bluuebunny/crossref_metadata_2025_split huggingface dataset:
Remote sensing classification approach to large‐scale crop cultivation identification: A case study of the Aral Sea Basin
Authors: Wen Zhuojian , Jiang Desheng , Jing Ye , Liu Guilin 
Published: November 2023

AbstractSince the collapse of the Soviet Union, the crop cultivation structure in the Aral Sea Basin has changed dramatically, and these changes are worth studying. However, historical crop remote sensing mapping at the watershed scale remains challenging, especially crop misclassification at the cropland edge due to mixed pixels. Therefore, we proposed a field segmentation approach to constrain field edges based on time‐series Sentinel‐2 remote sensing images and the Google Earth Engine platform and then employed the random forest algorithm to perform crop classification based on time series Landsat/Sentinel‐2 images and crop phenology information to produce historical crop maps in the Aral Sea Basin from the 1990s onward. The results showed that the intersection over union between the extracted field edges and in situ‐measured field size data was 0.65. The overall accuracy of crop mapping was 95.2% in 2019. Then, we extended our method to historical mapping over the 1991–2015 period with accuracies ranging from 82.8% to 91.3%. Moreover, our method applied to historical mapping works well in terms of accuracy and policy matching. These findings indicate that our method can accurately distinguish cropland edges to reduce classification errors due to mixed pixels. This method is promising for solving the cropland edge problem for historical crop mapping in the Aral Sea Basin and can potentially provide a reference for historical crop classification in other watersheds of the world.
GhMYB30‐GhMUR3 affects fiber elongation and secondary wall thickening in cotton
Authors: Wu Aimin , Lian Boying , Hao Pengbo , Fu Xiaokang , Zhang Meng , Lu Jianhua , Ma Liang , Yu Shuxun , Wei Hengling , Wang Hantao 
Published: November 2023

SUMMARYXyloglucan, an important hemicellulose, plays a crucial role in maintaining cell wall structure and cell elongation. However, the effects of xyloglucan on cotton fiber development are not well understood. GhMUR3 encodes a xyloglucan galactosyltransferase that is essential for xyloglucan synthesis and is highly expressed during fiber elongation. In this study, we report that GhMUR3 participates in cotton fiber development under the regulation of GhMYB30. Overexpression GhMUR3 affects the fiber elongation and cell wall thickening. Transcriptome showed that the expression of genes involved in secondary cell wall synthesis was prematurely activated in OE‐MUR3 lines. In addition, GhMYB30 was identified as a key regulator of GhMUR3 by Y1H, Dual‐Luc, and electrophoretic mobility shift assay (EMSA) assays. GhMYB30 directly bound the GhMUR3 promoter and activated GhMUR3 expression. Furthermore, DAP‐seq of GhMYB30 was performed to identify its target genes in the whole genome. The results showed that many target genes were associated with fiber development, including cell wall synthesis‐related genes, BR‐related genes, reactive oxygen species pathway genes, and VLCFA synthesis genes. It was demonstrated that GhMYB30 may regulate fiber development through multiple pathways. Additionally, GhMYB46 was confirmed to be a target gene of GhMYB30 by EMSA, and GhMYB46 was significantly increased in GhMYB30‐silenced lines, indicating that GhMYB30 inhibited GhMYB46 expression. Overall, these results revealed that GhMUR3 under the regulation of GhMYB30 and plays an essential role in cotton fiber elongation and secondary wall thickening. Additionally, GhMYB30 plays an important role in the regulation of fiber development and regulates fiber secondary wall synthesis by inhibiting the expression of GhMYB46.
Establishment of a reference interval for thiamine concentrations in healthy dogs and evaluation of the prevalence of absolute thiamine deficiency in critically ill dogs with and without sepsis using high‐performance liquid chromatography
Authors: Berlin Noa , Pfaff Alexandra , Rozanski Elizabeth A. , Chalifoux Nolan V. , Hess Rebecka S. , Donnino Michael W. , Silverstein Deborah C. 
Published: November 2023

