bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome-level genome of butterflyfish unveils genomic features of unique colour patterns and morphological traits
Authors: Zhang Suyu , Song Yue , Liu Meiru , Yuan Zengbao , Zhang Mengqi , Zhang He , Seim Inge , Fan Guangyi , Liu Shanshan , Liu Xin 
Published: August 2023

Abstract
Chaetodontidae, known as butterflyfishes, are typical fish in coral ecosystems, exhibiting remarkable interspecific differences including body colour patterns and feeding ecology. In this study, we report genomes of three butterflyfish species (Chelmon rostratus, Chaetodon trifasciatus and Chaetodon auriga) and a closely related species from the Pomacanthidae family, Centropyge bicolour, with an average genome size of 65,611 Mb. Chelmon rostratus, comprising 24 chromosomes assembled to the chromosome level, could be served as a reference genome for butterflyfish. By conducting a collinearity analysis between butterflyfishes and several fishes, we elucidated the specific and conserved genomic features of butterflyfish, with particular emphasis on novel genes arising from tandem duplications and their potential functions. In addition to the two melanocyte-specific tyr genes commonly found in fish, we found the gene tyrp3, a new tyrosinase-related proteins gene in the reef fish, including butterflyfish and clownfish, implicating their involvement in the pigmentation diversity of fish. Additionally, we observed a tandem duplication expansion of three copies of nell1 gene in C. rostratus genome, which likely contribute to its unique jaw development and distinctive morphology of its sharp mouth. These results provided valuable genomic resources for further investigations into the genetic diversity and evolutionary adaptations of reef fish.
Blind spot in endocarditis guidelines: Mycobacterium chimaera prosthetic valve endocarditis after cardiac surgery—a case series
Authors: Trauth Janina , Matt Ulrich , Kohl Thomas A , Niemann Stefan , Herold Susanne 
Published: August 2023

Abstract

Background
The recently published 2023 Duke-ISCVID Criteria for Infective Endocarditis for the first time consider mycobacteria (esp. Mycobacterium chimaera) as ‘typical’ microorganisms for prosthetic valve endocarditis (major criteria). This reflects the ongoing worldwide outbreak of M. chimaera prosthetic valve endocarditis.

Case summary
Our case series demonstrates a diagnostic pathway for mycobacterial endocarditis. Symptoms are unspecific, and standard microbiological testing does not result in identification of the causative agent (see Graphical Abstract); therefore patients require special microbiological and imaging diagnostics. One patient with early diagnosis and stringent antibiotic and surgical therapy survived. Two patients with disseminated infection at the time point of diagnosis had fatal outcomes.

Discussion
The diagnostic approach in our small retrospective case series is in line with the new modified Duke criteria and underlines the diagnostic gap in the previous definitions. Outcome of M. chimaera prosthetic valve endocarditis is related to timely diagnosis and anti-mycobacterial as well as surgical treatment. Non-tuberculous mycobacteria should be given more attention in future endocarditis guidelines.
The impact of malperfusion patterns in elderly patients undergoing surgery for acute type A aortic dissection
Authors: Pitts Leonard , Kofler Markus , Montagner Matteo , Heck Roland , Kurz Stephan D , Buz Semih , Falk Volkmar , Kempfert Jörg 
Published: August 2023

Abstract

OBJECTIVES
The aim of this study is to investigate the outcome of elderly patients with surgically treated acute type A aortic dissection (ATAAD) complicated by malperfusion.

METHODS
Patients ≥70 years old who underwent surgical treatment for ATAAD between January 2000 and December 2020 were enrolled in this study and stratified by their specific Penn Classification into 4 different subgroups, where Penn Abc was defined as multilevel malperfusion. Short- and long-term outcomes were investigated. Multivariable binary logistic regression was performed to identify risk factors for 1-year mortality.

RESULTS
Four hundred elderly patients underwent surgical treatment for ATAAD. A total of 204 (51%) patients had no evidence of malperfusion (Penn Aa), 106 (26.5%) had localized organic malperfusion (Penn Ab), 44 (11%) patients had systemic malperfusion (Penn Ac) and 46 (11.5%) suffered from multilevel malperfusion (Penn Abc). For the latter, in-hospital mortality was 70% (P &lt; 0.001). Age (P &lt; 0.006) and multilevel malperfusion (P &lt; 0.001) were independent risk factors for 1-year mortality. Patients with multilevel malperfusion showed the worst 1-year survival (P &lt; 0.001). In the case of Penn Aa, in-hospital mortality was 13% (P &lt; 0.001).

