bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morphological and molecular identification reveals a high diversity of Anopheles species in the forest region of the Cambodia–Laos border
Authors: Zhang Canglin , Luo Chunhai , Yang Rui , Yang Yaming , Guo Xiaofang , Deng Yan , Zhou Hongning , Zhang Yilong 
Published: March 2022

AbstractBackgroundTo develop an effective malaria vector intervention method in forested international border regions within the Greater Mekong Subregion (GMS), more in-depth studies should be conducted on localAnophelesspecies composition and bionomic features. There is a paucity of comprehensive surveys of biodiversity integrating morphological and molecular species identification conducted within the border of Laos and Cambodia.MethodsA total of 2394 adult mosquitoes were trapped in the Cambodia–Laos border region. We first performed morphological identification ofAnophelesmosquitoes and subsequently performed molecular identification using 412 recombinant DNA–internal transcribed spacer 2 (rDNA-ITS2) and 391 mitochondrial DNA–cytochrome c oxidase subunit 2 (mtDNA-COII) sequences. The molecular and morphological identification results were compared, and phylogenetic analysis of rDNA-ITS2 andmtDNA-COIIwas conducted for the sequence divergence among species.ResultsThirteen distinct species ofAnopheleswere molecularly identified in a 26,415 km2border region in Siem Pang (Cambodia) and Pathoomphone (Laos). According to the comparisons of morphological and molecular identity, the interpretation of local species composition for dominant species in the Cambodia–Laos border (An. dirus,An. maculatus,An. philippinensis,An. kochiandAn. sinensis) achieved the highest accuracy of morphological identification, from 98.37 to 100%. In contrast, the other species which were molecularly identified were less frequently identified correctly (0–58.3%) by morphological methods. The average rDNA-ITS2 andmtDNA-COIIinterspecific divergence was respectively 318 times and 15 times higher than their average intraspecific divergence. The barcoding gap ranged from 0.042 to 0.193 for rDNA-ITS2, and from 0.033 to 0.047 formtDNA-COII.ConclusionsThe Cambodia–Laos border hosts a high diversity ofAnophelesspecies. The morphological identification ofAnophelesspecies provides higher accuracy for dominant species than for other species. Molecular methods combined with morphological analysis to determine species composition, population dynamics and bionomic characteristics can facilitate a better understanding of the factors driving malaria transmission and the effects of interventions, and can aid in achieving the goal of eliminating malaria.Graphical Abstract
Canine microfilaraemia in some regions of Iran
Authors: Hosseini Seyed Hossein , Manshori-Ghaishghorshagh Fateme , Ramezani Mohammad , Nayebzadeh Hassan , Ahoo Mohammad Bagher , Eslamian Ahdieh , Soltani Minoo , Jamshidi Shahram , Bezerra-Santos Marcos Antonio , Jalousian Fatemeh , Sazmand Alireza , Otranto Domenico 
Published: March 2022

Abstract
Background
Dirofilaria immitis and Dirofilaria repens are vector-borne zoonotic parasites which affect mainly dogs and humans worldwide. In Iran, information about the distribution of those nematodes is scant in several regions. Therefore, we investigated the prevalence of these filarial parasites in stray dogs from five Iranian provinces where no information about these parasites is available.

Methods
Blood samples were collected from 344 stray dogs in five provinces of Iran (i.e. Mazandaran, Gilan, Esfahan, Qazvin and Loresan). The presence of microfilariae was assessed using direct smear, modified Knott’s test, molecular detection of filarial DNA (cox1 gene) and Wolbachia endosymbiont of parasitic nematodes (ftsZ gene) by conventional PCR (cPCR). All of the PCR products were sequenced and phylogenetic analysis was performed.

Results
In total, 75 dogs (21.8%) were found to be positive for D. immitis by cPCR. Infection was detected in all provinces, with the highest prevalence in Gilan province (22/28; 78.6%). Acanthocheilonema reconditum was diagnosed in five dogs (1.4%) from three provinces (i.e. Esfahan, Mazandaran, Gilan). Two dogs were infected with both parasites and three were only infected with A. reconditum. Dirofilaria repens infection was not found in the examined population. Representative sequences of the D. immitis cox1 gene from dogs from the northern provinces (Mazandaran, Gilan, Qazvin) were grouped together and distinctly separate from the ones from western and central provinces (Lorestan and Esfahan), suggesting that different nematode populations are present in the country.

