bluuebunny/crossref_metadata_2025_split huggingface dataset:
PMIpred: a physics-informed web server for quantitative protein–membrane interaction prediction
Authors: van Hilten Niek , Verwei Nino , Methorst Jeroen , Nase Carsten , Bernatavicius Andrius , Risselada Herre Jelger 
Published: February 2024

Abstract

Motivation
Many membrane peripheral proteins have evolved to transiently interact with the surface of (curved) lipid bilayers. Currently, methods to quantitatively predict sensing and binding free energies for protein sequences or structures are lacking, and such tools could greatly benefit the discovery of membrane-interacting motifs, as well as their de novo design.

Results
Here, we trained a transformer neural network model on molecular dynamics data for &gt;50 000 peptides that is able to accurately predict the (relative) membrane-binding free energy for any given amino acid sequence. Using this information, our physics-informed model is able to classify a peptide’s membrane-associative activity as either non-binding, curvature sensing, or membrane binding. Moreover, this method can be applied to detect membrane-interaction regions in a wide variety of proteins, with comparable predictive performance as state-of-the-art data-driven tools like DREAMM, PPM3, and MODA, but with a wider applicability regarding protein diversity, and the added feature to distinguish curvature sensing from general membrane binding.

Availability and implementation
We made these tools available as a web server, coined Protein-Membrane Interaction predictor (PMIpred), which can be accessed at https://pmipred.fkt.physik.tu-dortmund.de.
Synthesis of yolk–shell COF with corrole and electrocatalytic property of Co-doped COF for oxygen reduction reaction
Authors: Miyabayashi Keiko , Kondo Junna 
Published: February 2024

Abstract
Covalent organic polymers (COP) were synthesized by polymerizing 5,10,15-tris(4-aminophenyl)corrole (TAPC) and terephthalaldehyde in the presence of acetic acid. Yolk–shells and filled structures were obtained after ripening of COP synthesized with low and high acetic acid/TAPC, respectively. The low cross-linking degree of COP synthesized by low acetic acid/TAPC resulted in a yolk–shell structure due to the easy dissolution of the interior. The Co-doped yolk–shell showed higher electrocatalytic activity for the oxygen reduction reaction than the filled structure.
Early Mortality After the First Dose of COVID-19 Vaccination: A Target Trial Emulation
Authors: McConeghy Kevin W , Hur Kwan , Dahabreh Issa J , Jiang Rong , Pandey Lucy , Gellad Walid F , Glassman Peter , Good Chester B , Miller Donald R , Zullo Andrew R , Gravenstein Stefan , Cunningham Francesca 
Published: February 2024

Abstract

Background
Vaccine hesitancy persists alongside concerns about the safety of coronavirus disease 2019 (COVID-19) vaccines. We aimed to examine the effect of COVID-19 vaccination on risk of death among US veterans.

Methods
We conducted a target trial emulation to estimate and compare risk of death up to 60 days under two COVID-19 vaccination strategies: vaccination within 7 days of enrollment versus no vaccination through follow-up. The study cohort included individuals aged ≥18 years enrolled in the Veterans Health Administration system and eligible to receive a COVID-19 vaccination according to guideline recommendations from 1 March 2021 through 1 July 2021. The outcomes of interest included deaths from any cause and excluding a COVID-19 diagnosis. Observations were cloned to both treatment strategies, censored, and weighted to estimate per-protocol effects.

Results
We included 3 158 507 veterans. Under the vaccination strategy, 364 993 received vaccine within 7 days. At 60 days, there were 156 deaths per 100 000 veterans under the vaccination strategy versus 185 deaths under the no vaccination strategy, corresponding to an absolute risk difference of −25.9 (95% confidence limit [CL], −59.5 to 2.7) and relative risk of 0.86 (95% CL, .7 to 1.0). When those with a COVID-19 infection in the first 60 days were censored, the absolute risk difference was −20.6 (95% CL, −53.4 to 16.0) with a relative risk of 0.88 (95% CL, .7 to 1.1).

