bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virus expression detection reveals RNA-sequencing contamination in TCGA
Authors: Selitsky Sara R. , Marron David , Hollern Daniel , Mose Lisle E. , Hoadley Katherine A. , Jones Corbin , Parker Joel S. , Dittmer Dirk P. , Perou Charles M. 
Published: January 2020

Abstract
Background
Contamination of reagents and cross contamination across samples is a long-recognized issue in molecular biology laboratories. While often innocuous, contamination can lead to inaccurate results. Cantalupo et al., for example, found HeLa-derived human papillomavirus 18 (H-HPV18) in several of The Cancer Genome Atlas (TCGA) RNA-sequencing samples. This work motivated us to assess a greater number of samples and determine the origin of possible contaminations using viral sequences. To detect viruses with high specificity, we developed the publicly available workflow, VirDetect, that detects virus and laboratory vector sequences in RNA-seq samples. We applied VirDetect to 9143 RNA-seq samples sequenced at one TCGA sequencing center (28/33 cancer types) over 5 years.

Results
We confirmed that H-HPV18 was present in many samples and determined that viral transcripts from H-HPV18 significantly co-occurred with those from xenotropic mouse leukemia virus-related virus (XMRV). Using laboratory metadata and viral transcription, we determined that the likely contaminant was a pool of cell lines known as the “common reference”, which was sequenced alongside TCGA RNA-seq samples as a control to monitor quality across technology transitions (i.e. microarray to GAII to HiSeq), and to link RNA-seq to previous generation microarrays that standardly used the “common reference”. One of the cell lines in the pool was a laboratory isolate of MCF-7, which we discovered was infected with XMRV; another constituent of the pool was likely HeLa cells.

Conclusions
Altogether, this indicates a multi-step contamination process. First, MCF-7 was infected with an XMRV. Second, this infected cell line was added to a pool of cell lines, which contained HeLa. Finally, RNA from this pool of cell lines contaminated several TCGA tumor samples most-likely during library construction. Thus, these human tumors with H-HPV or XMRV reads were likely not infected with H-HPV 18 or XMRV.
Coexpression and Transcriptome analyses identify active Apomixis-related genes in Paspalum notatum leaves
Authors: de Oliveira Fernanda A. , Vigna Bianca B. Z. , da Silva Carla C. , Fávero Alessandra P. , de Matta Frederico P. , Azevedo Ana L. S. , de Souza Anete P. 
Published: January 2020

Abstract
Background
Paspalum notatum exhibits both sexual and apomictic cytotypes and, thus, is considered a good model for studies of apomixis because it facilitates comparative approaches. In this work, transcriptome sequencing was used to compare contrasting P. notatum cytotypes to identify differential expression patterns and candidate genes involved in the regulation of expression of this trait.

Results
We built a comprehensive transcriptome using leaf and inflorescence from apomictic tetraploids and sexual diploids/tetraploids and a coexpression network based on pairwise correlations between transcript expression profiles. We identified genes exclusively expressed in each cytotype and genes differentially expressed between pairs of cytotypes. Gene Ontology enrichment analyses were performed to better interpret the data. We de novo assembled 114,306 reference transcripts. In total, 536 candidate genes possibly associated with apomixis were detected through statistical analyses of the differential expression data, and several interacting genes potentially linked to the apomixis-controlling region, genes that have already been reported in the literature, and their neighbors were transcriptionally related in the coexpression network.

Conclusions
Apomixis is a highly desirable trait in modern agriculture due to the maintenance of the characteristics of the mother plant in the progeny. The reference transcriptome, candidate genes and their coexpression network identified in this work represent rich resources for future grass breeding programs.
High concentration of coagulase-negative staphylococci carriage among bioaerosols of henhouses in Central China
Authors: Lu Yuanqing , Lu Qin , Cheng Yiluo , Wen Guoyuan , Luo Qingping , Shao Huabin , Zhang Tengfei 
Published: January 2020

Abstract
Background
Coagulase-negative staphylococci (CoNS) are a group of opportunistic pathogens, which are widely spread in the environment. Animal breeding is an important source of pathogen spreading. However, the concentration and characteristics of CoNS in the bioaerosols of henhouses are unclear.

Results
In this study, we showed that CoNS were significantly increased in bioaerosols of henhouses during the first 60 days, and reached 2.0 × 106 CFU/m3, which account for 75.4% of total bacteria. One hundred and two CoNS isolates from bioaerosols and nasal swabs of farmers were further identified, covering seven species. Among these, 41.2% isolates were Staphylococcus sciuri, which was the predominant species, followed by S. equorum, S. saprophyticus, S. haemolyticus, S. xylosus, S. arlettae and S. gallinarum. There were high rates of resistance to oxacillin in CoNS (49.0%), which were defined as Methicillin-Resistant CoNS (MRCoNS), and 36.3% isolates contained resistance gene mecA. Bioaerosol infection models showed that, chickens exposed to aerosolized S. sciuri had significant induction of inflammatory cytokines interleukin (IL)-1β, IL-6, IL-8 and IL-10 at 5 days post-infection (dpi) in lungs and at 7 dpi in spleens.

