bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of nasopharyngeal viruses and pathogenic bacteria in children and their parents with and without HIV
Authors: Khan Tila , Das Ranjan Saurav , Chaudhary Amrita , Chatterjee Jyotirmoy , Bhattacharya Sangeeta Das 
Published: January 2021

Abstract
Background: Bacteria and respiratory viruses co-occur in the nasopharynx, and their interactions may impact pathogenesis of invasive disease. Associations of viruses and bacteria in the nasopharynx may be affected by HIV.Methods: We conducted a nested case-control study from a larger cohort study of banked nasopharyngeal swabs from families with and without HIV in West Bengal India, to look at the association of viruses and bacteria in the nasopharynx of parents and children when they are asymptomatic. Quantitative polymerase chain reaction for 4 bacteria and 21 respiratory viruses was run on 92 random nasopharyngeal swabs from children--49 from children living with HIV (CLH) and 43 from HIV uninfected children(HUC)-- and 77 swabs from their parents (44 parents of CLH and 33 parents of HUC).Results: Bacteria was found in 67% of children, viruses in 45%, and both in 27% of child samples. Staphylococcus aureus (53%) was the most common bacteria, followed by Streptococcus pneumoniae (pneumococcus) (37%) in children and parents (53%, 20%). Regardless of HIV status, viruses were detected in higher numbers (44%) in children than their parents (30%) (p=0.049), particularly rhinovirus (p=0.02). Human rhinovirus was the most frequently found virus in both CLH and HUC. Children with adenovirus were at six times increased risk of also having pneumococcus (Odds ratio OR 6, 95% CI 1.12-31.9) regardless of HIV status. In addition, the presence of rhinovirus in children was associated with increased pneumococcal density (Regression coeff 4.5, 1.14-7.9). In CLH the presence of rhinovirus increased the risk of pneumococcal colonization by nearly sixteen times (OR 15.6, 1.66-146.4) and pneumococcus and S. aureus dual colonization by nearly nine times (OR 8.7).Conclusions Children more frequently carried viruses regardless of HIV status. In CLH the presence of rhinovirus, the most frequently detected virus, significantly increased co-colonization with pneumococcus and S. aureus.
Preliminary study of the toxicity and radioprotective effects of zymosan in vitro and in vivo
Authors: Zhang Yue-zhi , Ge Shu-jing , Leng Qing-zhen , Ma Jian-jun , Liu Hanchen 
Published: January 2021

Abstract
Background: This study aimed to confirm the cytotoxicity of zymosan in vitro and in vivo and determine the appropriate treatment time and dose of zymosan.Methods: AHH-1 cells and HIECs were administered by 0, 20, 40, 80 or 160 μg/mL zymosan. The CCK-8 assay and flow cytometry were used to evaluate the cell viability and apoptosis 24 h, 48 h, and 72 h after administration. Furthermore, 12 h before irradiation, the cells were treated with 0, 5, 10, or 20 μg/mL zymosan and then irradiated with 4 Gy X-rays. Cell viability and apoptosis were measured by the CCK-8 assay and flow cytometry at 24 h. In addition, the protective effect of zymosan against radiation in vitro was compared to that of 20 μg/mL LPS. In vivo, weight, the spleen index and the thymus index were measured to evaluate the toxicity of 0, 5, 10, 20 and 10 mg/kg zymosan. In addition, rats were treated with 0, 2, 4, 8 or 10 mg/kg zymosan and then irradiated with 7 Gy X-rays. The survival rate, organ index were evaluated. The protective effect of zymosan against radiation in vivo was compared to that of 10 mg/kg LPS a positive control. Results: The viability and apoptosis of cells treated with different doses and treatment times of zymosan were not different from those of control cells (p<0.05). Furthermore, cell viability and apoptosis were clearly improved after zymosan preadministration (p<0.05). The radioprotective effect of zymosan was dose-dependent. In addition, the viability of cells pretreated with zymosan was higher than that of cells pretreated with LPS, and the apoptosis rate of zymosan-treated cells was lower than that of cells pretreated with LPS (p<0.05). In vivo, weight, the spleen index and the thymus index were significantly decreased by zymosan at a concentration of 20 mg/kg (p<0.05). Further experiments showed that the concentration at which zymosan exerted radioprotective effects was 10 mg/kg. The survival curves in the irradiated rats were barely separated between the LPS treatment and zymosan treatment. Conclusion: Zymosan administration before radiation exposure significantly increased cell viability and the survival rates of rats.
Identification of molecular regulation on difference of lipid deposition in dedifferentiated preadipocytes from different chicken tissues
Authors: ma zheng , Luo Na , Liu Lu , Cui Huanxian , Li Jing , Xiang Hai , Kang Huimin , Li Hua , Zhao Guiping 
Published: January 2021

