bluuebunny/crossref_metadata_2025_split huggingface dataset:
The evolution of mini-chromosomes in the fungal genus
Colletotrichum
Authors: Wang Haoming , Huang Rong , Ren Jingyi , Tang Lihua , Huang Suiping , Chen Xiaolin , Fan Jun , Li Bintao , Wang Qinhu , Hsiang Tom , Liu Huiquan , Li Qili 
Published: June 2023

ABSTRACT

Anthracnose diseases caused by
Colletotrichum
species are among the most common fungal diseases. These symptoms typically manifest as dark, sunken lesions on leaves, stems, and fruit. In China, mango anthracnose seriously affects fruit yield and quality. Genome sequencing of several species shows the presence of mini-chromosomes. These are thought to contribute to virulence, but their formation and activity remain to be fully elucidated. Here, we assembled 17
Colletotrichum
genomes (16 isolated from mango plus one from persimmon) through PacBio long-read sequencing. Half of the assembled scaffolds had telomeric repeats at both ends indicating full-length chromosomes. Based on comparative genomics analysis at interspecies and intraspecies levels, we identified extensive chromosomal rearrangements events. We analyzed mini-chromosomes of
Colletotrichum
spp. and found large variation among close relatives. In
C. fructicola
, homology between core chromosomes and mini-chromosomes suggested that some mini-chromosomes were generated by recombination of core chromosomes. In
C. musae
GZ23-3, we found 26 horizontally transferred genes arranged in clusters on mini-chromosomes. In
C. asianum
FJ11-1, several potential pathogenesis-related genes on mini-chromosomes were upregulated, especially in strains with highly pathogenic phenotypes. Mutants of these upregulated genes showed obvious defects in virulence. Our findings provide insights into the evolution and potential relationships to virulence associated with mini-chromosomes.

IMPORTANCE

Colletotrichum
is a cosmopolitan fungal genus that seriously affects fruit yield and quality of many plant species. Mini-chromosomes have been found to be related to virulence in
Colletotrichum
. Further examination of mini-chromosomes can help us elucidate some pathogenic mechanisms of
Colletotrichum
. In this study, we generated novel assemblies of several
Colletotrichum
strains. Comparative genomic analyses within and between
Colletotrichum
species were conducted. We then identified mini-chromosomes in our sequenced strains systematically. The characteristics and generation of mini-chromosomes were investigated. Transcriptome analysis and gene knockout revealed pathogenesis-related genes located on mini-chromosomes of
C. asianum
FJ11-1. This study represents the most comprehensive investigation of chromosome evolution and potential pathogenicity of mini-chromosomes in the
Colletotrichum
genus.
Spatial organization and proteome of a dual-species cyanobacterial biofilm alter among N
2
-fixing and non-fixing conditions
Authors: Bozan Mahir , Schmidt Matthias , Musat Niculina , Schmid Andreas , Adrian Lorenz , Bühler Katja 
Published: June 2023

ABSTRACT

Many disciplines have become increasingly interested in cyanobacteria, due to their ability to fix CO
2
while using water and sunlight as electron and energy sources. Further, several species of cyanobacteria are also capable of fixing molecular nitrogen, making them independent of the addition of nitrate or ammonia. Thereby they hold huge potential as sustainable biocatalysts. Here, we look into a dual-species biofilm consisting of filamentous diazotrophic cyanobacteria
Tolypothrix
sp. PCC 7712 and heterotrophic bacteria
Pseudomonas taiwanensis
VLB 120 growing in a capillary biofilm reactor. Such systems have been reported to enable high cell densities continuous process operation. By combining confocal laser scanning and helium-ion microscopy with a proteomics approach, we examined these organisms’ interactions under two nitrogen-feeding strategies: N
2
-fixing and nitrate assimilation. Not only did
Pseudomonas
facilitate the biofilm formation by forming a carpet layer on the surface area but also did N
2
-fixing biofilms show greater attachment to the surface.
Pseudomonas
proteins related to surface and cell attachments were observed in N
2
-fixing biofilms in particular. Furthermore, co-localized biofilm cells displayed a resilient response to extra shear forces induced by segmented media/air flows. This study highlights the role of
Pseudomonas
in the initial attachment process, as well as the effects of different nitrogen-feeding strategies and operation regimes on biofilm composition and growth.

