bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete hybrid genome assembly of
Mannheimia haemolytica
serotype A2 strain D95 isolated from ovine lung
Authors: Goldkamp Anna K. , Menghwar Harish , Dassanayake Rohana P. , Tatum Fred M. , Briggs Robert E. , Casas Eduardo 
Published: October 2024

ABSTRACT

Mannheimia haemolytica
is a major bacterial pathogen associated with broncho- and fibrinous pneumonia in ruminants. Here, we report the complete genome sequence of an isolate of serotype A2
M. haemolytica
(D95) recovered from a pneumonic ovine lung. The D95 genome has a size of 2.7 Mb and contains 2,720 genes.
Draft genome of
Aeromonas veronii
DFR01, the inactivated bacterial agent in a fish oral vaccine against motile aeromonad septicemia
Authors: Argayosa Anacleto M. , Gloria Paul Christian T. , Argayosa Vina B. , Santos Mary Nia M. 
Published: October 2024

ABSTRACT

Aeromonas veronii
DFR01 was isolated from Nile tilapia (
Oreochromis niloticus
) infected with motile aeromonad septicemia and has been developed as an oral vaccine. We report a 4.538-Mb draft genome with 99.4% BUSCO and 98.85% CheckM completeness.
Complete genome sequence of
Glycocaulis abyssi
type strain LMG 27140, a prosthecate bacterium isolated from an abyssal hydrothermal vent
Authors: LaSarre Breah , Kierstead Eva M. , Randich Amelia M. 
Published: October 2024

ABSTRACT

Glycocaulis abyssi
is a dimorphic, prosthecate member of the family
Maricaulaceae
, order Caulobacterales, in the class Alphaproteobacteria, originally isolated from an abyssal hydrothermal vent. Here, we report the complete genome sequence of type strain LMG 27140
T
(MCS33
T
) obtained using Oxford Nanopore technology.
Direct genome sequencing of respiratory viruses from low viral load clinical specimens using the target capture sequencing technology
Authors: Takemae Nobuhiro , Kuba Yumani , Oba Kunihiro , Kageyama Tsutomu 
Published: October 2024

ABSTRACT

The use of metagenomic next-generation sequencing technology to obtain complete viral genome sequences directly from clinical samples with low viral load remains challenging—especially in the case of respiratory viruses—due to the low copy number of viral versus host genomes. To overcome this limitation, target capture sequencing for the enrichment of specific genomes has been developed and applied for direct genome sequencing of viruses. However, as the efficiency of enrichment varies depending on the probes, the type of clinical sample, etc., validation is essential before target capture sequencing can be applied to clinical diagnostics. In this study, we evaluated the utility of target capture sequencing with a comprehensive viral probe panel for clinical respiratory specimens collected from patients diagnosed with SARS-CoV-2 or influenza type A. We focused on clinical specimens containing low copy numbers of viral genomes. Target capture sequencing yielded approximately 180- and 2,000-fold higher read counts of SARS-CoV-2 and influenza A virus, respectively, than metagenomic sequencing when the RNA extracted from specimens contained 59.3 copies/µL of SARS-CoV-2 or 625.1 copies/µL of influenza A virus. In addition, the target capture sequencing identified sequence reads in all SARS-CoV-2- or influenza type A-positive specimens with <26 RNA copies/µL, some of which also yielded >70% of the full-length genomes of SARS-CoV-2 or influenza A virus. Furthermore, the target capture sequencing using comprehensive probes identified co-infections with viruses other than SARS-CoV-2, suggesting that this approach will not only detect a wide range of viruses but also contribute to epidemiological studies.

IMPORTANCE
Target capture sequencing has been developed and applied for direct genome sequencing of viruses in clinical specimens to overcome the low detection sensitivity of metagenomic next-generation sequencing. In this study, we evaluated the utility of target capture sequencing with a comprehensive viral probe panel for clinical respiratory specimens collected from patients diagnosed with SARS-CoV-2 or influenza type A, focusing on clinical specimens containing low copy numbers of viral genomes. Our results showed that the target capture sequencing yielded dramatically higher read counts than metagenomic sequencing for both viruses. Furthermore, the target capture sequencing using comprehensive probes identified co-infections with other viruses, suggesting that this approach will not only detect a wide range of viruses but also contribute to epidemiological studies.
Is CMV DNAemia an early marker of CMV colitis in patients with active ulcerative colitis?
Authors: Melotti Laura , Rinaldi Matteo , Salice Marco , Dussias Nikolas K. , Vanigli Nicholas , Calabrese Carlo , Scaioli Eleonora , Gabrielli Liliana , Lazzarotto Tiziana , Rosini Francesca , Viale Pierluigi , Gionchetti Paolo , Giannella Maddalena , Rizzello Fernando 
Published: October 2024

