bluuebunny/crossref_metadata_2025 huggingface dataset:
ESM-PVP: Identification and classification of phage virion proteins with a large pretrained protein language model and an MLP neural network
Authors: Li Bowen , Liang Guanxiang
Published: December 2023

Bacteriophages, also known as phages, are essential for the stability of the microbiome system due to their ability to infect prokaryotes, another significant component of the microbiome. Thus, understanding the functions of phage proteins could help us unravel the nature of phages and their roles in the microbiome. However, limited by the low throughput of experimental techniques, a vast number of phage proteins remain unannotated in terms of their functions. Computational methods are expected to solve this restriction due to their high throughput and cost-effectiveness. In this study, we focused on one aspect of functional annotation for phage proteins, the identification and classification of phage virion proteins, and the integration of a large pretrained protein language model and an MLP neural network dramatically improved the performance of these two tasks. Additionally, we compared our model with some previous deep learning models using a newly collected, independent benchmark dataset, demonstrating the strong generalization ability of our model for both tasks. The source codes of ESM-PVP and the software for the PVP identification task have been uploaded to:https://github.com/li-bw18/ESM-PVP.
Diversity and connectivity of principal neurons in the lateral and basal nuclei of the mouse amygdala
Authors: Reéb Zsófia , Magyar Dániel , Weisz Filippo , Fekete Zsuzsanna , Müller Kinga , Vikór Attila , Péterfi Zoltán , Andrási Tibor , Veres Judit M. , Hájos Norbert
Published: December 2023

The basolateral amygdala is a non-layered cortical structure playing a role in various cognitive processes. Despite many studies focusing on local information processing within the circuits of the basolateral amygdala, the characteristics of excitatory principal neurons (PNs) are still not fully revealed. Here, we combined neuroanatomical, electrophysiological, and tracing techniques to determine the single-cell features, dendritic and axonal projections of PNs within the lateral (LA) and basal amygdala (BA). Using a mouse reporter line, we found that cholecystokinin (CCK) expression defines two spatially and functionally segregated groups of PNs both in the LA and BA. PNs in CCK-positive (CCK+) areas of the LA (LAa) had small somata and short dendrites which matched their single-cell electrophysiological properties. PNs in CCK-negative (CCK-) areas of the LA (LAp) and all BA had similarly ramified dendrites and single-cell features with some differences. Importantly, the dendritic arbors of PNs were restricted to the subnuclei defined by CCK expression, which corresponded to various extra-amygdalar afferents indicating specific inputs on distinct PN groups. Axonal arborization patterns of PNs within the basolateral amygdala and surrounding areas showed consistency to their soma location. For instance, BA PNs that projected to the medial prefrontal cortex but not to the lateral nucleus of the central amygdala were present in CCK+ areas. In contrast, those BA PNs that projected to the lateral part of the central nucleus were found in the subnucleus lacking CCK. Our study revealed that the basolateral amygdala is composed of functionally different subnuclei with specific inputs and outputs. This structural arrangement may empower the LA and BA to flexibly channel processed information toward their downstream regions, which can be a key requirement for diverse amygdala functions in cognitive operation.
maGENEgerZ: An Efficient AI-Based Framework Can Extract More Expressed Genes and Biological Insights Underlying Breast Cancer Drug Response Mechanism
Authors: Turki Turki , Taguchi Y-h.
Published: December 2023

Understanding breast cancer drug response mechanism can play a crucial role in improving the treatment outcomes and survival rates. Existing bioinformatics-based approaches are far from perfect and do not adopt computational methods based on advanced artificial intelligence concepts. Therefore, we introduce a novel computational framework based on an efficient support vector machines (esvm) working as follows. First, we downloaded and processed three gene expression datasets related to breast cancer responding and non-responding to the treatments from the gene expression omnibus (GEO) according to the following GEO accession numbers: GSE130787, GSE140494, and GSE196093. Our method esvm is formulated as a constrained optimization problem in the dual form as a function of λ. We recover the importance of each gene as a function of λ, y, and x. Then, we selectpgenes out ofn,provided as input to enrichment analysis tools, Enrichr and Metascape. Compared to existing baseline methods including deep learning, results demonstrate superiority and efficiency of esvm achieving high performance results and having more expressed genes in well-established breast cancer cell lines including MD-MB231, MCF7, and HS578T. Moreover, esvm is able to identify (1) various drugs including clinically approved ones (e.g., tamoxifen and erlotinib); (2) seventy-four unique genes (including tumor suppression genes such as TP53 and BRCA1); and (3) thirty-six unique TFs (including SP1 and RELA). These results have been reported to be linked to breast cancer drug response mechanism, progression, and metastasizing. Our method is available publicly in the maGENEgerZ web server athttps://aibio.shinyapps.io/maGENEgerZ/.
Pronounced early differentiation underlies zebra finch gonadal germ cell development
Authors: Biegler Matthew T. , Belay Kirubel , Wang Wei , Szi Christina , Collier Paul , Luo Ji-Dung , Haase Bettina , Gedman Gregory L. , Sidhu Asha V. , Harter Elijah , Rivera-López Carlos , Amoako-Boadu Kwame , Fedrigo Olivier , Tilgner Hagen U. , Carroll Thomas , Jarvis Erich D. , Keyte Anna L.
Published: December 2023

