bluuebunny/crossref_metadata_2025 huggingface dataset:
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

Although 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

Obstructive 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

Background

Gestational 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.

Objectives

To 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.

Methods

This 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.

Results

The 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.

Conclusions

Early 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

There 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.
A practical approach to determine minimal quantum gate durations using amplitude-bounded quantum controls
Authors: Günther Stefanie , Petersson N. Anders
Published: December 2023

We present an iterative scheme to estimate the minimal duration in which a quantum gate can be realized while satisfying hardware constraints on the control pulse amplitudes. The scheme performs a sequence of unconstrained numerical optimal control cycles that each minimize the gate fidelity for a given gate duration alongside an additional penalty term for the control pulse amplitudes. After each cycle, the gate duration is adjusted based on the inverse of the resulting maximum control pulse amplitudes by re-scaling the dynamics to a new duration where control pulses satisfy the amplitude constraints. Those scaled controls then serve as an initial guess for the next unconstrained optimal control cycle, using the adjusted gate duration. We provide multiple numerical examples that each demonstrate fast convergence of the scheme toward a gate duration that is close to the quantum speed limit, given the control pulse amplitude bound. The proposed technique is agnostic to the underlying system and control Hamiltonian models, as well as the target unitary gate operation, making the time-scaling iteration an easy to implement and practically useful scheme for reducing the durations of quantum gate operations.
Short-term exposure alters adult listeners' perception of segmental phonotactics
Authors: Steffman Jeremy , Sundara Megha
Published: December 2023

This study evaluates the malleability of adults' perception of probabilistic phonotactic (biphone) probabilities, building on a body of literature on statistical phonotactic learning. It was first replicated that listeners categorize phonetic continua as sounds that create higher-probability sequences in their native language. Listeners were also exposed to skewed distributions of biphone contexts, which resulted in the enhancement or reversal of these effects. Thus, listeners dynamically update biphone probabilities (BPs) and bring this to bear on perception of ambiguous acoustic information. These effects can override long-term BP effects rooted in native language experience.
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

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

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

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

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

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.
Domestication signatures in the non-conventional yeast
Lachancea cidri
Authors: Villarreal Pablo , O'Donnell Samuel , Agier Nicolas , Muñoz-Guzman Felipe , Benavides-Parra Jose , Urbina Kami , Peña Tomas A. , Solomon Mark , Nespolo Roberto F. , Fischer Gilles , Varela Cristian , Cubillos Francisco A.
Published: December 2023

Evaluating domestication signatures beyond model organisms is essential for a thorough understanding of the genotype-phenotype relationship in wild and human-related environments. Structural variations (SVs) can significantly impact phenotypes playing an important role in the physiological adaptation of species to different niches, including during domestication. A detailed characterization of the fitness consequences of these genomic rearrangements, however, is still limited in non-model systems, largely due to the paucity of direct comparisons between domesticated and wild isolates. Here, we used a combination of sequencing strategies to explore major genomic rearrangements in a
Lachancea cidri
yeast strain isolated from cider (CBS2950) and compared them to those in eight wild isolates from primary forests. Genomic analysis revealed dozens of SVs, including a large reciprocal translocation (~16 kb and 500 kb) present in the cider strain, but absent from all wild strains. Interestingly, the number of SVs was higher relative to single-nucleotide polymorphisms in the cider strain, suggesting a significant role in the strain’s phenotypic variation. The set of SVs identified directly impacts dozens of genes and likely underpins the greater fermentation performance in the
L. cidri
CBS2950. In addition, the large reciprocal translocation affects a proline permease (
PUT4
) regulatory region, resulting in higher
PUT4
transcript levels, which agrees with higher ethanol tolerance, improved cell growth when using proline, and higher amino acid consumption during fermentation. These results suggest that SVs are responsible for the rapid physiological adaptation of yeast to a human-related environment and demonstrate the key contribution of SVs in adaptive fermentative traits in non-model species.