AbstractObjectiveTo determine the normal reference interval (RI) for thiamine concentrations in healthy dogs and investigate the prevalence of thiamine deficiency in critically ill dogs with and without sepsis.DesignProspective, observational, multicenter study, conducted between 2019 and 2021.SettingTwo veterinary university teaching hospitals.AnimalsA total of 109 dogs were enrolled into 3 groups: 40 healthy dogs, 33 dogs with suspected or confirmed sepsis and evidence of tissue hypoperfusion (Doppler blood pressure ≤90 mm Hg or plasma lactate ≥3 mmol/L), and 36 dogs with other critical illnesses and evidence of tissue hypoperfusion.InterventionsFor each dog, CBC, serum biochemistry, plasma lactate concentration, whole‐blood thiamine concentration, blood pressure, vital parameters, Acute Patient Physiologic and Laboratory Evaluation (APPLE)fast score, and clinical outcomes were recorded, alongside basic patient parameters and dietary history. Whole‐blood thiamine pyrophosphate (TPP) concentrations were measured using high‐performance liquid chromatography.Measurements and Main ResultsThe RI for whole‐blood TPP in healthy dogs was 70.9–135.3 μg/L. Median TPP concentrations were significantly lower in septic dogs compared to healthy controls (P = 0.036). No significant difference in median TPP concentrations was found between septic dogs and nonseptic critically ill dogs, or between healthy dogs and nonseptic critically ill dogs. TPP concentrations were below the normal RI in 27.3% of septic dogs, compared to 19.4% of nonseptic critically ill dogs (P = 0.57). No correlations were found between TPP concentrations and lactate concentrations, age, body condition scores, time since last meal, RBC count, serum alanine aminotransferase, APPLEfast scores, or patient outcomes.ConclusionsTPP concentrations were significantly lower in septic dogs compared to healthy controls, with an absolute thiamine deficiency found in 27.3% of septic dogs. The established TPP RI allows for further investigation of thiamine deficiency in critically ill dogs.
Correlates of Fundamental Motor Skills in the Early Years (0–4 Years): A Systematic Review
Authors: Veldman Sanne L.C. , Gubbels Jessica S. , Singh Amika S. , Koedijker Johan M. , Chinapaw Mai J.M. , Altenburg Teatske M. 
Published: November 2023

Aim: This systematic review aims to summarize evidence on correlates of fundamental motor skills in typically developing children aged 0–4 years. Methods: A literature search (PubMed, Embase, PsycINFO, and SPORTDiscus) was performed from 2000 till 23 May 2022. Inclusion criteria was cross-sectional and prospective studies examining associations between a potential correlate and fundamental motor skills in typically developing, apparently healthy children aged 0–4 years. Two independent reviewers performed screening and methodological quality assessment. Results: Eighty-three studies met eligibility criteria and were included. Thirteen studies were of high methodological quality. In children aged <1 year, we found no evidence for family income, breastfeeding-related, sleep-related, home environment, and socioeconomic variables. In children aged 1–2 years, we found no evidence for sex, growth-related variables, singleton birth, and family income. In children aged 2–4 years, we found no evidence for screen behavior, toxicity, parental education, family income, socioeconomic variables, and maternal depression/anxiety and moderate evidence for a positive association with early childhood education and care setting type. For other examined correlates, we found insufficient evidence (inconsistent findings or only one study available). Conclusions: We found insufficient evidence for over half of examined potential correlates of fundamental motor skills. We recommend investing in better research methodologies and improved reporting.
Efficacy of a
Pseudomonas aeruginosa
serogroup O9 vaccine
Authors: Moustafa Dina A. , DiGiandomenico Antonio , Raghuram Vishnu , Schulman Marc , Scarff Jennifer M. , Davis Michael R. , Varga John J. , Dean Charles R. , Goldberg Joanna B. 
Published: November 2023

ABSTRACT

There are currently no approved vaccines against the opportunistic pathogen
Pseudomonas aeruginosa
. Among vaccine targets, the lipopolysaccharide (LPS) O antigen of
P. aeruginosa
is the most immunodominant protective candidate. There are 20 different O antigens composed of different repeat sugar structures conferring serogroup specificity, and 10 are found most frequently in infection. Thus, one approach to combat infection by
P. aeruginosa
could be to generate immunity with a vaccine cocktail that includes all these serogroups. Serogroup O9 is 1 of the 10 serogroups commonly found in infection, but it has never been developed into a vaccine, due in part to the acid-labile nature of the O9 polysaccharide. Our laboratory has previously shown that intranasal administration of an attenuated
Salmonella
strain expressing the
P. aeruginosa
serogroup O11 LPS O antigen was effective in clearing bacteria and preventing mortality in mice following intranasal challenge with serogroup O11
P. aeruginosa
. Consequently, we set out to develop a
P. aeruginosa
serogroup O9 vaccine using a similar approach. Here, we show that
Salmonella
expressing serogroup O9 triggered an antibody-mediated immune response following intranasal administration to mice and that it conferred protection from
P. aeruginosa
serogroup O9 in a murine model of acute pneumonia.
Shigella flexneri
remodeling and consumption of host lipids during infection
Authors: Ascari Alice , Frölich Sonja , Zang Maoge , Tran Elizabeth N. H. , Wilson Danny W. , Morona Renato , Eijkelkamp Bart A. 
Published: November 2023