The diversity of germ cell developmental strategies has been well documented across many vertebrate clades. However, much of our understanding of avian primordial germ cell (PGC) specification and differentiation has derived from only one species, the chicken (Gallus gallus). Of the three major classes of birds, chickens belong to Galloanserae, representing less than 4% of species, while nearly 95% of extant bird species belong to Neoaves. This represents a significant gap in our knowledge of germ cell development across avian species, hampering efforts to adapt genome editing and reproductive technologies developed in chicken to other birds. We therefore applied single-cell RNA sequencing to investigate inter-species differences in germ cell development between chicken and zebra finch (Taeniopygia castanotis), a Neoaves songbird species and a common model of vocal learning. Analysis of early embryonic male and female gonads revealed the presence of two distinct early germ cell types in zebra finch and only one in chicken. Both germ cell types expressed zebra finch Germline Restricted Chromosome (GRC) genes, present only in songbirds among birds. One of the zebra finch germ cell types expressed the canonical PGC markers, as did chicken, but with expression differences in several signaling pathways and biological processes. The second zebra finch germ cell cluster was marked by proliferation and fate determination markers, indicating beginning of differentiation. Notably, these two zebra finch germ cell populations were present in both male and female zebra finch gonads as early as HH25. Using additional chicken developmental stages, similar germ cell heterogeneity was identified in the more developed gonads of females, but not males. Overall, our study demonstrates a substantial heterochrony in zebra finch germ cell development compared to chicken, indicating a richer diversity of avian germ cell developmental strategies than previously known.
The risks of chronic exposure to ultraviolet light in laboratory environment
Authors: Xavier Eric Almeida
Published: December 2023

The use of ultraviolet (UV) sources in laboratories requires safety practices. For example, when the ultraviolet light of laminar flow is on, it is important that the researcher or team members do not remain in the environment. There are laminar flows that have glasses with an ultraviolet light filter, but many models do not have any protection against ultraviolet light. Thus, we measured the irradiance inside and outside two types of laminar flows without UV filter and with UV filter respectively. And calculated the radiation levels that a researcher could receive at one meter distance for one hour daily in a time interval of one year. Thus, we found that chronic exposure to UV radiation from laminar flow can cause health risks. And we concluded that all laboratories must adopt safety measures, for example does not allow the presence of people during the disinfection stage of laminar flow with UV light.
Activity-assembled nBAF complex mediates rapid immediate early gene transcription by regulating RNA Polymerase II productive elongation
Authors: Cornejo Karen G. , Venegas Andie , Sono Morgan H. , Door Madeline , Gutierrez-Ruiz Brenda , Karabedian Lucy B. , Nandi Supratik G. , Dykhuizen Emily C , Saha Ramendra N
Published: December 2023

Signal-dependent RNA Polymerase II (Pol2) productive elongation is an integral component of gene transcription, including those of immediate early genes (IEGs) induced by neuronal activity. However, it remains unclear how productively elongating Pol2 overcome nucleosomal barriers. Using RNAi, three degraders, and several small molecule inhibitors, we show that the mammalian SWI/SNF complex of neurons (neuronal BAF, or nBAF) is required for activity-induced transcription of neuronal IEGs, includingArc. The nBAF complex facilitates promoter-proximal Pol2 pausing, signal-dependent Pol2 recruitment (loading), and importantly, mediates productive elongation in the gene body via interaction with the elongation complex and elongation-competent Pol2. Mechanistically, Pol2 elongation is mediated by activity-induced nBAF assembly (especially, ARID1A recruitment) and its ATPase activity. Together, our data demonstrate that the nBAF complex regulates several aspects of Pol2 transcription and reveal mechanisms underlying activity-induced Pol2 elongation. These findings may offer insights into human maladies etiologically associated with mutational interdiction of BAF functions.
Differential substrate specificity of ERK, JNK, and p38 MAP kinases toward Connexin 43
Authors: Latchford Lauren P. , Perez Liz S. , Conage-Pough Jason E. , Turk Reem , Cusimano Marissa A. , Vargas Victoria I. , Arora Sonal , Shienvold Sophia R. , Kulp Ryan R. , Belverio Hailey M. , White Forest M. , Thévenin Anastasia F.
Published: December 2023

Phosphorylation of connexin 43 (Cx43) is an important regulatory mechanism of gap junction (GJ) function. Cx43 is modified by several kinases on over 15 sites within its ∼140 amino acid-long C-terminus (CT). Phosphorylation of Cx43CT on S255, S262, S279, and S282 by ERK has been widely documented in several cell lines, by many investigators. Phosphorylation of these sites by JNK and p38, on the other hand, is not well-established. Indeed, ERK is a kinase activated by growth factors and is upregulated in diseases, such as cancer. JNK and p38, however, have a largely tumor-suppressive function due to their stress-activated and apoptotic role. We investigated substrate specificity of all three MAPKs toward Cx43CT, first by using purified proteins, and then in two cell lines (MDCK - non-cancerous, epithelial cells and porcine PAECs – pulmonary artery endothelial cells). Cx43 phosphorylation was monitored through gel-shift assays on an SDS-PAGE, immunodetection with phospho-Cx43 antibodies, and LC-MS/MS phosphoproteomic analyses. Our results demonstrate that p38 and JNK specificity differ from each other and from ERK. JNK has a strong preference for S255, S262, and S279, while p38 readily phosphorylates S262, S279, and S282. While we confirmed that ERK can phosphorylate all four serines (255, 262, 279, and 282), we also identified T290 as a novel ERK phosphorylation site. In addition, we assessed Cx43 GJ function upon activation or inhibition of each MAPK in PAECs. This work underscores the importance of delineating the effects of ERK, JNK, and p38 signaling on Cx43 and GJ function.
RepeatOBserver: tandem repeat visualization and centromere detection
Authors: Elphinstone Cassandra , Elphinstone Rob , Todesco Marco , Rieseberg Loren
Published: December 2023