Abstract
Background: The body distribution with high intramuscular fat and low abdominal fat is ideal goal for broiler breeding. Preadipocytes with different origins have differences in metabolism and gene expression. This transcriptome analysis of intramuscular preadipocytes (DIMPs) and adipose tissue-derived preadipocytes (DAFPs) is aim to explore the characteristics in lipid deposition of different chicken preadipocytes by dedifferentiation in vitro. Results: Compared to DAFPs, the total lipid content was decreased (P <0.05) in DIMFPs after two days with 100% confluence. Moreover, 72 DEGs related to lipid metabolism were screened, which are involved in the adipocyte differentiation, fatty acid transport and fatty acid synthesis, lipid stabilization, and lipolysis. Among the 72 DEGs, 19 DEGs were enriched in the PPAR signaling pathway, indicating a main contribution to the regulation of the difference of lipid deposition between DAFPs and DIMFPs. Among these 19 genes, the representative APOA1, ADIPOQ, FABP3, FABP4, FABP7, HMGCS2, LPL and RXRG genes were down-regulated, but ACSL1, FABP5, PCK2, PDPK1, PPARG, SCD, SCD5, SLC27A6 genes were up-regulated (P < 0.05 or P < 0.01) in the DIMFPs. In addition, the well-known pathways affecting lipid metabolism (MAPK-, TGF beta-, Calcium-, PPAR signaling pathway) and the pathways related to cell communication were enriched, which may also contribute to the regulation of lipid deposition. Finally, the regulatory network for the difference of lipid deposition between chicken DAFPs and DIMFPs were proposed based on the above information.Conclusions: Our data suggested the difference of lipid deposition between DIMPs and DAFPs of chicken in vitro, and proposed the molecular regulatory network for the difference of lipid deposition between chicken DAFPs and DIMFPs. The lipid content was significantly increased in DAFPs by the direct mediation of PPAR signaling pathways. These findings provide new insights into the regulation of tissue-specific fat deposition and optimizing body fat distribution in broilers.
Alterations of RNA splicing patterns in esophagus squamous cell carcinoma
Authors: Ding Jiyu , Li Chunquan , Cheng Yinwei , Du Zepeng , Wang Qiuyu , Tang Zhidong , Song Chao , Xia Qiaoxi , Bai Wenjing , Lin Ling , Liu Wei , Xu Liyan , Li Enmin , Wu Bingli 
Published: January 2021

Abstract
Alternative splicing (AS) is an important biological process for regulating the expression of various isoforms from a single gene and thus to promote proteome diversity. In this study, RNA-seq data from 15 pairs of matched esophageal squamous cell carcinoma (ESCC) and normal tissue samples as well as two cell lines were analyzed. AS events with significant differences were identified between ESCC and matched normal tissues, which were re-annotated to find protein coding genes or non-coding RNAs. A total of 45,439 AS events were found. Of these, 6,019 (13.25%) significant differentially AS events were identified. Exon skipping (SE) events occupied the largest proportion of abnormal splicing events. Fifteen differential splicing events with the same trends of ΔΨ values in ESCC tissues, as well in the two cell lines were found. Four pathways and 20 biological processes related to pro-metastasis cell junction and migration were significantly enriched for the differentially spliced genes. The upregulated splicing factor SF3B4, which regulates 92 gene splicing events, could be a potential prognostic factor of ESCC. Differentially spliced genes, including HNRNPC, VCL, ZNF207, KIAA1217, TPM1 and CALD1 are shown with a sashimi plot. These results suggest that cell junction- and migration-related biological processes are influenced by AS abnormalities, and aberrant splicing events can be affected by splicing factor expression changes. The involved splicing factor SF3B4 was found to be a survival-related gene in ESCC and is presumed to regulate AS in multiple cancers. In summary, we identified significant differentially expressed AS events which may be related to the development of ESCC.
Sheep nemabiome diversity and its response to anthelmintic treatment in Swedish sheep herds
Authors: Halvarsson Peter , Höglund Johan 
Published: January 2021

