bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome streamlining in CPR bacteria transitioning from soil to groundwater
Authors: Chaudhari Narendrakumar M. , Pérez-Carrascal Olga M. , Overholt Will A. , Totsche Kai U. , Küsel Kirsten 
Published: May 2023

AbstractTo better understand the influence of habitat on the genetic content of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil to groundwater on genomic divergences of these organisms. Bacterial metagenome-assembled genomes (318 total, 35 of CPR bacteria) were generated from seepage waters and compared directly to groundwater counterparts. Seepage water CPR bacteria exhibited 1.24-fold greater mean genome size, while their inferred mean replication rate was 21.1% lower than groundwater lineages. While exploring gene loss and adaptive gains in closely related lineages in groundwater, we identified a zinc transporter, a surface protein, and a lipogylcopeptide resistance gene unique to a seepage Parcubacterium. A nitrite reductase gene unique to the groundwater Parcubacterium, likely acquired from pelagic microbes via horizontal gene transfer, was also identified. Groundwater Parcubacteria harbored nearly double the fraction (9.4%) of pseudogenes than their seepage kin (4.9%), suggesting further genome streamlining.
PandoGen: Generating complete instances of future SARS-CoV-2 sequences using Deep Learning
Authors: Ramachandran Anand , Lumetta Steven S. , Chen Deming 
Published: May 2023

AbstractOne of the challenges in a viral pandemic is the emergence of novel variants with different phenotypical characteristics. An ability to forecast future viral individuals at the sequence level enables advance preparation by characterizing the sequences and closing vulnerabilities in current preventative and therapeutic methods. In this article, we explore, in the context of a viral pandemic, the problem of generating complete instances of undiscovered viral protein sequences, which have a high likelihood of being discovered in the future using protein language models. Current approaches to training these models fit model parameters to a known sequence set, which does not suit pandemic forecasting as future sequences differ from known sequences in some respects. To address this, we develop a novel method, called PandoGen, to train protein language models towards the pandemic protein forecasting task. PandoGen combines techniques such as synthetic data generation, conditional sequence generation, and reward-based learning, enabling the model to forecast future sequences, with a high propensity to spread. Applying our method to modeling the SARS-CoV-2 Spike protein sequence, we find empirically that our model forecasts twice as many novel sequences with five times the case counts compared to a model that is thirty times larger. Our method forecasts unseen lineages months in advance, whereas models 4× and 30× larger forecast almost no new lineages. When trained on data available up to a month before the onset of important Variants of Concern, our method consistently forecasts sequences belonging to those variants within tight sequence budgets.PandoGen is available at:https://github.com/UIUC-ChenLab/PandoGen
YidC fromEscherichia coliforms an ion-conducting pore upon activation by ribosomes
Authors: Knyazev Denis G. , Winter Lukas , Vogt Andreas , Posch Sandra , Siligan Christine , Goessweiner-Mohr Nikolaus , Hagleitner-Ertugrul Nora , Koch Hans-Georg , Pohl Peter 
Published: May 2023

AbstractThe universally conserved protein YidC aids the insertion and folding of transmembrane polypeptides independently or as a part of the SecYEG translocon complex. In the former scenario, the lipid-exposed YidC surface equipped with a highly conserved positively charged arginine is thought to facilitate membrane insertion of the nascent chain by providing a countercharge for the acidic residues at the polypeptide’s N-terminal region. Here we show that the purified and reconstitutedE. coliYidC forms an ion-conducting transmembrane pore upon binding a ribosome or ribosome-nascent chain complex (RNC). This pore is closed in the absence of ribosomes. As this pore is not visible in the published monomeric YidC structure, we used AlphaFold to construct the model of a parallel YidC dimer. Experimental evidence for a dimeric assembly comes from our BN-PAGE analysis of native vesicles, fluorescence correlation spectroscopy studies, and single-molecule fluorescence microscopy. In the dimeric model, the conserved positively charged arginine and many residues interacting with nascent chains point into the putative pore. This result suggests the possibility of an alternative mode of YidC-assisted membrane protein insertion.
Analysis ofin-patientevolution ofEscherichia colireveals potential links to relapse of bone and joint infections
Authors: Thiriet-Rupert Stanislas , Josse Jérôme , Perez-Pascual David , Tasse Jason , Andre Camille , Abad Léila , Lebeaux David , Ghigo Jean-Marc , Laurent Frédéric , Beloin Christophe 
Published: May 2023