Conclusions
Vaccination against COVID-19 was associated with a lower but not statistically significantly different risk of death in the first 60 days. These results agree with prior scientific knowledge suggesting vaccination is safe with the potential for substantial health benefits.
Incremental dialysis: two complementary views
Authors: Casino Debaters: Francesco Gaetano , Murea Mariana , Floege Moderators: Jürgen , Zoccali Carmine 
Published: February 2024

ABSTRACT
Franco Casino and Mariana Murea discuss today's knowledge about the ‘incremental dialysis’ concept. Franco Casino frames the problem by saying that, in the presence of substantial residual kidney function, kidney replacement therapy can begin with low doses and/or frequencies, to be gradually increased to compensate for any subsequent losses of residual kidney function, keeping the total clearance above the minimum levels of adequacy. He remarks that studies so far have documented that this approach is safe. He recognizes that adequate randomized controlled trials (RCTs) are necessary to confirm the safety and simplify and standardize the practical aspects of this approach. Mariana Murea objects that most of the evidence gathered so far primarily derives from retrospective and observational studies, which can be influenced by socioeconomic constraints. She argues for the need for RCTs to provide compelling empirical evidence on the efficacy of incremental dialysis. Nephrologists are still reluctant to adopt this approach for various reasons, including unfamiliarity with the method, lack of practical guidance and financial disincentives. Several countries have ongoing or planned RCTs comparing incremental dialysis with conventional dialysis. These trials can shift the haemodialysis paradigm if they validate the safety and effectiveness of this approach. The moderators believe that the results of ongoing trials must be carefully interpreted, and further validation may be needed across different patient populations or healthcare settings. The ultimate goal is to gather robust evidence that could lead to widespread adoption of incremental haemodialysis, optimizing treatment, reducing overtreatment, preserving resources and improving patients’ quality of life.
The many channels of firm’s adjustment to energy shocks: evidence from France
Authors: Fontagné Lionel , Martin Philippe , Orefice Gianluca 
Published: February 2024

Abstract
Based on firm-level data in the French manufacturing sector, we find that firms adapt quickly, strongly and through multiple channels to energy shocks, even though electricity and gas bills represent a small share of their total costs. Over the period 1996–2019, faced with an idiosyncratic energy price increase, firms reduce their energy demand, improve their energy efficiency, increase intermediate inputs imports and optimize energy use across plants. Firms are also able to pass-through the cost shock fully into their export prices. Their production, exports and employment fall. A consequence of these multiple adjustment mechanisms is that the fall in profits is either non-significant, small or specific to only the most energy-intensive firms. We also find that the impact of electricity shocks has weakened over time, suggesting that only firms able to adapt their production process to energy cost shocks have survived. Importantly, when faced with large electricity and gas price increases, firms are less able to reduce their consumption. These results shed light on the mechanisms of resilience of the European manufacturing sector in the context of the present energy crisis.
Sibling influence on migration pathways from the French overseas to mainland France
Authors: Haddad Marine 
Published: February 2024

Abstract
Research shows that economic, political and social factors all drive migration, but we still know little about their interaction, especially the interplay between increasingly selective migration policies and family relations. Studies stress the role played by social capital in responding to migration restrictions and the importance of intermediaries in encouraging access to institutional resources, but we lack systematic analyses linking migrant networks and recourse to migration-facilitating programs. This paper fills this gap by investigating how siblings’ influence and migration programs combine in shaping migration from the French Overseas departments (DOM). Using a survey with detailed information on DOM families’ migration histories (MFV, INED, 2010), it assesses whether individuals stay, migrate with or without the support of migration programs, depending on their siblings’ past trajectories. A longitudinal approach and the nesting of individuals within families allow controlling for unobserved heterogeneity. Siblings migrating without the programs’ support decrease the chances of migration with it and increase the chances of migration without it. Siblings migrating with the programs’ support increase the chances of migration with it and decrease the chances of migration without it. This work shows how DOM populations engage with selective pro-migration policies, stressing the role of family relations in driving cumulative patterns of migration. It contributes to uncovering the way social and political factors interact in contexts of high migration prevalence with increased selectivity of migration and especially pro-migration policies.
Impact of the 2021 European Society for Cardiology prevention guideline’s stepwise approach for cardiovascular risk factor treatment in patients with established atherosclerotic cardiovascular disease
Authors: Holtrop Joris , Bhatt Deepak L , Ray Kausik K , Mach François , Smulders Yvo M , Carballo David , Steg Philippe Gabriel , Visseren Frank L J , Dorresteijn Jannick A N 
Published: February 2024

Abstract

Aims
This study aimed to evaluate the stepwise approach for cardiovascular (CV) risk factor treatment as outlined by the European Society for Cardiology 2021 guidelines on CV disease (CVD) prevention in patients with established atherosclerotic CVD (ASCVD).