IMPORTANCE

The exploration of domestication signatures associated with human-related environments has predominantly focused on studies conducted on model organisms, such as
Saccharomyces cerevisiae
, overlooking the potential for comparisons across other non-Saccharomyces species. In our research, employing a combination of long- and short-read data, we found domestication signatures in
Lachancea cidri
, a non-model species recently isolated from fermentative environments in cider in France. The significance of our study lies in the identification of large array of major genomic rearrangements in a cider strain compared to wild isolates, which underly several fermentative traits. These domestication signatures result from structural variants, which are likely responsible for the phenotypic differences between strains, providing a rapid path of adaptation to human-related environments.
Evidence for novel polycyclic aromatic hydrocarbon degradation pathways in culturable marine isolates
Authors: Walton Jillian L. , Buchan Alison
Published: December 2023

Polycyclic aromatic hydrocarbons (PAHs) are common toxic and carcinogenic pollutants in marine ecosystems. Despite their prevalence in these habitats, relatively little is known about the natural microflora and biochemical pathways that contribute to their degradation. Approaches to investigate marine microbial PAH degraders often heavily rely on genetic biomarkers, which requires prior knowledge of specific degradative enzymes and genes encoding them. As such, these biomarker-reliant approaches cannot efficiently identify novel degradation pathways or degraders. Here, we screen 18 marine bacterial strains representing the Pseudomonadota, Bacillota, and Bacteroidota phyla for degradation of two model PAHs, pyrene (high molecular weight) and phenanthrene (low molecular weight). Using a qualitative PAH plate screening assay, we determined that 16 of 18 strains show some ability to degrade either or both compounds. Degradative ability was subsequently confirmed with a quantitative high-performance liquid chromatography approach, where an additional strain showed some degradation in liquid culture. Several members of the prominent marine
Roseobacteraceae
family degraded pyrene and phenanthrene with varying efficiency (1.2%–29.6% and 5.2%–52.2%, respectively) over 26 days. Described PAH genetic biomarkers were absent in all PAH degrading strains for which genome sequences are available, suggesting that these strains harbor novel transformation pathways. These results demonstrate the utility of culture-based approaches in expanding the knowledge landscape concerning PAH degradation in marine systems.

IMPORTANCE

Polycyclic aromatic hydrocarbon (PAH) pollution is widespread throughout marine environments and significantly affects native flora and fauna. Investigating microbes responsible for degrading PAHs in these environments provides a greater understanding of natural attenuation in these systems. In addition, the use of culture-based approaches to inform bioinformatic and omics-based approaches is useful in identifying novel mechanisms of PAH degradation that elude genetic biomarker-based investigations. Furthermore, culture-based approaches allow for the study of PAH co-metabolism, which increasingly appears to be a prominent mechanism for PAH degradation in marine microbes.
PlAtg8-mediated autophagy regulates vegetative growth, sporangial cleavage, and pathogenesis in
Peronophythora litchii
Authors: Yu Ge , Li Wenqiang , Yang Chengdong , Zhang Xue , Luo Manfei , Chen Taixu , Wang Xuejian , Wang Rongbo , Chen Qinghe
Published: December 2023

Autophagy is a conserved cellular metabolic process in eukaryotes that transports damaged or redundant intracellular organelles and proteins to lysosomes or vacuoles for degradation and recycling. Atg8 is not only essential for autophagosome formation but also required for fungal development and pathogenicity, but its function is unknown in
Peronophythora litchii
. In this study, PlAtg8, a yeast Atg8 homolog, is deleted by the CRISPR/Cas9 system coupled with PEG-mediated protoplast transformation in
P. litchii
. Compared with the wild-type strain, the absence of PlAtg8 affects autophagosome formation. The colony growth rate, number of sporangia, and zoospore release rate are significantly decreased, and the oospores are undetected in Δ
Platg8
. The pathogenicity test shows that the lesion areas on litchi leaves and fruits caused by Δ
Platg8
are significantly attenuated compared with the wild type, indicating that PlAtg8 is also required for the pathogenicity of
P. litchii
. Moreover, the cleavage rate of sporangia in Δ
Platg8
is significantly decreased compared to the wild type by FM4-64 staining, which is probably the main reason for the lower zoospores release rate in Δ
Platg8
. These results suggest that PlAtg8 not only regulates autophagy but also participates in the growth and development of
P. litchii
.

IMPORTANCE

Peronophythora litchii
is the pathogen of litchi downy blight, which is the most serious disease in litchi. Autophagy is an evolutionarily conserved catabolic process in eukaryotes. Atg8 is a core protein of the autophagic pathway, which modulates growth and pathogenicity in the oomycete
P. litchii
. In
P. litchii
, CRISPR/Cas9-mediated knockout of the
PlATG8
impaired autophagosome formation.
PlATG8
knockout mutants exhibited attenuated colony expansion, sporangia production, zoospore discharge, and virulence on litchi leaves and fruits. The reduction in zoospore release was likely underpinned by impaired sporangial cleavage. Thus, in addition to governing autophagic flux, PlAtg8 is indispensable for vegetative growth and infection of
P. litchii
.
Supplemental Material: Early uplift and exhumation of the Tanggula granitoid pluton since the Late Cretaceous: Implications for the stepwise topographic growth model in the eastern Qiangtang terrane
Authors: Lu Lu , et al.
Published: December 2023

