bluuebunny/crossref_metadata_2025_split huggingface dataset:
Barriers to chimpanzee gene flow at the south‐east edge of their distribution
Authors: Bonnin Noémie , Piel Alex K. , Brown Richard P. , Li Yingying , Connell Andrew Jesse , Avitto Alexa N. , Boubli Jean P. , Chitayat Adrienne , Giles Jasmin , Gundlapally Madhurima S. , Lipende Iddi , Lonsdorf Elizabeth V. , Mjungu Deus , Mwacha Dismas , Pintea Lilian , Pusey Anne E. , Raphael Jane , Wich Serge A. , Wilson Michael L. , Wroblewski Emily E. , Hahn Beatrice H. , Stewart Fiona A. 
Published: June 2023

AbstractPopulations on the edge of a species' distribution may represent an important source of adaptive diversity, yet these populations tend to be more fragmented and are more likely to be geographically isolated. Lack of genetic exchanges between such populations, due to barriers to animal movement, can not only compromise adaptive potential but also lead to the fixation of deleterious alleles. The south‐eastern edge of chimpanzee distribution is particularly fragmented, and conflicting hypotheses have been proposed about population connectivity and viability. To address this uncertainty, we generated both mitochondrial and MiSeq‐based microsatellite genotypes for 290 individuals ranging across western Tanzania. While shared mitochondrial haplotypes confirmed historical gene flow, our microsatellite analyses revealed two distinct clusters, suggesting two populations currently isolated from one another. However, we found evidence of high levels of gene flow maintained within each of these clusters, one of which covers an 18,000 km2 ecosystem. Landscape genetic analyses confirmed the presence of barriers to gene flow with rivers and bare habitats highly restricting chimpanzee movement. Our study demonstrates how advances in sequencing technologies, combined with the development of landscape genetics approaches, can resolve ambiguities in the genetic history of critical populations and better inform conservation efforts of endangered species.
The sublingual microcirculation and frailty index in chronic kidney disease patients
Authors: Homes Ryan A. P. , Giddens Fiona , Francis Ross S. , Hubbard Ruth E. , Gordon Emily H. , Midwinter Mark J. 
Published: June 2023

AbstractObjectiveTo examine the relationship between sublingual microcirculatory measures and frailty index in those attending a kidney transplant assessment clinic.MethodsPatients recruited had their sublingual microcirculation taken using sidestream dark field videomicroscopy (MicroScan, Micro Vision Medical, Amsterdam, the Netherlands) and their frailty index score using a validated short form via interview.ResultsA total of 44 patients were recruited with two being excluded due to microcirculatory image quality scores exceeding 10. The frailty index score indicated significant correlations with total vessel density (p < .0001, r = −.56), microvascular flow index (p = .004, r = −.43), portion of perfused vessels (p = .0004, r = −.52), heterogeneity index (p = .015, r = .32), and perfused vessel density (p < .0001, r = −.66). No correlation was shown between the frailty index and age (p = .08, r = .27).ConclusionsThere is a relationship between the frailty index and microcirculatory health in those attending a kidney transplant assessment clinic, that is not confounded by age. These findings suggest that the impaired microcirculation may be an underlying cause of frailty.
Flagella‐mediated cytosolic motility of Salmonella enterica Paratyphi A aids in evasion of xenophagy but does not impact egress from host cells
Authors: Scharte Felix , Franzkoch Rico , Hensel Michael 
Published: June 2023