ABSTRACT

Shigella flexneri
is a major cause of bacillary dysentery in the developing world, predominantly affecting the pediatric age group, with malnutrition being a common co-morbidity. Lipids are key nutritional components, and their abundance and composition are likely to influence the pathobiology of
S. flexneri. S. flexneri
expresses a plethora of polysaccharides on its cell surface, but how this hydrophilic surface layer influences
S. flexneri
interaction with hydrophobic host molecules, such as fatty acids and lipids, is not well understood. In this study, we sought to interrogate how this hydrophilic layer affects
S. flexneri
during its intracellular lifestyle and how lipid homeostasis changes in both the host and pathogen. We characterized changes in
S. flexneri
cell envelope composition and surface-associated glycolipids, in particular lipopolysaccharide (LPS), during different phases of infection. We found that a dynamic capacity in LPS expression is necessary for the pathogen to manage delicate interaction with host fatty acids and maintain optimum virulence. Additionally, through confocal immunofluorescent microscopy, coupled with transcriptional and lipid analyses, we demonstrate that
S. flexneri
induces major host lipid remodeling during infection, by hijacking host lipid homeostasis pathways to its own benefit. Finally, this study suggests that fatty acid supplementation can influence the persistence and magnitude of
S. flexneri
infection. This work provides novel insights into the potential roles of balanced and sufficient dietary fatty acid intake in protection against gastroenteric pathogen infection.

IMPORTANCE

Bacterial pathogens have vastly distinct sites that they inhabit during infection. This requires adaptation due to changes in nutrient availability and antimicrobial stress. The bacterial surface is a primary barrier, and here, we show that the bacterial pathogen
Shigella flexneri
increases its surface decorations when it transitions to an intracellular lifestyle. We also observed changes in bacterial and host cell fatty acid homeostasis. Specifically, intracellular
S. flexneri
increased the expression of their fatty acid degradation pathway, while the host cell lipid pool was significantly depleted. Importantly, bacterial proliferation could be inhibited by fatty acid supplementation of host cells, thereby providing novel insights into the possible link between human malnutrition and susceptibility to
S. flexneri
.
HIV-1 Gag co-localizes with euchromatin histone marks at the nuclear periphery
Authors: Chang Jordan , Parent Leslie J. 
Published: November 2023

ABSTRACT
The retroviral Gag protein of human immunodeficiency virus type 1 (HIV-1) plays a central role in the selection of unspliced viral genomic RNA (gRNA) for packaging into new virions. Previously, we demonstrated that full-length HIV-1 Gag undergoes nuclear trafficking, where it associates with unspliced viral RNA (USvRNA) at transcription sites. To further examine the kinetics of HIV-1 Gag nuclear localization, we used biochemical and imaging techniques to determine the timing of HIV-1 entry into the nucleus. We also aimed to determine more precisely Gag’s subnuclear distribution to test the hypothesis that Gag associates with euchromatin, the transcriptionally active region of the nucleus. We observed that HIV-1 Gag localized to the nucleus at low expression levels shortly after its synthesis in the cytoplasm, suggesting that nuclear trafficking was not strictly concentration dependent. Furthermore, we found that HIV-1 Gag preferentially localized to the transcriptionally active euchromatin fraction compared to the heterochromatin-rich region in a latently infected T-cell line (J-Lat 10.6) treated with latency-reversal agents. Interestingly, HIV-1 Gag was more closely co-localized with euchromatin-associated histone marks near the nuclear periphery, the preferred location of HIV-1 proviral integration. Although the precise function of Gag’s association with histones in transcriptionally active chromatin regions remains uncertain, together with previous reports, this finding is consistent with a potential role for euchromatin-associated Gag molecules to initiate the selection of newly transcribed USvRNA in the nucleus for incorporation into virions.