CONCLUSIONS
Surgery may lead to satisfactory results in the absence of malperfusion, even in octogenarians. Elderly patients with multilevel malperfusion show very poor surgical outcome. In these patients, the decision for surgery should be taken with caution. Operation, if performed, should be carried out by experienced teams only.
Performance of DNA-based biomarkers for classification of adrenocortical carcinoma: a prognostic study
Authors: Lippert Juliane , Dischinger Ulrich , Appenzeller Silke , Prete Alessandro , Kircher Stefan , Skordilis Kassiani , Elhassan Yasir S , Altieri Barbara , Fassnacht Martin , Ronchi Cristina L 
Published: August 2023

Abstract

Objective
Adrenocortical carcinoma (ACC) is a rare aggressive malignancy with heterogeneous clinical outcomes. Recent studies proposed a combination of clinical/histopathological parameters (S-GRAS score) or molecular biomarkers (BMs) to improve prognostication. We performed a comparative analysis of DNA-based BMs by evaluating their added prognostic value to the S-GRAS score.

Design and methods
A total of 194 formalin-fixed, paraffin-embedded (FFPE) ACC samples were analysed, including a retrospective training cohort (n = 107) and a prospective validation cohort (n = 87). Targeted DNA sequencing and pyrosequencing were used to detect somatic single-nucleotide variations in ACC-specific genes and methylation in the promoter region of paired box 5 (PAX5). The European Network for the Study of Adrenocortical Tumors (ENSAT) tumour stage, age, symptoms at presentation, resection status, and Ki-67 were combined to calculate S-GRAS. Endpoints were overall (OS), progression-free (PFS), and disease-free survival (DFS). Prognostic role was evaluated by multivariable survival analysis and their performance compared by Harrell's concordance index (C index).

Results
In training cohort, an independent prognostic role was confirmed at multivariate analysis for two DNA-based BMs: alterations in Wnt/β-catenin and Rb/p53 pathways and hypermethylated PAX5 (both P&lt; .05 for PFS and DFS, hazard ratio [HR] 1.47-2.33). These were combined to S-GRAS to obtain a combined (COMBI) score. At comparative analysis, the best discriminative prognostic model was COMBI score in both cohorts for all endpoints, followed by S-GRAS score (C index for OS 0.724 and 0.765, PFS 0.717 and 0.670, and DFS 0.699 and 0.644, respectively).

Conclusions
Targeted DNA-based BM evaluated on routinely available FFPE samples improves prognostication of ACC beyond routinely available clinical and histopathological parameters. This approach may help to better individualise patient's management.
Fish biogeography and hybridization: do contemporary distributions predict introgression history?
Authors: Waters Jonathan M , Campbell Ciaran S M , Dutoit Ludovic 
Published: August 2023

Abstract
Freshwater ecosystems frequently house diverse assemblages of closely related fish taxa, which can be particularly prone to hybridization and introgression. While extensive introgression may be expected among biogeographically proximate lineages, recent analyses imply that contemporary distributions do not always accurately predict hybridization history. Here, we use the ABBA–BABA approach to test biogeographic hypotheses regarding the extent of hybridization in the recent evolution of New Zealand’s species-rich freshwater Galaxias vulgaris fish complex. Genome-wide comparisons reveal significant increases in introgression associated with increasing geographic overlap of taxa. The estimator DP, which assesses the net proportion of a genome originating from introgression, shows a particularly strong relationship with biogeographic overlap (R2 = .43; p = .005). Our analyses nevertheless reveal surprisingly substantial signatures of introgression among taxa that currently have disjunct distributions within drainages (e.g., separate subcatchments). These “anomalies” imply that current biogeography is not always an accurate predictor of introgression history. Our study suggests that both modern and ancient biogeographic shifts, including recent anthropogenic range fragmentation and tectonically driven riven capture events, have influenced introgression histories in this dynamic freshwater fish radiation.
Fabric controls fault stability in serpentinite gouges
Authors: Pozzi G , Collettini C , Scuderi M M , Tesei T , Marone C , Amodio A , Cocco M 
Published: August 2023

