bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel pathogenic avipoxvirus infecting oriental turtle dove (
Streptopelia orientalis
) in China shows a high genomic and evolutionary proximity with the pigeon avipoxviruses isolated globally
Authors: He Lei , Zhang Yuhao , Jia Yanyan , Li Zedian , Li Jing , Shang Ke , Ding Ke , Yu Haotong , Sarker Subir 
Published: September 2023

ABSTRACT

Avipoxviruses are considered as significant viral pathogen infecting a wide range of domestic and wild bird species globally, yet the majority of avipoxviruses that infect the wild bird species remain uncharacterized and their genetic diversities remain unclear. In this study, we present a novel pathogenic avipoxvirus isolated from the cutaneous pox lesions of a wild oriental turtle dove (
Streptopelia orientalis
), tentatively named as turtle dovepox virus (TDPV). The avipoxvirus was isolated by using the chorioallantoic membranes of specific pathogen-free chicken embryos which showed characteristic focal pock lesions, followed by cytopathic effects in host cells infected with oriental turtle dovepox virus. An effort in sequencing the whole genome of the poxvirus using next-generation sequencing was given, and the first whole genome sequence of TDPV was obtained. The TDPV genome was 281,386 bp in length and contained 380 predicted open reading frames (ORFs). While 336 of the predicted ORFs showed homology to other characterized avipoxviruses, the other 44 ORFs were unique. Subsequent phylogenetic analyses showed that the novel TDPV shared the closest genetic evolutionary linkage with the avipoxviruses isolated from pigeon in South Africa and India, of which the TDPV genome had the highest sequence similarity (92.5%) with South African pigeonpox virus (FeP2). In conclusion, the sequenced TDPV is significantly different from any other avipoxviruses isolated from avian or other natural host species considering genomic architecture and observed sequence similarity index. Thus, it likely should be considered a separate species.

IMPORTANCE

Over the past few decades, avipoxviruses have been found in a number of wild bird species including the oriental turtle dove. However, there is no whole genome sequence information on avipoxviruses isolated from oriental turtle dove, leaving us unclear about the evolutionary linkage of avipoxviruses in oriental turtle dove and other wild bird species. Thus, we believe that our study makes a significant contribution because it is the first report of the whole genome sequence of TDPV isolated from a wild oriental turtle dove, which enriches the genomic information of the genus
Avipoxvirus
, furthermore, contributes to tracking the genetic evolution of avipoxviruses-infected oriental turtle dove species.
A large-scale phylogeny-guided analysis of pseudogenes in
Pseudomonas aeruginosa
bacterium
Authors: Cohen Nimrod , Veksler-Lublinsky Isana 
Published: September 2023

ABSTRACT

Pseudogenes, once considered "junk DNA" based on the incorrect assumption that the absence of full coding potential means a complete lack of functionality, have recently become a subject of significant interest in the scientific community. Concurrently, it is widely assumed that bacterial genomes are compact and have a high density of coding genes with little room for non-coding genes, including pseudogenes. A key aspect of genome annotation is the correct identification of genes and the distinction between coding genes and pseudogenes, as it directly impacts functional and comparative genomics studies. In this study, we analyzed the genomic data of 4,699 strains of the bacterium
Pseudomonas aeruginosa
(
P. aeruginosa
) as they exhibit high variability in the number of annotated pseudogenes. In particular, we looked for correlations between the number of pseudogenes and other genomic and meta-features of the strains. We identified clusters of orthologous genes and pseudogenes and compared cluster size distributions and length homogeneity within clusters. We then mapped and examined orthology relationships between genes and pseudogenes. Additionally, we generated a phylogenetic tree of the strains and found that phylogenetically related strains are more homogeneous in the number of pseudogenes and share a significant amount of pseudogenes. Finally, we delved into clusters of orthologous genes and pseudogenes and quantified their phylogenetic neighborhood, classifying pseudogenes into evolutionary preserved pseudogenes, mis-annotated pseudogenes, or pseudogenes formed by failed horizontal transfer events. This in-depth study provides important insights that can be incorporated into pseudogene annotation pipelines in the future.