ABSTRACT

Cytomegalovirus (CMV) colitis is a serious concern worsening the prognosis of patients with ulcerative colitis (UC). We aimed to assess risk factors and prognostic impact of CMV colitis in patients with moderate-to-severe UC flare. We conducted a retrospective, observational, single-center study. Consecutive adult patients hospitalized for moderate-to-severe UC from January 2020 to June 2023 were included. The primary endpoint was a diagnosis of CMV-colitis according to immunohistochemistry on tissue biopsies. The secondary endpoint was the need for colectomy within 30 days. Overall, 135 patients were included. CMV colitis was diagnosed in
n
= 37 (27.4%):
n
= 19 (51.4%) endoscopically, the remaining on surgical specimens. Of them,
n
= 23 (62.2%) had positive CMV-DNAemia with a median value of 1,008 cp/mL (interquartile range 318–2,980). Differences between the two groups (CMV colitis vs non-CMV) included age (60 vs 41 years,
P
= 0.004), Charlson Comorbidity Index (1 vs 0,
P
= 0.003), steroid refractoriness (86.5% vs 62.2%,
P
= 0.007), and positive CMV-DNAemia (62.2% vs 10.1%,
P
< 0.001). At multivariable analysis, steroid-refractory disease, Charlson Comorbidity Index, and CMV-DNAemia were associated with CMV colitis. Overall,
n
= 54 (39.7%) patients underwent colectomy, and this was significantly more common in patients with CMV colitis vs non-CMV group (54.1% vs 34.4%,
P
= 0.049). Kaplan-Meier showed that antiviral therapy seems to have a relevant impact on colectomy (
P
< 0.001). CMV-DNA blood detection is independently associated with CMV-positive refractory UC. Since CMV colitis may increase the risk of colectomy and antiviral treatment seems to reduce such risk, prospective studies are needed to confirm the role of CMV-DNA blood detection to early diagnose CMV colitis.

IMPORTANCE
Cytomegalovirus (CMV) colonic reactivation worsens the prognosis of patients with active ulcerative colitis. Blood CMV-DNA reactivation is strongly associated with CMV colitis. Prompt diagnosis and treatment of CMV colitis can avoid surgery in most cases.
The
Streptococcus agalactiae
LytSR two-component regulatory system promotes vaginal colonization and virulence
in vivo
Authors: AlQadeeb Hajar , Baltazar Murielle , Cazares Adrian , Poonpanichakul Tiraput , Kjos Morten , French Neil , Kadioglu Aras , O’Brien Marie 
Published: October 2024

ABSTRACT

Streptococcus agalactiae
(or group B
Streptococcus
, GBS) is a leading cause of neonatal sepsis and meningitis globally. To sense and respond to variations in its environment, GBS possesses multiple two-component regulatory systems (TCSs), such as LytSR. Here, we aimed to investigate the role of LytSR in GBS pathogenicity. We generated an isogenic
lytS
knockout mutant in a clinical GBS isolate and used a combination of phenotypic
in vitro
assays and
in vivo
murine models to investigate the contribution of
lytS
to the colonization and invasive properties of GBS. Deletion of the
lytS
gene in the GBS chromosome resulted in significantly higher survival rates in mice during sepsis, accompanied by reduced bacterial loads in blood, lung, spleen, kidney, and brain tissues compared to infection with the wild-type strain. In a mouse model of GBS vaginal colonization, we also observed that the
lytS
knockout mutant was cleared more readily from the vaginal tract compared to its wild-type counterpart. Interestingly, lower levels of proinflammatory cytokines were found in the serum of mice infected with the
lytS
mutant. Our results demonstrate that the LytSR TCS plays a key role in GBS tissue invasion and pathogenesis, and persistence of mucosal colonization.

