bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reliability and validity of intervention characteristic measures for assessing barriers to evidence-based practice use
Authors: Jones Salene M W , Weiner Bryan J 
Published: March 2024

Abstract
Assessing barriers before implementing an evidence-based practice can increase the chances of successful implementation. This project evaluated measures of intervention characteristics that could affect implementation: evidence strength and quality; relative advantage; adaptability; trialability; complexity; design quality and packaging; perceived cost; compatibility; observability; risk; and burden. Measures (109 items total) for each intervention characteristic were developed in a previous study, using prior measures, and expert feedback. Measures were scored such that higher scores meant a more positive view. Healthcare personnel implementing a new practice (n = 175) completed two surveys, 1 month apart. Participants completed the intervention characteristic item banks and questions on the use of the evidence-based practice. Reliability and validity were assessed for each item bank. All measures had Cronbach’s alphas over 0.7 (range: 0.700–0.932) indicating good reliability. Frequent users of the practice reported better levels of each determinant at the first (Cohen’s d range: −0.239 to −0.687) and second surveys (Cohen’s d range: −0.043 to −1.081) except for costs (0.096) with use on the second survey. This preliminary test of measures to assess determinants of implementing evidence-based practice supports the validity and reliability of these tools. Additional studies are needed to further test the psychometric properties of the measures and develop short forms of each intervention characteristic measure.
Biosafety and toxicity assessment of transgenic cotton-harboring insecticide and herbicide tolerant genes on albino mice
Authors: Bhutta Muhammad Saad , Awais Muhammad , Raouf Abdul , Anjum Aqsa , Azam Saira , Shahid Naila , Malik Kausar , Shahid Ahmed Ali , Rao Abdul Qayyum 
Published: March 2024

Abstract

Introduction
Genetic engineering has revolutionized agriculture by transforming biotic and abiotic stress-resistance genes in plants. The biosafety of GM crops is a major concern for consumers and regulatory authorities.

Methodology
A 14-week biosafety and toxicity analysis of transgenic cotton, containing 5 transgenes ((Cry1Ac, Cry2A, CP4 EPSPS, VIP3Aa, and ASAL)), was conducted on albino mice. Thirty mice were divided into three groups (Conventional, Non-transgenic, without Bt, and transgenic, containing targeted crop) according to the feed given, with 10 mice in each group, with 5 male and 5 female mice in each group.

Results
During the study, no biologically significant changes were observed in the non-transgenic and transgenic groups compared to the control group in any of the study’s parameters i.e. increase in weight of mice, physiological, pathological, and molecular analysis, irrespective of the gender of the mice. However, a statistically significant change was observed in the hematological parameters of the male mice, while no such change was observed in the female study group mice. The expression analysis, however, of the TNF gene increases many folds in the transgenic group as compared to the non-transgenic and conventional groups.

Conclusion
Overall, no physiological, pathological, or molecular toxicity was observed in the mice fed with transgenic feed. Therefore, it can be speculated that the targeted transgenic crop is biologically safe. However, more study is required to confirm the biosafety of the product on the animal by expression profiling.
Otic Capsule Demineralization and Hearing Outcome of Stapes Surgery for Osteogenesis Imperfecta in Comparison With Otosclerosis
Authors: Kimura Akira , Morita Yuka , Kitazawa Meiko , Yagi Chihiro , Takahashi Kuniyuki , Ohshima Shinsuke , Yamagishi Tatsuya , Izumi Shuji , Horii Arata 
Published: March 2024

Objective
To assess the location/number of otic capsule demineralization and hearing outcomes of stapes surgery (SS) for osteogenesis imperfecta (OI) compared with otosclerosis (OS).

Patients
This study included 11 and 181 consecutive ears from 6 and 152 patients with OI and OS, respectively.

Interventions
Demineralization loci observed as hypodense area of the otic capsule were examined using high-resolution computed tomography. All patients underwent SS.

