bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathogen change of avian influenza virus in the live poultry market before and after vaccination of poultry in southern China
Authors: Guo Jin , Song Wentao , Ni Xiansheng , Liu Wei , Wu Jingwen , Xia Wen , Zhou Xianfeng , Wang Wei , He Fenglan , Wang Xi , Fan Guoyin , Zhou Kun , Chen Haiying , Chen Shengen 
Published: October 2021

Abstract
Background
The fifth wave of H7N9 avian influenza virus caused a large number of human infections and a large number of poultry deaths in China. Since September 2017, mainland China has begun to vaccinate poultry with H5 + H7 avian influenza vaccine. We investigated the avian influenza virus infections in different types of live poultry markets and samples before and after genotype H5 + H7 vaccination in Nanchang, and analyzed the changes of the HA subtypes of AIVs.

Methods
From 2016 to 2019, we monitored different live poultry markets and collected specimens, using real-time reverse transcription polymerase chain reaction (RT-PCR) technology to detect the nucleic acid of type A avian influenza virus in the samples. The H5, H7 and H9 subtypes of influenza viruses were further classified for the positive results. The χ2 test was used to compare the differences in the separation rates of different avian influenza subtypes.

Results
We analyzed 5,196 samples collected before and after vaccination and found that the infection rate of AIV in wholesale market (21.73%) was lower than that in retail market (24.74%) (P < 0.05). Among all the samples, the positive rate of sewage samples (33.90%) was the highest (P < 0.001). After vaccination, the positive rate of H5 and H7 subtypes decreased, and the positive rate of H9 subtype and untypable HA type increased significantly (P < 0.001). The positive rates of H9 subtype in different types of LPMs and different types of samples increased significantly (P < 0.01), and the positive rates of untypable HA type increased significantly in all environmental samples (P < 0.05).

Conclusions
Since vaccination, the positive rates of H5 and H7 subtypes have decreased, but the positive rates of H9 subtypes have increased to varying degrees in different testing locations and all samples. This results show that the government should establish more complete measures to achieve long-term control of the avian influenza virus.
Thirty-eight-year follow-up of the first patient of mandibular reconstruction with free vascularized fibula flap
Authors: Puricelli Edela , Chem Roberto Correa 
Published: October 2021

Abstract
Background
The mandible is responsible for vital functions of the stomatognathic system, and its loss results in functional and aesthetic impairment. Mandibular reconstruction with free fibula flap is considered the gold standard for mandibular reconstruction.

Case presentation
We describe here the 38-year follow-up of the patient who was the first case of mandibular reconstruction with free fibula flap reported in the literature. The original report describes a 27-year-old woman who had undergone extensive mandibulectomy due to an osteosarcoma. A microvascularized fibula flap was used for mandibular reconstruction in 1983. Two years later, a vestibulo-lingual sulcoplasty with skin graft was performed to allow the construction of a total dental prosthesis. Fifteen years after the initial treatment, an autologous iliac crest graft was placed in the fibula flap, aimed at increasing bone thickness and height for rehabilitation with implant supported prosthesis. In 2015, a rib graft was positioned in the mental region, enhancing the support to the soft tissues of the face and improving the oral function. A recent review of the patient shows well-balanced facial morphology and optimal functional results of the procedure.

Conclusions
The fibula flap method, described in 1975 and first reported for mandibular reconstruction in 1985, continues to be applied as originally described, especially where soft tissue damage is not extensive. Its use in reconstructive surgery was expanded by advancements in surgery and techniques such as virtual surgical planning. However, there is still a lack of evidence related to the long-term evaluation of outcomes. The present work represents the longest-term follow-up of a patient undergoing mandibular reconstruction with free vascularized fibula flap, presenting results showing that, even after 38 years, the procedure continues to provide excellent results.
A systematic study of independently-tuned room-specific PBS beam model in a beam-matched multiroom proton therapy system
Authors: Huang Yu-Hua , Fang Chunfeng , Yang Tao , Cao Lin , Zhang Gaolong , Qu Baolin , Zhang Yihang , Wang Zishen , Xu Shouping 
Published: October 2021

Abstract
Background
In the existing application of beam-matched multiroom proton therapy system, the model based on the commissioning data from the leading treatment room was used as the shared model. The purpose of this study is to investigate the ability of independently-tuned room-specific beam models of beam-matched gantries to reproduce the agreement between gantries’ performance when considering the errors introduced by the modeling process.