Conclusions
We reported a high concentration of CoNS in henhouses, and S. sciuri was the preponderant CoNS species. Antibiotic resistance analysis and bioaerosols infection of CoNS further highlighted its hazards on resistance and immunological challenge. These results suggested that, CoNS in bioaerosols could be one serious factor in the henhouses for not only poultry industry but also public health.
Efficacy of continuous epidural infusion with epidural electric stimulation compared to that of conventional continuous epidural infusion for acute herpes zoster management: a retrospective study
Authors: Lee Chung Hun , Choi Sang Sik , Lee Mi Kyoung , Lee Yeon Joo , Park Jong Sun 
Published: January 2020

Abstract
Background
Continuous epidural infusions are commonly used in clinical settings to reduce the likelihood of transition to postherpetic neuralgia via pain control. The purpose of this study was to compare the efficacy of conventional continuous epidural infusion to that of continuous epidural infusion in which the catheter is guided by electric stimulation to areas with neurological damage for the treatment of zoster-related pain and prevention of postherpetic neuralgia.

Methods
We analyzed the medical records of 114 patients in this study. The patients were divided into two groups: contrast (conventional continuous epidural infusion) and stimulation (continuous epidural infusion with epidural electric stimulation). In the contrast group, the position of the epidural catheter was confirmed using contrast medium alone, whereas in the stimulation group, the site of herpes zoster infection was identified through electric stimulation using a guidewire in the catheter. Clinical efficacy was assessed using a numerical rating scale (pain score) up to 6 months after the procedures. We compared the percentage of patients who showed complete remission (pain score less than 2 and no further medication) in each group. We also investigated whether the patients required additional interventional treatment due to insufficient pain control during the 6-month follow-up period after each procedure.

Results
After adjusting for confounding variables, the pain score was significantly lower in the stimulation group than in the contrast group for 6 months after the procedure. After adjustment, the odds of complete remission were 1.9-times higher in the stimulation group than in the contrast group (95% confidence interval [CI]: 0.81–4.44, P = 0.14). Patients in the contrast group were significantly more likely to require other interventions within 6 months of the procedure than patients in the stimulation group (odds ratio: 3.62, 95% CI: 1.17–11.19, P = 0.03).

Conclusion
Epidural drug administration to specific spinal segments using electric stimulation catheters may be more helpful than conventional continuous epidural infusion for improving pain and preventing postherpetic neuralgia in the acute phase of herpes zoster.
Immune classification for the PD-L1 expression and tumour-infiltrating lymphocytes in colorectal adenocarcinoma
Authors: Noh Byeong-Joo , Kwak Jae Young , Eom Dae-Woon 
Published: January 2020

Abstract
Background
Colorectal adenocarcinoma is the third most common cancer worldwide and a leading cause of cancer-related death. The recent emergence of diverse immunotherapeutic agents has made it crucial to interpret a complex tumour microenvironment intermingled with tumour-infiltrating immune cells to predict the immunotherapeutic response rate. However, in colorectal adenocarcinoma, studies are lacking that provide detailed analyses of programmed death-ligand 1 (PD-L1) and tumour-infiltrating lymphocytes (TIL) to elucidate their prognostic values and to identify immunotherapy-targetable subgroups, preferably with multiple immune-related biomarkers. In the present study, we categorize colorectal adenocarcinomas into four types of tumour immune microenvironments according to PD-L1 expression and TIL, analyse their prognostic values, and propose an immunotherapy-targetable subgroup.

Methods
Formalin-fixed, paraffin-embedded tissue samples of surgically resected primary colorectal adenocarcinomas (n = 489) were obtained and arrayed on tissue microarray blocks. Immunohistochemical stains for PD-L1, programmed cell death protein 1 (PD-1), cluster of differentiation 8 (CD8), and deficient mismatch repair (dMMR) were performed and evaluated.

Results
Tumour microenvironment immune type (TMIT) I (PD-L1-positive tumour cells and CD8-high TIL) and type II (PD-L1-negative tumour cells and CD8-low TIL) showed the best and worst prognoses, respectively. PD-L1 overexpression was significantly associated with dMMR status. PD-L1 immunoreactivity was positively correlated with TIL having CD8 or PD-1 overexpression.