Conclusion
The data reported herein fill existing gaps in knowledge about canine filarial infection in two Iranian provinces and record the highest prevalence of D. immitis ever reported in the country (i.e. 78.6%). A geographical review of the literature about Dirofilaria spp. and A. reconditum infections in dogs and humans has also been summarized, indicating that D. immitis and D. repens are distributed in 22 of 31 provinces in Iran, whereas A. reconditum is present in fewer regions. Effective control strategies are advocated for owned dogs, and a national program for the management of stray dogs is needed to minimize the risk of infection in animals and humans.

Graphical Abstract
Evaluating type and amount of dietary protein in relation to metabolic syndrome among Iranian adults: cross-sectional analysis of Fasa Persian cohort study
Authors: Jamshidi Ali , Farjam Mojtaba , Ekramzadeh Maryam , Homayounfar Reza 
Published: March 2022

Abstract
Background and aim
Metabolic syndrome is characterized by several conditions including abdominal obesity, dyslipidemia, impaired glucose levels, and hypertension; which all are directly associated with an increased risk of cardiovascular disease and type 2 diabetes mellitus. This study aimed to evaluate the association of the amount and source of dietary protein with the risk of metabolic syndrome and its components in adult men and women.

Material and method
This study was performed using Persian cohort data, Fasa branch, which included 3660 men and 5262 women. Individuals were divided into five groups for total dietary proteins, plant proteins, and animal proteins using the quintiles, and the odds of incidence for metabolic syndrome and each component was evaluated.

Results
A higher intake of total protein was associated with lower odds of having metabolic syndrome (OR: 0.24 95% CI 0.18–0.33, P-trend < 0.001 in men, OR: 0.42 95% CI 0.34–0.51, P-trend < 0.001 in women) and all of its components. men (OR: 0.35 95% CI 0.25–0.48, P-trend < 0.001) and women (OR: 0.41 95% CI 0.33–0.52, P-trend < 0.001) in the highest quintile of plant protein intake had a reduced prevalence of metabolic syndrome and its components. An increased animal protein intake was associated with a lower prevalence of metabolic syndrome (P-trend < 0.001), a declined risk of having elevated triglycerides (P-trend = 0.016) in men, and a reduced risk of having abdominal obesity in men (P-trend < 0.001) and women (P-trend < 0.001).

Conclusion
A higher consumption of total protein and plant protein was associated with a lower prevalence of metabolic syndrome and its components. Increased consumption of animal protein seemed to be related to a lower prevalence abdominal obesity. Also, only in men, animal protein was associated with decreased risk of having metabolic syndrome.
Bacterial microbiome of faecal samples of naked mole-rat collected from the toilet chamber
Authors: Chua Kah-Ooi , Fatima Iqra , Lau Yin Yin , Hong Kar Wai , Yin Wai-Fong , Mardaryev Andrei , Chan Kok-Gan , Chang Chien-Yi 
Published: March 2022

Abstract
Objective
The naked mole rats (NMRs, Heterocephalus glaber) are subterranean rodents that belong to the family Bathyergidae. They gained the attention of the scientific community for their exceptionally long lifespan of up to 30 years and have become an animal model of biomedical research on neurodegenerative diseases, aging and cancer. NMRs dig and survive in a maze of underground tunnels and chambers and demarcate toilet chambers for defecation and urination. Due to their coprophagic behaviours, we believed that the toilet chamber might play a role in maintaining optimal health of the NMRs. A 16S rRNA gene amplicon sequencing was performed to characterize the bacterial microbiome of faecal samples collected from the toilet chamber of a laboratory NMR colony.

Results
Four faecal samples were collected at different time points from the same toilet chamber of a laboratory NMR colony for analysis. The 16S rRNA gene amplicon sequencing revealed that bacterial phyla Firmicutes and Bacteroidetes were the dominant taxa in the bacterial microbiome of NMRs. The relative abundance of the bacterial taxa shifted substantially between time points, indicating a dynamic microbiome in the toilet chamber. The data provided an insight to the faecal microbiome of NMRs in the toilet chamber.
Giant anogenital tumor of Buschke–Löwenstein in a patient living with human immunodeficiency virus/acquired immunodeficiency syndrome: a case report
Authors: Kowo Mathurin , Nzoume Nsope Mengang Jude-Marcel , Simeni Njonnou Sylvain Raoul , Kouotou Emmanuel Armand , Atangana Paul Jean Adrien , Ankouane Andoulo Firmin 
Published: March 2022

Abstract
Background
Buschke–Löwenstein tumor is a giant condyloma acuminata infection that is characterized by degeneration, invasion, and recurrence. It is associated with human papilloma virus infection. It develops around the genital and perineal area, sometimes causing a large budding ulcerated lesion. Although human immunodeficiency virus infection is frequent in Africa, there are few descriptions of Buschke–Löwenstein tumor diagnosis and its management. Screening for other sexually transmitted infections must be systematic among these patients.