SUMMARY
Serpentinites are polymineralic rocks distributed almost ubiquitously across the globe in active tectonic regions. Magnetite-rich serpentinites are found in the low-strain domains of serpentinite shear zones, which act as potential sites of nucleation of unstable slip. To assess the potential of earthquake nucleation in these materials, we investigate the link between mechanical properties and fabric of these rocks through a suite of laboratory shear experiments. Our experiments were done at room temperature and cover a range of normal stress and slip velocity from 25 to 100 MPa and 0.3 to 300 µm s−1, respectively. We show that magnetite-rich serpentinites are ideal materials since they display strong sensitivity to the loading rate and are susceptible to nucleation of unstable slip, especially at low forcing slip velocities. We also aim at the integration of mechanical and microstructural results to describe the underlying mechanisms that produce the macroscopic behaviour. We show that mineralogical composition and mineral structure dictates the coexistence of two deformation mechanisms leading to stable and unstable slip. The weakness of phyllosilicates allows for creep during the interseismic phase of the laboratory seismic cycle while favouring the restoration of a load-bearing granular framework, responsible of the nucleation of unstable events. During dynamic slip, fault zone shear fabric determines the mode of slip, producing either asymmetric or Gaussian slip time functions for either fast or slow events. We report rate/state friction parameters and integrate our mechanical data with microstructural observations to shed light on the mechanisms dictating the complexity of laboratory earthquakes. We show that mineralogical and fabric heterogeneities control fault slip behaviour.
Effectiveness and Safety Profile of Budesonide Maintenance in Microscopic Colitis: A Systematic Review and Meta-Analysis
Authors: Tome June , Tariq Raseen , Hassett Leslie C , Khanna Sahil , Pardi Darrell S 
Published: August 2023

Abstract

Background
Microscopic colitis (MC) is a common cause of chronic diarrhea. Randomized controlled trials (RCTs) have demonstrated the efficacy of budesonide treatment for MC. However, relapse is frequent after discontinuation of budesonide, and data on maintenance therapy are limited. We performed a systematic review and meta-analysis evaluating these outcomes in clinical trials and real-world settings.

Methods
A systematic search was performed on October 31, 2022, of Medline, Embase, Cochrane, and Scopus. Case series, case-control, cohort studies, and RCTs of adults with MC were included. Data were pooled using random effects models to calculate weighted pooled estimates and 95% confidence intervals. Heterogeneity was assessed using the I2 statistic.

Results
We included 35 studies (11 RCTs, 24 observational studies) with 1657 MC patients treated with budesonide induction and 146 for maintenance. The overall pooled clinical remission rate with budesonide treatment was similar between RCTs and observational studies. The pooled remission rate with budesonide maintenance therapy was 84% (95% CI, 0.60-1.00; I2 = 91%). After budesonide discontinuation, the pooled relapse rate was 53% (95% CI, 0.42-0.63; I2 = 76%). On maintenance therapy, no differences were noted in adverse events (eg, metabolic bone disease, hypertension, hyperglycemia, cataracts/glaucoma) in those on budesonide vs placebo or other noncorticosteroid medications for MC (P = .9).

Conclusions
Budesonide is an effective maintenance treatment for MC. There is a high risk of recurrence after budesonide discontinuation, but long-term use at the lowest effective dose appears to be relatively safe and have limited adverse effects.
Applying the ‘Ceased Circumstances’ Cessation Clause: More Politics than Law?
Authors: Cole Georgia 
Published: August 2023

Abstract
Drawing on a detailed history of the ‘ceased circumstances’ cessation clause that was invoked for Eritrean refugees in 2002, this article highlights why the starting point for any analysis of the application of article 1C(5) of the 1951 Convention relating to the Status of Refugees must focus as much on politics as on law. This is not only because of the impossibility of insulating States and the United Nations High Commissioner for Refugees (UNHCR) from the political pressures that surround any determination of ‘ceased circumstances’ in a particular country, but also because the very standards on which such a determination rests are inherently relational, circumstantial, and political. Despite guidelines on the application of the clause promoting an ‘objective and verifiable’ approach, they rest on assessments of a ‘functioning’ government and ‘effective’ protection, of acceptable standards of human rights, and of the ‘best interests’ of refugees, all of which are geographically and historically contingent. The article thus argues that focusing on the legal standards that ostensibly underpin any invocation of article 1C(5) may perpetuate the fallacy that these standards can ever be objectively determined and, in focusing attention on how to better clarify these thresholds and conditions, this approach may, in certain instances, divert attention from confronting the political pressures that govern the application of the clause.
Effective Density for Inhomogeneous Quadratic Forms II: Fixed Forms and Generic Shifts
Authors: Ghosh Anish , Kelmer Dubi , Yu Shucheng 
Published: August 2023