Table S1: A compilation of low-temperature thermochronology (LTT) data in the eastern Qiangtang terrane. Table S2: Apatite U-Pb dating results for samples from the Tanggula granitoid pluton. Table S3: Biotite 40Ar-39Ar furnace step-heating analytical results for samples from the Tanggula granitoid pluton. Table S4: K-feldspar 40Ar-39Ar furnace step-heating analytical results for samples from the Tanggula granitoid pluton. Table S5: Zircon fission-track data of samples from the Tanggula granitoid pluton. Table S6: Apatite fission-track data of samples from the Tanggula granitoid pluton. Table S7: Single-grain zircon (U-Th)He data of samples from the Tanggula granitoid pluton. 
Local Quench within the Keldysh Technique
Authors: Radovskaya A. A. , Semenov A. G.
Published: December 2023

The problem of quantum scalar field evolution after an instantaneous local perturbation (quench) is considered. A new approach to descriptions of a quench from an arbitrary initial state is developed in the framework of the Keldysh technique. This approach does not require the procedure of the analytical continuation, which can be ambiguous in some cases. The evolution of the energy density after local quench is calculated for a simple case, and its dependence on the interaction region width and the initial conditions is analyzed.
Treatment of complex iatrogenic common hepatic duct injury following laparoscopic cholecystectomy
Authors: Guimarães Andreia , Lemos Mariana , Donato Paulo , Bernardes António
Published: December 2023

We report the case of a woman in her 40s, with no significant medical history, submitted to a laparoscopic cholecystectomy in our institution for symptomatic gallbladder lithiasis. On postoperative day 4, she presented to our emergency room with severe abdominal pain and elevated inflammatory markers. Abdominal CT scan revealed a mass filled with liquid and air in the gallbladder fossa. Surgical exploration was performed revealing a major common hepatic duct iatrogenic injury, which was managed using suture over a T-tube. Three months after surgery, cholangiography showed a biliary stenosis, and a biodegradable stent was inserted through percutaneous transhepatic access. The difficulties in the management of this condition and its outcomes are discussed in this report.
Convexal subarachnoid haemorrhage in a patient under pembrolizumab-lenvatinib combination therapy
Authors: Simao Paulo , Almeida Marco José , Catela João , Matias Fernando
Published: December 2023

A woman in her 60s was brought to the emergency department due to a new-onset seizure. She was drowsy on arrival and unable to provide a clinical history. She had a medical history of advanced endometrial cancer, for which she was under the therapeutic protocol pembrolizumab plus lenvatinib. Laboratorial investigations were unremarkable. The brain CT angiography provided further insight into the case by detecting a bilateral convexal subarachnoid haemorrhage with discrete bilateral opercular vasogenic oedema, without other noticeable structural changes. Cerebrospinal fluid analysis was macroscopically haemorrhagic, but otherwise unremarkable. The brain MRI did not provide additional information. Although considered a rare adverse reaction, cerebral haemorrhage has been described for both pembrolizumab and lenvatinib. We cautiously assumed a probable drug aetiology after a thorough review of potential causes. Following discontinuation of these drugs and under anti-convulsive therapy, the patient remained asymptomatic and was discharged home.
Safety and efficacy of a nitrous oxide procedural sedation programme in a paediatric emergency department: a decade of outcomes
Authors: Croughan Sean , Barrett Michael , O'Sullivan Ronan , Beegan Aidan , Blackburn Carol
Published: December 2023

Background

Nitrous oxide (N2O) has multiple benefits in paediatric procedural sedation (PPS), but use is restricted by its limited analgesic properties. Analgesic potency could be increased by combining N2O and intranasal fentanyl (INF). We assessed safety and efficacy data from 10 years (2011–2021) of our N2O PPS programme.

Methods

Prospectively collected data from a sedation registry at a paediatric emergency department (PED) were reviewed. Total procedures performed with N2O alone or with INF, success rate, sedation depth and adverse events were determined. Contributing factors for these outcomes were assessed via regression analysis and compared between different N2O concentrations, N2O in combination with INF, and for physician versus nurse administered sedation. A post hoc analysis on factors associated with vomiting was also performed.