Conclusions
TMIT I subgroup showed stronger CD8/PD-L1/PD-1 signalling interaction compared to the other TMIT. Therefore, we propose that the TMIT I subgroup is a candidate TMIT to predict effective response rate for existing immune checkpoint inhibitors and determine targetable subgroups for emerging therapies.
Online self-compassion training to improve the wellbeing of youth with chronic medical conditions: protocol for a randomised control trial
Authors: Finlay-Jones Amy , Boyes Mark , Perry Yael , Sirois Fuschia , Lee Rachael , Rees Clare 
Published: January 2020

Abstract
Background
Chronic medical conditions (CMCs) affect up to 35% of children and adolescents. Youth with chronic medical conditions are at an increased risk of psychological distress and reduced health-related quality of life, and report rates of mental illness up to double that of their physically healthy peers. Accessible, evidence-based interventions for young people with chronic illness are urgently required to improve their mental health and daily functioning. Self-compassion involves taking a mindful, accepting approach to difficult experiences, being aware that one is not alone in one’s suffering, and being kind and understanding with oneself during challenging times. Self-compassion shares strong associations with mental health outcomes among young people and preliminary work indicates that interventions that build self-compassion have the potential to substantially improve youth mental health. Self-compassion is also associated with better physical and mental health outcomes among individuals living with CMCs. While face-to-face self-compassion training is available, there are several barriers to access for youth with CMCs. Online self-compassion training potentially offers an accessible alternative for this high-risk group.

Methods
Self-Compassion Online (SCO) is a self-compassion program that has been tested with a non-clinical adult group. For the proposed trial, a reference group of youth (16–25 years) with chronic illness reviewed the program and proposed adaptations to improve its suitability for youth with chronic illness. In alignment with the SPIRIT Checklist, this paper outlines the protocol for a CONSORT-compliant, single-blind randomised controlled trial to test the efficacy of the adapted program, relative to a waitlist control, for improving self-compassion, wellbeing, distress, emotion regulation, coping and quality of life among young Australians with CMCs. Mechanisms of action and feasibility of SCO will be analysed using quantitative data and participant interviews, respectively. Finally, cost-utility will be analysed using health-related quality of life data.

Discussion
The SCO program could provide a scalable solution for improving psychological outcomes and quality of life among youth with chronic illness. The proposed trial will be the first to determine its efficacy for improving these outcomes, relative to waitlist control.

Trial registration
The trial was registered on the Australian New Zealand Clinical Trials Registry on the 11th April 2019, ACTRN12619000572167.
Protocol version: Version 2, 21 December 2019.
Studying the urine microbiome in superficial bladder cancer: samples obtained by midstream voiding versus cystoscopy
Authors: Hourigan Suchitra K. , Zhu Wei , S.W.Wong Wendy , Clemency Nicole C. , Provenzano Marina , Vilboux Thierry , Niederhuber John E. , Deeken John , Chung Simon , McDaniel-Wiley Kim , Trump Donald 
Published: January 2020

Abstract
Background
Preliminary data suggest that the urinary microbiome may play a role in bladder cancer. Information regarding the most suitable method of collecting urine specimens is needed for the large population studies needed to address this. To compare microbiome metrics resulting from 16S ribosomal RNA gene sequencing between midstream, voided specimens and those obtained at cystoscopy.

Methods
Adults, with a history of superficial urothelial cell carcinoma (non-muscle invasive bladder cancer) being followed with periodic surveillance cystoscopy had a urine sample collected by a mid-stream, voided technique and then from the bladder at cystoscopy. Urine samples underwent 16S ribosomal RNA gene sequencing on the Illumina MiSeq platform.

Results
22 subjects (8 female, 14 male) were included. There was no significant difference in beta diversity (diversity between samples) in all samples between collection methods. However, analysis by sex revealed a difference between voided and cystoscopy samples from the same individual in males (p = 0.006, Adonis test) but not in females (p = 0.317, Adonis test). No differences were seen by collection method in any alpha diversity (diversity within a sample) measurement or differential abundance of taxa.

Conclusions
Beta diversity of the urine microbiome did differ by collection method for males only. This suggests that the urinary microbiomes of the two collection methods are not equivalent to each other, at least in males, which is the sex that bladder cancer occurs most frequently in. Therefore, the same collection method within a given study should be used.
Exploring barriers to seeking health care among Kenyan Somali women with female genital mutilation: a qualitative study
Authors: Kimani Samuel , Kabiru Caroline W. , Muteshi Jacinta , Guyo Jaldesa 
Published: January 2020