IMPORTANCE
Accurate annotation of genes and pseudogenes is vital for comparative genomics analysis. Recent studies have shown that bacterial pseudogenes have an important role in regulatory processes and can provide insight into the evolutionary history of homologous genes or the genome as a whole. Due to pseudogenes’ nature as non-functional genes, there is no commonly accepted definition of a pseudogene, which poses difficulties in verifying the annotation through experimental methods and resolving discrepancies among different annotation techniques. Our study introduces an in-depth analysis of annotated genes and pseudogenes and insights that can be incorporated into improved pseudogene annotation pipelines in the future.
Gut microbiota-driven regulation of queen bee ovarian metabolism
Authors: Li Wan-Li , Huang Qi , Li Jia-Li , Wu Ping , Wei Bangrong , Li Xi-Jie , Tang Qi-He , Dong Zhi-Xiang , Xiong Jian , Tang Hong , Zhang Jun , Zhao Chong-Hui , Cao Zhe , Chen Yuan , Zhao Wen-zheng , Wang Kai , Guo Jun 
Published: September 2023

ABSTRACT

With the global prevalence of
Varroa
mites, more and more beekeepers resort to confining the queen bee in a queen cage to control mite infestation or to breed superior and robust queen bees. However, the impact of such practices on the queen bee remains largely unknown. Therefore, we subjected the queen bees to a 21-day egg-laying restriction treatment (from the egg stage to the emergence of adult worker bees) and analyzed the queen bees’ ovarian metabolites and gut microbiota after 21 days, aiming to assess the queen bees’ quality and assist beekeepers in better hive management. Our findings revealed a significant reduction in the relative expression levels of
Vg
and
Hex110
genes in the ovaries of egg laying-restricted queen bees compared to unrestricted egg-laying queens. The diversity of gut microbiota in the queen bee exhibited a notable decrease, accompanied by corresponding changes in the core bacteria of the microbial community, the relative abundance of
Lactobacillus
and
Bifidobacterium
increased from 22.34% to 53.14% (
P
= 0.01) and from 0.053% to 0.580% (
P
= 0.04), respectively. The relative abundance of
Bombella
decreased from 25.85% to 1.720% (
P
= 0.002). Following egg-laying restriction, the activity of the queen bee’s ovaries decreased, while the metabolism of glycerophospholipids remained or stored more lipid molecules, awaiting environmental changes for the queen bee to resume egg laying promptly. Furthermore, we observed that
Bombella
in the queen bee’s gut may regulate the queen’s ovarian metabolism through tryptophan metabolism. These findings provide novel insights into the interplay among queen egg laying, gut microbiota, and ovarian metabolism.

IMPORTANCE

With
Varroa
mite infestation, beekeepers often confine the queen bee in cages for control or breeding. However, the impact on the queen bee is largely unknown. We evaluated queen bee quality by restricting egg laying and analyzing ovarian metabolites and gut microbiota. In this study, we provided a comprehensive explanation of the expression of ovarian genes, the diversity of gut microbiota, and changes in ovarian metabolism in the queen bee. Through integrated analysis of the queen bee’s gut microbiota and ovarian metabolism, we discovered that the gut microbiota can regulate the queen bee’s ovarian metabolism. These findings provide valuable insights into the interplay among egg laying, gut microbiota, and the reproductive health of the queen bee. Understanding these relationships can contribute to the development of better strategies for
Varroa
mite control and queen bee breeding.
Synthetic seismic-stratigraphic interpretation from a sedimentological forward model in a pre-salt field in the Santos Basin
Authors: Benac Pedro , Faria Desiree Liechoscki de Paula , Maul Alexandre , Silva Cleverson Guizan 
Published: September 2023

Forward modelling of sedimentary systems is a method that simulates sedimentation processes over geological time to generate a set of facies distributed in a depositional space. The objective of using forward modelling in this work was to build a 3D facies model from which a synthetic seismic simulation was generated, and then to analyse the relation of seismic-stratigraphic interpretations with the knowledge of the
a priori
generated sedimentological model. This modelling methodology was applied in a pre-salt field in the Santos Basin, Brazilian offshore, focused on the Barra Velha Formation. The modelling parameters used were: (i) the initial surface of bathymetric depth; (ii) the lake-level variation; (iii) the subsidence map; and (iv) the deposition rates of the facies. Average-constant of acoustic impedance values were assigned to each facies and a synthetic seismic was obtained. With the facies and synthetic models available, it was possible to analyse: (i) the distribution of thicknesses and proportion of facies by region; (ii) the vertical stacking pattern and lateral facies variation; (iii) the Wheeler distance
×
time diagram; and (iv) the seismic reflector patterns through the seismic facies classification. Through these analyses it was possible to better understand the possibilities and limitations of seismic stratigraphy as an interpretation auxiliary tool in pre-salt carbonate environments.
New localities and sexual dichromatism in Blue-green eyed Spotted Cuscus Spilocuscus wilsoni Helgen et Flannery, 2004 (Mammalia: Marsupialia: Phalangeridae) from Biak Island, Indonesia
Authors: Yohanita Aksamina Maria , Widayati Kanthi Arum , Atmowidi Tri , Imai Hiroo , Suryobroto Bambang 
Published: September 2023