Abstract
BackgroundA novel way to study the species composition and diversity of nematode parasites in livestock is to perform deep sequencing on composite samples containing a mixture of different species. Herein we describe for the first-time the nematode community structures (nemabiomes) inhabiting Swedish sheep and how these are/were affected by host age and recent anthelmintic treatments.MethodsA total of 158 fecal samples were collected (n=35 in 2007 and n=123 in 2013-2016) and cultured from groups of sheep on 61 commercial farms in the south-central part of the country where most animals are grazed. Among the samples, 2 x 44 (56%) were paired collections from the same groups pre- and post-treatment with anthelmintics such as macrocyclic lactones, benzimidazoles or levamisole. Samples were analyzed for their nemabiome using the PacBio platform followed by bioinformatic sequence analysis with SCATA. Species richness and diversity were calculated and analyzed in R.ResultsNematode ITS2 sequences were found in all larval culture samples except two, even though the fecal egg counts were below the McMaster threshold in 20 samples. Sequencing yielded, on average, 1,008 sequences per sample. In total 16 operational taxonomical units (OTU), all had ≥98 % identity to sequences in the NCBI database, were recognized. The OTUs found represented nematode species of which 10 are commonly associated with sheep. Multiple species were identified in all pre anthelmintic treatment larval culture samples. No effects on nematode diversity were found in relation to host age. On the other hand, recent anthelmintic treatment lowered species richness, especially after use of ivermectin and albendazole. Interestingly, despite zero egg counts after use of levamisole, these samples still contained nematode DNA and especially H. contortus.ConclusionsOur findings provide evidence that nemabiome analysis combined with diversity index analysis provide an objective methodology in the study of the efficacy of anthelmintic treatment, as both high and low abundant species were detected.
Self-reported psychological problems and coping strategies: a web-based study in Peruvian population during the COVID-19 pandemic.
Authors: Guerrero Rita Judith Ames , Parra Victoria Aymé Barreda , Cahua Julio Cesar Huamani , Holl Jane Banaszak 
Published: January 2021

Abstract
BACKGROUND: The Coronavirus pandemic has disrupted health systems across the world and led to major shifts in individual behavior by forcing people into isolation in home settings. Its rapid spread has overwhelmed populations in all corners of Latin-American countries resulting in individual psychological reactions that may aggravate the health crisis. OBJECTIVE: This study reports on demographics, self-reported psychological disturbance and associated coping styles during the COVID-19 pandemic for the Peruvian population. METHODS: This cross-sectional study uses an online survey with snowball sampling that was conducted after the state of emergency was declared in Perú (on April 2nd). The General Health Questionnaire (GHQ-28) was used to identify somatic symptoms, incidence of anxiety/ insomnia, social dysfunction and depression and the Coping Strategy Questionnaire (COPE-28) mapped personal strategies to address recent stress. RESULTS: 434 self-selected participants ranging in age from 18 to 68 years old (ME =33.87) completed the survey. The majority of participants were women (61.3%), aged between 18 and 28 (41.7%), well-educated (>=85.0 %), Peruvian (94.2%), employed (57.4%) and single (71.20 %). 40.8% reported psychological problems, expressing fear of coronavirus infection (71.43%). Regression analysis shows that women developed more somatic symptoms (p<0.001*, C.I: -2.75 to -.99) and greater anxiety/insomnia (p=0.00*, C.I: -2.98 to 0.84) than men. Depression and social dysfunction were equally likely at any age. Educational status was protective against developing psychological disorders (p<0.05). While active responses (acceptance and social support) are scarcely used by individuals with psychological problems; passive strategies (such as denial, self-distraction, self-blame, disconnection, and emotional discharge) are more commonly reported.CONCLUSION: This study provides a better understanding of psychological disorders occurring during the COVID-19 pandemic in the Peruvian population. About half of the respondents reported psychological disturbance and poor coping responses. This evidence informs the need for broader promotional health policies focused on strengthening individual’s active strategies to improve mental health, especially in underprivileged groups during and after the COVID-19 pandemic.
BMSCs Seeding in Different Scaffold Incorporation with Hyperbaric Oxygen Treat Seawater Immersed Bony Defect
Authors: zhang gan , Chen Xiaosong , Cheng Xunsheng , Ma Xiuwu , Chen Congcong 
Published: January 2021