Results

831 N2O procedural sedations were performed, 358 (43.1%) involved a combination INF and N2O. Nurses managed sedation in 728 (87.6%) cases. Median sedation depth on the University of Michigan Sedation Scale was 1 (IQR 1–2). Sedation was successful in 809 (97.4%) cases. Combination INF/N2O demonstrated higher median sedation scores (2 vs 1, p<0.001) and increased vomiting (RR 1.8, 95% CI 1.3 to 2.5), with no difference in sedation success compared with N2O alone. No serious adverse events (SAEs) were reported (desaturation, apnoea, aspiration, bradycardia or hypotension) regardless of N2O concentration or use of INF. 137 (16.5%) minor adverse events occurred. Vomiting occurred in 113 (13.6%) cases and was associated with higher concentrations of N2O and INF use, but not associated with fasting status. There were no differences in adverse events (RR 0.98, 95% CI 0.97 to 1.04) or success rates (RR 0.93, 95% CI 0.56 to 1.7) between physician provided and nurse provided sedation.

Conclusion

N2O can provide effective PED PPS. No SAEs were recorded. INF may be an effective PPS adjunct but remains limited by increased rates of vomiting.
Evolving educational landscape in pathology: a comprehensive bibliometric and visual analysis including digital teaching and learning resources
Authors: Cima Luca , Bussola Nicole , Hassell Lewis A , Kiehl Tim-Rasmus , Schukow Casey , Zerbe Norman , Munari Enrico , Torresani Evelin , Barbareschi Mattia , Cecchini Matthew J , Cirielli Vito , Pagliuca Francesca , Ahsan Muhammad , Mohanty Sambit K , Arbitrio Ernesto , Hughes Griffin , Mirza Kamran M
Published: December 2023

Aims

Pathology education is a core component of medical training, and its literature is critical for refining educational modalities. We performed a cross-sectional bibliometric analysis to explore publications on pathology education, focusing on new medical education technologies.

Methods

The analysis identified 64 pathology journals and 53 keywords. Relevant articles were collected using a web application, PaperScraper, developed to accelerate literature search. Citation data were collected from multiple sources. Descriptive statistics, with time period analysis, were performed using Microsoft Excel and visualised with Flourish Studio. Two article groups were further investigated with a bibliometric software, VOSViewer, to establish co-authorship and keyword relationships.

Results

8946 citations were retrieved from 905 selected articles. Most articles were published in the last decade (447, 49.4%). The top journals wereArchives of Pathology & Laboratory Medicine(184),Human Pathology(122) and theAmerican Journal of Clinical Pathology(117). The highest number of citations was found forHuman Pathology(2120), followed byArchives of Pathology & Laboratory Medicine(2098) andAmerican Journal of Clinical Pathology(1142). Authors with different backgrounds had the greatest number of articles and citations. 12 co-authorship, 3 keyword and 8 co-citation clusters were found for the social media/online resources group, 8 co-authorship, 4 keyword and 7 co-citation clusters for the digital pathology/virtual microscopy/mobile technologies group.

Conclusions

The analysis revealed a significant increase in publications over time. The emergence of digital teaching and learning resources played a major role in this growth. Overall, these findings underscore the transformative potential of technology in pathology education.
Identification of critical mitochondrial hub gene for facial nerve regeneration
Authors: Cao Xiaofang , Zhang Yan , Shi Yu , Li Ying , Gao Li , Wang Xiumei , Sun Liang
Published: December 2023

Mitochondria play a critical role in nerve regeneration, yet the impact of gene expression changes related to mitochondria in facial nerve regeneration remains unknown. To address this knowledge gap, we analyzed the expression profile of the facial motor nucleus (FMN) using data obtained from the Gene Expression Omnibus (GEO) database (GSE162977). By comparing different time points in the data, we identified differentially expressed genes (DEGs). Additionally, we collected mitochondria-related genes from the Gene Ontology (GO) database and intersected them with the DEGs, resulting in the identification of mitochondria-related DEGs (MIT-DEGs). To gain further insights, we performed functional enrichment and pathway analysis of the MIT-DEGs. To explore the interactions among these MIT-DEGs, we constructed a protein–protein interaction (PPI) network using the STRING database and identified hub genes using the Degree algorithm of Cytoscape software. To validate the relevance of these genes to nerve regeneration, we established a rat facial nerve injury (FNI) model and conducted a series of experiments. Through these experiments, we confirmed three MIT-DEGs (Myc, Lyn, and Cdk1) associated with facial nerve regeneration. Our findings provide valuable insights into the transcriptional changes of mitochondria-related genes in the FMN following FNI, which can contribute to the development of new treatment strategies for FNI.
Additional Albertosaurus sarcophagus (Tyrannosauridae, Albertosaurinae) material from the Danek bonebed of Edmonton, Alberta, Canada with evidence of cannibalism
Authors: Coppock Colton C. , Currie Philip J.
Published: December 2023