Spotted cuscuses are medium-sized tree-dwelling mammals native to tropical forests of Australo-Papua that primarily feed on fruits and leaves. They belong to the phalangerid genus Spilocuscus (Gray, 1862). The difference in pelage color between male and female Spilocuscus wilsoni has not yet been well described morphologically. In the present study, we describe the coat color of four S. wilsoni individuals: a male adult, a sub-adult male, a sub-adult female, and a juvenile female. Dorsal, lateral, and ventral body section images were captured on camera, and body weight & length, tail & ear length were measured. The adult male S. wilsoni had brown spot and blotch patterns on the dorsal and lateral regions, and the ventral region was plain beige. The sub-adult male had distinct spot patterns without blotches on the dorsal and lateral regions, while the ventral region was plain with a cream base color. The sub-adult female had a mottled pattern that blended with the base color, making a silvery appearance. The female juvenile was spotless throughout, with a foundation hue ranging from creamy to somewhat yellow.
Kukumseri: a home to Colchicum luteum Baker (Colchicaceae), a rare and endangered medicinal herb
Authors: Sharma Rajender Kumar 
Published: September 2023

Colchicum luteum Baker (Colchicaceae), an economically and medicinally important threatened medicinal herb has been poorly investigated for its distribution, propagation, and conservation. We observed very restricted distribution of the species in Lahaul, Himachal Pradesh. The species were found in two locations only (Mailing & Kukumseri).
Clinical Features and Outcomes Among Patients With Refractory Out-of-Hospital Cardiac Arrest and an Initial Shockable Rhythm
Authors: Zheng Wayne C. , Zheng Maye C. , Ho Felicia C.S. , Noaman Samer , Haji Kawa , Batchelor Riley J. , Hanson Laura B. , Bloom Jason E. , Shaw James A. , Yang Yang , Stub Dion , Cox Nicholas , Kaye David M. , Chan William 
Published: September 2023

BACKGROUND:
Clinical features among patients with refractory out-of-hospital cardiac arrest (OHCA) and initial shockable rhythms of ventricular fibrillation/pulseless ventricular tachycardia are not well-characterized.

METHODS:
We compared clinical characteristics and coronary angiographic findings between patients with refractory OHCA (incessant ventricular fibrillation/pulseless ventricular tachycardia after ≥3 direct-current shocks) and those without refractory OHCA.

RESULTS:

Between 2014 and 2018, a total of 204 patients with ventricular fibrillation/pulseless ventricular tachycardia OHCA (median age 62; males 78%) were divided into groups with (36%, 74/204) and without refractory arrest (64%, 130/204). Refractory OHCA patients had longer cardiopulmonary resuscitation (23 versus 15 minutes), more frequently required ≥450 mg amiodarone (34% versus 3.8%), and had cardiogenic shock (80% versus 55%) necessitating higher adrenaline dose (4.0 versus 1.0 mg) and higher rates of mechanical ventilation (92% versus 74%; all
P
<0.01). Of 167 patients (82%) selected for coronary angiography, 33% (n=55) had refractory OHCA (
P
=0.035). Significant coronary artery disease (≥1 major vessel with >70% stenosis) was present in >70% of patients. Refractory OHCA patients frequently had acute coronary occlusion (64% versus 47%), especially left circumflex (20% versus 6.4%) and graft vessel (7.3% versus 0.9%; all
P
<0.05) compared with those without refractory OHCA. Refractory OHCA group had higher in-hospital mortality (45% versus 30%,
P
=0.036) and greater new requirement for dialysis (18% versus 6.3%,
P
=0.011). After adjustment, refractory OHCA was associated with over 2-fold higher odds of in-hospital mortality (odds ratio, 2.28 [95% CI, 1.06–4.89];
P
=0.034).