Abstract
Introduction: The experiment was undertaken to estimate the effect of BMSCs seeding in different scaffold incorporation with HBO on the repair of seawater immersed bone defect. And future compared n-HA/PLGA with β-TCP/PLGA as scaffold in treatment effect of seawater immersed bone defect.Methods: 60 New Zealand White rabbits with standard seawater defect in radius were randomly divided to group A (implant with nothing), group B (implanted with atuogenous bone), group C (implanted with n-HA/PLGA/BMSCs, and Group D ( implanted with β-TCP/PLGA/BMSCs). After implant, each rabbit receive HBO treatment at 2.4 ATA 100% oxygen for 120 minutes per day for 2 weeeks. Radiograph, histological and biomechanical examination were used to analyze osteogenesis.Result: X-ray analysis show that n-HA/PLGA/BMSCs and β-TCP/PLGA/BMSCs could accelerate the new bone formation, and the new bone formation in group C was lager than in group D or group A, and close to group B (P<0.05). After 12 weeks, in group A, defect without scaffold show a loose connect tissue filled in the areas. The medullary canal in group B was recanalizated. Defect in group C and D show a larger number of wove bone formation. The new wove bone formation in defect areas in group C was lager than D. The mechanical examination revealed ultimate strength at 12 weeks were group D>group C>group B>group A(P<0.05).Conclusion: Scaffold of n-HA/PLGA and β-TCP/PLGA incorporation with HBO and BMSCs were effective to treat seawater immersed bone defect, and n-HA/PLGA was more excellent than β-TCP/PLGA.
Is Preexisting Mental Illness Associated with Lower Patient Satisfaction for Older Trauma Patients? A Cross-sectional Descriptive Study
Authors: McGraw Constance , Pekarek Jennifer , Redmond Diane , Vogel Rebecca , Tanner Allen , Bar-Or David 
Published: January 2021

Abstract
Background: The purpose of this study was to examine if satisfaction with care differs among older trauma patients with and without preexisting mental illness (PMI+/PMI-).Methods: Data from two level I trauma centers were examined from 11/2016 through 12/2017. Trauma patients ≥55 years were included and satisfaction of those who had a diagnosis of mental illness prior to the trauma admission (PMI+) to those without a diagnosis (PMI-) (n=299; 62 PMI+ and 237 PMI-) were compared. Enrolled patients completed the Family Satisfaction with Advanced Care Cancer Scale Patient Survey (FAMCARE-P13) prior to discharge. Associations between mental illness status and patient baseline characteristics, overall mean satisfaction, and mean satisfaction by question were compared. Generalized linear models adjusted for differences in patient satisfaction by mental illness status. Analyses were stratified by hospital to account for the interaction between hospital and mental illness status.Results: Compared to PMI- patients, PMI+ patients were more likely to be younger, female, have multiple comorbidities, and to report lower overall satisfaction with care. Among PMI+ patients, the most common diagnoses were depression and anxiety. After adjustment, PMI+ was associated with lower patient satisfaction at hospital 1; after examining individual questions lower satisfaction was associated with information provided on procedures and questions surrounding “Physical care.” Conversely, PMI+ did not affect satisfaction at hospital 2 after adjustment.Conclusions: At hospital 1, room for improvement was identified in providing information about prognosis and procedures, symptom management, and continuity of care. Reexamining practices for older PMI+ trauma patients is warranted.
Predictive value of the neutrophil to lymphocyte ratio for disease deterioration and serious adverse outcomes in patients with COVID-19: a prospective cohort study
Authors: Zeng Zhi-Yong , Feng Shao-Dan , Chen Gong-Ping , Wu Jiang-Nan 
Published: January 2021