Abstract
We establish effective versions of Oppenheim’s conjecture for generic inhomogeneous quadratic forms. We prove such results for fixed quadratic forms and generic shifts. Our results complement our previous paper [13] where we considered generic forms and fixed shifts. In this paper, we use ergodic theorems and in particular we establish a strong spectral gap with effective bounds for some representations of orthogonal groups, which do not possess Kazhdan’s property $(T)$.
Collagen microgel to simulate the adipocyte microenvironment for in vitro research on obesity
Authors: Moreno-Castellanos Natalia , Cuartas-Gómez Elías , Vargas-Ceballos Oscar 
Published: August 2023

Abstract
Obesity is linked to adipose tissue dysfunction, a dynamic endocrine organ. Two-dimensional cultures present technical hurdles hampering their ability to follow individual or cell groups for metabolic disease research. Three-dimensional type I collagen microgels with embedded adipocytes have not been thoroughly investigated to evaluate adipogenic maintenance as instrument for studying metabolic disorders. We aimed to develop a novel tunable Col-I microgel simulating the adipocyte microenvironment to maintain differentiated cells with only insulin as in vitro model for obesity research. Adipocytes were cultured and encapsulated in collagen microgels at different concentrations (2, 3 and 4 mg/mL). Collagen microgels at 3 and 4 mg/mL were more stable after 8 days of culture. However, cell viability and metabolic activity were maintained at 2 and 3 mg/mL, respectively. Cell morphology, lipid mobilization and adipogenic gene expression demonstrated the maintenance of adipocyte phenotype in an in vitro microenvironment. We demonstrated the adequate stability and biocompatibility of the collagen microgel at 3 mg/mL. Cell and molecular analysis confirmed that adipocyte phenotype is maintained over time in the absence of adipogenic factors. These findings will help better understand and open new avenues for research on adipocyte metabolism and obesity.
Insight box In the context of adipose tissue dysfunction research, new struggles have arisen owing to the difficulty of cellular maintenance in 2D cultures. Herein, we sought a novel approach using a 3D type I collagen-based biomaterial to adipocyte culture with only insulin. This component was tailored as a microgel in different concentrations to support the growth and survival of adipocytes. We demonstrate that adipocyte phenotype is maintained and key adipogenesis regulators and markers are over time. The cumulative results unveil the practical advantage of this microgel platform as an in vitro model to study adipocyte dysfunction and obesity.
Exposure of Salmonella enterica serovar 1,4,[5],12:i:- to benzalkonium chloride leads to acquired resistance to this disinfectant and antibiotics
Authors: Yang Mingzhe , Dong Qingli , Niu Hongmei , Li Jiaming , Lin Zijie , Aslam Muhammad Zohaib , Wang Xiang , Li Zhuosi , Liu Yangtai , Ma Yue , Qin Xiaojie 
Published: August 2023

Abstract

Aims
Disinfectants such as benzalkonium chloride (BC), extensively used in animal farms and food-processing industries, contribute to the development of adaptive and cross-resistance in foodborne pathogens, posing a serious threat to food safety and human health. The purpose of this study is to explore whether continuous exposure of Salmonella enterica serovar 1,4,[5],12:i:- (S. 1,4,[5],12:i:-) to sublethal concentrations of BC could result in acquired resistance to this agent and other environmental stresses (e.g. antibiotics, heat, and acid).

Methods and Results
BC tolerance increased in all tested strains after exposure to gradually increasing concentrations of BC, with increases in minimum inhibitory concentrations between two and sixfold. The survival rate of BC-adapted strains was significantly (P &lt; 0.05) higher than that of their wild-type (non-adapted) counterparts in lethal concentrations of BC. In addition, significant reductions (P &lt; 0.05) in zeta potential were observed in BC-adapted strains compared to wild-type ones, indicating that a reduction in cell surface charge was a cause of adaptative resistance. More importantly, two BC-adapted strains exhibited increased antibiotic resistance to levofloxacin, ceftazidime, and tigecycline, while gene mutations (gyrA, parC) and antibiotic efflux-related genes (acrB, mdsA, mdsB) were detected by genomic sequencing analysis. Moreover, the tolerance of BC-adapted strains to heat (50, 55, and 60°C) and acid (pH 2.0, 2.5) was strain-dependent and condition-dependent.