Tandem repeats can play an important role in centromere structure, subtelomeric regions, DNA methylation, recombination, and the regulation of gene activity. There is a growing need for bioinformatics tools that can visualize and explore chromosome-scale repeats. Here we present RepeatOBserver, a new tool for visualizing tandem repeats and clustered transposable elements and for identifying potential natural centromere locations, using a Fourier transform of DNA walks:https://github.com/celphin/RepeatOBserverV1. RepeatOBserver can identify a broad range of repeats (3-20, 000bp long) in genome assemblies without anya prioriknowledge of repeat sequences or the need for optimizing parameters. RepeatOBserver allows for easy visualization of the positions of both perfect and imperfect repeating sequences across each chromosome. We use RepeatOBserver to compare DNA walks, repeat patterns and centromere positions across genome assemblies in a wide range of well-studied species (e.g., human, mouse-ear cress), crops, and non-model organisms (e.g., fern, yew). Analyzing 107 chromosomes with known centromere positions, we find that centromeres consistently occur in regions that have the least diversity in repeat types (i.e. one or a few repeated sequences are present in very high numbers). Taking advantage of this information, we use a genomic Shannon diversity index to predict centromere locations in several other chromosome-scale genome assemblies. The Fourier spectra produced by RepeatOBserver can help visualize historic centromere positions, potential neocentromeres, retrotransposon clusters and gene copy variation. Identification of patterns of split and inverted tandem repeats at inversion boundaries suggests that at least some chromosomal inversions or misassemblies can be predicted with RepeatOBserver. RepeatOBserver is therefore a flexible tool for comprehensive characterization of tandem repeat patterns that can be used to visualize and identify a variety of regions of interest in genome assemblies.
Genomic Underground: Unraveling NUMTs in Mole Voles
Authors: Prokopov Dmitry , Saluev Tigran , Romanenko Svetlana , Bakloushinskaya Irina , Graphodatsky Alexander
Published: December 2023

Nuclear mitochondrial DNA segments (NUMTs) are pervasive elements of eukaryotic genomes. This study focuses onEllobius talpinusandEllobius lutescens, for which we assembled full mitochondrial DNA sequences. Our study identified NUMTs encompassing approximately 0.0052% and 0.0086% of genome assembly length inE. talpinusandE. lutescens, respectively. These NUMTs collectively spanned a total length of 122,294 bp inE. talpinusand 194,875 bp inE. lutescens. Notably, the majority of NUMTs in both species were short, with lengths of less than 500 bp. InE. talpinus, the data indicated the presence of comparatively recent NUMT insertions. More than half of the NUMTs in each species are organized into clusters, primarily situated in intergenic regions or within introns. RNA genes are the most frequently occurring fragments within these NUMTs. Furthermore, our analysis identified LINE, SINE, and LTR retrotransposons within and flanking NUMT clusters. Our results demonstrate the intricate dynamics of NUMT integration and distribution inEllobiusspecies and provide insights into their genomic architecture and evolutionary history. This study contributes to the broader understanding of mitochondrial DNA contributions to nuclear genomes and underscores the complexity of distinguishing between mtDNA and nuclear DNA in genomic studies.
Sex- and strain-dependent effects of ageing on sleep and activity patterns inDrosophila
Authors: Woodling Nathan
Published: December 2023

The fruit flyDrosophilais a major discovery platform in the biology of ageing due to its balance of relatively short lifespan and relatively complex physiology and behaviour. Previous studies have suggested that some important phenotypes of ageing, for instance increasingly fragmented sleep, are shared from humans toDrosophilaand can be useful measures of behavioural change with age: these phenotypes therefore hold potential as readouts of healthy ageing for genetic or pharmacological interventions aimed at the underpinning biology of ageing. However, some age-related phenotypes inDrosophilashow differing results among studies, leading to questions regarding the source of discrepancies among experiments. In this study, I have tested females and males from three common laboratory strains ofDrosophilato determine the extent to which sex and background strain influence age-related behavioural changes in sleep and activity patterns. Surprisingly, I find that some phenotypes – including age-related changes in total activity, total sleep, and sleep fragmentation – depend strongly on sex and strain, to the extent that some phenotypes show opposing age-related changes in different sexes or strains. Conversely, I identify other phenotypes, including age-related decreases in morning and evening anticipation, that are more uniform across sexes and strains. These results reinforce the importance of controlling for background strain in both behavioural and ageing experiments, and they imply that caution should be used when drawing conclusions from studies on a single sex or strain ofDrosophila. At the same time, these findings also offer suggestions for behavioural measures that merit further investigation as potentially more consistent phenotypes of ageing.
Do agency costs and business risk affect the corporate sustainability–financial performance relationship?
Authors: Kalash Ismail
Published: December 2023

Purpose

The aim of this research is to examine the effect of corporate sustainability performance on financial performance and the role of agency costs and business risk in determining this effect.