AbstractBone and joint infections (BJIs) are difficult to treat and affect a growing number of patients, in which relapses are observed in 10-20% of the case. These relapses, which call for prolonged antibiotic treatment and increase the risk of emergence of resistance, may originate from ill understood adaptation of the pathogen to the host. Here, we studied three pairs ofEscherichia colistrains corresponding to three cases of BJIs and their relapse to better understand in-patient adaptation.Whole genome comparison presented evidence for positive selection with prevalence of non-synonymous and loss of function mutations. Phenotypic characterization showed that biofilm formation capacity was not modified, contrary to what is usually described in such relapse cases. Although virulence was not modified, we identified the loss of two virulence factors (namely an AFA afimbrial adhesin and a YadA-like adhesin) contributing to immune system evasion in one of the studied relapse strain. Other selected strategies likely helped the relapse strains to outcompete competitors through global growth optimization and colicin production. This work highlights the variety of strategies allowing in-patient adaptation in BJIs.
Influence of expression and purification protocols on Gα biochemical activity: kinetics of plant and mammalian G protein cycles
Authors: Gookin Timothy E. , Chakravorty David , Assmann Sarah M. 
Published: May 2023

AbstractHeterotrimeric G proteins are a class of signal transduction complexes with broad roles in human health and agriculturally important plant traits. In the classic paradigm, guanine nucleotide binding to the Gα subunit regulates the activation status of the complex. Using theArabidopsis thalianaGα subunit, GPA1, we developed a rapid StrepII-tag mediated purification method that facilitates isolation of protein with increased enzymatic activities as compared to conventional methods, and is demonstrably also applicable to mammalian Gα subunits. We subsequently utilized domain swaps of GPA1 and human GNAO1 to demonstrate the instability of recombinant GPA1 is a function of the interaction between the Ras and helical domains, and can be partially uncoupled from the rapid nucleotide binding kinetics displayed by GPA1.
Severe liver damage, low bone mineral content, and PDXDC1/TTC39B gene variations linked to NAFLD with metabolic syndrome
Authors: Chatterjee Ankita , Mondal Bandana , Das Kausik , Mondal Dipankar , Ghosh Ranajoy , Chowdhury Abhijit , Basu Priyadarshi 
Published: May 2023

AbstractBackgroundFatty liver disease is a pathologic condition of liver due to excess deposition of fat in the liver and is considered as hepatic manifestation of metabolic syndrome (MetS). Metabolic syndrome is comorbid with multiorgan abnormalities and diseases. However, the phenotypic uniqueness and genetic background of fatty liver patients in the presence/absence of metabolic syndrome are unclear.MethodsA cohort of 551 individuals with (FLD+) or without fatty liver (FLD-) was recruited.We subdivided the study cohort based on the presence or absence of metabolic syndrome (MetS) into four groups-Group4FLD+/MetS+; n=221, Group3FLD+/MetS-; n=39, Group2FLD-/MetS+; n=175 and Group1FLD-/MetS-n=116. Pathophysiology was compared between the study groups. Association of genomic variants with Group4FLD+/MetS+; n=167 was studied compared to Group1FLD-/MetS-; n=74. The effects of the associated variants on gene expression were studied using eQTL mapping.Results and conclusionsAmong 551 individuals, 47.2% had fatty liver (FLD+) and 71.87% had metabolic syndrome (MetS+). Compared to Group3FLD+/MetS-, Group4FLD+/MetS+ patients had significantly higher age, higher adiposity, severe diabetic and lipid profile, liver damage marker, CRP, low bone mineral content and higher liver damage, both among the obese and the non-obese. Non-obese Group2FLD-/MetS+ patients had significantly higher serum TG and lower HDL, while obese Group3FLD+/MetS-patients had higher liver damage markers. Additionally, we also showed that in our population, Group4FLD+/MetS+ patients carried higher risk allele frequency in rs3761472-G(SAMM50,OR=2.9(2.0-4.1); p=0.002), rs738409-G(PNPLA3,OR=2.8(1.9-4.07)p=0.003),rs58542926-A(TM6SF2,OR=2.7(1.9-3.9)p=0.021),rs35665085-A(CECR5,OR=2.7(1.9-3.9)p=0.038),rs471364-G(TTC39B,OR=3.1(2.1-4.5)p=0.001),rs2800-G(SLC9A9,OR=3.1(2-4.5)p=0.028),rs7200543-A(PDXDC1,OR=2.261(1.1-4.8)p=0.031). Group4 patients with rs7200543-AA showed poor skeletal health. Thus, fatty liver with metabolic syndrome showed the most severe disease phenotype.
“Not enough yet”: CSR communication of stigmatized industries through news coverage
Authors: Jeong Hyun Ju , Chung Deborah S. 
Published: May 2023

