hunter , Turaga Kiran , Mueller Jeffrey , Krausz Thomas , Husain Aliya N. , Li Huihua 
Published: December 2023

AimDiagnosis of mesothelioma in situ (MIS) is historically controversial and, until recently, specific features defining the entity have not been well characterized. Most reported cases of MIS occurred in the pleura; peritoneal MIS is very rare. This study investigates the morphologic features and results of ancillary testing in peritoneal MIS.MethodsWe present three patients with peritoneal MIS, as defined by a single layer of mesothelial cells with loss of nuclear BRCA‐1‐associated protein‐1 (BAP1) immunostaining and without evidence of invasive tumour by microscopic evaluation, imaging, or direct examination of the peritoneum. Histology and immunostains were reviewed by three expert thoracic pathologists with multidisciplinary input. Next‐generation sequencing (NGS) was performed in all three cases. A literature review was conducted to characterize this rare precursor lesion.ResultsBAP1 was lost in all three lesions, while methylthioadenosine phosphorylase (MTAP) was retained in two (not performed in the third). NGS revealed BAP1 pathogenic alterations in all three cases as well as mutations of SMO, ERCC3, TET2, and U2AF1. Progression to invasive mesothelioma occurred in one patient at 13 months postdiagnosis (case 1). One patient was diagnosed at age 24 and was later found to harbour a BAP1 germline mutation (case 3).ConclusionThis work describes the histologic features and clinicopathologic characteristics of peritoneal MIS in three cases, highlights BAP1 somatic and germline mutations in peritoneal MIS, and strengthens the importance of ancillary studies (including immunohistochemical and molecular studies) in the diagnosis of MIS.
NR1D1‐rearranged soft tissue tumour: A clinicopathological and molecular analysis of four additional cases
Authors: Yin Tangchen , Zhu Peipei , Lao I Weng , Yu Lin , Bai Qianming , Zhou Xiaoyan , Wang Jian 
Published: December 2023

AimsNuclear receptor subfamily 1 group D member 1 (NR1D1)‐rearranged soft tissue tumour is a newly described entity with an epithelioid morphology and a potential for aggressive behaviour. Largely due to under‐recognition, this tumour type has not yet been widely acknowledged. Herein, we report four additional cases to further expand its clinicopathological and molecular spectrum.Methods and resultsFour mesenchymal tumours with NR1D1 rearrangement were identified from our consultation files. There were one male and three females with ages ranging from 19 to 47 years (median = 28.5 years). Tumour occurred in the tongue, neck, hip and index finger, respectively. Histologically, two tumours were composed predominantly of epithelioid cells; one tumour had admixed epithelioid‐spindle cells and one tumour consisted of monomorphic small round to ovoid cells. By immunohistochemistry, none of the tumours expressed lineage‐specific markers. Targeted RNA‐sequencing identified NR1D1 fusions in all four tumours, the partner genes being MAML2, MAML3, KMT2A and NCOA2, respectively. The novel MAML3 and NCOA2 rearrangements were confirmed by fluorescence in‐situ hybridisation analysis. On follow‐up (2–23 months), one patient experienced local recurrence due to incomplete resection and one patient developed lung metastasis. The other two patients were alive without disease.ConclusionsThis study adds more support for NR1D1‐rearranged soft tissue tumour as an emerging entity. The occurrence of two additional tumours in the head and neck region, description of a small round cell variant and identification of novel MAML3, KMT2A and NCOA2 partners further expand its clinicopathological and molecular spectrum. More studies on larger series are necessary to validate the fully malignant potential of NR1D1‐rearranged soft tissue tumour.
Antecedents and outcomes of open innovation over the past 20 years: A framework and meta‐analysis
Authors: Zhang Hao , Ma Zengguang , Liang Xiaoning , Garrett Tony C. 
Published: December 2023