AbstractSalmonella enterica is a common foodborne, facultative intracellular enteropathogen. Typhoidal serovars like Paratyphi A (SPA) are human restricted and cause severe systemic diseases, while many serovars like Typhimurium (STM) have a broad host range, and usually lead to self‐limiting gastroenteritis. There are key differences between typhoidal and non‐typhoidal Salmonella in pathogenesis, but underlying mechanisms remain largely unknown. Transcriptomes and phenotypes in epithelial cells revealed induction of motility, flagella and chemotaxis genes for SPA but not STM. SPA exhibited cytosolic motility mediated by flagella. In this study, we applied single‐cell microscopy to analyze triggers and cellular consequences of cytosolic motility. Live‐cell imaging (LCI) revealed that SPA invades host cells in a highly cooperative manner. Extensive membrane ruffling at invasion sites led to increased membrane damage in nascent Salmonella‐containing vacuole, and subsequent cytosolic release. After release into the cytosol, motile bacteria showed the same velocity as under culture conditions in media. Reduced capture of SPA by autophagosomal membranes was observed by LCI and electron microscopy. Prior work showed that SPA does not use flagella‐mediated motility for cell exit via the intercellular spread. However, cytosolic motile SPA was invasion‐primed if released from host cells. Our results reveal flagella‐mediated cytosolic motility as a possible xenophagy evasion mechanism that could drive disease progression and contributes to the dissemination of systemic infection.
Cultivating a new ecosystem in English language teaching: A focus on researchers in a textbook development project
Authors: Shu Dingfang , Yang Shanshan , Sato Masatoshi 
Published: June 2023

AbstractIn addressing the widening research–practice gap in the field of second language (L2) education, an increasing emphasis has been placed on a bidirectional and mutually beneficial relationship between L2 researchers and practitioners. Through the lens of an ecosystems model, this qualitative study explored how seven researchers at a research center in China, who collaborated with practitioners and other stakeholders in developing English textbooks, impacted the local English language teaching (ELT) ecosystem and built a bridge between research and practice. Data sources included semistructured interviews, written reflections, and official documents, in an effort to provide a holistic perspective of researchers’ experiences and changes in the textbook project. Results showed that with researchers’ engagement, which was influenced by other participants at distinct levels of the ecosystem, a healthy ecosystem emerged as a result of the project. The engagement of the researchers with other participants contributed to value co‐creation in the local ELT ecosystem, which was facilitated by the research center. The evolving new ecosystem is characterized by rich, multidirectional, and reciprocal energy flows among the stakeholders with differing roles. In particular, active agents, government support, dialogue platforms, and collaborative mindsets played important roles in facilitating researchers’ engagement in the ecosystem.
Comparative acetylomic analysis reveals differentially acetylated proteins regulating fungal metabolism in hypovirus‐infected chestnut blight fungus
Authors: Li Ru , Chen Fengyue , Li Shuangcai , Yuan Luying , Zhao Lijiu , Tian Shigen , Chen Baoshan 
Published: June 2023

AbstractCryphonectria parasitica, the chestnut blight fungus, and hypoviruses are excellent models for examining fungal pathogenesis and virus–host interactions. Increasing evidence suggests that lysine acetylation plays a regulatory role in cell processes and signalling. To understand protein regulation in C. parasitica by hypoviruses at the level of posttranslational modification, a label‐free comparative acetylome analysis was performed in the fungus with or without Cryphonectria hypovirus 1 (CHV1) infection. Using enrichment of acetyl‐peptides with a specific anti‐acetyl‐lysine antibody, followed by high accuracy liquid chromatography–tandem mass spectrometry analysis, 638 lysine acetylation sites were identified on 616 peptides, corresponding to 325 unique proteins. Further analysis revealed that 80 of 325 proteins were differentially acetylated between C. parasitica strain EP155 and EP155/CHV1‐EP713, with 43 and 37 characterized as up‐ and down‐regulated, respectively. Moreover, 75 and 65 distinct acetylated proteins were found in EP155 and EP155/CHV1‐EP713, respectively. Bioinformatics analysis revealed that the differentially acetylated proteins were involved in various biological processes and were particularly enriched in metabolic processes. Differences in acetylation in C. parasitica citrate synthase, a key enzyme in the tricarboxylic acid cycle, were further validated by immunoprecipitation and western blotting. Site‐specific mutagenesis and biochemical studies demonstrated that the acetylation of lysine‐55 plays a vital role in the regulation of the enzymatic activity of C. parasitica citrate synthase in vitro and in vivo. These findings provide a valuable resource for the functional analysis of lysine acetylation in C. parasitica, as well as improving our understanding of fungal protein regulation by hypoviruses from a protein acetylation perspective.
Change in prefilter pressure as a key determinant in the decision to return blood in continuous renal replacement therapy: An observational study
Authors: Mateos‐Dávila Almudena , Betbesé Roig Antonio Jorge , Santos Rodríguez José Alberto , Guix‐Comellas Eva Maria 
Published: June 2023