PurposeCorporate social responsibility (CSR) communication covered by the news media is considered as more credible and effective in shaping public perceptions toward corporations than CSR shared by corporations themselves. This is particularly true when CSR is about corporations with social stigma inherent in business practices. This study examines the CSR publicity of stigmatized industries from the journalism lens.Design/methodology/approachA content analysis was conducted with CSR stories from 2019 to 2020 by USA newspapers (n = 348).FindingsResults of this study showed that the overall volume of CSR from stigmatized industries has decreased, with fewer responses to the recent pandemic. Further, the media brought promotional CSR activities and the business motives behind the activities into focus. Opposing patterns were found for CSR of non-stigmatized industries presented with philanthropic activities based on corporations' social motives to help communities. Similarly, economic and legal responsibilities reflected in the CSR pyramid were more prominently reported for stigmatized industries, and ethical and discretionary responsibilities appeared more frequently for non-stigmatized industries.Practical implicationsIntegrating business and media literature, this study enriches scholarly discussions on media processes and effects for CSR communication. This study also provides practical implications for stigmatized industries by highlighting more authentic and careful approaches for CSR communication to earn positive publicity.Social implicationsThis study provides social implications by highlighting the importance of CSR communications through the lens of news media when corporations are socially stigmatized.Originality/valueStigmatized industries are known to be active in CSR communication to nullify social stigma surrounding themselves. The authors' findings provide empirical evidence suggesting that not all publicity benefits CSR communication for stigmatized corporations.
The future of sports tourism in the light of the COVID-19 pandemic – Developing a new paradigm model
Authors: Pashaie Sajjad , Perić Marko 
Published: May 2023

PurposeSports tourism was strongly affected by the COVID-19 pandemic, but there is no consensus on what sports tourism should look like in the post-pandemic period. This study explores the future of sports tourism in light of the COVID-19 pandemic and provides an alternative paradigm model.Design/methodology/approachData were collected by interviewing sports tourism experts. Data analysis was based on the continuous comparison method during three stages of open, axial and selective coding.FindingsThe findings point to the complexity of the future sports tourism industry. Post-COVID-19 sports tourism strongly depends on environmental forces and targeted support, with strategies focused on tourists’ safety and security, digitalization of the industry, and new employment opportunities.Originality/valueThis study contributes to the body of knowledge on sports tourism by providing answers to the current challenges, threats and opportunities associated with the pandemic. The proposed paradigm model could be a guideline for sports tourism practitioners and policymakers to accelerate recovery from COVID-19 in a sustainable and resilient manner.
Inspiring academic confidence in university students: perceived digital experience as a source of self-efficacy
Authors: Shaikh Imran Mehboob , Alsharief Ahmed , Amin Hanudin , Noordin Kamaruzaman , Shaikh Junaid 
Published: May 2023

Purpose
This study aims to introduce a research framework that identifies the potential sources of design self-efficacy that emerge from the digital class by covering the teaching for professional competence model (TPCM) to enhance students’ design self-efficacy.

Design/methodology/approach
The multistage and purposive sampling technique is used, and the respondents considered are Malaysian university students. Further, the students who completed the survey included both local and international students so as to capture responses through primary data.

Findings
The findings of this research study reveal that design self-efficacy is determined not only by feedback and collaborative learning but also by perceived digital class experience.

Research limitations/implications
Moreover, this study is limited in offering a theoretical framework using the TPCM; therefore, future studies may incorporate Bronfenbrenner’s ecological systems theory and may also use the theory integration approach. Also, in terms of geographic coverage, the current work is limited to an area in Klang Valley. Future studies may be carried out in other parts or regions of the country. Future researchers may also focus on technological self-efficacy to capture the other related factors that may be related.