Design/methodology/approach

This study uses the data of 83 non-financial Turkish firms listed on Istanbul Stock Exchange during the period 2014–2021. Two-step system GMM models are applied to examine the study’s hypotheses.

Findings

The results indicate a positive effect of corporate sustainability performance on financial performance, and that this effect is significant only for firms that are more likely to suffer agency costs of equity, firms with R&D expenditures and firms with lower business risk.

Practical implications

The results of this study confirm the importance of regulations introduced by regulators to support the sustainability initiatives for firms that have less ability to access funds required for their investments. In addition, the findings provide important insight into the role of the persistence of corporate sustainability performance in enhancing financial performance through mitigating managers' opportunistic behavior.

Originality/value

To the author’s knowledge, this research is one of few that examine the effect of agency costs and business risk on the corporate sustainability–financial performance relationship in emerging markets.
Outbound open innovation effectiveness measurement between big organizations and startups using Fuzzy MCDM
Authors: Quaiser Raunaque Mujeeb , Srivastava Praveen Ranjan
Published: December 2023

Purpose

This research aims to identify the key factors affecting Outbound Open Innovation between Startups and Big organizations using the multiple criteria decision-making analysis (MCDM) approach. The MCDM technique ranks the four key factors identified from the literature study that can help to improve collaboration opportunities with Startups.

Design/methodology/approach

Identification of key factors affecting Outbound Open Innovation between Startups and big organizations based on extant literature. A questionnaire is prepared based on these four identified key factors to gather views of the startup's employees, from the designer level to the startup's founder. MCDM techniques are used to evaluate the questionnaire. The ensemble technique is used to rank the key factors coming from three different MCDM methods.

Findings

The findings from the MCDM approach and Ensemble techniques give insight to the big organizations to facilitate outbound Open Innovation effectively. It also provides insight into the requirements of the startups and the kind of support they seek from the big organizations. The ranking can help the big organization close the gaps and make an informed decision to increase the effectiveness of the collaborations and boost innovation.

Originality/value

This is a unique research work where the MCDM approach is used to identify the ranking of key factors affecting outbound open innovation between startups and big organizations. The MCDM technique is followed by the ensemble method to rationalize the findings. Technology Relevance ranks highest, followed by Innovation Ecosystem, Organization commitment and Knowledge Sharing.
Asymmetric effect of environmental tax on CO2 emissions embodied in domestic final demand in South Africa: A NARDL approach
Authors: Ibe Godwin Imo , Ezeaku Hillary Chijindu , Okpara Itiri Idam , Eze Eze Festus , Igwemeka Ebele , Ubani Obinna
Published: December 2023

Motivated by the pressing need to address environmental concerns, this study explores the relationship between environmental taxes and CO2 emissions embodied in domestic final demand in South Africa. The study uses a non‐linear autoregressive distributed lag (NARDL) model to analyse the asymmetric impact of environmental taxes. Results indicate that environmental taxes have an asymmetric impact on CO2 emissions embodied in domestic final demand in both the short and long runs. Specifically, both positive and negative shifts in environmental taxes are linked with a respective 0.06% decrease and a more pronounced 0.22% decrease in CO2 emissions embodied in domestic final demand. Moreover, positive shocks in the GDP growth rate are associated with an approximately 0.002% uptick in CO2 emissions, while negative shocks lead to a 0.012% decrease. Additionally, both positive and negative shocks in population growth exhibit a significant positive correlation with the response variable. The baseline estimates demonstrate that the joint effect of environmental taxes and the GDP growth rate is correlated with reductions in CO2 emissions embodied in domestic final demand. Similarly, the joint influence of environmental taxes and population growth rate is linked to declines in CO2 emissions. The study highlights the practical policy implications of these findings.
Therapy for the Dead: Working Clinically with Jung's Black Books and The Red Book
Authors: Hill Ginny
Published: December 2023

With the 2020 publication of the facsimile edition of The Black Books, we have an opportunity to study the layers of C. G. Jung's creative writing process for the first time. In this paper, I explore Jung's practice of active imagination in relation to his fantasy dialogues with the dead during two specific episodes in 1914 and 1916. I discuss Jung's concept of the collective unconscious corresponding to the “mythic land of the dead” and I show how this idea develops in The Black Books and The Red Book, or Liber Novus, culminating in Septem Sermones ad Mortuos. I describe my work with a patient, who, in an early session, said she felt like the "living dead". I recount how the patient's experience of her own internal world began to change as we were able to wonder about the inner world of the patient's late mother and, together, to imagine her mother's lament. I consider the use of imagination when working with the concept of "therapy for the dead" (Hillman & Shamdasani, 2013, p. 164) in the context of intergenerational trauma.
Fraud Power Laws
Authors: CHEYNEL EDWIGE , CIANCIARUSO DAVIDE , ZHOU FRANK S.
Published: December 2023