Methods
Raw measurements of two gantries’ dosimetric characteristics were quantitatively compared to ensure their agreement after initially beam-matched. Two gantries’ beam model parameters, as well as the model-based computed dosimetric characteristics, were analyzed to study the introduced errors and gantries’ post-modeling consistency. We forced two gantries to share the same beam model. The model-sharing patient-specific quality assurance (QA) tasks were retrospectively performed with 36 cancer patients to study the clinical impact of beam model discrepancies.

Results
Intra-gantry comparisons demonstrate that the modeling process introduced the errors to a certain extent indeed, which made the model-based reproduced results deviate from the raw measurements. Among them, the deviation introduced to the IDD curves was generally larger than that to the beam spots during modeling. Cross-gantry comparisons show that, from the beam model perspective, the introduced deviations deteriorated the high agreement of the dosimetric characteristics originally shown between two beam-matched gantries, but the cross-gantry discrepancy was still within the clinically acceptable tolerance. In model-sharing patient-specific QA, for the particular gantry, the beam model usage for intensity-modulated proton therapy (IMPT) QA plan generation had no significant effect on the actual delivering performance. All reached a high level of 95.0% passing rate with a 3 mm/3% criterion.

Conclusions
It was preliminary recognized that among beam-matched gantries, the independently-tuned room-specific beam model from any gantry is reasonable to be chosen as the shared beam model without affecting the treatment efficacy.
Degradation-driven changes in fine root carbon stocks, productivity, mortality, and decomposition rates in a palm swamp peat forest of the Peruvian Amazon
Authors: Dezzeo Nelda , Grandez-Rios Julio , Martius Christopher , Hergoualc’h Kristell 
Published: October 2021

AbstractBackgroundAmazon palm swamp peatlands are major carbon (C) sinks and reservoirs. In Peru, this ecosystem is widely threatened owing to the recurrent practice of cuttingMauritia flexuosapalms for fruit harvesting. Such degradation could significantly damage peat deposits by altering C fluxes through fine root productivity, mortality, and decomposition rates which contribute to and regulate peat accumulation. Along a same peat formation, we studied an undegraded site (Intact), a moderately degraded site (mDeg) and a heavily degraded site (hDeg) over 11 months. Fine root C stocks and fluxes were monthly sampled by sequential coring. Concomitantly, fine root decomposition was investigated using litter bags. In the experimental design, fine root stocks and dynamics were assessed separately according to vegetation type (M. flexuosapalm and other tree species) andM. flexuosaage class. Furthermore, results obtained from individual palms and trees were site-scaled by using forest composition and structure.ResultsAt the scale of individuals, fine root C biomass inM. flexuosaadults was higher at the mDeg site than at the Intact and hDeg sites, while in trees it was lowest at the hDeg site. Site-scale fine root biomass (Mg C ha−1) was higher at the mDeg site (0.58 ± 0.05) than at the Intact (0.48 ± 0.05) and hDeg sites (0.32 ± 0.03). Site-scale annual fine root mortality rate was not significantly different between sites (3.4 ± 1.3, 2.0 ± 0.8, 1.5 ± 0.7 Mg C ha−1 yr−1at the Intact, mDeg, and hDeg sites) while productivity (same unit) was lower at the hDeg site (1.5 ± 0.8) than at the Intact site (3.7 ± 1.2), the mDeg site being intermediate (2.3 ± 0.9). Decomposition was slow with 63.5−74.4% of mass remaining after 300 days and it was similar among sites and vegetation types.ConclusionsThe significant lower fine root C stock and annual productivity rate at the hDeg site than at the Intact site suggests a potential for strong degradation to disrupt peat accretion. These results stress the need for a sustainable management of these forests to maintain their C sink function.
Determinants of low birth weight deliveries at five referral hospitals in Western Area Urban district, Sierra Leone
Authors: Kargbo David Kabba , Nyarko Kofi , Sackey Samuel , Addo-Lartey Adolphina , Kenu Ernest , Anto Francis 
Published: October 2021

Abstract
Background
Low birth weight (LBW) contributes significantly to infant and child mortality. Each year, about 20 1million deliveries are LBW with 96.5% occurring in developing countries. Whiles the incidence of LBW is reducing in other districts of Sierra Leone, it has been reported to be increasing in the Western Area Urban district. Determining the risk factors in a specific geographic area is important for identifying mothers at risk and thereby for planning and taking appropriate action. The current study sought to identify factors associated with LBW deliveries in the Western Area Urban district of Sierra Leone.