IMPORTANCE
The traditional view of retrovirus assembly posits that packaging of gRNA by HIV-1 Gag occurs in the cytoplasm or at the plasma membrane. However, our previous studies showing that HIV-1 Gag enters the nucleus and binds to USvRNA at transcription sites suggest that gRNA selection may occur in the nucleus. In the present study, we observed that HIV-1 Gag trafficked to the nucleus and co-localized with USvRNA within 8 hours of expression. In infected T cells (J-Lat 10.6) reactivated from latency and in a HeLa cell line stably expressing an inducible Rev-dependent HIV-1 construct, we found that Gag preferentially localized with euchromatin histone marks associated with enhancer and promoter regions near the nuclear periphery, which is the favored site HIV-1 integration. These observations support the innovative hypothesis that HIV-1 Gag associates with euchromatin-associated histones to localize to active transcription sites, promoting capture of newly synthesized gRNA for packaging.
Diversity and conservation of the genome architecture of phages infecting the Alphaproteobacteria
Authors: Hyde Jonathan R. , Armond Thomas , Herring Jacob A. , Hope Sandra , Grose Julianne H. , Breakwell Donald P. , Pickett Brett E. 
Published: November 2023

ABSTRACT
Bacteriophages are viruses that are only capable of replicating inside a suitable bacterial host cell. Here, we performed a comprehensive meta-analysis of all 103 publicly available phage genomes that are known to infect members of the Alphaproteobacteria. We combined the sequence data and associated metadata with results from various comparative genomic and phylogenetic methods to quantify gene presence, families of orthologous gene products, and assign the phages into clusters and subclusters. Comparative genomic analyses, such as this one, allow differentiation of phages based on their evolutionary relatedness. The results of our analyses justify the classification of these phages into 16 clusters and 6 subclusters to ideally balance sequence diversity, protein orthologs, and core genes with host range. This study is the first to group phages infecting the Alphaproteobacteria. We expect that these results will inform future studies and that our classification schema will improve the classification of phages that infect bacterial taxa in the Alphaproteobacteria class.

IMPORTANCE
This study reports the results of the largest analysis of genome sequences from phages that infect the Alphaproteobacteria class of bacterial hosts. We analyzed over 100 whole genome sequences of phages to construct dotplots, categorize them into genetically distinct clusters, generate a bootstrapped phylogenetic tree, compute protein orthologs, and predict packaging strategies. We determined that the phage sequences primarily cluster by the bacterial host family, phage morphotype, and genome size. We expect that the findings reported in this seminal study will facilitate future analyses that will improve our knowledge of the phages that infect these hosts.
Early offering transcatheter aortic valve replacement to patients with moderate aortic stenosis: quantifying costs and benefits – a Markov model-based simulation study
Authors: Nguyen Dieu , Marwick Tom , Moodie Marj , Gao Lan 
Published: November 2023

ObjectiveAortic stenosis (AS) is one of the most common acquired cardiac valvular diseases. The success of transcatheter aortic valve implantation (TAVI) for severe AS has led to increasing interest in its use to earlier disease—moderate AS (MAS).DesignModel-based study using a Markov microsimulation technique to evaluate the long-term costs and benefits associated with ‘early’ TAVI. Key data inputs were sourced from the international literature and costs were obtained from Australian sources.SettingAustralian health care system perspective.Participants10 000 hypothetical MAS patients with or without left ventricular diastolic dysfunction or impaired left ventricular ejection fraction.InterventionComparing early TAVI to medical management over a life time horizon for MAS patients aged >65 years. We evaluated the cost-effectiveness of offering early TAVI in five scenarios (10%, 25%, 50%, 75% and 90% take-up rates).Primary and secondary outcome measuresThe primary outcome measure is quality-adjusted life years (QALY) gained and the incremental cost–utility ratio (ICUR). Secondary outcomes are life-years gained and the number of heart failure case avoided.ResultsOffering early TAVI for MAS patients resulted in both higher healthcare costs and greater benefits (an increase of 3.02 QALYs or 3.99 life-years) per person treated. The ICUR was around $A10 867 and $A11 926 per QALY gained for all five scenarios, with the total cost of early TAVI to the healthcare system being anticipated to be up to $A3.66 billion. Sensitivity analyses indicated a 100% probability of being cost-effective with a willingness to pay threshold of $A50 000/QALY. The benefits remained, even with assumptions of high levels of repeat valve replacement after TAVI.ConclusionWhile ongoing randomised controlled trials will define the benefit of TAVI to MAS patients, these results suggest that this intervention is likely to be cost-effective.
Mandatory Monthly Sales Disclosure and the Information Content of Earnings
Authors: Lu Hsueh-Tien , Xin Hua Christine 
Published: November 2023