Using misstatement data, we find that the distribution of detected fraud features a heavy tail. We propose a theoretical mechanism that explains such a relatively high frequency of extreme frauds. In our dynamic model, a manager manipulates earnings for personal gain. A monitor of uncertain quality can detect fraud and punish the manager. As the monitor fails to detect fraud, the manager's posterior belief about the monitor's effectiveness decreases. Over time, the manager's learning leads to a slippery slope, in which the size of frauds grows steeply, and to a power law for detected fraud. Empirical analyses corroborate the slippery slope and the learning channel. As a policy implication, we establish that a higher detection intensity can increase fraud by enabling the manager to identify an ineffective monitor more quickly. Further, nondetection of frauds below a materiality threshold, paired with a sufficiently steep punishment scheme, can prevent large frauds.
Difficulty differentiating primary mediastinal classical Hodgkin lymphoma from inflammatory myofibroblastic tumor: A case report
Authors: Akata Kentaro , Yamasaki Kei , Chiba Yosuke , Kawaguchi Takako , Dosaka Hiroki , Morimoto Toshiki , Higashi Yasuyuki , Nishida Chinatsu , Shimajiri Shohei , Yatera Kazuhiro
Published: December 2023

A 20‐year‐old Japanese man visited our hospital because an enlarged mediastinal shadow had been detected on chest x‐ray. Chest computed tomography revealed a large mediastinal mass with multiple lymph node enlargement, pericardial effusion, and bilateral pleural effusion. He was diagnosed with inflammatory myofibroblastic tumor (IMT) based on a thoracoscopic tumor biopsy. Initial corticosteroid and celecoxib treatment was only partially effective; therefore, additional tumor rebiopsy and left axillary lymph node biopsy were performed. Based on the findings, the patient was rediagnosed with classical Hodgkin lymphoma (CHL). To date, there has only been one report of a case initially diagnosed as IMT and rediagnosed as CHL, as in our case, and only three reports of malignant lymphoma mimicking IMT. When IMT is suspected based on pathological findings and subsequently with treatment failure, possible CHL and performing rebiopsy should be considered.
Appropriateness of antibiotic prescribing for patients with sepsis in rural hospital emergency departments
Authors: Heffernan A. J. , Smedley A. , Stickley T. , Oomen S. , Carrigan B. , Heffernan R. , Woodall H. , Pinidiyapathirage J. , Brumpton K.
Published: December 2023

Design/Participants

This was a multicentre retrospective cohort study of adult patients (≥18 years) presenting with a process associated International Classification of Diseases code (ICD‐AM‐10) pertaining to sepsis between January 2017 and July 2020 to rural Emergency Departments.

Main Outcome Measures

Our primary outcome was antibiotic appropriateness as defined by the Australian Therapeutic Guidelines (for antibiotic selection relative to infecting source) and the National Antimicrobial Prescribing Survey tool. Our secondary outcome was in‐hospital mortality.

Methods

Relevant clinical and non‐clinical, physiological and laboratory data were collected retrospectively. Multivariate logistic regression was used to estimate the odds of both inappropriate antibiotic prescribing and in‐hospital mortality based on clinical and non‐clinical factors.

Results

A total of 378 patients were included who primarily presented with sepsis of unknown origin (36.8%), a genitourinary (22.22%) or respiratory (18.78%) source. Antibiotics were appropriately prescribed in 59% of patients. A positive Quick Sequential Organ Failure Assessment score (qSOFA) (odds ratio [OR] = 0.49; 95% confidence interval [CI], 0.29–0.83), a respiratory infection source (OR = 0.5; 95% CI, 0.29–0.86) and documented allergy (OR = 0.42; 95% CI, 0.25–0.72) were associated with a lower risk of appropriate prescribing in multivariate analysis. Forty‐one percent of patients received antibiotics within 1 h of presentation. Inappropriate antibiotic prescribing was not associated with in‐hospital mortality.

Conclusion

The rates of appropriate antibiotic prescribing in rural Emergency Departments for patients presenting with sepsis is low, but comparable to other referral metropolitan centres.
Prevalence of steatotic liver disease, MASLD, MetALD and significant fibrosis in people with HIV in the United States
Authors: Gawrieh Samer , Vilar‐Gomez Eduardo , Woreta Tinsay A. , Lake Jordan E. , Wilson Laura A. , Price Jennifer C. , Naggie Susanna , Sterling Richard K. , Heath Sonya , Corey Kathleen E. , Cachay Edward R. , Ajmera Veeral , Tonascia James , Sulkowski Mark S. , Chalasani Naga , Loomba Rohit
Published: December 2023

Background

Metabolic dysfunction‐associated steatotic liver disease (MASLD) has recently been proposed as a replacement term for NAFLD.

Aims

To assess the effects of this new nomenclature on the prevalence and distribution of different SLD categories in people with HIV (PWH) and identified factors associated with MASLD and clinically significant fibrosis (CSF).

Methods

PWH were prospectively enrolled from 9 US centres and underwent clinical evaluation and vibration‐controlled transient elastography for controlled attenuation parameter (CAP) and liver stiffness measurement (LSM). SLD was defined as CAP ≥ 263 dB/m, CSF as LSM of ≥8 kPa, and advanced fibrosis (AF) as LSM ≥ 12 kPa. The prevalence of SLD, MASLD, metabolic dysfunction and alcohol‐associated liver disease (MetALD), ALD, cryptogenic (cSLD), CSF and AF were determined. Uni‐ and multivariate logistic regression models were used to assess factors associated with MASLD and CSF risk.

Results

Of 1065 participants, 74% were male, mean (SD) age 51.6 ± 11.9 years, 46% non‐Hispanic Black and 74% with undetectable HIV RNA. The prevalence of SLD was 52%, MASLD 39%, MetALD 10%, ALD 3%, CSF 15% and AF 4%. Only 0.6% had cSLD. Black race was protective whereas obesity, ALT and AST levels were associated with increased risk of MASLD and CSF in MASLD. HIV or antiretroviral therapy did not affect MASLD risk.