CONCLUSIONS:
Refractory ventricular fibrillation/pulseless ventricular tachycardia OHCA was associated with more intensive resuscitation, higher rates of acute coronary occlusion, and poorer in-hospital outcomes, underscoring the need for future studies in this extreme-risk subgroup.
Nomogram for Predicting Risk of Cancer Therapy–Related Cardiac Dysfunction in Patients With Human Epidermal Growth Factor Receptor 2–Positive Breast Cancer
Authors: Yu Anthony F. , Lin I‐Hsin , Jorgensen Justine , Copeland‐Halperin Robert , Feldman Stephanie , Ibtida Ishmam , Assefa Amare , Johnson Michelle N. , Dang Chau T. , Liu Jennifer E. , Steingart Richard M. 
Published: September 2023

Background
Cancer therapy–related cardiac dysfunction (CTRCD) is an important treatment‐limiting toxicity for patients with human epidermal growth factor receptor 2 (HER2)–positive breast cancer that adversely affects cancer and cardiovascular outcomes. Easy‐to‐use tools that incorporate readily accessible clinical variables for individual estimation of CTRCD risk are needed.

Methods and Results
From 2004 to 2013, 1440 patients with stage I to III HER2‐positive breast cancer treated with trastuzumab‐based therapy were identified. A multivariable Cox proportional hazards model was constructed to identify risk factors for CTRCD and included the 1377 patients in whom data were complete. Nine clinical variables, including age, race, body mass index, left ventricular ejection fraction, systolic blood pressure, coronary artery disease, diabetes, arrhythmia, and anthracycline exposure were built into a nomogram estimating risk of CTRCD at 1 year. The nomogram was validated for calibration and discrimination using bootstrap resampling. A total of 177 CTRCD events occurred within 1 year of HER2‐targeted treatment. The nomogram for prediction of 1‐year CTRCD probability demonstrated good discrimination, with a concordance index of 0.687. The predicted and observed probabilities of CTRCD were similar, demonstrating good model calibration.

Conclusions
A nomogram composed of 9 readily accessible clinical variables provides an individualized 1‐year risk estimate of CTRCD among women with HER2‐positive breast cancer receiving HER2‐targeted therapy. This nomogram represents a simple‐to‐use tool for clinicians and patients that can inform clinical decision‐making on breast cancer treatment options, optimal frequency of cardiac surveillance, and role of cardioprotective strategies.
Misdiagnosis of Posterior Reversible Encephalopathy Syndrome and Reversible Cerebral Vasoconstriction Syndrome in the Emergency Department
Authors: Liberman Ava L. , Zhang Cenai , Parikh Neal S. , Salehi Omran Setareh , Navi Babak B. , Lappin Richard I. , Merkler Alexander E. , Kaiser Jed H. , Kamel Hooman 
Published: September 2023

Background
Cerebrovascular dysregulation syndromes, posterior reversible encephalopathy syndrome (PRES) and reversible cerebral vasoconstriction syndrome (RCVS), are challenging to diagnose because they are rare and require advanced neuroimaging for confirmation. We sought to estimate PRES/RCVS misdiagnosis in the emergency department and its associated factors.

Methods and Results

We conducted a retrospective cohort study of PRES/RCVS patients using administrative claims data from 11 states (2016–2018). We defined patients with a probable PRES/RCVS misdiagnosis as those with an emergency department visit for a neurological symptom resulting in discharge to home that occurred ≤14 days before PRES/RCVS hospitalization. Proportions of patients with probable misdiagnosis were calculated, characteristics of patients with and without probable misdiagnosis were compared, and regression analyses adjusted for demographics and comorbidities were performed to identify factors affecting probable misdiagnosis. We identified 4633 patients with PRES/RCVS. A total of 210 patients (4.53% [95% CI, 3.97–5.17]) had a probable preceding emergency department misdiagnosis; these patients were younger (mean age, 48 versus 54 years;
P
<0.001) and more often female (80.4% versus 69.3%;
P
<0.001). Misdiagnosed patients had fewer vascular risk factors except prior stroke (36.3% versus 24.2%;
P
<0.001) and more often had comorbid headache (84% versus 21.4%;
P
<0.001) and substance use disorder (48.8% versus 37.9%;
P
<0.001). Facility‐level factors associated with probable misdiagnosis included smaller facility, lacking a residency program (62.2% versus 73.7%;
P
<0.001), and not having on‐site neurological services (75.7% versus 84.3%;
P
<0.001). Probable misdiagnosis was not associated with higher likelihood of stroke or subarachnoid hemorrhage during PRES/RCVS hospitalization.