IMPORTANCE

Cyanobacteria are highly interesting microorganisms due to their ability to synthesize sugars from CO
2
while using water and sunlight as electron and energy sources. Further, many species are also capable of utilizing molecular nitrogen, making them independent of artificial fertilizers. In this study, such organisms are cultivated in a technical system, which enables them to attach to the reactor surface, and form three-dimensional structures termed biofilms. Biofilms achieve extraordinarily high cell densities. Furthermore, this growth format allows for continuous processing, both being essential features in biotechnological process development. Understanding biofilm growth and the influence technical settings and media composition have on biofilm maturation and stability are crucial for reaction and reactor design. These findings will help to open up these fascinating organisms for applications as sustainable, resource-efficient industrial workhorses.
Risk of admission to hospital with arterial or venous thromboembolism among patients diagnosed in the ambulatory setting with covid-19 compared with influenza: retrospective cohort study
Authors: Lo Re Vincent , Dutcher Sarah K , Connolly John G , Perez-Vilar Silvia , Carbonari Dena M , DeFor Terese A , Djibo Djeneba Audrey , Harrington Laura B , Hou Laura , Hennessy Sean , Hubbard Rebecca A , Kempner Maria E , Kuntz Jennifer L , McMahill-Walraven Cheryl N , Mosley Jolene , Pawloski Pamala A , Petrone Andrew B , Pishko Allyson M , Rogers Driscoll Meighan , Steiner Claudia A , Zhou Yunping , Cocoros Noelle M 
Published: June 2023

ObjectiveTo measure the 90 day risk of arterial thromboembolism and venous thromboembolism among patients diagnosed with covid-19 in the ambulatory (ie, outpatient, emergency department, or institutional) setting during periods before and during covid-19 vaccine availability and compare results to patients with ambulatory diagnosed influenza.DesignRetrospective cohort study.SettingFour integrated health systems and two national health insurers in the US Food and Drug Administration's Sentinel System.ParticipantsPatients with ambulatory diagnosed covid-19 when vaccines were unavailable in the US (period 1, 1 April-30 November 2020; n=272 065) and when vaccines were available in the US (period 2, 1 December 2020-31 May 2021; n=342 103), and patients with ambulatory diagnosed influenza (1 October 2018-30 April 2019; n=118 618).Main outcome measuresArterial thromboembolism (hospital diagnosis of acute myocardial infarction or ischemic stroke) and venous thromboembolism (hospital diagnosis of acute deep venous thrombosis or pulmonary embolism) within 90 days after ambulatory covid-19 or influenza diagnosis. We developed propensity scores to account for differences between the cohorts and used weighted Cox regression to estimate adjusted hazard ratios of outcomes with 95% confidence intervals for covid-19 during periods 1 and 2 versus influenza.Results90 day absolute risk of arterial thromboembolism with covid-19 was 1.01% (95% confidence interval 0.97% to 1.05%) during period 1, 1.06% (1.03% to 1.10%) during period 2, and with influenza was 0.45% (0.41% to 0.49%). The risk of arterial thromboembolism was higher for patients with covid-19 during period 1 (adjusted hazard ratio 1.53 (95% confidence interval 1.38 to 1.69)) and period 2 (1.69 (1.53 to 1.86)) than for patients with influenza. 90 day absolute risk of venous thromboembolism with covid-19 was 0.73% (0.70% to 0.77%) during period 1, 0.88% (0.84 to 0.91%) during period 2, and with influenza was 0.18% (0.16% to 0.21%). Risk of venous thromboembolism was higher with covid-19 during period 1 (adjusted hazard ratio 2.86 (2.46 to 3.32)) and period 2 (3.56 (3.08 to 4.12)) than with influenza.ConclusionsPatients diagnosed with covid-19 in the ambulatory setting had a higher 90 day risk of admission to hospital with arterial thromboembolism and venous thromboembolism both before and after covid-19 vaccine availability compared with patients with influenza.
Evaluating residual anti-Xa levels following discontinuation of treatment-dose enoxaparin in patients presenting for elective surgery: a prospective observational trial
Authors: Henshaw Daryl S , Edwards Christopher J , Dobson Sean W , Jaffe Doug , Turner James D , Reynolds J Wells , Thompson Garrett R , Russell Greg , Weller Robert 
Published: June 2023