Main Outcome Measures
Locations of the hypodense areas were classified into the anterior oval window, anterior internal auditory canal, and pericochlear area. The location/number of hypodense areas and preoperative/postoperative hearing parameters were correlated. Postoperative hearing outcome was evaluated 12 months after surgery.

Results
Hypodense area was more frequently observed in OI (9 of 11 ears [81.8%]) than in OS (96 of 181 ears [53.0%]), with significant differences. Multiple sites were involved in 81.8% OI and 18.8% OS patients, showing significant differences. Preoperative air conduction (AC), bone conduction, and air-bone gap (ABG) were 48.9 ± 17.8, 28.0 ± 11.3, and 20.7 ± 8.4 dB, respectively, in OI and 56.2 ± 13.5, 30.5 ± 9.9, and 26.4 ± 9.7 dB, respectively, in OS, demonstrating greater AC and ABG in OS than in OI. Postoperative AC (31.3 ± 20.5 dB), ABG (10.6 ± 10.0 dB), and closure of ABG (12.1 ± 4.7 dB), that is, preoperative ABG minus postoperative ABG of OI, were comparable to those of OS (AC, 30.9 ± 13.3 dB; ABG, 7.0 ± 7.4 dB; closure of ABG, 20.1 ± 11.6 dB).

Conclusion
OI ears showed more severe demineralization of otic capsule than OS ears. However, favorable hearing outcomes could be obtained through SS for OI and OS ears.
MRI Safety of Stapes Prostheses: A Systematic Review
Authors: Daher Ghazal S. , Kocharyan Armine , Carlson Matthew L. , Dillon William P. , Fischbein Nancy J. , Jackler Robert , Rassner Ulrich , Gurgel Richard K. 
Published: March 2024

Objective
To assess magnetic resonance imaging (MRI) safety of stapes prostheses.

Data Sources
Ovid MEDLINE, Embase, Cochrane Central Register of Controlled Trials, Web of Science, and Scopus databases were searched from inception to November 2021 following PRISMA guidelines.

Review Methods
Studies reporting evidence of stapes prosthesis displacement or interaction in adult or pediatric implant recipients undergoing MRI. Cadaveric, animal, and basic studies with nonhuman data were also included.

Results
From an initial search of 123 articles, 42 full-text studies were evaluated for eligibility and 19 studies that met the inclusion criteria were included. Motion artifact was reported in a few stainless steel prosthesis types in vitro; however, such displacement was not observed in human cadaver temporal bone studies and had no adverse reported outcomes. A small subgroup of patients in the 1980s received a ferromagnetic stainless steel stapes implant that was recalled and has not been used since 1987. Patients with implants performed in the 1980s should be directed to 1.5T scanners from an abundance of caution.

Conclusion
Modern (post-1987) stapes prostheses do not pose a risk in vivo when exposed to the magnetic fields of MRI scanners.
Single RNA molecule resolution spatial imaging of immunotherapy response in triple negative breast tumors harboring tertiary lymphoid structures
Authors: Mebane Richard H. , Noel Teia , Ing Nathan , Gouin Kenneth , Shah Aagam , Zitser David , Martinez Andrew , Gupta Gaorav , Ho Alice , McArthur Heather , Shiao Stephen S. , Knott Simon. R.V. 
Published: March 2024