IMPORTANCE

Streptococcus agalactiae (
group B
Streptococcus,
or GBS) is a common commensal of the female urogenital tract and one of WHO’s priority pathogens. The bacterium has evolved mechanisms to adapt and survive in its host, many of which are regulated via two-component signal transduction systems (TCSs); however, the exact contributions of TCSs toward GBS pathogenicity remain largely obscure. We have constructed a TCS
lytS-
deficient mutant in a CC-17 hypervirulent GBS clinical isolate. Using murine models, we showed that LytSR regulatory system is essential for vaginal colonization via promoting biofilm production. We also observed that
lytS
deficiency led to significantly attenuated virulence properties and lower levels of proinflammatory cytokines in blood. Our findings are of significant importance in that they unveil a previously unreported role for LytSR in GBS and pave the way toward a better understanding of its ability to transition from an innocuous commensal to a deadly pathogen.
Redox Status and Protein Glutathionylation in Binase-Treated HPV16-Positive SiHa Carcinoma Cells
Authors: Nadyrova A. I. , Petrushanko I. Y. , Mitkevich V. A. , Ilinskaya O. N. 
Published: October 2024

Abstract
Human papillomavirus type 16 (HPV16) belongs to viruses of the high-risk type and is associated by overexpression of E6 and E7 oncoproteins, which determine the oncogenic properties of the virus, such as immortalization and malignant transformation of proliferating epithelial cells. The biogenesis of redox-sensitive proteins E6 and E7 at the early stages of viral infection leads to blocking of the cell antioxidant defense system and ubiquintin-dependent degradation of p53 and Rb tumor suppressors. Maintaining high rates of tumor cell proliferation contributes to an increase in the level of reactive oxygen species (ROS) and a shift in the redox balance towards oxidative processes. Reduced glutathione (GSH) provides antioxidant protection to tumor cells through S-glutathionylation of thiol groups of redox-sensitive proteins, which leads to the appearance of multidrug-resistant forms of cancer. In this regard, drugs restoring redox balance and increasing susceptibility to antitumor therapy are of particular importance. We have established that, Bacillus pumilus RNase (binase) modulates the redox-dependent regulatory mechanisms that ensure tumor cell resistance to apoptosis in HPV-16-positive SiHa cells of cervical squamous cell carcinoma,. Binase in nontoxic concentrations initiates a number of pre-apoptogenic changes, i.e., decreases ROS and reduced glutathione (GSH) levels, suppresses the expression of the E6 oncoprotein, activates the expression of the p53 tumor suppressor, and reduces the mitochondrial potential of tumor cells. Binase-induced disruption of the integrity of the mitochondrial membrane is a signal for activation of the mitochondrial apoptosis pathway.
Prevalence of risky sexual behaviour and its associated factors among youths of Pokhara metropolitan city, Nepal: a cross-sectional study
Authors: Wagle Aakriti , Karki Khem B 
Published: October 2024

IntroductionRisky sexual behaviour, which puts young people at greater risk of acquiring HIV AIDS and sexually transmitted infection, is a significant public health concern all around the world. In 2020, 15% of ever reported HIV positive cases were youths in Nepal. This study aimed to estimate the prevalence of risky sexual behaviour and its associated factors among youths of Pokhara metropolitan city.MethodologyA cross-sectional study was done. The study population was youths aged 15–24 who were currently studying in grades 11/12 or at the bachelor level. The sample size was 850, interviewed in two strata (male and female). A multistage cluster sampling technique was used. A self-administered, structured questionnaire was used to obtain information. Bivariate (χ2test) and multivariate (logistic regression) analyses were performed to assess the statistically significant relationship between the dependent and independent variables.ResultsOverall, nearly a third (31%) respondents ever had sexual intercourse. Similarly, the overall prevalence of risky sexual behaviour was 18.6% (95% CI=16% to 21.2%), while the prevalence among sexually active respondents was 60% (95% CI=53.7% to 65.5%). The prevalence varied greatly among two sexes where 72% male and 31% female were involved in risky sexual behaviour. The logistic regression analysis showed that females were 72% (AOR=0.28, 95% CI=0.12 to 0.69) less likely than males and youths aged 20–24 were 72% (AOR=0.28, 95% CI=0.13 to 0.57) less likely than adolescents aged 15–19 to engage in risky sexual behaviour. Similarly, in regard to caste, Janajatis were almost six times (AOR=5.56, 95% CI=2.47 to 12.5) and Dalits/Madhesi/others were almost two times more likely to involve in risky sexual behaviour than Brahmin/Chhetri.ConclusionThis study shows a significantly higher prevalence of risky sexual behaviour among adolescents, males and Janajatis than their counterparts. Hence, youths should be educated and empowered to practice safe sexual behaviour through appropriate educational and behaviour change interventions with a special focus on adolescents, males and Janajatis.
Examining associations between social vulnerability and maternal morbidity among a multicentre cohort of pregnancies complicated by placenta accreta spectrum disorder in New York City
Authors: Tavella Nicola Francesco , Rosenberg Henri Mitchell , Mills Alexandra , Owens Thomas , Brustman Lois , Doulaveris Georgios , Haberman Shoshana , Limaye Meghana , Janevic Teresa , Jessel Rebecca Hope , Bianco Angela Teresa 
Published: October 2024