IntroductionPrior studies have demonstrated that patients presenting for elective surgery may have higher-than-expected residual anti-Xa level activity at or beyond 24 hours following their last treatment dose of enoxaparin. Given that 24 hours of abstinence is currently recommended by both European and American societies before the performance of neuraxial or deep anesthetic/analgesic procedures, determining the actual timeframe at which residual anti-Xa level activity reliably falls below 0.2 IU/mL, the lower limit of the target range for thromboprophylaxis, is critical.MethodsThis was a prospective observational trial. Consenting patients on treatment-dose enoxaparin were randomized to either a 24-hour group (last dose at 07:00 the day prior to surgery) or a 36-hour group (last dose at 19:00 2 days prior to surgery). On arrival for surgery, blood samples were obtained to assess residual anti-Xa level activity and renal function. The primary outcome was residual anti-Xa level activity following the last treatment dose of enoxaparin. Incorporating all patients, linear regression modeling was performed to predict the timepoint at which the level of anti-Xa activity reliably fell below 0.2 IU/mL.Results103 patients were analyzed. Time from the last dose at which residual anti-Xa activity fell below 0.2 IU/mL, based on the upper bound of the 95% CI, was 31.5 hours. No correlation overall between age, renal function, or sex was found.ConclusionResidual levels of anti-Xa activity do not reliably fall below 0.2 IU/mL 24 hours following discontinuation of treatment-dose enoxaparin. Therefore, current time-based guidelines are not conservative enough. Routine anti-Xa testing should be strongly considered, or current time-based guidelines should be reassessed.Trial registration numberNCT03296033.
National review of acute pain service utilization, models of care, and clinical practices within the Veterans Health Administration
Authors: Mahyar Lauren , Missair Andres , Buys Michael J , Kou Alex , Benedetti de Marrero Esther , Sandbrink Friedhelm , Matadial Christina M , Mariano Edward R 
Published: June 2023

IntroductionThe Veterans Health Administration (VHA) is the largest healthcare network in the USA and has been a national leader in opioid safety for acute pain management. However, detailed information on the availability and characteristics of acute pain services within its facilities is lacking. We designed this project to assess the current state of acute pain services within the VHA.MethodsA 50-question electronic survey developed by the VHA national acute pain medicine committee was emailed to anesthesiology service chiefs at 140 VHA surgical facilities within the USA. Data collected were analyzed by facility complexity level and service characteristics.ResultsOf the 140 VHA surgical facilities contacted, 84 (60%) completed the survey. Thirty-nine (46%) responding facilities had an acute pain service. The presence of an acute pain service was associated with higher facility complexity level designation. The most common staffing model was 2.0 full-time equivalents, which typically included at least one physician. Services performed most by formal acute pain programs included peripheral nerve catheters, inpatient consult services, and ward ketamine infusions.ConclusionsDespite widespread efforts to promote opioid safety and improve pain management, the availability of dedicated acute pain services within the VHA is not universal. Higher complexity programs are more likely to have acute pain services, which may reflect differential resource distribution, but the barriers to implementation have not yet been fully explored.
Quantum equations of motion and the geometrical imperative: relativistic
Authors: Henriksen R.N. 
Published: June 2023

We extract the square root of the Minkowski metric using Dirac/Clifford matrices. The resulting 4 × 4 operator dS that represents the square root can be used to transform four vectors between relatively moving observers. This effects the usual Lorentz transformation. In addition, it acts on a Dirac bi-spinor. The operator is essentially a Hamiltonian that can be used to write an equation of motion for a relativistic spinor. This turns out to be the Dirac equation for electrons in standard form. We believe that it is a new approach to familiar results.
Assessment of Employability Skills of Technical-Vocational Education and Training (TVET) Graduates: Basis for an Enhancement Program
Authors: Mariano Rayhanah P. , Tantoco Luzviminda F. 
Published: June 2023