Abstract
Background: Early identification of patients who are at high risk of poor clinical outcomes is of great importance in saving the lives of patients with novel coronavirus disease 2019 (COVID-19) in the context of limited medical resources.Objective: To evaluate the value of the neutrophil to lymphocyte ratio (NLR), calculated at hospital admission and in isolation, for the prediction of the subsequent presence of disease progression and serious clinical outcomes (e.g., shock, death).Methods: We designed a prospective cohort study of 352 hospitalized patients with COVID-19 between January 9 and February 26, 2020, in Yichang City, Hubei Province. Patients with an NLR equal to or higher than the cutoff value derived from the receiver operating characteristic curve method were classified as the exposed group. The primary outcome was disease deterioration, defined as an increase of the clinical disease severity classification during hospitalization (e.g., moderate to severe/critical; severe to critical). The secondary outcomes were shock and death during the treatment.Results: During the follow-up period, 51 (14.5%) patients’ conditions deteriorated, 15 patients (4.3%) had complicated septic shock, and 15 patients (4.3%) died. The NLR was higher in patients with deterioration than in those without deterioration (median: 5.33 vs. 2.14, P <0.001), and higher in patients with serious clinical outcomes than in those without serious clinical outcomes (shock vs. no shock: 6.19 vs. 2.25, P <0.001; death vs. survival: 7.19 vs. 2.25, P <0.001). The NLR measured at hospital admission had high value in predicting subsequent disease deterioration, shock and death (all the areas under the curve > 0.80). The sensitivity of an NLR ≥ 2.6937 for predicting subsequent disease deterioration, shock and death was 82.0% (95% confidence interval, 69.0 to 91.0), 93.3% (68.0 to 100), and 92.9% (66.0 to 100), and the corresponding negative predictive values were 95.7% (93.0 to 99.2), 99.5% (98.6 to 100) and 99.5% (98.6 to 100), respectively.Conclusions: The NLR measured at admission and in isolation can be used to effectively predict the subsequent presence of disease deterioration and serious clinical outcomes in patients with COVID-19.
Detection of SARS-CoV-2 from Patient Fecal Samples by Whole Genome Sequencing
Authors: Papoutsis Andreas , Borody Thomas , Dolai Siba , Daniels Jordan , Steinberg Skylar , Barrows Brad , Hazan Sabine 
Published: January 2021

Abstract
Background

SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections. Here were sought to identify SARS-CoV-2 by enrichment NGS from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients.

Results

Study participants underwent testing for SARS-CoV-2 from fecal samples by whole genome enrichment NGS (n = 14), and RT-PCR nasopharyngeal swab analysis (n = 12). The concordance of SARS-CoV-2 detection by enrichment NGS from stools with RT-PCR nasopharyngeal analysis was 100%. Unique variants were identified in four patients, with a total of 33 different mutations among those in which SARS-CoV-2 was detected by whole genome enrichment NGS.

Conclusion

These results highlight the potential viability of SARS-CoV-2 in feces, its ongoing mutational accumulation, and its possible role in fecal-oral transmission. This study also elucidates the advantages of SARS-CoV-2 enrichment NGS, which may be a key methodology to document complete viral eradication.
Early visual quality outcomes after small-incision lenticule extraction surgery for correcting high myopic astigmatism
Authors: Hou Xiangtao , Du Kaixuan , Wen Dan , Hu Shengfa , Hu Tu , Li Chenling , Tang Yanhui , Wu Xiaoying 
Published: January 2021

Abstract
Background: To evaluate early optical quality outcomes after small-incision lenticule extraction (SMILE) surgery for correcting high myopic astigmatism.Methods: This retrospective study enrolled 55 eyes from 37 patients who had preoperative myopic astigmatism of ≥2.00 diopters (D) who had been treated with SMILE surgery. Preoperatively, the mean cylinder was -2.41 ± 0.54 D (range, -2.00 D to -4.50 D). The preoperative and postoperative visual outcomes, refraction, and higher-order aberration (HOA) at 1 and 3 months were compared. Refractive astigmatism changes were analyzed by the Alpins vector method.Results: Three months after SMILE surgery, the average cylinder was -0.14 ± 0.31 D, and the average astigmatism vector was -0.09 D × 6.34°. The angle of error (AofE) was limited to within ±10°, and the magnitude of error was limited to within ±1.0 D in all patients. The correction index (CI) was 0.98 ± 0.07, the index of success (IOS) was 0.08 ± 0.13, and the flattening index (FI) was 0.97 ± 0.07. Significant positive correlations were found between IOS and |AofE| (P = 0.000); negative correlations were found between FI and |AofE| (P = 0.000). The postoperative total HOA, spherical aberration, vertical coma aberration, and trefoil 30° were increased significantly compared with preoperative measurements, and the increase in HOA was closely related to preoperative astigmatism (P < 0.05).Conclusions: SMILE has preferable outcomes for correcting high myopic astigmatism. Axis rotation during the surgery might influence the undercorrection of astigmatism. The increase of HOA after surgery is related to preoperative astigmatism.