Methods
A hospital-based unmatched 1:2 case-control study was conducted among mothers who delivered live singleton babies from November, 2019 to February, 2020 in five referral health facilities. Mothers were conveniently sampled and sequentially enrolled into the study after delivery. Their antenatal care cards were reviewed and a pre-tested questionnaire administered to the mothers. Data analysis was done using Stata 15.0 and association between maternal socio-demographic, socio-economic, obstetric and lifestyle factors and LBW assessed using bivariable and multivariable logistic regression analyses.

Results
A total of 438 mothers (146 cases and 292 controls), mean age: 24.2 (±5.8) and 26.1 (±5.5) years for cases and controls respectively participated in the study. Multivariable analysis revealed that being unemployed (AoR = 2.52, 95% CI 1.16–5.49, p = 0.020), having anaemia during pregnancy (AoR = 3.88, 95% CI 1.90–7.90, p <  0.001), having less than 2 years inter-pregnancy interval (AoR = 2.53, 95% CI 1.11–5.73, p = 0.026), and smoking cigarettes during pregnancy (AoR = 4.36, 95% CI 1.94–9.80, p <  0.001) were significantly associated with having LBW babies.

Conclusion
Factors associated with LBW identified were unemployment, anaemia during pregnancy, < 2 years inter-pregnancy interval and cigarette smoking during pregnancy. Health care providers should screen and sensitize mothers on the risk factors of LBW during antenatal sessions.
Insecticide resistance to insect growth regulators, avermectins, spinosyns and diamides in Culex quinquefasciatus in Saudi Arabia
Authors: Hafez Abdulwahab M. , Abbas Naeem 
Published: October 2021

Abstract
Background
Culex quinquefasciatus is not only a biting nuisance but also an important vector of fatal diseases. In Saudi Arabia, management measures to control this mosquito and thereby prevent associated disease transmission have focused on insecticides. Nevertheless, information on the resistance status of C. quinquefasciatus is insufficient, especially concerning insecticides containing novel classes of insecticides.

Methods
We evaluated six insecticides belonging to four classes of insecticides (insect growth regulators [3], avermectins [1], diamides [1] and spinosyns [1]) for toxicity and resistance in eight C. quinquefasciatus populations (from Ishbiliya, Al-Masfa, Al-Masanie, Al-Washlah, Al-Nakhil, Irqah, Al-Suwaidi and Al-Ghanemiya) following World Health Organisation protocols.

Results
Resistance status ranging from susceptibility/low resistance to high resistance, in comparison with the susceptible strain, was detected for cyromazine in the eight C. quinquefasciatus populations: Ishbiliya (resistance ratio [RR] = 3.33), Al-Masfa (RR = 4.33), Al-Masanie (RR = 3.67), Al-Washlah (RR = 2.33), Al-Nakhil (RR = 5.33), Irqah (RR = 7.00), Al-Suwaidi (RR = 21.33) and Al-Ghanemiya (RR = 16.00). All C. quinquefasciatus populations exhibited a high level of resistance to diflubenzuron (RR = 13.33–43.33), with the exception of Al-Nakhil which exhibited moderate resistance (RR = 10.00). Susceptibility/low resistance to high resistance was observed for triflumuron in the eight C. quinquefasciatus populations: Ishbiliya (RR = 0.50), Al-Ghanemiya (RR =  3.00), Al-Suwaidi (RR =  10.00), Al-Masfa (RR =  5.00), Al-Masanie (RR =  10.00), Al-Nakhil (RR =  5.00), Irqah (RR =  5.00) and Al-Washlah (RR =  15.00). Susceptibility/low resistance was assessed for abamectin, chlorantraniliprole and spinosad in all C. quinquefasciatus populations, with RR ranges of 0.25–3.50, 0.17–2.19, and 0.02–0.50, respectively. However, the population collected from Irqah showed high resistance to chlorantraniliprole (RR = 11.93).