The study aims to determine the employability skills of Technical-Vocational Education and Training Graduates of Valenzuela City Polytechnic College.
This study was carried out to 423 graduates of TVET using convenience sampling and forty-five (45) employers who were selected purposively in the City of Valenzuela. The respondents had completed the TVET program. A survey questionnaire, document analysis and an interview guide were used. Frequency, percentage, and weighted mean were utilized in the statistical analysis and handling of the data.
Among 423 TVET graduates of ValPoly from 2015 to 2019, majority are employed which had an employment rate of 87.94 percent, compared to a rate of 12.06 percent for those who were unemployed. Carpentry obtained the highest employment rate while the bread and pastry production got the lowest employment rate. The year 2019 also has the highest rate while respondents who graduated in 2016 have the lowest employment rate.
Half of the employed graduates acquired a "regular status". Despite the skills mismatch, graduates have managed to seek employment related to their training right after graduation. Communication skills is the most useful skill in the workplace.
ValPoly has provided comprehensive and effective programs and provisions that enhance graduates' employability skills. TVET graduates employed were assessed as highly competent by their employers. Several factors that facilitate the acquisition of employment. A proposed enhancement program for the employability skills of TVET graduates is formulated based on findings of this study to ensure that all graduates will be equipped with skills for employment.
Characteristics and Prognosis of Patients With Hypertensive Encephalopathy: A French Nationwide Cohort Study
Authors: Halimi Jean-Michel , de Fréminville Jean-Baptiste , Gatault Philippe , Bisson Arnaud , Sautenet Bénédicte , Maisons Valentin , Vigny Pascal , Angoulvant Denis , Fauchier Laurent 
Published: June 2023

BACKGROUND:
Hypertensive encephalopathy (HE) constitutes a serious condition, usually observed in patients with long-lasting hypertension. Hypertension-associated HE is sometimes differentiated from the stroke-associated hypertensive emergency. Whether prognosis of hypertension-associated and stroke-associated HE is different is unclear.

METHODS:
Characteristics and prognosis of HE were assessed in this nationwide retrospective cohort study in all patients with an administrative code of HE compared with age-, sex- and year of inclusion-matched controls admitted to French hospitals during the 2014 to 2022 period.

RESULTS:
HE was identified in 7769 patients. Chronic kidney disease (19.3%), coronary artery disease (13.8%), diabetes (22.1%), and ischemic stroke (5.2%) were frequent but thrombotic microangiopathy, hemolytic-uremic syndrome, systemic sclerosis or renal infarction were <1%. HE prognosis was poor (death: 10.4%/y, heart failure: 8.6%/y, end-stage kidney disease: 9.0%/y, ischemic stroke: 3.6%/y, hemorrhagic stroke: 1.6%/y, dementia: 4.1%/y). The risk of death was increased to a similar extent in patients with HE, regardless of the presence of known hypertension or concomitant stroke (versus patients without HE). Among patients with HE, known hypertension was significantly associated with increased risks of ischemic stroke, hemorrhagic stroke, heart failure, vascular dementia, and all-cause dementia and to a lesser extent with chronic dialysis in multivariable analyses including adjustment on concomitant stroke.

CONCLUSIONS:
HE remains a considerable health burden and is associated with a poor prognosis. The distinction between hypertension- versus stroke-associated HE is relevant as these 2 situations convey different risks of stroke, heart failure, vascular dementia, and end-stage kidney disease.
Analysis of RNA-Seq data using self-supervised learning for vital status prediction of colorectal cancer patients
Authors: Padegal Girivinay , Rao Murali Krishna , Boggaram Ravishankar Om Amitesh , Acharya Sathwik , Athri Prashanth , Srinivasa Gowri 
Published: June 2023

Abstract
Background
RNA sequencing (RNA-Seq) is a technique that utilises the capabilities of next-generation sequencing to study a cellular transcriptome i.e., to determine the amount of RNA at a given time for a given biological sample. The advancement of RNA-Seq technology has resulted in a large volume of gene expression data for analysis.

Results
Our computational model (built on top of TabNet) is first pretrained on an unlabelled dataset of multiple types of adenomas and adenocarcinomas and later fine-tuned on the labelled dataset, showing promising results in the context of the estimation of the vital status of colorectal cancer patients. We achieve a final cross-validated (ROC-AUC) Score of 0.88 by using multiple modalities of data.