Practical implications
This study not only contributed to the theoretical extensions but also to practical implications, which would benefit the policymakers of higher education providers in Malaysia.

Originality/value
TPCM components, which are students’ personal characteristics, teaching practices and student’s perceptions of the classroom climate, are mapped into the digital class context as potential sources of design self-efficacy and collectively labelled as digital class experience. To the authors’ knowledge, the digital class environment variable is yet to be tested as a component of TPCM.
Opportunism in headhunter‐client relations: An agency theory perspective
Authors: Peltokorpi Vesa 
Published: May 2023

AbstractRecruitment is one of the most important human resource functions for organizational success and survival. While organizations increasingly use headhunters to recruit employees, little research has focused on client‐headhunter relations. This paper draws on agency theory and interviews with 130 contingency‐based headhunters and corporate clients to examine clients' opportunistic behaviors and how headhunters sought to mitigate these opportunistic behaviors. Our analysis shows that clients used several headhunters in search assignments, negotiated and refused to pay placement fees, contacted candidates directly, changed search criteria and terminated search assignments, and used headhunters to poach employees from their competitors. Our analysis also shows that headhunters used various social interaction and contract‐based approaches to mitigate these behaviors, which affected recruitment‐related outcomes. This paper contributes to the literature by providing the first agency theory‐based study on clients' opportunist behaviors, bringing principals into agency theory‐based research, and showing that clients' opportunism affects recruitment‐related outcomes.
Full‐surface defect detection of navel orange based on hyperspectral online sorting technology
Authors: Shang Mengmeng , Xue Long , Zhang Yifan , Liu Muhua , Li Jing 
Published: May 2023

AbstractThe whole‐surface hyperspectral image acquisition of navel orange is particularly important for surface defect detection and quality classification. Because the light intensity at the edge of the navel orange is lower than that in the middle, the defects on the surface of the navel orange cannot be effectively identified. In this paper, a hyperspectral online sorting device for the whole‐surface defects of navel orange is proposed. First of all, the image data of navel orange is collected by online detection sorting equipment and the spectral image of the characteristic wave peak of 1655.72 nm was extracted. Then, the light intensity at the edge of the navel orange is enhanced by nonuniformity correction based on quadratic curve fitting, and the light intensity correction of the navel orange is realized. Finally, the corrected image is segmented by the threshold to obtain surface defects, and the number of surface defect pixels is improved effectively compared with that before light intensity correction. Ultimately, the online sorting test is carried out, and the detection accuracy is 100%. This indicates that this method effectively improves the sensitivity of defect detection. At the same time, the dimensionality reduction of hyperspectral data is also carried out, which is conducive to improving the efficiency of online detection.
Emergency laparoscopic sigmoid colectomy with primary anastomosis for Hinchey stages III and IV diverticulitis
Authors: Chikaraishi Kentaro , Kaneko Kenjiro , Kanai Hideki , Kobayashi Tetsuya , Tanabe Yoshiaki 
Published: May 2023

AbstractFor patients with perforated diverticulitis, many reports have focused on laparoscopic surgery without primary anastomosis. We performed laparoscopic surgery with primary anastomosis in three patients (two with Hinchey stage III, one with IV), with a median age of 53 years, all female, and no prior medical history. They all were hemodynamically stable. The median operation time was 91 minutes (range: 56–227 minutes) and the median blood loss was 50 mL (range: 0–200 mL). Their post‐operative course was uneventful, and patients commenced oral intake at a median of 5 post‐operative days and were discharged at a median of 12 post‐operative days. This procedure may be an option for Hinchey stages III and IV diverticulitis.
A scoring tool to predict mortality and dependency after cerebral venous thrombosis
Authors: Lindgren Erik , Krzywicka Katarzyna , de Winter Maria A. , Sánchez Van Kammen Mayte , Heldner Mirjam R. , Hiltunen Sini , Aguiar de Sousa Diana , Mansour Maryam , Canhão Patrícia , Ekizoğlu Esme , Rodrigues Miguel , Martins Silva Elisa , Garcia‐Esperon Carlos , Arnao Valentina , Aridon Paolo , Simaan Naaem Moin , Silvis Suzanne M. , Zuurbier Susanna M. , Scutelnic Adrian , Sezgin Mine , Alasheev Andrey Marisovich , Smolkin Andrey , Guisado‐Alonso Daniel , Yesilot Nilufer , Barboza Miguel , Ghiasian Masoud , Leker Ronen R. , Arauz Antonio , Arnold Marcel , Putaala Jukka , Tatlisumak Turgut , Coutinho Jonathan M. , Jood Katarina 
Published: May 2023