AbstractBackgroundDuring continuous renal replacement therapy (CRRT), circuit coagulation is an important event that can result in suboptimal outcomes. Nurses must remain alert throughout the treatment and observe machine pressures. Transmembrane pressure (TMP) is commonly used for monitoring but it is sometimes too late to return blood to the patient.AimTo compare the capacity of prefilter pressure (FP) versus TMP to predict the risk of circuit coagulation in adult patients with acute renal failure on CRRT.Study DesignAn observational, longitudinal, prospective study. This study was carried out in a tertiary referral hospital over 2 years. Data collected included the following variables: TMP, filter or FP, effluent pressure, venous and arterial pressure, filtration fraction, and ultrafiltration constant of each circuit. Means and their trends over time were collected, for both diffusive and convective therapy and for two membrane types.ResultsA total of 151 circuits (24 polysulfone and 127 acrylonitrile) were analysed, from 71 patients (n = 22 [34%] women; mean age, 66.5 [36–84] years). Of the total treatments, 80 were diffusive, and the rest were convective or mixed. In the diffusive circuits, a progressive rise in FP was observed without an increase in TMP and with an increasing trend in effluent pressure. Circuit lifespan was between 2 and 90 h. In 11% (n = 17) of the cases, the blood could not be returned to the patient.ConclusionThese findings allowed the creation of graphs that indicate the appropriate point to return blood to the patient. FP was a major determinant in this decision; in most cases, TMP was not a reliable parameter. Our findings are applicable to convective, diffusive, and mixed treatments as well as both types of membranes used in this acute setting.Relevance to Clinical PracticeThis study provides two clear reference graphs showing risk scales for the assessment of circuit pressures in CRRT. The graphs proposed here can be used to evaluate any machine on the market and the two types of membranes used in this acute setting. Both convective and diffusive circuits can be assessed, allowing safer evaluation in patients who change treatment.
Diagnostic methods to measure spastic segment and guide tailored myotomy length in type 3 achalasia
Authors: Low Eric E. , Hasan Aws , Fehmi Syed Abbas , Chang Michael A. , Kwong Wilson , Krinsky Mary L. , Anand Gobind , Greytak Madeline , Kaizer Alexander , Yadlapati Rena 
Published: June 2023

AbstractBackgroundMyotomy length in type 3 achalasia is generally tailored based on segment of spasticity on high‐resolution manometry (HRM). Potential of length of tertiary contractions on barium esophagram (BE) or length of thickened circular muscle on endoscopic ultrasound (EUS) to guide tailored myotomy is less understood. This study aimed to assess agreement between spastic segments lengths on HRM, BE, and EUS among patients with type 3 achalasia.MethodsThis retrospective study included adults with type 3 achalasia on HRM between November 2019 and August 2022 who underwent evaluation with EUS and/or BE. Spastic segments were defined as HRM—distance between proximal borders of lower esophageal sphincter and high‐pressure area (isobaric contour ≥70 mmHg); EUS—length of thickened circular muscle (≥1.2 mm) from proximal border of esophagogastric junction (EGJ) to the transition to a non‐thickened circular muscle; BE—distance between EGJ to proximal border of tertiary contractions. Pairwise comparisons assessed for correlation (Pearson's) and intraclass correlation classification (ICC) agreement.Key ResultsTwenty‐six patients were included: mean age 66.9 years (SD 13.8), 15 (57.7%) male. Spastic segments were positively correlated on HRM and BE with good agreement (ICC 0.751, [95% CI 0.51, 0.88]). Spastic segments were negatively correlated with poor agreement on HRM and EUS (ICC −0.04, [−0.45, 0.39]) as well as BE and EUS (ICC −0.03, [−0.47, 0.42]).Conclusions & InferencesLength of spastic segment was positively correlated on HRM and BE while negatively correlated when compared to EUS, supporting the common use of HRM and highlighting the uncertain role for EUS in tailoring myotomy length for type 3 achalasia.
Fermentation‐mediated growth, signaling, and defense in plants
Authors: Jardine Kolby J. , McDowell Nate 
Published: June 2023