SummaryCancer immunotherapy trials have had variable success, prompting a search for biomarkers of response. Tertiary lymphoid structures (TLS) have emerged as prognostic for multiple tumor types. These ectopic immunological bodies resemble secondary lymphoid organs with segregated B and T cell zones, but they are heterogeneous in their organization and cellular composition. These features have consequences in terms of prognostication and disease clearance, so there is interest in what drives TLS heterogeneity and corresponding immunological responses. We applied single RNA molecule resolution imaging to study biopsies from triple negative breast tumors harboring TLS where the biopsies were taken longitudinally, prior to therapy, after pembrolizumab and after pembrolizumab with radiation therapy. We developed a computational framework to identify TLS and tumor beds and to align spatial trajectories between the immune and malignant structures for systematic analyses. We identified two tumor types based on immune infiltration profiles in the tumor bed. Immune “infiltrated” tumors were eliminated after pembrolizumab, while “non-infiltrated” tumors saw gains in effector T cells and myeloid cells after pembrolizumab and were cleared after pembrolizumab with RT. TLS from infiltrated tumors had better separation of B and T cell zones and had higher expression of immunoreactivity gene pathways in most cell types. Further, malignant cell MHC expression was higher in the tumor beds of infiltrated tumors, providing one plausible mechanism for the groupings. In non-infiltrated tumors, classical dendritic cells enter the tumor bed from TLS proximal zones after pembrolizumab and bring transcription of the CXCL9 chemokine, which can recruit T cells and promote T cell effector phenotypes and was higher in infiltrated tumors at baseline.
What do we know about the missing millions of Earth’s insect species and can we improve their collection: evidence from bark beetles?
Authors: Stork Nigel E , Boyle Michael J. W. , Wardhaugh Carl , Beaver Roger 
Published: March 2024

AbstractOnly 20% of the estimated five million species of insects on Earth are named despite over 240 years of taxonomy. Yet insects are poorly represented in protected area assessments, and insect declines are of concern globally. Here we explore how to increase the discovery of new species and understanding of this group through analysis of 10,097 tropical rainforest bark beetles (Scolytinae) from eight different ecological studies using beetles between 2000 and 2018 in the Australian Wet Tropics. Of the 107 species identified, 58 are undescribed: an increase of 35% on the 166 species known from Australia. As hypothesised, new species are significantly smaller, less abundant and less widespread than described species making them more extinction prone than named species. Rarefaction indicates doubling sampling would increase the number of species by 17. Flight Interception Traps (FIT) collected 84% of individuals and 98% of species confirming the effectiveness of a single sampling method for some beetles. Increased locations and collection from the canopy may sample further species rather than additional collecting methods. Scolytines are relatively well studied with a cadre of taxonomists at the forefront of using modern methods to resolve formerly intractable groups. These new species are more likely to be named than others in many other beetle groups where taxonomy has largely stalled. To increase species description rates and to avoid most species becoming extinct before being named, we call on taxonomists to use new character systems provided by DNA methods and to look at working with Artificial Intelligence tools.Significance StatementIn an era of rapid biodiversity loss, current conservation decisions for insects will continue to be based on a small and almost certainly biased sample of the world’s biota until more species are named. We demonstrate how large-scale sampling can dramatically increase the number of species discovered for one group of beetles and how these undescribed species are significantly smaller, less abundant and less widespread than named species. The identification and determination of undescribed species is rarely possible except when taxonomic expertise is available, as in the present study. Addressing the insect taxonomic bottleneck and increasing the rate of description will require the adoption of new and developing tools.
Identifyingin vivogenetic dependencies of melanocyte and melanoma development
Authors: Perlee Sarah , Ma Yilun , Hunter Miranda V. , Swanson Jacob B. , Ming Zhitao , Xia Julia , Lionnet Timothée , McGrail Maura , White Richard M. 
Published: March 2024

AbstractThe advent of large-scale sequencing in both development and disease has identified large numbers of candidate genes that may be linked to important phenotypes. Validating the function of these candidatesin vivois challenging, due to low efficiency and low throughput of most model systems. We have developed a rapid, scalable system for assessing the role of candidate genes using zebrafish. We generated transgenic zebrafish in which Cas9 was knocked-in to the endogenousmitfalocus, a master transcription factor of the melanocyte lineage. We used this system to identify both cell-autonomous and non-cell autonomous regulators of normal melanocyte development. We then applied this to the melanoma setting to demonstrate that loss of genes required for melanocyte survival can paradoxically promote more aggressive phenotypes, highlighting thatin vitroscreens can maskin vivophenotypes. Our high-efficiency genetic approach offers a versatile tool for exploring developmental processes and disease mechanisms that can readily be applied to other cell lineages.
Discovery, Characterization and Synthetic Potential of Two Novel Bacterial Alcohol Oxidases
Authors: Cinca-Fernando Paula , Ascaso-Alegre Christian , Sevilla Emma , Martínez-Júlvez Marta , Mangas-Sánchez Juan , Ferreira Patricia 
Published: March 2024