AbstractBackground and purposeA prognostic score was developed to predict dependency and death after cerebral venous thrombosis (CVT) to identify patients for targeted therapy in future clinical trials.MethodsData from the International CVT Consortium were used. Patients with pre‐existent functional dependency were excluded. Logistic regression was used to predict poor outcome (modified Rankin Scale score 3–6) at 6 months and Cox regression to predict 30‐day and 1‐year all‐cause mortality. Potential predictors derived from previous studies were selected with backward stepwise selection. Coefficients were shrunk using ridge regression to adjust for optimism in internal validation.ResultsOf 1454 patients with CVT, the cumulative number of deaths was 44 (3%) and 70 (5%) for 30 days and 1 year, respectively. Of 1126 patients evaluated regarding functional outcome, 137 (12%) were dependent or dead at 6 months. From the retained predictors for both models, the SI2NCAL2C score was derived utilizing the following components: absence of female‐sex‐specific risk factor, intracerebral hemorrhage, infection of the central nervous system, neurological focal deficits, coma, age, lower level of hemoglobin (g/l), higher level of glucose (mmol/l) at admission, and cancer. C‐statistics were 0.80 (95% confidence interval [CI] 0.75–0.84), 0.84 (95% CI 0.80–0.88) and 0.84 (95% CI 0.80–0.88) for the poor outcome, 30‐day and 1‐year mortality model, respectively. Calibration plots indicated a good model fit between predicted and observed values. The SI2NCAL2C score calculator is freely available at www.cerebralvenousthrombosis.com.ConclusionsThe SI2NCAL2C score shows adequate performance for estimating individual risk of mortality and dependency after CVT but external validation of the score is warranted.
Influences of no‐tillage on the yield and silage fermentation quality of Italian ryegrass
Authors: Xu Liuxing , Li Xinqin , Tian Jing , Wu Dan , Zhang Jianguo 
Published: May 2023

AbstractIt is common in southern China that rice (Oryza sativa L.) fields are sown with a cover crop like Italian ryegrass (Lolium multiflorum L.) following autumn harvest. The objective of the present research was to compare the effects of different no‐tillage methods on the yield, nutritive composition and silage fermentation quality of Italian ryegrass. Italian ryegrass was planted in winter fallow paddy fields on 9 days (NT9) and 5 days (NT5) prior to rice harvest and on 1 day after rice harvest for 2 years. Sowing prior to harvest was no‐tillage, and sowing after rice harvest was either no‐tillage (NT1) or conventional tillage (CK). The grass was harvested and ensiled two times each year. The growing year had no significant effects on the yield and most nutrition components, while it had significant effects on pH value, butyric acid and NH3‐N contents of silage. There were no differences in the yield, nutritional composition and silage fermentation quality among sowing methods. The neutral detergent fiber and acid detergent fiber of NT1 decreased slightly compared with NT9, NT5 and CK (p > .05). There was no difference in silage fermentation quality among the four treatments. The best sowing method for Italian ryegrass with second cut in winter fallow paddy was no‐tillage sowing after rice harvest.
Reducing sex work by targeting ‘vulnerable’ sex workers: A post‐structural analysis of policies regulating Danish exit programmes directed at people involved in sex work
Authors: Karlsson Henrik 
Published: May 2023

AbstractDespite the increased popularity of exit programmes targeting people involved in sex work, the research community has yet not critically scrutinised policies that regulate these programmes. This study aimed to start filling this research gap by studying the example of Denmark, a country that has implemented exit programmes although sex work remains partly decriminalised since 1999. In specific, this study has analysed policy documents that were formulated by the government and four Danish municipalities in relation to the government's latest grant called ‘Exit Package for People in Prostitution’, which was issued in 2019 to finance municipal exit programmes running between 2020 and 2023. The key finding indicates that the ‘problem’ of sex work is the sex work of the ‘vulnerable’ sex workers. Their sex work must be reduced because they risk being seriously harmed by their sex work activities. Implications from the findings of the study are discussed.