AbstractThe open innovation paradigm emphasizes that firms can improve their innovation performance by collaborating with other firms. However, there is no consensus in the open innovation literature regarding what drives firms' implementation of inbound and outbound open innovation and how the two types of open innovation influence innovation and firm performance. The present meta‐analysis synthesizes previous research to advance our understanding of open innovation by reexamining its antecedents and its moderating effects on innovation and firm performance. Using data from 157 articles, our results show that appropriation strategy, formal organizational structure, learning culture and top manager competence drive inbound open innovation, while innovation strategy, appropriation strategy, learning culture, and top manager competence drive outbound open innovation. In addition, we find that absorptive capacity positively moderates the positive impact of inbound and outbound open innovation on innovation performance. However, industry type (i.e., high‐ and low‐tech) is not found to moderate the effect of open innovation on innovation or firm performance, suggesting that both high‐ and low‐tech firms can equally reap benefits from open innovation. Furthermore, this study also partially supports the moderating effects of firm size and cultural value (individualism vs. collectivism) on the open innovation—performance relationship. These findings collectively suggest that the effects of inbound and outbound open innovation on performance are subject to contextual factors. Although this meta‐analysis does not allow us to generate new theories in the open innovation literature, it offers valuable insights to both academics and practitioners regarding factors affecting the implementation of open innovation and its performance implications.
Analysing the impact of body position shift on sleep architecture and stage transition: A comprehensive multidimensional study using event‐synchronised polysomnography data
Authors: Ahn Hyun Keun , Kang Yun Jin , Yoon Wonhyuck , Shin Hyun‐Woo 
Published: December 2023

SummaryAlthough understanding the physiological mechanisms of obstructive sleep apnea (OSA) is important for treating OSA, limited studies have examined OSA patients’ sleep architecture at the epoch‐by‐epoch level and analysed the impact of sleep position and stage on OSA pathogenesis. The epoch‐labelled polysomnogram was analysed multidimensionally to investigate the effect of sleep position on the sleep architecture and risk factors of apnea in patients with OSA. This retrospective multicentric case–control study reviewed full‐night diagnostic polysomnography of 6983 participants. The difference in the proportion of time spent supine during non‐rapid eye movement (NREM) and REM stages, and the mean duration of respiratory events per body position were evaluated. The frequency of sleep stage transition per body position shift type was computed. Further subgroup analysis was performed based on OSA severity and positional dependency. Supine time in patients with OSA varied across sleep stages, with lower proportions in N3 and REM, and shorter durations with severity. Patients with OSA spent less time in supine positions during N3 and REM, and experienced longer apnea events in both positions compared to the control group. The frequency of all sleep stage transitions increased with OSA severity and was higher among non‐positional OSA than positional OSA and the control group, regardless of body position shift type. The sleep stage transition from N3 and REM to wakefulness was notably heightened during position shift. Understanding the sleep architecture of patients with OSA requires analysing various sleep characteristics including sleep position simultaneously, with future studies focusing on position detection to predict sleep stages and respiratory events.
Bed partner perception of CPAP therapy on relationship satisfaction and intimacy—A European perspective from the ESADA network
Authors: Laharnar Naima , Bailly Sebastien , Basoglu Ozen K. , Buskova Jitka , Drummond Marta , Fanfulla Francesco , Mihaicuta Stefan , Pataka Athanasia , Riha Renata L. , Bouloukaki Izolde , Testelmans Dries , Trakada Georgia , Verbraecken Johan , Zimmermann Sandra , Penzel Thomas , Fietze Ingo 
Published: December 2023

SummaryObstructive sleep apnea increases morbidity and mortality risks. The most common treatment is continuous positive airway pressure, with nasal mask usage being important, but not always optimal. While most research on treatment adherence focuses on the patient, the bed partner's involvement may be detrimental. Our study aim is to obtain a European‐wide picture of the bed partner's attitude and support towards continuous positive airway pressure therapy, including effects on relationship satisfaction and intimacy. The English translation of a German bed partner questionnaire, assessing relationship satisfaction and three major components (general attitude, perceived mask looks, intimacy effects) was distributed within the European Sleep Apnea Database Network and translated in participating countries' local language. Data were collected for 2 years. In total, 10 European countries (13 sleep centres) participated with 1546 questionnaires. Overall, 91% of bed partners had a positive attitude towards continuous positive airway pressure therapy, 86% perceived mask looks not negative, 64% stated no negative intimacy effects. More specifically, 71% mentioned improved sleep quality, 68% supported nightly device usage. For 41% of bed partners, relationship satisfaction increased (no change for 47%). These results were significantly more pronounced in Eastern/Southern Europe compared with Middle Europe, especially regarding intimacy effects. However, increased continuous positive airway pressure therapy length affected attitude negatively. These results provide necessary information to improve treatment strategies by including educational couple‐focused approaches. Among others, we revealed that negative intimacy effects are not considered a barrier to continuous positive airway pressure adherence. These results may inspire more research identifying regional gaps with need for treatment adjustments.
Unveiling sex bias and adverse neonatal outcomes in ultrasound estimation of gestational age: A population‐based cohort study
Authors: Einum Anders , Sørbye Linn Marie , Nilsen Roy Miodini , Ebbing Cathrine , Morken Nils‐Halvdan 
Published: December 2023