SummaryWhile traditionally considered important mainly in hypoxic roots during flooding, upregulation of fermentation pathways in plants has recently been described as an evolutionarily conserved drought survival strategy, with acetate signaling mediating reprograming of transcription and cellular carbon and energy metabolism from roots to leaves. The amount of acetate produced directly correlates with survival through potential mechanisms including defense gene activation, biosynthesis of primary and secondary metabolites, and aerobic respiration. Here, we review root ethanolic fermentation responses to hypoxia during saturated soil conditions and summarize studies highlighting acetate fermentation under aerobic conditions coupled with respiration during growth and drought responses. Recent work is discussed demonstrating long‐distance transport of acetate via the transpiration stream as a respiratory substrate. While maintenance and growth respiration are often modeled separately in terrestrial models, here we propose the concept of ‘Defense Respiration’ fueled by acetate fermentation in which upregulation of acetate fermentation contributes acetate substrate for alternative energy production via aerobic respiration, biosynthesis of primary and secondary metabolites, and the acetylation of proteins involved in defense gene regulation. Finally, we highlight new frontiers in leaf‐atmosphere emission measurements as a potential way to study acetate fermentation responses of individual leaves, branches, ecosystems, and regions.
Beyond knockouts: fine‐tuning regulation of gene expression in plants with CRISPR‐Cas‐based promoter editing
Authors: Tang Xu , Zhang Yong 
Published: June 2023

SummaryThe CRISPR‐Cas‐based genome editing field in plants is expanding rapidly. Editing plant promoters to obtain cis‐regulatory alleles with altered expression levels or patterns of target genes is a highly promising topic. However, primarily used CRISPR‐Cas9 has significant limitations when editing noncoding sequences like promoters, which have unique structures and regulatory mechanisms, including A‐T richness, repetitive redundancy, difficulty in identifying key regulatory regions, and a higher frequency of DNA structure, epigenetic modification, and protein binding accessibility issues. Researchers urgently require efficient and feasible editing tools and strategies to address these obstacles, enhance promoter editing efficiency, increase diversity in promoter polymorphism, and, most importantly, enable ‘non‐silent’ editing events that achieve precise target gene expression regulation. This article provides insights into the key challenges and references for implementing promoter editing‐based research in plants.
A paler shade of green: engineering cellular chlorophyll content to enhance photosynthesis in crowded environments
Authors: Cutolo Edoardo Andrea , Guardini Zeno , Dall'Osto Luca , Bassi Roberto 
Published: June 2023

SummaryIn natural ecosystems, plants compete for space, nutrients and light. The optically dense canopies limit the penetration of photosynthetically active radiation and light often becomes a growth‐limiting factor for the understory. The reduced availability of photons in the lower leaf layers is also a major constraint for yield potential in canopies of crop monocultures. Traditionally, crop breeding has selected traits related to plant architecture and nutrient assimilation rather than light use efficiency. Leaf optical density is primarily determined by tissue morphology and by the foliar concentration of photosynthetic pigments (chlorophylls and carotenoids). Most pigment molecules are bound to light‐harvesting antenna proteins in the chloroplast thylakoid membranes, where they serve photon capture and excitation energy transfer toward reaction centers of photosystems. Engineering the abundance and composition of antenna proteins has been suggested as a strategy to improve light distribution within canopies and reduce the gap between theoretical and field productivity. Since the assembly of the photosynthetic antennas relies on several coordinated biological processes, many genetic targets are available for modulating cellular chlorophyll levels. In this review, we outline the rationale behind the advantages of developing pale green phenotypes and describe possible approaches toward engineering light‐harvesting systems.
Management of oral herpes simplex virus infections: The problem of resistance. A narrative review
Authors: Piperi Evangelia , Papadopoulou Erofili , Georgaki Maria , Dovrat Sara , Bar Illan Mor , Nikitakis Nikolaos G. , Yarom Noam 
Published: June 2023