Conclusions
Probable emergency department misdiagnosis occurred in ≈1 of every 20 patients with PRES/RCVS in a large, multistate cohort.
Prognostic Value of Patient‐Reported Outcomes in Predicting Long‐Term Mortality After Transcatheter Aortic Valve Replacement
Authors: Alarouri Hasan S. , El Shaer Ahmed , Ponce Alejandra Chavez , Mahayni Abdulah , Sulaiman Samian , Samimi Sahar , Alkhouli Mohamad 
Published: September 2023

Background
Patient‐reported outcome measures have been shown to have important prognostic value after various cardiac interventions. We assessed the association between the change in Kansas City Cardiomyopathy Questionnaire 12 (KCCQ‐12) score after transcatheter aortic valve replacement and mortality.

Methods and Results

We included patients who underwent transcatheter aortic valve replacement at Mayo Clinic between February 2012 to June 2022 and who completed a KCCQ‐12 before and 30 to 45 days after the procedure. Patients were categorized into 3 groups: those who experienced significant (>+19 points; group 1), modest (1–19 points; group 2), and no (≤0 points; group 3) improvement. A total of 1124 patients were included: 60.8% men; 97.6% White. Mean age was 79.4±8.3 years, baseline KCCQ‐12 score was 53.9±24.5, and median Society of Thoracic Surgeons score was 4.9% (interquartile range, 3.1–8.0). At 45 days, the mean change in KCCQ‐12 score was 19±24 points; 46.3% (n=520) of patients had a significant improvement in their KCCQ‐12 score, while 33.4% (n=375) and 20.4% (n=229) had modest and no improvement, respectively. Median survival was higher in group 1 (5.7±0.2 years) compared with groups 2 and 3 (5.1±0.3 and 4.1±0.4 years, respectively;
P
<0.001). Compared with patients in group 1, those in groups 2 and 3 had higher long‐term risk‐adjusted mortality (adjusted hazard ratios, 1.54 [95% CI, 1.20–1.96], and 2.30 [95% CI, 1.74–3.04], respectively).

Conclusions
Patients who experience modest or no improvement in KCCQ‐12 score after transcatheter aortic valve replacement have substantially higher long‐term mortality. Delta KCCQ‐12 is a cost‐effective, efficient tool that can identify patients at increased risk of death at long‐term follow‐up post‐transcatheter aortic valve replacement.
Association of High‐Deductible Health Plans With Health Care Use and Costs for Patients With Cardiovascular Disease
Authors: Gupta Ravi , Yang Lin , Lewey Jennifer , Navathe Amol S. , Groeneveld Peter W. , Khatana Sameed Ahmed M. 
Published: September 2023

Background
By increasing cost sharing, high‐deductible health plans (HDHPs) aim to reduce low‐value health care use. The association of HDHPs with health care use and costs in patients with chronic cardiovascular disease is unknown.

Methods and Results
This longitudinal cohort study analyzed 57 690 privately insured patients, aged 18 to 64 years, from a large commercial claims database with chronic cardiovascular disease from 2011 to 2019. Health care entities in which all or most beneficiaries switched from being in a traditional plan to an HDHP were identified. A difference‐in‐differences design was used to account for differences between individuals who remained in traditional plans and those who switched to HDHPs and to assess changes in health care use and costs. Among the 934 individuals in the HDHP group and the 56 756 in the traditional plan group, switching to an HDHP was not associated with statistically significant changes in annual outpatient visits, hospitalizations, or emergency department visits (−8.3% [95% CI, −16.8 to 1.1], −28.5% [95% CI, −62.1 to 34.6], and 11.2% [95% CI, −20.9 to 56.5], respectively). Switching to an HDHP was associated with an increase of $921 (95% CI, $743–$1099) in out‐of‐pocket costs but no statistically significant difference in total health care costs.

Conclusions
Among commercially insured patients with chronic cardiovascular disease, switching to an HDHP was not associated with a change in health care use but was associated with an increase in out‐of‐pocket costs. Although health care use by individuals with chronic cardiovascular disease may not be sensitive to higher cost sharing associated with HDHP enrollment, there may be a significant increase in patients' financial burden.