AbstractThe search for novel synthetic tools to prepare industrial chemicals in a safer and greener manner is a continuing challenge in synthetic chemistry. In this manuscript, we report the discovery, characterization, and synthetic potential of two novel aryl-alcohol oxidases from bacteria which are able to oxidize a variety of aliphatic and aromatic alcohols in high efficiencies (up to 4970 min-1mM-1). Crystal structures revealed unusually wide-open entrance to the active-site pockets compared to that previously described for traditional fungal aryl-alcohol oxidases, which could correlate with differences in substrate scope, catalytic efficiency, and other functional properties. Preparative-scale reactions and ability to operate at high substrate loadings also demonstrate the potential of these enzymes in synthetic chemistry with turnover numbers > 30000. Moreover, their availability as soluble and active recombinant proteins enabled their use as cell-free extracts which further highlights their potential for the large-scale production of carbonyl compounds.
The Relationship ofpqsGene Expression to Acylhomoserine Lactone Signaling inPseudomonas aeruginosa
Authors: Soto-Aceves Martin P. , Smalley Nicole E. , Schaefer Amy L. , Greenberg E. Peter 
Published: March 2024

ABSTRACTThe opportunistic pathogenPseudomonas aeruginosahas complex quorum sensing (QS) circuitry, which involves two acylhomoserine lactone (AHL) systems, the LasI AHL synthase and LasR AHL-dependent transcriptional activator system and the RhlI AHL synthase-RhlR AHL-responsive transcriptional activator. There is also a quinoline signaling system (thePseudomonasquinolone signal, PQS, system). Although there is a core set of genes regulated by the AHL circuits, there is substantial strain-to-strain variation in the non-core QS regulated genes. Reductive evolution of the QS regulon, and variation in specific genes activated by QS, occurs in laboratory evolution experiments with the model strain PAO1. We used a transcriptomics approach to test the hypothesis that reductive evolution in the PAO1 QS regulon can in large part be explained by a simple null mutation inpqsR, the gene encoding the transcriptional activator of thepqsoperon. We found that PqsR had very little influence on the AHL QS regulon. This was a surprising finding because the last gene in the PqsR-dependentpqsoperon,pqsE, codes for a protein, which physically interacts with RhlR and this interaction is required for RhlR-dependent activation of some genes. We used comparative transcriptomics to examine the influence of apqsEmutation on the QS regulon and identified only three transcripts, which were strictly dependent on PqsE. By using reporter constructs we showed that the PqsE influence on other genes was dependent on experimental conditions and we have gained some insight about those conditions. This work adds to our understanding of the plasticity of theP. aeruginosaQS regulon and to the role PqsE plays in RhlR-dependent gene activation.
Cohesin supercoils DNA during loop extrusion
Authors: Davidson Iain F. , Barth Roman , Horn Sabrina , Janissen Richard , Nagasaka Kota , Wutz Gordana , Stocsits Roman R. , Bauer Benedikt , Dekker Cees , Peters Jan-Michael 
Published: March 2024

AbstractCohesin extrudes genomic DNA into loops that promote chromatin assembly, gene regulation and recombination. Here we show that cohesin introduces negative supercoils into extruded DNA. Supercoiling requires engagement of cohesin’s ATPase heads, DNA clamping by these heads, and a DNA binding site on cohesin’s hinge, indicating that cohesin supercoils DNA when constraining it between the hinge and the clamp. Our results suggest that DNA extrusion stops once cohesin reaches its stall torque during supercoiling, and a cohesin mutant predicted to stall at lower torque forms shorter loops in cells. These results indicate that supercoiling is an integral part of the loop extrusion mechanism and that cohesin controls genome architecture not only by looping DNA but also by supercoiling it.
Design of Antigen-Specific Antibody CDRH3 Sequences Using AI and Germline-Based Templates
Authors: Marinov Toma M. , Abu-Shmais Alexandra A. , Janke Alexis K. , Georgiev Ivelin S. 
Published: March 2024