Conclusions
The detection of widespread resistance to insect growth regulators in C. quinquefasciatus highlights an urgent need to establish integrated vector management strategies. Our results may facilitate the selection of potent insecticides for integrated vector management programmes for C. quinquefasciatus.

Graphical Abstract
Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes
Authors: Vysotskiy Mikhail , Zhong Xue , Miller-Fleming Tyne W. , Zhou Dan ,   Autism Working Group of the Psychiatric Genomics Consortium^,   Bipolar Disorder Working Group of the Psychiatric Genomics Consortium^,   Schizophrenia Working Group of the Psychiatric Genomics Consortium^, Cox Nancy J. , Weiss Lauren A. 
Published: October 2021

Abstract
Background
Deletions and duplications of the multigenic 16p11.2 and 22q11.2 copy number variant (CNV) regions are associated with brain-related disorders including schizophrenia, intellectual disability, obesity, bipolar disorder, and autism spectrum disorder (ASD). The contribution of individual CNV genes to each of these identified phenotypes is unknown, as well as the contribution of these CNV genes to other potentially subtler health implications for carriers. Hypothesizing that DNA copy number exerts most effects via impacts on RNA expression, we attempted a novel in silico fine-mapping approach in non-CNV carriers using both GWAS and biobank data.

Methods
We first asked whether gene expression level in any individual gene in the CNV region alters risk for a known CNV-associated behavioral phenotype(s). Using transcriptomic imputation, we performed association testing for CNV genes within large genotyped cohorts for schizophrenia, IQ, BMI, bipolar disorder, and ASD. Second, we used a biobank containing electronic health data to compare the medical phenome of CNV carriers to controls within 700,000 individuals in order to investigate the full spectrum of health effects of the CNVs. Third, we used genotypes for over 48,000 individuals within the biobank to perform phenome-wide association studies between imputed expressions of individual 16p11.2 and 22q11.2 genes and over 1500 health traits.

Results
Using large genotyped cohorts, we found individual genes within 16p11.2 associated with schizophrenia (TMEM219, INO80E, YPEL3), BMI (TMEM219, SPN, TAOK2, INO80E), and IQ (SPN), using conditional analysis to identify upregulation of INO80E as the driver of schizophrenia, and downregulation of SPN and INO80E as increasing BMI. We identified both novel and previously observed over-represented traits within the electronic health records of 16p11.2 and 22q11.2 CNV carriers. In the phenome-wide association study, we found seventeen significant gene-trait pairs, including psychosis (NPIPB11, SLX1B) and mood disorders (SCARF2), and overall enrichment of mental traits.

Conclusions
Our results demonstrate how integration of genetic and clinical data aids in understanding CNV gene function and implicates pleiotropy and multigenicity in CNV biology.
The complete genome sequence of a bile-isolated Stenotrophomonas maltophilia ZT1
Authors: Zhang Min , Li Lixiang , Pan Hongwei , Zhou Tao 
Published: October 2021

Abstract
Background
Stenotrophomonas maltophilia is one of the most frequently isolated opportunistic pathogens that can cause infections in humans. Many researches concerned the mechanism of antibiotic resistance displayed by S. maltophilia, however, the mechanism of its pathogenesis and its adaptation to special niches, such as bile, remain unclear.

Results
In this study, the S. maltophilia strain ZT1 was isolated from human bile. Its genome was sequenced and a circular chromosome of 4,391,471 bp was obtained with a GC content of 66.51%. There were 3962 protein-coding sequences, 7 rRNAs and 74 tRNAs in the chromosome. Compared with Virulence Factor Database, we identified more than 500 candidate virulence genes including genes encoding fimbrial assembly protein, enterobactin synthesis pathway proteins, efflux pumps, and the DNA and/or proteins secretion system in the genome of strain ZT1. Additionally, there were at least 22 genes related to bile adaption, including emrAB, acrRAB, galU, rfbC, tolC and mdtABC.