Case presentation
We report herein the case of a 21-year-old African origin male patient who developed a perineal swelling. Physical examination showed evidence of a huge exophytic tumor made up of budding pinkish vegetations, with serrated crests, a ‘’butterfly wing’’ structure, and a cauliflower-like appearance crowned with centrifugal circinate lesions. Multiple condylomatous lesions of the anal margin were also present. The patient tested positive for human immunodeficiency virus (cluster of differentiation 4 count of 119 cells/mm3) and hepatitis B infections. Real-time polymerase chain reaction revealed human papilloma virus-16 and other high-risk human papilloma virus deoxyribonucleic acid. The diagnosis of Buschke–Löwenstein tumor was made on mass biopsy, and the patient underwent multidisciplinary intervention (surgery, podophyllin application, and antiretroviral therapy). Medium-term evolution was, however, fatal due to opportunistic infection.

Conclusion
Buschke–Löwenstein tumor is a rare tumor associated with human immunodeficiency virus infection. It is more frequent in male human immunodeficiency virus-positive patients. There is a need to screen for other sexually transmitted infections. In most cases, the treatment is surgical, in association with local therapies. However, recurrences are common.
Influence of Mycoplasma hyopneumoniae natural infection on the respiratory microbiome diversity of finishing pigs
Authors: Sonalio Karina , Almeida Henrique M. S. , Mechler-Dreibi Marina L. , Storino Gabriel Y. , Haesebrouck Freddy , Maes Dominiek , de Oliveira Luís Guilherme 
Published: March 2022

AbstractMycoplasma (M.) hyopneumoniaeinteracts with the respiratory microbiota and facilitates colonization of other pathogens. The present study investigated the pulmonary and nasal microbiota ofM. hyopneumoniae-infected andM. hyopneumoniae-free pigs. Sixty-six pigs from three commercial herds were selected at the end of the finishing phase: 44 originated from twoM. hyopneumoniae-positive herds and 22 from aM. hyopneumoniae-negative farm. At the slaughterhouse, samples of nasal turbinate (NT) and bronchus-alveolar lavage fluid (BALF) were collected. DNA was extracted with a commercial kit and the infection status was confirmed by qPCR. All samples from the same herd were pooled, and next-generation sequencing based on the hypervariable region V3–V4 of the 16 s bacterial rDNA was performed. Data analysis included the taxonomic analysis, Alpha diversity indexes, and Principal coordinates analysis (Pcoa) using Jaccard, Bray–Curtis, Weighted Unifrac, and Unweighted Unifrac distances. All pigs from the infected herds tested PCR positive forM. hyopneumoniae, whereas all pigs from the negative farm were negative. There was a greater diversity of microorganisms in BALF when compared to NT samples in all the farms. BALF samples from infected animals showed higher abundance ofM. hyopneumoniaethan NT samples and a predominance ofPasteurella multocidaamong the main species identified, which was also abundant in theM. hyopneumoniae-free herd. PCoa diagrams indicated that for most of the samples, dissimilarity on bacterial composition was observed, regardless of infection status and sample type. Therefore, the lung microbiota was modulated byM. hyopneumoniaeinfection, which could play a role in the pathogenesis ofM. hyopneumoniae-disease.
Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates
Authors: Estrada April A. , Gottschalk Marcelo , Gebhart Connie J. , Marthaler Douglas G. 
Published: March 2022