AbstractHerpes Simplex Virus (HSV) type 1 (HSV‐1) and type 2 (HSV‐2) are among the most common human viral pathogens, affecting several billion people worldwide. Although in healthy patients clinical signs and symptoms of HSV infection are usually mild and self‐limiting, HSV‐infections in immunocompromised patients are frequently more aggressive, persistent, and even life‐threatening. Acyclovir and its derivatives are the gold standard antiviral drugs for the prevention and treatment of HSV infections. Although the development of acyclovir resistance is a rather uncommon condition, it may be associated with serious complications, especially in immunocompromised patients. In this review, we aim to address the problem of drug resistant HSV infection and discuss the available alternative therapeutic interventions. All relative studies concerning alternative treatment modalities of acyclovir resistant HSV infection published in PubMed between 1989 to 2022 were reviewed. Long‐term treatment and prophylaxis with antiviral agents predisposes to drug resistance, especially in immunocompromised patients. Cidofovir and foscarnet could serve as alternative treatments in these cases. Although rare, acyclovir resistance may be associated with severe complications. Hopefully, in the future, novel antiviral drugs and vaccines will be available in order to avoid the existing drug resistance.
Optimal return shipping insurance policy with consumers' anticipated regret
Authors: Li Yiming , Li Gang , Pan Xiajun Amy 
Published: June 2023

We study return shipping insurance (RSI) policies prevalent on platforms such as JD.com and Taobao.com. Retailers on those platforms can purchase and provide RSI for consumers (RRSI) or offer an option for consumers to buy RSI themselves (CRSI). With either RSI, consumers will be partially compensated by an insurer for their shipping fees associated with product returns. As the consumers' uncertainty about product fit is realized only after purchase, their decisions whether to purchase CRSI may lead to postpurchase regret. Considering these anticipated regret behaviors, we investigate the optimal RSI policy for a monopolistic online retailer and an insurer. We show that the retailer offers RRSI only if the retailer's return handling cost is relatively low and consumers' return shipping cost is in an intermediate range; otherwise, the consumers' strong propensity for uninsured regret may stimulate them to purchase CRSI. Under the optimal RRSI policy, the retailer always charges a higher product price than under no RSI, and surprisingly the consumer demand could expand. In contrast, under the optimal CRSI policy, the retailer always sets a lower product price, but resulting in consumer demand shrinkage. Counterintuitively, CRSI may become a “win‐win‐win” policy for the retailer, insurer, and consumers.
COVID‐19 associated oral and oropharyngeal microbiome: Systematic review and meta‐analysis
Authors: Ganesan Sukirth M. , Peter Tabitha K. , Withanage Miyuraj H. H. , Boksa Frank , Zeng Erliang , Martinez April , Dabdoub Shareef M. , Dhingra Kunaal , Hernandez‐Kapila Yvonne 
Published: June 2023

AbstractThree years into the coronavirus disease 2019 (COVID‐19) pandemic, there are still growing concerns with

the emergence of different variants,
unknown long‐ and short‐term effects of the virus, and
potential biological mechanisms underlying etiopathogenesis and increased risk for morbidity and mortality.
The role of the microbiome in human physiology and the initiation and progression of several oral and systemic diseases have been actively studied in the past decade. With the proof of viral transmission, carriage, and a potential role in etiopathogenesis, saliva and the oral environment have been a focus of COVID‐19 research beyond diagnostic purposes. The oral environment hosts diverse microbial communities and contributes to human oral and systemic health. Several investigations have identified disruptions in the oral microbiome in COVID‐19 patients. However, all these studies are cross‐sectional in nature and present heterogeneity in study design, techniques, and analysis. Therefore, in this undertaking, we (a) systematically reviewed the current literature associating COVID‐19 with changes in the microbiome; (b) performed a re‐analysis of publicly available data as a means to standardize the analysis, and (c) reported alterations in the microbial characteristics in COVID‐19 patients compared to negative controls. Overall, we identified that COVID‐19 is associated with oral microbial dysbiosis with significant reduction in diversity. However, alterations in specific bacterial members differed across the study. Re‐analysis from our pipeline shed light on Neisseria as the potential key microbial member associated with COVID‐19.