Conclusions
Repeated exposure to sublethal concentrations of BC could result in the emergence of BC- and antibiotic-resistant S. 1,4,[5],12:i:- strains.
Diet production and utilization of corn fermented protein compared to traditional yeast in healthy adult cats
Authors: Kilburn-Kappeler Logan R , Paulk Chad B , Aldrich Charles G 
Published: August 2023

Abstract
The inclusion of yeast in pet food can provide health benefits and increase palatability. Corn fermented protein is a co-product from ethanol production which contains approximately 20% to 25% yeast. The objective of this study was to determine the effects of the yeast in CFP on diet production and utilization when fed to healthy adult cats. The four experimental diets included a control with 15% soybean meal (CON) and diets containing either 3.5% brewer’s dried yeast (BDY), 2.5% brewer’s dried yeast plus 17.5% distillers dried grains with solubles (BDY+DDGS), or 17.5% corn fermented protein (CFP). All treatments except CON were formulated to contain 3.5% yeast. Experimental diets were fed to adult cats (n = 11) in an incomplete 4 × 4 replicated Latin square design. Cats were adapted to diet for 9 d followed by a 5-d total fecal collection. Titanium dioxide (0.4%) was added to all diets as an external marker to estimate digestibility. Data were analyzed using a mixed model in SAS (version 9.4, SAS Institute, Inc., Cary, NC) with treatment as a fixed effect and cat and period as random effects. Preconditioner discharge temperature was greater (P &lt; 0.05) for CON and BDY (average, 96 °C) compared to BDY + DDGS and CFP (average, 91 °C). Extruder screw speed, die temperature, kibble toughness, and kibble hardness were greatest (P &lt; 0.05) for CFP. The bulk density of BDY + DDGS at 392 g/L was greater (P &lt; 0.05) than BDY and CFP (average, 342 g/L). The sectional expansion index of kibble for CFP was greater (P &lt; 0.05) than BDY + DDGS and smaller (P &lt; 0.05) than CON but similar to BDY. Fecal output was greatest (P &lt; 0.05) for cats fed BDY + DDGS. Nutrient digestibility was lowest (P &lt; 0.05) for BDY + DDGS. The concentrations of short-chain and branched-chain fatty acids in fecal samples were not altered (P &gt; 0.05) by dietary treatment. Cats had no preference (P &gt; 0.05) when comparing CON to BDY or BDY + DDGS. However, cats consumed significantly less CFP compared to CON. The significant differences for bulk density, fecal output, and nutrient digestibility among dietary treatments are likely due to a greater fiber effect of DDGS compared to CFP. Therefore, the yeast component in CFP may provide greater kibble expansion and nutrient utilization compared to DDGS when fed to cats.
Small molecule inducers of actinobacteria natural product biosynthesis
Authors: Alwali Amir Y , Parkinson Elizabeth I 
Published: August 2023

Abstract

Actinobacteria are a large and diverse group of bacteria that are known to produce a wide range of secondary metabolites, many of which have important biological activities, including antibiotics, anti-cancer agents, and immunosuppressants. The biosynthesis of these compounds is often highly regulated with many natural products (NPs) being produced at very low levels in laboratory settings. Environmental factors, such as small molecule elicitors, can induce the production of secondary metabolites. Specifically, they can increase titers of known NPs as well as enabling discovery of novel NPs typically produced at undetectable levels. These elicitors can be NPs, including antibiotics or hormones, or synthetic compounds. In recent years, there has been a growing interest in the use of small molecule elicitors to induce the production of secondary metabolites from actinobacteria, especially for the discovery of NPs from “silent” biosynthetic gene clusters. This review aims to highlight classes of molecules that induce secondary metabolite production in actinobacteria and to describe the potential mechanisms of induction.

One-Sentence Summary
This review describes chemical elicitors of actinobacteria natural products described to date and the proposed mechanisms of induction.