AbstractStreptococcus suis is a significant economic and welfare concern in the swine industry. Pan-genome analysis provides an in-silico approach for the discovery of genes involved in pathogenesis in bacterial pathogens. In this study, we performed pan-genome analysis of 208 S. suis isolates classified into the pathogenic, possibly opportunistic, and commensal pathotypes to identify novel candidate virulence-associated genes (VAGs) of S. suis. Using chi-square tests and LASSO regression models, three accessory pan-genes corresponding to S. suis strain P1/7 markers SSU_RS09525, SSU_RS09155, and SSU_RS03100 (>95% identity) were identified as having a significant association with the pathogenic pathotype. The proposed novel SSU_RS09525 + /SSU_RS09155 + /SSU_RS03100 + genotype identified 96% of the pathogenic pathotype strains, suggesting a novel genotyping scheme for predicting the pathogenicity of S. suis isolates in North America. In addition, mobile genetic elements carrying antimicrobial resistance genes (ARGs) and VAGs were identified but did not appear to play a major role in the spread of ARGs and VAGs.
Legendre spectral collocation method for distributed and Riesz fractional convection–diffusion and Schrödinger-type equation
Authors: Abdelkawy M. A. , Jeelani Mdi Begum , Alnahdi Abeer S. , Taha T. M. , Soluma E. M. 
Published: March 2022

AbstractThe numerical analysis of the temporal distributed and spatial Riesz fractional problem (TDSRFP) is presented in this work. To address the two independent variables, the suggested technique employs a completely spectral Legendre collocation approach. For the current model, our technique is proven to be more accurate, efficient, and practical. The results confirmed that the spectral scheme is exponentially convergent.
Occupational and community risk of SARS-CoV-2 infection among employees of a long-term care facility: an observational study
Authors: Lenggenhager Lauriane , Martischang Romain , Sauser Julien , Perez Monica , Vieux Laure , Graf Christophe , Cordey Samuel , Laubscher Florian , Nunes Tomás Robalo , Zingg Walter , Cori Anne , Harbarth Stephan , Abbas Mohamed 
Published: March 2022

AbstractBackgroundWe investigated the contribution of both occupational and community exposure for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among employees of a university-affiliated long-term care facility (LTCF), during the 1stpandemic wave in Switzerland (March–June 2020).MethodsWe performed a nested analysis of a seroprevalence study among all volunteering LTCF staff to determine community and nosocomial risk factors for SARS-CoV-2 seropositivity using modified Poison regression. We also combined epidemiological and genetic sequencing data from a coronavirus disease 2019 (COVID-19) outbreak investigation in a LTCF ward to infer transmission dynamics and acquisition routes of SARS-CoV-2, and evaluated strain relatedness using a maximum likelihood phylogenetic tree.ResultsAmong 285 LTCF employees, 176 participated in the seroprevalence study, of whom 30 (17%) were seropositive for SARS-CoV-2. Most (141/176, 80%) were healthcare workers (HCWs). Risk factors for seropositivity included exposure to a COVID-19 inpatient (adjusted prevalence ratio [aPR] 2.6; 95% CI 0.9–8.1) and community contact with a COVID-19 case (aPR 1.7; 95% CI 0.8–3.5). Among 18 employees included in the outbreak investigation, the outbreak reconstruction suggests 4 likely importation events by HCWs with secondary transmissions to other HCWs and patients.ConclusionsThese two complementary epidemiologic and molecular approaches suggest a substantial contribution of both occupational and community exposures to COVID-19 risk among HCWs in LTCFs. These data may help to better assess the importance of occupational health hazards and related legal implications during the COVID-19 pandemic.
Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study
Authors: Almiñana C. , Dubuisson F. , Bauersachs S. , Royer E. , Mermillod P. , Blesbois E. , Guignot F. 
Published: March 2022

Abstract
Background
Currently, there is a high demand for efficient pig embryo cryopreservation procedures in the porcine industry as well as for genetic diversity preservation and research purposes. To date, vitrification (VIT) is the most efficient method for pig embryo cryopreservation. Despite a high number of embryos survives in vitro after vitrification/warming procedures, the in vivo embryo survival rates after embryo transfer are variable among laboratories. So far, most studies have focused on cryoprotective agents and devices, while the VIT effects on porcine embryonic gene expression remained unclear. The few studies performed were based on vitrified/warmed embryos that were cultured in vitro (IVC) to allow them to re–expand. Thus, the specific alterations of VIT, IVC, and the cumulative effect of both remained unknown. To unveil the VIT-specific embryonic alterations, gene expression in VIT versus (vs.) IVC embryos was analyzed. Additionally, changes derived from both VIT and IVC vs. control embryos (CO) were analyzed to confirm the VIT embryonic alterations. Three groups of in vivo embryos at the blastocyst stage were analyzed by RNA–sequencing: (1) VIT embryos (vitrified/warmed and cultured in vitro), (2) IVC embryos and (3) CO embryos.