Methods and results
In patients with ASCVD, included in UCC-SMART (n = 8730) and European parts of the REACH registry (n = 18 364), the 10-year CV risk was estimated using SMART2. Treatment effects were derived from meta-analyses and trials. Step 1 recommendations were LDL cholesterol (LDLc) &lt; 1.8 mmol/L, systolic blood pressure (SBP) &lt; 140 mmHg, using any antithrombotic medication, sodium–glucose co-transporter 2 (SGLT2) inhibition, and smoking cessation. Step 2 recommendations were LDLc &lt; 1.4 mmol/L, SBP &lt; 130 mmHg, dual-pathway inhibition (DPI, aspirin plus low-dose rivaroxaban), colchicine, glucagon-like peptide (GLP)-1 receptor agonists, and eicosapentaenoic acid. Step 2 was modelled accounting for Step 1 non-attainment. With current treatment, residual CV risk was 22%, 32%, and 60% in the low, moderate, and pooled (very) high European risk regions, respectively. Step 2 could prevent up to 198, 223 and 245 events per 1000 patients treated, respectively. Intensified LDLc reduction, colchicine, and DPI could be applied to most patients, preventing up to 57, 74, and 59 events per 1000 patients treated, respectively. Following Step 2, the number of patients with a CV risk of &lt;10% could increase from 20%, 6.4%, and 0.5%, following Step 1, to 63%, 48%, and 12%, in the respective risk regions.

Conclusion
With current treatment, residual CV risk in patients with ASCVD remains high across all European risk regions. The intensified Step 2 treatment options result in marked further reduction of residual CV risk in patients with established ASCVD.

Key findings
Guideline-recommended intensive treatment of patients with cardiovascular disease could prevent additional 198–245 new cardiovascular events for every 1000 patients treated.
Microbial community and network responses across strong environmental gradients: How do they compare with macroorganisms?
Authors: Arboleda-Baena Clara , Freilich Mara , Pareja Claudia Belén , Logares Ramiro , De la Iglesia Rodrigo , Navarrete Sergio A 
Published: February 2024

AbstractThe way strong environmental gradients shape multispecific assemblages has allowed us to examine a suite of ecological and evolutionary hypotheses about structure, regulation and community responses to fluctuating environments. But whether the highly diverse co-occurring microorganisms are shaped in similar ways as macroscopic organisms across the same gradients has yet to be addressed in most ecosystems. Here, we characterize intertidal biofilm bacteria communities, comparing zonation at both the “species” and community levels, as well as network attributes, with co-occurring macroalgae and invertebrates in the same rocky shore system. The results revealed that the desiccation gradient has a more significant impact on smaller communities, while both desiccation and submersion gradients (surge) affect the larger, macroscopic communities. At the community level, we also confirmed the existence of distinct communities within each intertidal zone for microorganisms, similar to what has been previously described for macroorganisms. But our results indicated that dominant microbial organisms along the same environmental gradient exhibited less differentiation across tidal levels than their macroscopic counterparts. However, despite the substantial differences in richness, size and attributes of co-occurrence networks, both macro- and micro-communities respond to stress gradients, leading to the formation of similar zonation patterns in the intertidal rocky shore.
Fermenting the future – on the benefits of a bioart collaboration
Authors: Mattanovich Diethard , Altvater Martin , Ata Özge , Bachleitner Simone 
Published: February 2024