AbstractBackgroundGestational age estimation by second‐trimester ultrasound biometry introduces systematic errors due to sex differences in early foetal growth, consequently increasing the risk of adverse neonatal outcomes. Ultrasound estimation earlier in pregnancy may reduce this bias.ObjectivesTo investigate the distribution of sex ratio by gestational age and estimate the risk of adverse outcomes in male foetuses born early‐term and female foetuses born post‐term by first‐ and second‐trimester ultrasound estimations.MethodsThis population‐based study compared two cohorts of births with gestational age based on first‐ and second‐trimester ultrasound in the Medical Birth Registry of Norway between 2016 and 2020. We used a log‐binomial regression model to estimate adjusted relative risk (RR) with 95% confidence interval (CI) for Apgar score <7 at 5 min, umbilical artery pH <7.05, neonatal intensive care unit (NICU) admission and respiratory morbidity in relation to foetal sex.ResultsThe sex ratio at birth in gestational weeks 36–43 showed less male predominance in pregnancies estimated in first compared to second trimester. Any adverse outcome was registered in 627 of 4470 male infants born in gestational weeks 37–38 and 618 of 6406 females born ≥41 weeks. Male infants born in weeks 37–38 had lower risk of NICU admission (RR 0.76, 95% CI 0.58, 0.99), Apgar score <7 at 5 min (RR 0.63, 95% CI 0.28, 1.41) and respiratory morbidity (RR 0.68, 95% CI 0.37, 1.25) in first‐ compared to second‐trimester estimations. Female infants estimated in first trimester born ≥41 weeks had lower risk of umbilical artery pH <7.05, NICU admissions and respiratory morbidity; however, CIs were wide.ConclusionsEarly ultrasound estimation of gestational age may reduce the excess risk of adverse neonatal outcomes and highlight the role of foetal sex and the timing of ultrasound assessment in the clinical evaluation of preterm and post‐term pregnancies.
Long‐term soil organic carbon changes after cropland conversion to grazed grassland in Southern Sweden
Authors: Johansson Anna , Livsey John , Guasconi Daniela , Hugelius Gustaf , Lindborg Regina , Manzoni Stefano 
Published: December 2023

AbstractThere is growing awareness of the potential value of agricultural land for climate change mitigation. In Sweden, cropland areas have decreased by approximately 30% over recent decades, creating opportunities for these former croplands to be managed for climate change mitigation by increasing soil organic carbon (SOC) stocks. One potential land‐use change is conversion of cropland to grazed grasslands, but the long‐term effect of such change in management is not well understood and likely varies with soil type and site‐specific conditions. Through sampling of mineral and peatland soils within a 75‐year chronosequence of land converted from crop production to grazed grassland, we assessed how time since conversion, catenary position, and soil depth affected SOC storage. The SOC stocks calculated at an equivalent soil or ash mass increased through time since conversion in mineral soils at all topographic positions, at a rate of ~0.65% year−1. Soils at low topographic positions gained the most carbon. Peat SOC stock gains after conversion were large, but only marginally significant and only when calculated at an equivalent ash mass. We conclude that the conversion of mineral soil to grazed grassland promotes SOC accumulation at our sites, but climate change mitigation potential would need to be evaluated through a full greenhouse gas balance.
Overexpression of T3SS translocation signals in
Salmonella
causes delayed attenuation
Authors: Abele Taylor J. , Billman Zachary P. , Harvest Carissa K. , Bryan Alexia K. , Larson Heather N. , Coers Jörn , Miao Edward A. 
Published: December 2023