BackgroundPlacenta accreta spectrum (PAS) disorder is a source of severe obstetric morbidity and mortality worldwide. The objective of this paper was to evaluate the potential relationship between social vulnerability and severe maternal morbidity in a cohort of patients delivering a pregnancy complicated by PAS.MethodsA retrospective review of 323 deliveries at three academic medical institutions between January 2013 and June 2022 was included in the analyses. Patients were those with a histopathologically confirmed case of PAS. The composite morbidity outcome included such maternal complications as mechanical ventilation, injury to organs and transfusion of 4+units of red blood cells. Social vulnerability was measured by assigning subjects a value of the Childhood Opportunity Index based on their home zip code. Logistic regression models were employed and adjusted for potential confounders.Results73% of our sample experienced composite severe maternal morbidity at the time of their delivery. There were no statistically significant associations between social vulnerability and severe surgical morbidity, either as a composite or individually, within the multivariate regression models.ConclusionOur results do not support the hypothesis that social vulnerability is associated with severe maternal morbidity in deliveries complicated by PAS. The present study suggests that the relationship between social vulnerability and obstetrical surgical morbidity is more complicated than can be assessed by the present linear regression models.
Granulocyte colony-stimulating factor for stem cell mobilisation in acute myocardial infarction: a randomised controlled trial
Authors: Achilli Felice , Maggiolini Stefano , Madotto Fabiana , Bassetti Beatrice , Gentile Francesco , Maggioni Aldo Pietro , Colombo Gualtiero I , Pompilio Giulio 
Published: October 2024

BackgroundTo determine whether granulocyte colony-stimulating factor (G-CSF) improves clinical outcomes after large ST-elevation myocardial infarction (STEMI) when administered early in patients with left ventricular (LV) dysfunction after successful percutaneous coronary intervention (PCI).MethodsSTEM-AMI OUTCOME was designed as a prospective, multicentre, nationwide, randomised, open-label, phase III trial (ClinicalTrials.gov ID:NCT01969890) to demonstrate the efficacy and safety of early G-CSF administration in reducing 2-year cardiac mortality and morbidity in patients with STEMI with LV ejection fraction ≤45% after PCI. The primary outcome was a composite of all-cause death, recurrence of myocardial infarction and hospitalisation for heart failure. Due to low recruitment and event rates, the study was discontinued and did not achieve adequate statistical power to verify the hypothesis.ResultsPatients were randomly allocated to G-CSF (n=260) or standard of care (SOC; n=261). No difference was found in the composite primary outcome between study groups (HR 1.20; 95% CI 0.63 to 2.28). The 2-year mortality was 2.31% in the G-CSF and 2.68% in the control group (HR 0.88; 95% CI 0.29 to 2.60). Adverse events did not differ between the G-CSF (n=65) and SOC groups (n=58; OR 1.17; 95% CI 0.78 to 1.75). In post hoc analyses on the intervention group, we observed a trend towards fewer composite primary outcomes in patients with low bone marrow (BM) cell mobilisation (n=108) versus those with high mobilisation (n=152, with peak leucocyte count >50×109/L; HR 2.86; 95% CI 0.96 to 8.56). Primary outcomes were lower in patients with severe LV systolic dysfunction at discharge treated with G-CSF than in controls (interaction β±SE, −0.08±0.04; p=0.034).ConclusionsAlthough inconclusive, this is the largest trial in the field of cell-based cardiac repair after STEMI providing evidence of the tolerability and long-term safety of G-CSF treatment. The results prompt further studies to understand which patient can benefit most from BM cell mobilisation.Trial registration numberNCT01969890.
Symmetry analysis in multi scalar-torsion cosmological model with quantum description
Authors: Hembrom Shriton , Bhaumik Roshni , Dutta Sourav , Chakraborty Subenoy 
Published: October 2024

AbstractA detailed symmetry analysis has been done for the present multi scalar-torsion gravity theory in the background of flat Friedmann Lema$$\hat{\text{ i }}$$

i

^

tre Robertson Walker (FLRW) space-time. Not only the Noether symmetry from the invariance of the Lagrangian has been determined and associated conserved quantities are evaluated, but also the conformal symmetry of the physical metric (i.e., metric of the kinetic part) has been investigated to evaluate homothetic and killing vector fields. Finally, a through study of quantum cosmology both by canonical approach and by considering quantum trajectories has been presented.
Pentaquark molecular states with hidden bottom and double strangeness
Authors: Song Jing , Duan Man-Yu , Roca Luis , Oset Eulogio 
Published: October 2024