Conclusions

MASLD and MetALD are the dominant causes of SLD in PWH, affecting almost half. Application of the new nomenclature resulted in minimal change in the proportion of patients with MASLD who would have been diagnosed previously with NAFLD.
The costs of lying: Consequences of telling lies on liar's self‐esteem and affect
Authors: Preuter Sanne , Jaeger Bastian , Stel Mariëlle
Published: December 2023

Deceiving others is generally viewed as immoral. However, most people lie on a daily basis. This article examines the psychological consequences for the liars themselves, as they are participating in what is generally perceived as immoral behaviour. More specifically, this article focuses on the effects of lying on the liar's self‐esteem and affect. We tested if lying, in comparison to telling the truth, lowers people's self‐esteem and increases negative experienced affect. In total, three cross sectional and one longitudinal studies were conducted (N = 783). Results showed that lying decreased people's self‐esteem and increased negative affect, regardless of the type of lie (self‐centred vs. other‐oriented). Furthermore, lying on a given day decreased people's self‐esteem compared to their self‐esteem on the previous day and to their average level of self‐esteem across 5 days.
Predictive model averaging with parameter instability and heteroskedasticity
Authors: Yin Anwen
Published: December 2023

This paper proposes a frequentist model averaging approach in the presence of parameter instability and heteroskedasticity. We derive optimal weights combining the stable and break specifications of a predictive model, with the weights from minimizing the leave‐one‐out cross‐validation information criterion (CV). We characterize the asymptotic distribution of the CV and provide the analytical expressions of the feasible optimal CV weights. Our simulations and applications forecasting the US and Taiwanese GDP growth demonstrate the superior performance of the CV model averaging relative to other methods such as the Mallows averaging, the approximate Bayesian averaging, and equal weighting.
Does geographic or market proximity matter? Evidence from institutional investor monitoring on earnings attributes in US cross‐listed stocks
Authors: Kang Sanggyu , Chung Chune Young , Fard Amirhossein
Published: December 2023

This study investigates institutional distance as a factor of investors’ monitoring of corporate earnings attributes. We analyze the US cross‐listing market to determine whether institutional monitoring depends on geographic or market proximity. We find that shareholdings of non‐US institutions headquartered in the same country as the investee firm are significantly and positively related to earnings quality. However, we do not find such a monitoring role in the United States, or in institutions not incorporated in the investee firm's home country. Our findings support a geographic proximity advantage over market proximity, which is more pronounced when firms’ information opacity is more severe; the results are not altered by the choice of earnings attribute variables.
Effectiveness of catch‐up and routine program of the 9‐valent vaccine on cervical cancer risk reduction in Japan
Authors: Yagi Asami , Nakagawa Satoshi , Ueda Yutaka , Oka Emiko , Ikeda Sayaka , Kakuda Mamoru , Kobayashi Eiji , Ito Yuri , Katayama Kayoko , Hirai Kei , Nakayama Tomio , Kimura Tadashi
Published: December 2023

In 2013, the national human papillomavirus (HPV) immunization program began. However, in June 2013, Japan's Ministry of Health, Labor and Welfare (MHLW) announced a “temporary” suspension of its recommendation for the human papillomavirus vaccine. Finally, in November 2021, the MHLW ended its suspension of the recommendation of the HPV vaccine. To address the 9‐year gap in HPV vaccinations the suspension had caused, the MHLW conducted a program of catch‐up vaccinations from April 2022 to March 2025. Finally, in April 2023, the 9‐valent HPV vaccine was approved for both the routine and catch‐up vaccination programs in Japan. In this study, we investigated the potential effects of the introduction of the 9‐valent vaccine on the increased risk of cervical cancer in females born after fiscal year (FY) 2000. We estimated the lifetime relative risk of cervical cancer incidence and death using the improved routine and catch‐up vaccination rates after the recent resumption of the governmental recommendation for women and girls to have the HPV vaccination. These relative risks were calculated using a lifetime risk of 1.000 for cervical cancer incidence and death for females born in FY 1993. We predicted that even if a 90% vaccination rate were to be achieved by FY 2024 with the 9‐valent vaccine among women born between FY 2000 and FY 2005, the risk would remain higher than for the vaccination generation. Therefore, for women born between FY 2000 and FY 2005, it will be necessary to significantly improve the cervical cancer screening rate to compensate for this increased risk.
Stapler size independently predicts postoperative complications following stapled ileocolic anastomosis: A retrospective cohort study
Authors: Garoufalia Zoe , Emile Sameh Hany , Zhou Peige , Gefen Rachel , Horesh Nir , Strassmann Victor , Ray‐Offor Emeka , DaSilva Giovanna , Wexner Steven D.
Published: December 2023

Aim

Staplers used in ileocolic anastomosis construction differ in length and height. We assessed the impact of stapler type in creating ileocolic anastomoses on postoperative outcomes.

Methods

This retrospective cohort study of an Institutional Review Board approved database included patients who underwent laparoscopic right colectomy for cancer between January 2011 and August 2021. All patients had construction of extracorporeal antiperistaltic stapled ileocolic anastomosis using a linear cutting stapler. Main outcome measures were short‐term (<30 day) morbidity and mortality.