ABSTRACT

Engineering pathogens is a useful method for discovering new details of microbial pathogenesis and host defense. However, engineering can result in off-target effects. We previously engineered
Salmonella enterica
serovar Typhimurium to overexpress the secretion signal of the type 3 secretion system effector SspH1 fused with domains of other proteins as cargo. Such engineering had no virulence cost to the bacteria for the first 48 hours post infection in mice. Here, we show that after 48 hours, the engineered bacteria manifest an attenuation that correlates with the quantity of the SspH1 translocation signal expressed. In IFN-γ-deficient mice, this attenuation was weakened. Conversely, the attenuation was accelerated in the context of a pre-existing infection. We speculate that inflammatory signals change aspects of the target cell’s physiology, which makes host cells less permissive to
S
. Typhimurium infection. This increased degree of difficulty requires the bacteria to utilize its T3SS at peak efficiency, which can be disrupted by engineered effectors.
In silico
discovery of the myxosortases that process MYXO-CTERM and three novel prokaryotic C-terminal protein-sorting signals that share invariant Cys residues
Authors: Haft Daniel H. 
Published: December 2023

ABSTRACT

The LPXTG protein-sorting signal, found in surface proteins of various Gram-positive pathogens, was the founding member of a growing panel of prokaryotic small C-terminal sorting domains. Sortase A cleaves LPXTG, exosortases (XrtA and XrtB) cleave the PEP-CTERM sorting signal, archaeosortase A cleaves PGF-CTERM, and rhombosortase cleaves GlyGly-CTERM domains. Four sorting signal domains without previously known processing proteases are the MYXO-CTERM, JDVT-CTERM, Synerg-CTERM, and CGP-CTERM domains. These exhibit the standard tripartite architecture of a short signature motif, a hydrophobic transmembrane segment, and an Arg-rich cluster. Each has an invariant cysteine in its signature motif. Computational evidence strongly suggests that each of these four Cys-containing sorting signals is processed, at least in part, by a cognate family of glutamic-type intramembrane endopeptidases related to the eukaryotic type II CAAX-processing protease Rce1. For the MYXO-CTERM sorting signals of different lineages, their sorting enzymes, called myxosortases, include MrtX (MXAN_2755 in
Myxococcus xanthus
), MrtC, and MrtP, all with radically different N-terminal domains but with a conserved core. Related predicted sorting enzymes were also identified for JDVT-CTERM (MrtJ), Synerg-CTERM (MrtS), and CGP-CTERM (MrtA). This work establishes a major new family of protein-sorting housekeeping endopeptidases contributing to the surface attachment of proteins in prokaryotes.

IMPORTANCE

Homologs of the eukaryotic type II CAAX-box protease Rce1, a membrane-embedded endopeptidase found in yeast and human ER and involved in sorting proteins to their proper cellular locations, are abundant in prokaryotes but not well understood there. This bioinformatics paper identifies several subgroups of the family as cognate endopeptidases for four protein-sorting signals processed by previously unknown machinery. Sorting signals with newly identified processing enzymes include three novel ones, but also MYXO-CTERM, which had been the focus of previous experimental work in the model fruiting and gliding bacterium
Myxococcus xanthus
. The new findings will substantially improve our understanding of Cys-containing C-terminal protein-sorting signals and of protein trafficking generally in bacteria and archaea.
HIV-1 capsid and viral DNA integration
Authors: Dwivedi Richa , Prakash Prem , Kumbhar Bajarang Vasant , Balasubramaniam Muthukumar , Dash Chandravanu 
Published: December 2023

ABSTRACT
The human immunodeficiency virus type 1 (HIV-1) genome encodes 15 proteins that perform structural, enzymatic, regulatory, and accessory functions. The capsid protein (CA) is the primary structural protein of HIV-1 and plays multiple functions during infection. Early studies predicted that HIV-1 CA mainly protected and delivered the viral genome to the target cell. However, it is now well established that CA plays a critical role after the cellular entry steps of infection. During the early stages, CA promotes reverse transcription of the RNA genome into a DNA copy and the nuclear import/entry step of HIV-1 infection. Emerging evidence also supports the functional role of CA in the post-nuclear entry steps of infection, such as HIV-1 integration. During the late stages of infection, CA coordinates hexameric lattice formation for the assembly of immature virion. CA also regulates theformation of the mature capsid that encases the viral genome and associated factors in the infectious progeny virion. Because of these indispensable roles, HIV-1 CA has emerged as a new and validated target for antiviral drug development. Accordingly, the first CA-targeting drug, lenacapavir (GS-6207), was recently approved to treat certain HIV-1-infected individuals whose viral load cannot be controlled by other antiviral drugs. Still, new and superior CA inhibitors are needed to qualify as part of the front-line antiviral therapy regimens for all infected individuals. The development of such inhibitors requires a clear understanding of CA’s role in HIV-1 infection. In this review, we will describe CA’s role during the early stages of HIV-1 infection, with particular emphasis on post-nuclear entry steps.