Conclusion
The results of this study demonstrate that self-supervised learning methods pretrained on a vast corpus of unlabelled data outperform traditional supervised learning methods such as XGBoost, Neural Networks, and Decision Trees that have been prevalent in the tabular domain. The results of this study are further boosted by the inclusion of multiple modalities of data pertaining to the patients in question. We find that genes such as RBM3, GSPT1, MAD2L1, and others important to the computation model’s prediction task obtained through model interpretability corroborate with pathological evidence in current literature.
Surface wax in the ancestral grapevine Vitis sylvestris correlate with partial resistance to Powdery Mildew
Authors: Ge Xinshuang , Hetzer Birgit , Tisch Christine , Kortekamp Andreas , Nick Peter 
Published: June 2023

Abstract
Background
Powdery Mildew of Grapevine belongs to the major diseases in viticulture and requires intensive use of fungicides. Genetic introgression of resistance factors from wild grapes from North America and, recently, China, has been successful, but wine made from those varieties is still confronted with low consumer acceptance, due to differences in taste.

Results
The current work explores the potential of Vitis vinifera sylvestris, the wild ancestor of domesticated Grapevine, with respect to containing Erysiphe necator, the causative agent of Powdery Mildew. Making use of a germplasm collection comprising the entire genetic variability remaining in Germany, we show that there is considerable genetic variation in the formation of leaf surface waxes exceeding wax formation in commercial varieties.

Conclusions
High wax formation correlates with reduced susceptibility to controlled infection with E. necator linked with perturbations of appressoria formation. We propose V. vinifera sylvestris as novel source for resistance breeding since it is genetically much closer to domesticated grapevine than the hitherto used sources from beyond the species barrier.
Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications
Authors: Zhao Yu-Juan , Liu Jian , Yin Gen-Shen , Gong Xun 
Published: June 2023

Abstract
Background
Ceratostigma, a genus in the Plumbaginaceae, is an ecologically dominant group of shrubs, subshrub and herb mainly distributed in Qinghai-Tibet Plateau and North China. Ceratostigma has been the focal group in several studies, owing to their importance in economic and ecological value and unique breeding styles. Despite this, the genome information is limited and interspecific relationships within the genus Cerotastigma remains unexplored. Here we sequenced, assembled and characterized the 14 plastomes of five species, and conducted phylogenetic analyses of Cerotastigma using plastomes and nuclear ribosomal DNA (nrDNA) data.

Results
Fourteen Cerotastigma plastomes possess typical quadripartite structures with lengths from 164,076 to 168,355 bp that consist of a large single copy, a small single copy and a pair of inverted repeats, and contain 127–128 genes, including 82–83 protein coding genes, 37 transfer RNAs and eight ribosomal RNAs. All plastomes are highly conservative and similar in gene order, simple sequence repeats (SSRs), long repeat repeats and codon usage patterns, but some structural variations in the border of single copy and inverted repeats. Mutation hotspots in coding (Pi values > 0.01: matK, ycf3, rps11, rps3, rpl22 and ndhF) and non-coding regions (Pi values > 0.02: trnH-psbA, rps16-trnQ, ndhF-rpl32 and rpl32-trnL) were identified among plastid genomes that could be served as potential molecular markers for species delimitation and genetic variation studies in Cerotastigma. Gene selective pressure analysis showed that most protein-coding genes have been under purifying selection except two genes. Phylogenetic analyses based on whole plastomes and nrDNA strongly support that the five species formed a monophyletic clade. Moreover, interspecific delimitation was well resolved except C. minus, individuals of which clustered into two main clades corresponding to their geographic distributions. The topology inferred from the nrDNA dataset was not congruent with the tree derived from the analyses of the plastid dataset.

Conclusion
These findings represent the first important step in elucidating plastome evolution in this widespread distribution genus Cerotastigma in the Qinghai-Tibet Plateau. The detailed information could provide a valuable resource for understanding the molecular dynamics and phylogenetic relationship in the family Plumbaginaceae. Lineage genetic divergence within C. minus was perhaps promoted by geographic barriers in the Himalaya and Hengduan Mountains region, but introgression or hybridization could not be completely excluded.