AbstractWe investigate the meson-baryon interaction in coupled channels with the quantum numbers of the pentaquarks $$P_{bss}$$

P

bss

and $$P_{bsss}$$

P

bsss

. The interaction is derived from an extension of the local hidden gauge approach to the heavy quark sector, which has demonstrated accurate results compared to experiments involving $$\Omega _{b}$$

Ω
b

, $$\Xi _{b}$$

Ξ
b

states, and pentaquarks $$P_{c}$$

P
c

and $$P_{cs}$$

P

cs

. In our study, we identify several molecular states with small decay widths within the chosen set of coupled channels. The spin-parity ($$J^P$$

J
P

) of these states is as follows: $$J^P={\frac{1}{2}}^-$$

J
P

=

1
2

-

for pseudoscalar-baryon ($${\frac{1}{2}}^+$$

1
2

+

) coupled channels, $$J^P={\frac{3}{2}}^-$$

J
P

=

3
2

-

for pseudoscalar-baryon ($${\frac{3}{2}}^+$$

3
2

+

) coupled channels, $$J^P={\frac{1}{2}}^-$$

J
P

=

1
2

-

and $${\frac{3}{2}}^-$$

3
2

-

for vector-baryon ($${\frac{1}{2}}^+$$

1
2

+

) coupled channels, and $$J^P={\frac{1}{2}}^-$$

J
P

=

1
2

-

, $${\frac{3}{2}}^-$$

3
2

-

, $${\frac{5}{2}}^-$$

5
2

-

for vector-baryon ($${\frac{3}{2}}^+$$

3
2

+

) coupled channels. We search for the poles of these states and evaluate their couplings to the different channels.
Clinical, Pathologic, and Genetic Spectrum of Collagen VI–Related Disorder in China—A Retrospective Observational Multicenter Study
Authors: Hu Chaoping , Shi Yiyun , Zhao Lei , Zhu Wenhua , Jiao Kexin , Yu Lifei , Li Xihua , Wang Yi 
Published: October 2024

Background: Collagen VI‐related disorder (COLVI‐RD) is one of the most common congenital muscular dystrophies. However, data is limited in China.Methods: We conducted a retrospective study at two tertiary centers. Clinical presentations, lab findings (including serum creatine kinase levels), muscle biopsy, and molecular test results for patients diagnosed with definite COLVI‐RD were collected.Results: A total of 82 patients were enrolled in the study, including 4 with early–severe Ullrich congenital muscular dystrophy (E–S UCMD) (4.8%), 45 with moderate–progressive Ullrich congenital muscular dystrophy (M–P UCMD, 54.9%), 19 with mild UCMD (23.2%), and 14 with Bethlem myopathy (BM, 17.1%). Feeding difficulty, DDH, and neurogenic damage were more common in E–S and M–P UCMD, while contracture of distal joints, atrophic scars, and hyperkeratosis was more prominent in mild UCMD and BM. Seventy patients harbored 64 pathogenic mutations in COLVI‐related genes: 28 patients in COL6A1 gene, 25 patients in the COL6A2 gene, and 17 patients in the COL6A3 gene, among which 33 mutations were novel. Missense and splicing mutations were predominant for COL6A1 and COL6A3 genes, which were mostly located in N‐terminus of THD, in a dominant pattern, while mutations in the COL6A2 gene were much more polymorphic, which spread throughout the whole length of the gene, in a dominant or recessive pattern. Immunofluorescence dual labeling of Collagen VI/IV in 44 patients showed complete deficiency of Collagen VI in 10 patients (22.7%), sarcolemma‐specific Collagen VI deficiency in 25 patients (56.8%), and normal Collagen VI staining in 9 patients (20.5%).Conclusion: Our study reported the largest cohort of COLVI‐RD in China, which showed M–P UCMD was the most common phenotype, followed by mild UCMD and BM. We identified 30 novel mutations and expanded the genetic spectrum. Missense and splicing mutations were predominant for COL6A1 and COL6A3 genes, while mutations in the COL6A2 gene were much more polymorphic. For severe phenotypes, most mutations are sporadic, while some are AD or recessive inherited. For milder phenotypes, sporadic and AD inherited were both common, while only 1 patient with recessive mutations was observed.