Albertosaurus sarcophagus Osborn, 1905 specimens from the Danek Bonebed of Edmonton, Alberta, Canada were first described in 2014. Since this initial report, the University of Alberta's annual field work has continued to yield additional tyrannosaurid material from the Danek Bonebed. In addition to nearly 200 tyrannosaurid shed teeth, five diagnostic tyrannosaurid cranial and postcranial bones have been identified to date. Three cranial bones were included in the initial description; here, the newly uncovered left and right tyrannosaurid pubes (UALVP 52709 and UALVP 56262, respectively) are described and mapped in relation to the previously known material. The pubes can be confidently diagnosed as tyrannosaurid based on a posterior bow of the pubic shaft and further classified as albertosaurine by a weakly expanded obturator plate. A. sarcophagus is the only tyrannosaurid and albertosaurine known from the Horseshoe Canyon Formation, which allows for the material to be confidently assigned to this taxon. The left pubis (UALVP 52709) possesses multiple tooth traces on the medial surface that were likely made post-mortem as the medial surface of the pubis would have been deep within the body cavity of the animal and reactive (healing) bone is absent. Given the numerous large gouge-like tooth traces on the medial surface of the pubis and the abundance of cf. Albertosaurus teeth from the bonebed, it seems likely that an A. sarcophagus took this opportunity to feed on a conspecific, providing evidence for the first case of cannibalism from an albertosaurine.
Exact rotating black hole solutions for f(R) gravity by modified Newman Janis algorithm
Authors: Chaturvedi Pankaj , Kumar Utkarsh , Thattarampilly Udaykrishna , Kakkat Vishnu
Published: December 2023

We show that the f(R)-gravity theories with constant Ricci scalar in the Jordan/Einstein frame can be described by Einstein or Einstein–Maxwell gravity with a cosmological term and a modified gravitational constant. To obtain the rotating axisymmetric solutions for the Einstein/Einstein–Maxwell gravity with a cosmological constant, we also propose a modified Newmann–Janis algorithm which involves the non-complexification of the radial coordinate and a complexification of the polar coordinate. Using the duality between the two gravity theories we show that the stationary or static solutions for the Einstein/Einstein–Maxwell gravity with a cosmological constant will also be the solutions for the dual f(R)-gravity with constant Ricci scalar.
Solving real-life BVPs via the second derivative Chebyshev pseudo-Galerkin method
Authors: Gamal Marwa , El-Kady M. , Abdelhakem M.
Published: December 2023

The aim of this paper is to use the second derivative of Chebyshev polynomials (SDCHPs) as basis functions for solving linear and nonlinear boundary value problems (BVPs). Then, the operational matrix for the derivative was established by using SDCHPs. The established matrix via mixing between two spectral methods, collocation and Galerkin, has been applied to solve BVPs. Consequently, an error analysis is investigated to ensure the convergence of the technique used. Finally, we solved some problems involving real-life applications and compared their solutions with exact and other solutions from different methods to verify the accuracy and efficiency of this method.
D-type photonic crystal fiber low refractive index sensor based on surface plasmon
Authors: Li Runhua , Liu Sitong , Wang Hongman , Yang Ziyi , Sun Lulu , Ma Ji
Published: December 2023

This study presents the design and analysis of a novel surface plasmon resonance sensor based on D-type photonic crystal fiber. The analyte channel in the sensor comprises an open ring with a thin gold film deposited on the channel, inducing the surface plasmon resonance effect to enhance the resonance effect and improve the spectral sensitivity of the sensor. The proposed design eliminates the need to introduce liquid into the analyte channel. Upon inserting the sensor into the vessel, the analyte automatically flows into the liquid channel. Simulations illustrate the capability of the proposed sensor to detect low refractive indices spanning from [Formula: see text] to [Formula: see text], exhibiting a remarkable spectral sensitivity of up to 9000[Formula: see text]nm/RIU. The surface plasmon resonance sensor presented in this study emerges as a competitive candidate for applications requiring low refractive index detection. It is all because of its promising sensing results, wide refractive index sensing range, and simple, compact fiber design.
Leader–follower coherence in multi-layer networks: Understanding allocations of leaders
Authors: Wang Yixin , Wang Jun , Sun Weigang
Published: December 2023