Results

In all, 270 patients (136 men; median age 70.2 years) were included. A 75 mm stapler was used in 49 (18.1%) patients, 80 mm in 97 (35.9%) and 100 mm in 124 (45.9%). Blue cartridge (stapler height 3.5 mm) was used in 175 (64.5%) and green cartridge (4.8 mm) in 18 (7%) patients; this information was unavailable in 77 (28.5%) cases. Apical enterotomy closure was performed by linear stapler in 54% and linear cutting stapler in 46%. Apical staple line reinforcement or imbrication suturing was used in 26.3%. The overall postoperative complication rate was 28.9%. The anastomotic leak rate was 2.6%. Independent predictors of complications after laparoscopic right colectomy were older age (OR 1.03, 95%CI 1–1.06; P = 0.01), extended colectomy (OR 2.76, 95%CI 1.07–7.08; P = 0.035) and emergency surgery (OR 4.5, 95%CI 1.3–14.9; P = 0.014). A 100‐mm linear cutting stapler was an independent protective factor against postoperative complications (OR 0.3, 95%CI 0.18–0.85; P = 0.019). Stapler height and closure technique of apical enterotomy did not affect postoperative complications.

Conclusion

Independent predictors of complications after laparoscopic right colectomy were older age, extended colectomy and emergency surgery. Using a 100 mm stapler was an independent protective factor against postoperative complications.
Do payday lending bans protect or constrain regional economies? Evidence from the Military Lending Act's final rule
Authors: Carpenter Craig Wesley , Deming Kristopher , Anders John , Lotspeich‐Yadao Michael , Tolbert Charles M. , Ingrao Adam
Published: December 2023

The 2007 Military Lending Act attempted to ban high‐interest loans to U.S. military members and the 2017 “Final Rule” further restricted access, causing regional shocks in payday lending exposure in counties with a military base. Difference‐in‐differences and dynamic estimators provide mixed evidence on the effect of this payday lending access shock on regional economic outcomes and local business outcomes. However, we consistently find statistically significant reduced entry and exit of firms. Given payday lenders congregate around low‐income and minoritized populations analogously to how they congregated around military bases, these results provide policy implications for more general usury bans.
Making the grade: The effect of teacher grading standards on student outcomes
Authors: Gershenson Seth , Holt Stephen B. , Tyner Adam
Published: December 2023

One mechanism by which teachers might affect student learning is through the grading standards they set for their classrooms. However, the effects of grading standards on student outcomes are understudied. Using administrative data that links individual students and teachers in Algebra I classrooms from 2006 to 2016, we examine the effects of teachers' grading standards on student learning and attendance. High teacher grading standards increase both contemporaneous student achievement in Algebra I and performance in subsequent math classes. Heterogeneity analyses find that these impacts are positive and similar in size for students of different backgrounds, aptitudes, and school contexts.
Single‐cell RNA sequencing to explore cancer‐associated fibroblasts heterogeneity: “Single” vision for “heterogeneous” environment
Authors: Zhang Xiangjian , Zhu Ruiqiu , Yu Die , Wang Juan , Yan Yuxiang , Xu Ke
Published: December 2023

Cancer‐associated fibroblasts (CAFs), a phenotypically and functionally heterogeneous stromal cell, are one of the most important components of the tumour microenvironment. Previous studies have consolidated it as a promising target against cancer. However, variable therapeutic efficacy—both protumor and antitumor effects have been observed not least owing to the strong heterogeneity of CAFs. Over the past 10 years, advances in single‐cell RNA sequencing (scRNA‐seq) technologies had a dramatic effect on biomedical research, enabling the analysis of single cell transcriptomes with unprecedented resolution and throughput. Specifically, scRNA‐seq facilitates our understanding of the complexity and heterogeneity of diverse CAF subtypes. In this review, we discuss the up‐to‐date knowledge about CAF heterogeneity with a focus on scRNA‐seq perspective to investigate the emerging strategies for integrating multimodal single‐cell platforms. Furthermore, we summarized the clinical application of scRNA‐seq on CAF research. We believe that the comprehensive understanding of the heterogeneity of CAFs form different visions will generate innovative solutions to cancer therapy and achieve clinical applications.
Concurrent Langerhans cell histiocytosis and acute myeloid leukemia: A rare presentation of a rare case
Authors: Gao Julia L. , Davis Matthew J. , Dagrosa Alicia T. , Momtahen Shabnam
Published: December 2023

A 72‐year‐old woman with no significant past medical history was admitted to the hospital for new‐onset of leukocytosis with neutropenia, anemia, and thrombocytopenia, as well as a pruritic skin eruption. She was found to have acute myeloid leukemia (AML) with myelomonocytic differentiation. Her skin eruption consisted of widespread hemorrhagic crusted papules on the scalp and trunk. A skin biopsy was performed, which revealed a proliferation of mononuclear cells in the dermis with prominent epidermotropism and positive expression of CD1a and langerin (CD207), supporting a diagnosis of Langerhans cell histiocytosis (LCH). LCH is an uncommon proliferative disorder of activated Langerhans cells, which generally presents in children. In adults, it is exceptionally infrequent. Associated malignancies and rare reports of AML developing in subsequent years after an initial presentation of LCH have been described. Here we present an unusual concurrent presentation of LCH and AML in an adult.
Value of drug level concentrations of brivaracetam, lacosamide, and perampanel in care of people with epilepsy
Authors: Hentschel Matthias , Stoffel‐Wagner Birgit , Surges Rainer , von Wrede Randi , Dolscheid‐Pommerich Ramona Christina
Published: December 2023

Objective

The aim of this study was to determine whether clinical efficacy and reported adverse effects (AEs) of the newer antiseizure medications (ASMs) brivaracetam (BRV), lacosamide (LCM), and perampanel (PER) have been associated with plasma levels of these ASMs. We also investigated whether plasma levels outside the reference range has led to dose adjustments.