Synopsis The research problem Taiwanese stock markets practice a unique form of reporting frequency, combining quarterly interim financial reports with mandatory monthly sales announcements. This unique setting allows us to compare the information content of quarterly earnings that are announced before, bundled with, or announced after the monthly sales disclosures. Motivation Monthly sales disclosures likely contribute to the pricing of earnings announcements (EAs) by providing investors with valuable information that helps them revise their expectations when forecasting earnings and cash flows. We examine whether monthly sales disclosures help investors to process earnings information. The test hypotheses Our first hypothesis is that the immediate market response to earnings news is lower if the previous quarter’s EAs are disclosed after the reporting of monthly sales for the first month of the next quarter. Our second hypothesis is that the subsequent market response to earnings news is lower if the previous quarter’s EAs are disclosed after the reporting of monthly sales for the first month of the next quarter. Target population We studied a sample of Taiwanese listed firms from 2014 through 2018. Adopted methodology We used multivariate regressions to test the hypotheses. Analyses We examined the monthly sales disclosures for the first month of quarter [Formula: see text], which are released within the first 10 days of the second month of quarter [Formula: see text]. We analyze the pricing of the content of the earnings of quarter q, conditional on whether the earnings are released before, simultaneously with, or released after the monthly sales disclosures. Findings We found that earnings disclosed after the monthly sales news are associated with weaker EA returns and post-EA drift, relative to earnings disclosed before or bundled with the monthly sales news. These results suggest that monthly sales disclosures preempt the information content of late EAs. More importantly, we found that late EAs are associated with less positive correlation between EA returns and post-EA returns than early and bundled EAs. Overall, these results suggest that by providing timely sales information, monthly sales disclosures improve the information environment.
Top Management Team Fault Lines and Stock Price Crash Risk: Evidence from China
Authors: Huang Jingjuan , Zhu Bo 
Published: November 2023

Synopsis The research problem This study examined whether and how top management team (TMT) fault lines formed by diversity and division affect stock price crash risk (hereafter, crash risk). Motivation Prior studies have documented how a single characteristic or the demographic diversity of managers affects real economic activities. However, TMT fault lines, formed by the structure of executives’ demographic diversity, remain untapped in crash risk research. Given the potential monopoly of the TMT on information, it is important to determine whether TMT fault lines influence the distribution of bad news. This study therefore explored how TMT fault lines reduce crash risk through the private leakage of bad news by subgroups and the moderating role of analysts in this process. The test hypotheses We hypothesized that firms with a strong TMT fault line have low stock price crash risk. Moreover, subgroups divided by TMT fault lines have a greater chance of leaking bad news when firms are followed by more analysts, thereby reducing the stock price crash risk to a greater extent. Target population We examined 19,228 annual observations of Chinese publicly listed firms from 2008 to 2021. Adopted methodology We applied ordinary least squares (OLS) regression and moderation analysis to our study. Analyses We evaluated the microgovernance factors affecting crash risk from a novel perspective — internal TMT conflict. First, we performed regression analysis on a sample of Chinese publicly listed firms to determine whether TMT fault lines reduce crash risk and the effect of analysts on this relationship. Second, we performed cross-sectional variation tests for the main regression. Finally, we investigated the effect of a CEO-CFO coalition on crash risk, given that the unequal status of subgroups may reduce the monitoring capacity of any subgroup in a weaker position. Findings We found that TMT task-related fault lines are negatively associated with crash risk and positively moderated by analysts. Meanwhile, the TMT biodemographic fault lines do not have a significant influence on crash risk. We also demonstrated that the monitoring effect of TMT task-related fault lines is stronger when external governance is weaker. Finally, additional analysis implies that the monitoring effect of a CEO-CFO coalition fault line remains effective, but this effect is weaker.