This paper investigates a leader–follower consensus problem of multi-layer networks and understands the role of leader’s allocations in the process of consensus. Leader–follower coherence quantified by the spectrum measures the extent of consensus between leaders and followers in the system under additive noise. In order to study the exact interplay between leader–follower coherence and leader’s allocations, we choose complete multi-partite networks as network models and assign the leaders into different layers. Based on the network construction, we obtain exact solutions of leader–follower coherence with freely assigned leaders and reveal that the allocations of leaders have a significant impact on the coherence. Finally, we compare the leader–follower coherence and leaderless coherence of bipartite networks when the number of leaders and network size satisfies certain conditions.
Medical Image Segmentation Using Grey Wolf-Based U-Net with Bi-Directional Convolutional LSTM
Authors: Tamilmani G. , Phaneendra Varma CH , Devi V. Brindha , Ramesh Babu G
Published: December 2023

In recent years, deep learning-based networks have been able to achieve state-of-the-art performance in medical image segmentation. U-Net, one of the currently available networks, has proven to be effective when applied to the segmentation of medical images. A Convolutional Neural Network’s (CNN) performance is heavily dependent on the network’s architecture and associated parameters. There are many layers and parameters that need to be set up in order to manually create a CNN, making it a complex procedure. Designing a network is made more difficult by using a variety of connections to increase the network’s complexity. Evolutionary computation can be used to set the parameters of CNN and/or organize the CNN layers as an optimization strategy. This paper proposes an automatic evolutionary method for detecting an optimal network topology and its parameters for the segmentation of clinical image using Grey Wolf Optimization algorithm. Also, Bi-Directional LSTM integrated in the skip connection to extract dense feature characteristics of image by combining feature maps extracted from encoded and previous decoded path in nonlinear way (MIS-GW-U-Net-BiDCLSTM) is proposed. The experimental results demonstrate that the proposed method attains 98.49% accuracy with minimal parameters, which is much better than that of the other methods.
UPQC-Based Hybrid Technique to Reduce Power Quality Problems in the Photovoltaic Grid System
Authors: Shankar C. Udhaya , Nithya devi N.
Published: December 2023

In addition to Power Quality (PQ) problems caused by solid state devices in the distribution side of grid connected Photo Voltaic (PV) system, quality of power also suffers in the source side by the usage of converters. Generally, PQ problems mitigation strategy has turned into a critical issue in grid-connected PV systems. This paper proposes a control topology for PQ issues mitigation scheme in grid connected PV systems. The primary goal of this study is to enhance the PQ in power distribution system through eradicating the voltage interruption, voltage swell and sag as well as voltage fluctuation. To accomplish these changes, Unified Power Quality Conditioners (UPQCs) with controllers were utilized. Then the faults are mitigated by the utilization of UPQC with Tree Seeds Algorithm (TSA) — Adaptive Neuro-Fuzzy Interference System (ANFIS). At first, the normal properties of the grid-connected PV systems are dissected. From that point forward, a few interruptions are made in the system and the abnormal characteristics are analyzed. Then the abnormal characteristics of PQ problems are diminished in the utilization of UPQC and TSA–ANFIS controllers. UPQC is one of the best filters topologies which can mitigate and control all PQ problems. The combined algorithms of TSA-ANFIS are used to keep the dc-link voltage in UPQC at consistent level. The proposed hybrid approach is executed in MATLAB/Simulink platform and the performance is studied. Further, the proposed method is compared with existing Elephant Herding Optimization (EHO) technique and also with hybrid EHO-ANFIS techniques. The comparison results showed that the proposed technique is superior to the EHO and EHO-ANFIS techniques.
Bifurcation Solutions to the Templator Model in Chemical Self-Replication
Authors: Cao Qian , Bao Xiongxiong
Published: December 2023

In this paper, we are concerned with a diffusive templator model in chemical self-replication, which describes the process of an individual molecule duplicating itself. Firstly, the stability of non-negative constant equilibrium solution is introduced. Then the existence of Hopf bifurcation is proved. Particularly, the stability and the direction of Hopf bifurcation for the spatially homogeneous model are discussed. Furthermore, by space decomposition and implicit function theorem, it is shown that the system may undergo a steady-state bifurcation with a two-dimensional kernel. Finally, several numerical simulations are completed to demonstrate the theoretical results.