Abstract
In this article we explore the intersection of science and art through a collaboration between us scientists and the bioartists Anna Dimitriu and Alex May, focusing on the interface of yeast biotechnology and art. The collaboration, originally initiated in 2018, resulted in three major artworks: CULTURE, depicting the evolution of yeast and human societies; FERMENTING FUTURES, illustrating a synthetic autotrophic yeast and its link to lactic acid production; and WOOD SPIRIT—AMBER ACID, inspired by the VIVALDI project targeting CO2 reduction to methanol. We emphasize the reciprocal nature of the collaboration, detailing the scientific insights gained and the impact of artistic perspectives on us as researchers. We also highlight the historical connection between art and science, particularly in the Renaissance periods, and underscore the educational value of integrating art into science not only to support public engagement and science dissemination, but also to widen our own perceptions in our research.
Lack of Dosage Balance and Incomplete Dosage Compensation in the ZZ/ZW Gila Monster (Heloderma suspectum) Revealed by De Novo Genome Assembly
Authors: Webster Timothy H , Vannan Annika , Pinto Brendan J , Denbrock Grant , Morales Matheo , Dolby Greer A , Fiddes Ian T , DeNardo Dale F , Wilson Melissa A 
Published: February 2024

Abstract
Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes. Here, we report the assembly and analysis of the Gila monster genome. We generated a de novo draft genome assembly for a male using 10X Genomics technology. We further generated and analyzed short-read whole genome sequencing and whole transcriptome sequencing data for three males and three females. By comparing female and male genomic data, we identified four putative Z chromosome scaffolds. These putative Z chromosome scaffolds are homologous to Z-linked scaffolds identified in the Komodo dragon. Further, by analyzing RNAseq data, we observed evidence of incomplete dosage compensation between the Gila monster Z chromosome and autosomes and a lack of balance in Z-linked expression between the sexes. In particular, we observe lower expression of the Z in females (ZW) than males (ZZ) on a global basis, though we find evidence suggesting local gene-by-gene compensation. This pattern has been observed in most other ZZ/ZW systems studied to date and may represent a general pattern for female heterogamety in vertebrates.
Constraints from GPS measurements on plate coupling within the Makran subduction zone and tsunami scenarios in the western Indian Ocean
Authors: Cheng Guo , Barnhart William D , Small David 
Published: February 2024

SUMMARY
Plate-coupling estimates and previous seismicity indicate that portions of the Makran megathrust of southern Pakistan and Iran are partially coupled and have the potential to produce future magnitude 7+ earthquakes. However, the GPS observations needed to constrain coupling models are sparse and lead to an incomplete understanding of regional earthquake and tsunami hazard. In this study, we assess GPS velocities for plate coupling of the Makran subduction zone with specific attention to model resolution and the accretionary prism rheology. We use finite element model-derived Green's functions to invert for the interseismic slip deficit under both elastic and viscoelastic Earth assumptions. We use the model resolution matrix to characterize plate-coupling scenarios that are consistent with the limited spatial resolution afforded by GPS observations. We then forward model the corresponding tsunami responses at major coastal cities within the western Indian Ocean basin. Our plate-coupling results show potential segmentation of the megathrust with varying coupling from west to east, but do not rule out a scenario where the entire length of the megathrust could rupture in a single earthquake. The full subduction zone rupture scenarios suggest that the Makran may be able to produce earthquakes up to Mw 9.2. The corresponding tsunami model from the largest earthquake event (Mw 9.2) estimates maximum wave heights reaching 2–5 m at major port cities in the northern Arabian Sea region. Cities on the west coast of India are less affected (1–2 m). Coastlines bounding eastern Africa, and the Strait of Hormuz, are the least affected (&lt;1 m).
Postoperative intra-abdominal hypertension predicts worse hospital outcomes in children after cardiac surgery: a pilot study
Authors: Zhang Yunyi , Luo Shuhua , Xie Yuxuan , Wang Yue , Fang Yibing , Wang Shouping , Deng Lijing 
Published: February 2024

Abstract

OBJECTIVES
Our goal was to determine the incidence and characteristics of postoperative intra-abdominal hypertension (IAH) in paediatric patients undergoing open-heart surgery.

METHODS
This single-centre study included consecutive children (aged &lt;16 years) who underwent open-heart surgery between July 2020 and February 2021. Patients who entered the study were followed until in-hospital death or hospital discharge. The study consisted of 2 parts. Part I was a prospective observational cohort study that was designed to discover the association between exposures and IAH. Postoperative intra-abdominal pressure was measured immediately after admission to the intensive care unit and every 6 h thereafter. Part II was a cross-sectional study to compare the hospital-related adverse outcomes between the IAH and the no-IAH cohorts.