IMPORTANCE
HIV-1 capsid protein (CA)—independently or by recruiting host factors—mediates several key steps of virus replication in the cytoplasm and nucleus of the target cell. Research in the recent years have established that CA is multifunctional and genetically fragile of all the HIV-1 proteins. Accordingly, CA has emerged as a validated and high priority therapeutic target, and the first CA-targeting antiviral drug was recently approved for treating multi-drug resistant HIV-1 infection. However, development of next generation CA inhibitors depends on a better understanding of CA’s known roles, as well as probing of CA’s novel roles, in HIV-1 replication. In this timely review, we present an updated overview of the current state of our understanding of CA’s multifunctional role in HIV-1 replication—with a special emphasis on CA’s newfound post-nuclear roles, highlight the pressing knowledge gaps, and discuss directions for future research.
Genome sequence of
Staphylococcus nepalensis
ZZ-2023a, isolated from
Nasonia vitripennis
Authors: Zhu Zhengyu , Wu Runbiao , Wang Guan-Hong 
Published: December 2023

ABSTRACT

We isolated a strain of
Staphylococcus nepalensis
from
Nasonia vitripennis
and presented the draft genome sequence of this strain. This research was conducted at the Institute of Zoology, Chinese Academy of Sciences (Beijing, China). The genome spans 2,910,033 bp, distributed over 144 contigs, with a G+C content of 33.33%.
Blanket antimicrobial resistance gene database with structural information, BOARDS, provides insights on historical landscape of resistance prevalence and effects of mutations in enzyme structure
Authors: Ko Seyoung , Kim Jaehyung , Lim Jaewon , Lee Sang-Mok , Park Joon Young , Woo Jihoon , Scott-Nevros Zoe K. , Kim Jong R. , Yoon Hyunjin , Kim Donghyuk 
Published: December 2023

ABSTRACT

Antimicrobial resistance (AMR) in pathogenic bacteria poses a significant threat to public health, yet there is still a need for development in the tools to deeply understand AMR genes based on genetic or structural information. In this study, we present an interactive web database named Blanket Overarching Antimicrobial-Resistance gene Database with Structural information (BOARDS,
sbml.unist.ac.kr
), a database that comprehensively includes 3,943 reported AMR gene information for 1,997 extended spectrum beta-lactamase (ESBL) and 1,946 other genes as well as a total of 27,395 predicted protein structures. These structures, which include both wild-type AMR genes and their mutants, were derived from 80,094 publicly available whole-genome sequences. In addition, we developed the rapid analysis and detection tool of antimicrobial-resistance (RADAR), a one-stop analysis pipeline to detect AMR genes across whole-genome sequencing (WGSs). By integrating BOARDS and RADAR, the AMR prevalence landscape for eight multi-drug resistant pathogens was reconstructed, leading to unexpected findings such as the pre-existence of the MCR genes before their official reports. Enzymatic structure prediction-based analysis revealed that the occurrence of mutations found in some ESBL genes was found to be closely related to the binding affinities with their antibiotic substrates. Overall, BOARDS can play a significant role in performing in-depth analysis on AMR.

IMPORTANCE
While the increasing antibiotic resistance (AMR) in pathogen has been a burden on public health, effective tools for deep understanding of AMR based on genetic or structural information remain limited. In this study, a blanket overarching antimicrobial-resistance gene database with structure information (BOARDS)—a web-based database that comprehensively collected AMR gene data with predictive protein structural information was constructed. Additionally, we report the development of a RADAR pipeline that can analyze whole-genome sequences as well. BOARDS, which includes sequence and structural information, has shown the historical landscape and prevalence of the AMR genes and can provide insight into single-nucleotide polymorphism effects on antibiotic degrading enzymes within protein structures.