Conclusions
This is the first study to reveal the whole genome sequence of the ZT1 strain of S. maltophilia isolated from human bile. We identified hundreds virulence factors and 22 bile adaptation-related genes in the genome of the S. maltophilia strain ZT1. Further comparative genomic analysis and functional verification would aid in understanding the pathogenesis and bile adaptation of S. maltophilia.
Malignant pericardial effusion as a primary manifestation of metastatic colon cancer: a case report
Authors: Neves Milena Brachmans Mascarenhas , Stival Mirella Velasco , Neves Yuri Costa Sarno , da Silva Jordânia Gonçalves Pereira , Macedo Daniela Borges da Rocha , Carnevalli Bianca Mendes , Silva Alana Moura Fé e , Sette Claudia Vaz de Melo , da Luz Stephane Tomaz , Cubero Daniel de Iracema Gomes 
Published: October 2021

Abstract
Background
Pericardial neoplastic involvement is rarely related to primary tumors of the pericardium and is most often caused by spread from other primary sites, such as lung and breast carcinomas, hematological malignancies (lymphoma and leukemia), and melanoma. Although pericardial metastasis from infradiaphragmatic tumors (such as colon cancers) are rare and poorly described in literature, any neoplasm has the potential to metastasize to the pericardium and heart by either contiguity, lymphatic, or hematological spread.

Case presentation
A 44-year-old previously healthy male Causasian patient had a sudden onset of dyspnea and wheezing. During investigation with echocardiogram, computed tomography and repeated pericardiocentesis, the cause of malignant pericardial effusion was confirmed as primary manifestation of metastatic colon cancer. The patient was treated with appropriate chemotherapy and presented satisfactory disease control.

Conclusions
This report emphasizes the importance of considering the diagnostic hypothesis of occult neoplasia in a patient with pericardial effusion.
Dietary supplementation of red-osier dogwood polyphenol extract changes the ileal microbiota structure and increases Lactobacillus in a pig model
Authors: Zheng Shugui , Song Jichen , Qin Xia , Yang Kai , Liu Mei , Yang Chengbo , Nyachoti Charles M. 
Published: October 2021

AbstractRed-osier dogwood (ROD) extract contains a lot of polyphenols that have the potential for modulation of gut microbiota. However, little information is available about its prebiotic properties. This study investigated the impact of ROD polyphenol extract on the ileal microbiota with dietary supplementation of ROD polyphenol extract in a pig model. The data indicated that supplementation of ROD polyphenol extract significantly increased class Bacilli, order Lactobacillales and family lactobacillaceae. Within family lactobacillaceae, Lactobacillus was the main responder by increasing from 5.92% to 35.09%. Further analysis showed that ROD polyphenol extract improved two species Lactobacillus delbrueckii and Lactobacillus mucus. The results of this study suggested that ROD polyphenol extract has the potential to play prebiotic role and confer health benefit through modifying gut microbiota.
Alcohol dependence in a community sample of Aboriginal and Torres Strait Islander Australians: harms, getting help and awareness of local treatments
Authors: Weatherall Teagan J. , Conigrave James H. , Conigrave Katherine M. , Perry Jimmy , Wilson Scott , Room Robin , Chikritzhs Tanya , Kylie Lee K. S. 
Published: October 2021

Abstract
Background
Few studies have examined links between current alcohol dependence and specific harms among Indigenous Australians. We investigated these associations as well as help seeking for drinking, awareness of local treatments and recommendations to help family or friends cut down or stop drinking in two Indigenous communities.

Methods
A representative sample of Indigenous Australians was surveyed in one urban and one remote community in South Australia. Data were collected via the Grog Survey App. Participants were dependent if they reported two or more symptoms of alcohol dependence (ICD-11). Pearson chi-square tests were used to describe relationships between employment by gender, and dependence by awareness of medicines and local treatment options. Multivariate logistic regressions were used to predict the odds of dependent drinkers experiencing harms and getting help for drinking, controlling for age, gender, schooling and income.

Results
A total of 775 Indigenous Australians took part in the study. After controlling for confounders, dependent drinkers were nearly eight times more likely to report a harm and nearly three times more likely to get help for their drinking—compared with non-dependent drinkers. Participants recommended accessing local support from an Aboriginal alcohol and other drugs worker, or a detoxification/ rehabilitation service.

Discussion and conclusions
More support and funding is needed for Indigenous Australians to ensure local treatment options for dependent drinkers are readily available, appropriate and accessible. Involvement of local Aboriginal or Torres Strait Islander health professionals in delivery of care can help ensure that it is appropriate to an individual’s culture and context.