RESULTS
Postoperatively, 24.7% (38/154) of the patients exhibited IAH, whereas 3.9% (6/154) developed abdominal compartment syndrome. The majority (29/38, 76.3%) of IAH cases occurred within the first 24 h in the intensive care unit. Multivariable analysis showed that the Society of Thoracic Surgeons–European Association for Cardio-Thoracic Surgery score [odds ratio (OR) = 1.86, 95% confidence interval (CI) 1.23–2.83, P = 0.004], right-sided heart lesion (OR = 5.60, 95% CI 2.34–13.43, P &lt; 0.001), redo sternotomy (OR = 4.35, 95% CI 1.64–11.57, P = 0.003), high baseline intra-abdominal pressure (OR = 1.43, 95% CI 1.11–1.83, P = 0.005), prolonged cardiopulmonary bypass duration (OR = 1.01, 95% CI 1.00–1.01, P = 0.005) and deep hypothermic circulatory arrest (OR = 5.14, 95% CI 1.15–22.98, P = 0.032) were independent predictors of IAH occurrence. IAH was associated with greater inotropic support (P &lt; 0.001), more gastrointestinal complications (P = 0.001), sepsis (P = 0.003), multiple organ dysfunction syndrome (P &lt; 0.001) and prolonged intensive care unit stay (z = -4.916, P &lt; 0.001) and hospitalization (z = -4.710, P &lt; 0.001). The occurrence of a composite outcome (P = 0.009) was significantly increased in patients with IAH.

CONCLUSIONS
IAH is common in children undergoing cardiac surgery and is associated with worse hospital outcomes. Several factors may be associated with the development of IAH, including basic cardiac physiology and perioperative factors.

Trial information
This study was registered in the Chinese Clinical Trial Registry (Trial number: ChiCTR2000034322)
URL site: https://www.chictr.org.cn/hvshowproject.html?id=41363&v=1.4
Detection of linezolid and vancomycin resistant Enterococcus isolates collected from healthy chicken caecum
Authors: Ben Yahia Houssem , Trabelsi Islem , Arous Fatma , García-Vela Sara , Torres Carmen , Ben Slama Karim 
Published: February 2024

Abstract

Aim
The poultry industry represents an important economic sector in Tunisia. This study aims to determine the antimicrobial resistance phenotypes and genotypes and virulence factors of enterococci collected from chicken caecum in Tunisia.

Methods and results
Forty-nine composite chicken caecum samples were recovered in 49 different Tunisian farms (December 2019–March 2020). Each composite sample corresponds to six individual caecum from each farm. Composite samples were plated on Slanetz–Bartley agar both supplemented (SB-Van) and not supplemented (SB) with vancomycin and isolates were identified by matrix-assisted laser desorption/ionization time-of-flight. Antibiotic resistance and virulence genes were tested by Polymerase Chain Reaction (PCR) and sequencing and multilocus-sequence-typing of selected enterococci was performed. One hundred sixty seven enterococci of six different species were recovered. Acquired linezolid resistance was detected in 6 enterococci of 4/49 samples (8.1%): (A) four optrA-carrying Enterococcus faecalis isolates assigned to ST792, ST478, and ST968 lineages; (B) two poxtA-carrying Enterococcus faecium assigned to ST2315 and new ST2330. Plasmid typing highlighted the presence of the rep10, rep14, rep7, rep8, and pLG1 in these strains. One vancomycin-resistant E. faecium isolate (typed as ST1091) with vanA gene (included in Tn1546) was detected in SB-Van plates. The gelE, agg, esp, and hyl virulence genes were found in linezolid- and vancomycin-resistant enterococci. High resistance rates were identified in the enterococci recovered in SB plates: tetracycline [74.8%, tet(M) and tet(L) genes], erythromycin [65.9%, erm(B)], and gentamicin [37.1%, aac(6′)-Ie–aph(2″)-Ia].

Conclusion
The detection of emerging mechanisms of resistance related to linezolid and vancomycin in the fecal enterococci of poultry farms has public health implications, and further surveillance should be carried out to control their dissemination by the food chain.