ABSTRACTAntibody-antigen specificity is engendered and refined through a number of complex B cell processes, including germline gene recombination and somatic hypermutation. Here, we present an AI-based technology for de novo generation of antigen-specific antibody CDRH3 sequences using germline-based templates, and validate this technology through the generation of antibodies against SARS-CoV-2. AI-based processes that mimic the outcome, but bypass the complexity of natural antibody generation, can be efficient and effective alternatives to traditional experimental approaches for antibody discovery.
Structure, substrate selectivity determinants and membrane interactions of a Glutamate-specific TAXI TRAP binding protein fromVibrio cholerae
Authors: Davies Joseph F.S. , Daab Andrew , Massouh Nicholas , Kirkland Corey , Strongitharm Bernadette , Leech Andrew , Farré Marta , Thomas Gavin H. , Mulligan Christopher 
Published: March 2024

AbstractTripartite ATP independent periplasmic (TRAP) transporters are widespread in prokaryotes and are responsible for the transport of a variety of different ligands, primarily organic acids. TRAP transporters are secondary active transporters that employ a substrate binding protein to bind and present the substrate to membrane embedded translocation component. TRAP transporters can be divided into two subclasses; DctP-type and TAXI type, which share the same overall architecture and requirement of the SBP for transport, but their SBPs share no similarity. The DctP-type transporters are very well studied and have been shown to transport a range of compounds including dicarboxylates, keto acids, sugar acids. However, the TAXI type transporters are relatively poorly understood, with the range of transportable compounds still to be discovered and selectivity requirements for binding unknown. To address these shortfalls in our understanding, we have structurally and biochemically characterized VC0430 fromVibrio choleraerevealing it to be a monomeric high affinity glutamate binding protein. VC0430 is stereoselective, binding the L-isomer preferentially, and can also bind L-glutamine and L-pyroglutamate, but with low affinity relative to L-glutamate. Structural characterization of ligand bound VC0430 reveals details of the binding site and biophysical characterization of binding site mutant reveal the substrate binding determinants, which differ substantially from the DctP-type TRAPs. Finally, we have analysedin silicothe interaction between VC0430 and its cognate membrane component revealing an architecture hitherto unseen. To our knowledge, this is the first transporter inV. choleraeto be identified as specific to glutamate, which plays a key role in osmoadaptation ofV. cholerae, making this transporter a potential therapeutic target.
Being politically connected: corporate charitable giving before and after the 2016 Charity Law
Authors: Ji Min , Deng Detian , Li Guangyu 
Published: March 2024

Purpose
Charitable giving in China has moved from being subjected to government attention and public skepticism to receiving government encouragement and public support. The role played by political connections in philanthropy is indisputable, although very few studies have explored their association from the perspective of the country’s first Charity Law of 2016. This study aims to contribute to the ongoing debate about the 2016 Charity Law and offers an understanding of the future trends in corporate charitable giving.

Design/methodology/approach
Using empirical analysis of data collected from listed companies in China, this study analyzes the impact of political connections on corporate charitable giving before and after the 2016 Charity Law. The study adopts three leading theories from previous research into corporate charitable giving and political connections: corporate social responsibility, resource dependence theory and stakeholder theory. A conceptual framework is outlined, and hypotheses are formulated accordingly.

Findings
The results show that political connections have a substantial positive impact on corporate charitable giving, both before and after the implementation of the 2016 Charity Law, which has significantly promoted and increased the amount and proportion of charitable giving. Although the 2016 Charity Law attempted to weaken the political connections of enterprises, the influence of political connections on corporate charitable giving has proved difficult to diminish or eliminate, as charity is dominated by the state.

Originality/value
This study explores the association between political connections and corporate charitable giving from the perspective of China’s Charity Law of 2016.