Results
RNA–sequencing revealed three clearly different mRNA profiles for VIT, IVC and CO embryos. Comparative analysis of mRNA profiles between VIT and IVC identified 321, differentially expressed genes (DEG) (FDR < 0.006). In VIT vs. CO and IVC vs. CO, 1901 and 1519 DEG were found, respectively, with an overlap of 1045 genes. VIT-specific functional alterations were associated to response to osmotic stress, response to hormones, and developmental growth. While alterations in response to hypoxia and mitophagy were related to the sum of VIT and IVC effects.

Conclusions
Our findings revealed new insights into the VIT procedure-specific alterations of embryonic gene expression by first comparing differences in VIT vs. IVC embryos and second by an integrative transcriptome analysis including in vivo control embryos. The identified VIT alterations might reflect the transcriptional signature of the embryo cryodamage but also the embryo healing process overcoming the VIT impacts. Selected validated genes were pointed as potential biomarkers that may help to improve vitrification.
Structured regularization based velocity structure estimation in local earthquake tomography for the adaptation to velocity discontinuities
Authors: Yamanaka Yohta , Kurata Sumito , Yano Keisuke , Komaki Fumiyasu , Shiina Takahiro , Kato Aitaro 
Published: March 2022

AbstractWe propose a local earthquake tomography method that applies a structured regularization technique to determine sharp changes in Earth’s seismic velocity structure using arrival time data of direct waves. Our approach focuses on the ability to better image two common features that are observed in Earth’s seismic velocity structure: sharp changes in velocities that correspond to material boundaries, such as the Conrad and Moho discontinuities; and gradual changes in velocity that are associated with pressure and temperature distributions in the crust and mantle. We employ different penalty terms in the vertical and horizontal directions to refine the earthquake tomography. We utilize a vertical-direction (depth) penalty that takes the form of the$${l}_{1}$$l1-sum of the$${l}_{2}$$l2-norms of the second-order differences of the horizontal units in the vertical direction. This penalty is intended to represent sharp velocity changes caused by discontinuities by creating a piecewise linear depth profile of seismic velocity. We set a horizontal-direction penalty term on the basis of the$${l}_{2}$$l2-norm to express gradual velocity tendencies in the horizontal direction, which has been often used in conventional tomography methods. We use a synthetic data set to demonstrate that our method provides significant improvements over velocity structures estimated using conventional methods by obtaining stable estimates of both steep and gradual changes in velocity. We also demonstrate that our proposed method is robust to variations in the amplitude of the velocity jump, the initial velocity model, and the number of observed arrival times, compared with conventional approaches, and verify the adaptability of the proposed method to dipping discontinuities. Furthermore, we apply our proposed method to real seismic data in central Japan and present the potential of our method for detecting velocity discontinuities using the observed arrival times from a small number of local earthquakes.Graphical Abstract
N6-methyladenosine-related lncRNAs is a potential marker for predicting prognosis and immunotherapy in ovarian cancer
Authors: Nie Xin , Tan Jichun 
Published: March 2022

Abstract
Background
With a lack of specific symptoms, ovarian cancer (OV) is often diagnosed at an advanced stage. This coupled with inadequate prognostic indicators and treatments with limited therapeutic effect make OV the deadliest type of gynecological tumor. Recent research indicates that N6-methyladenosine (m6A) and long-chain non-coding RNA (lncRNA) play important roles in the prognosis of OV and the efficacy of immunotherapy.

Results
Using the Cancer Genome Atlas (TCGA) OV-related data set and the expression profiles of 21 m6A-related genes, we identified two m6A subtypes, and the differentially expressed genes between the two. Based on the differentially expressed lncRNAs in the two m6A subtypes and the lncRNAs co-expressed with the 21 m6A-related genes, single-factor cox and LASSO regression were used to further isolate the 13 major lncRNAs. Finally, multi-factor cox regression was used to construct a m6A-related lncRNA risk score model for OV, with good performance in patient prognosis. Using risk score, OV tumor samples are divided into with high- and low-score groups. We explored the differences in clinical characteristics, tumor mutational burden, and tumor immune cell infiltration between the two groups, and evaluated the risk score’s ability to predict the benefit of immunotherapy.

Conclusion
Our m6A-based lncRNA risk model could be used to predict the prognosis and immunotherapy response of future OV patients.