Methods

Plasma levels of 300 people with epilepsy (PWE) seen at our tertiary epilepsy center were determined by liquid chromatography–tandem mass spectrometry.

PWE received BRV (n = 100), LCM (n = 100), or PER (n = 100), in most cases in polytherapy. Demographic and clinical data were retrospectively analyzed and related to plasma levels. Clinical efficacy of BRV, LCM, or PER was assessed retrospectively by comparing seizure frequency at the time of current blood draw with seizure frequency at the time of first administration. AEs were also recorded and, if reported, compared retrospectively with the time of first administration.

Results

No significant associations were found between plasma levels of BRV, LCM, or PER and seizure freedom (BRV, p = 1.000; LCM, p = .243; PER, p = .113) or responder status (BRV, p = .118; LCM, p = .478; PER, p = .069) at presentation. There was also no pattern between plasma levels and the occurrence of AEs. In the majority of cases, drug levels outside the reference ranges have not led to adjustments in the daily doses of BRV (93.5%), LCM (93.9%), or PER (89.1%).

Significance

Plasma levels at a given time point did not allow conclusions to be drawn about seizure control or the occurrence of AEs. Our findings indicate that efficacy and tolerability cannot be predicted based on averaged data from a single plasma measurement due to high interindividual variability. Instead, individual reference values should be established when sufficient clinical data are available, in line with the 2008 International League Against Epilepsy position paper on therapeutic drug monitoring.
Climatic niche differentiation between native and non‐native ranges is widespread in Ponto‐Caspian amphipods
Authors: Šidagytė‐Copilas Eglė , Copilaș‐Ciocianu Denis
Published: December 2023

1. Niche conservatism posits that a species' non‐native populations establish in areas that match their native environmental conditions. Although the Ponto‐Caspian biodiversity hotspot is a major source of freshwater alien species, the extent to which their climatic niches diverge between invaded and native ranges remains poorly understood.

2. Using an n‐dimensional hypervolume approach, we quantified climatic niche overlap and inferred patterns of niche differentiation (shift, contraction, or expansion) among native and invaded ranges for 12 widespread Ponto‐Caspian amphipod species (six genera in three families).

3. Our results show that all species experience substantially different climatic conditions in their invaded range compared to their native range. The invasive niche either contracted (five species), shifted (four species), expanded and shifted (two species), or shifted and contracted (one species) relative to the native niche.

4. We conclude that although the focal taxa share a common geographic origin and evolutionary history, they exhibit disparate patterns of climatic niche change outside their native range. The niche conservatism hypothesis receives mixed support given that half of the studied species underwent niche shifts/expansion. Furthermore, congeners exhibited both identical and contrasting patterns of niche differentiation, suggesting a limited phylogenetic effect.

5. The uncovered diversity of niche dynamics among closely related species indicates that each has a unique potential for invasiveness and long‐term persistence. This has important implications for predicting invasion risk and refining management strategies. Our study also underlines the importance of biodiversity hotspots as reservoirs of highly adaptable alien species.
Drug‐related sarcopenia as a secondary sarcopenia
Authors: Kuzuya Masafumi
Published: December 2023

Sarcopenia has a significant impact on falls, physical function, activities of daily living, and quality of life in older adults, and its prevention and treatment are becoming increasingly important as the global population ages. In addition to primary age‐related sarcopenia, activity‐related sarcopenia, disease‐related sarcopenia, and nutrition‐related sarcopenia have been proposed as secondary sarcopenia. Polypharmacy and potentially inappropriate medication based on multiple diseases cause health problems in older patients. In some cases, drugs used for therapeutic or preventive purposes act on skeletal muscle as adverse drug reactions and induce sarcopenia. Although sarcopenia caused by these adverse drug reactions may be more common in older patients, in particular those taking many medications, drug‐related sarcopenia has not yet received much attention. This review summarizes drugs that may induce sarcopenia and emphasizes the importance of drug‐related sarcopenia as a secondary sarcopenia. Geriatr Gerontol Int 2024; 24: 195–203.
THE UNCONSCIOUS IN INDIVIDUALS AND SOCIETY: ON THE APPLICATION OF PSYCHOANALYTIC CATEGORIES IN HISTORIOGRAPHY
Authors: KLÜNERS MARTIN
Published: December 2023

The long‐held conviction of a mutually exclusive relationship between psychoanalysis, which allegedly proceeds purely in terms of individual psychology, and historical social science, which is interested primarily in the analysis of collectives, has significantly hindered dialogue between the disciplines. Norbert Elias's “figurational” sociology, which has been strongly influenced by psychoanalysis and group therapy, has the potential to indicate a way in which social science‐oriented historical research might investigate the network of relations between individual and “collective” psychic processes without relying on artificial dichotomies. Elias's figurational theory, for its part, does not sufficiently take into account the question of a collective or social unconscious, so this article examines approaches that attempt to explore and conceptually define a supra‐individual unconscious.