AbstractBackgroundFemale genital mutilation/cutting (FGM/C) is a cultural practice associated with health consequences, women rights and deprivation of dignity. Despite FGM/C-related health consequences, circumcised women may encounter additional challenges while seeking interventions for reproductive health problems. Experiences of women/girls while accessing health services for reproductive health problems including FGM/C-related complications in poor, remote and hard to reach areas is poorly understood. We sought to explore barriers to care seeking among Somali women with complications related to FGM/C in public health facilities in Kenya.MethodsWe drew on qualitative data collected from purposively selected women aged 15–49 years living with FGM/C, their partners, community leaders, and health providers in Nairobi and Garissa Counties. Data were collected using in-depth interviews (n = 10), key informant interviews (n = 23) and 20 focus group discussions. Data were transcribed and analyzed thematically using NVivo version 12.ResultsBarriers were grouped into four thematic categories. Structural barriers to care-seeking, notably high cost of care, distance from health facilities, and lack of a referral system. Concerns regarding perceived quality of care also presented a barrier. Women questioned health professionals’ and health facilities’ capacity to offer culturally-sensitive FGM/C-specific care, plus ensuring confidentiality and privacy. Women faced socio-cultural barriers while seeking care particularly cultural taboos against discussing matters related to sexual health with male clinicians. Additionally, fear of legal sanctions given the anti-FGM/C law deterred women with FGM/C-related complications from seeking healthcare.ConclusionStructural, socio-cultural, quality of service, and legal factors limit health seeking for reproductive health problems including FGM/C-related complications. Strengthening health system should consider integration of FGM/C-related interventions with existing maternal child health services for cost effectiveness, efficiency and quality care. The interventions should address health-related financial, physical and communication barriers, while ensuring culturally-sensitive and confidential care.
Lessons learned, challenges and outlooks for decision-making after a decade of experience monitoring the impact of indoor residual spraying in Benin, West Africa
Authors: Akogbéto Martin C. , Dagnon Fortuné , Aïkpon Rock , Ossé Razaki , Salako Albert S. , Ahogni Idelphonse , Akinro Bruno , Sominahouin André , Sidick Aboubakar , Tokponnon Filémon , Padonou Germain G. 
Published: January 2020

Abstract
Background
Since 2008, Indoor Residual Spraying (IRS) has been performed in Benin in 19 districts, including 4 in southern Benin, 9 in Atacora, and 8 in Atacora, Alibori and Donga in northern Benin. However, Benin still struggles with questions about IRS cost–benefit and epidemiological impact. Lessons learned and challenges from 10 years of IRS in Benin to be shared with the stakeholders involved in vector control implementation for decision-making.

Methods
Entomological parameters have been assessed entomological parameters in IRS communes since 2008. In all IRS intervention communes, decreases in human biting rate (HBR) of Anopheles gambiae, blood feeding inhibition and entomological inoculation rate (EIR) as compared to control district have been measured.

Results
EIR was reduced by 80–90%, which is encouraging, but should be observed with caution because: (i) the reduction may be insufficient to decrease epidemiological indicators given that the residual EIR in IRS districts is still higher than it is in some regions of stable malaria; (ii) the reduction in EIR is based on comparisons with control communes, but it is difficult to select control areas with the same environmental characteristics as intervention areas; (iii) despite the reduction, half of all mosquitoes that entered IRS-treated houses succeeded in taking human blood meals. Further, there are behaviours among Benin’s population that limit IRS efficacy, including recent data showing that > 90% of people are not protected by IRS between 7 and 10 p.m. This is due to the fact that they remain outdoors and that most people are not protected from mosquito bites after 10 p.m. because they either sleep outdoors without IRS protection or indoors without an ITN. Moreover, people have large amounts of clothing hanging on walls where mosquitoes can rest instead of IRS-treated walls. Finally, other components are important to consider in implementing IRS among which: (i) Vector resistance management strategies are sometimes poorly understood; this is actually different from the need to replace one insecticide with another after the emergence of resistance; (ii) African countries should prepare to finance IRS themselves.

Conclusion
To curtail residual malaria transmission, additional interventions able to target vectors escaping IRS should be prioritized.
Child health, household environment, temperature and rainfall anomalies in Honduras: a socio-climate data linked analysis
Authors: Bradatan Cristina , Dennis Jeffrey A. , Flores-Yeffal Nadia , Swain Sharmistha 
Published: January 2020

Abstract
Background
As climate research continues to highlight the global shifts in temperature and precipitation, more research is needed to understand how climate anomalies impact human health outcomes. In this paper, we analyze one of the paths through which climate anomalies affect health (in particular, child’s health) within one of poorest countries in the world (Honduras).

Methods
Using the GPS location of the household, we link information on child health and house amenities from the Honduras Demographic Health Survey 2011–2012 dataset (a nationally representative sample) with climate data (1981–2012) from the Climate Research Unit (CRU TS3.21). We use generalized estimating equations for binary logistic models and spatial association to analyze these data.

Results
We show that 1) areas experiencing significant temperature anomalies are also the ones with the worst child respiratory problems and 2) in households with poor amenities – such as access to sanitation and clean water, children tend to have a high incidence of respiratory diseases and diarrhea .

Conclusions
We conclude that, as climate change increases the incidence of climate anomalies, tackling in advance those household environmental factors responsible for poor child health outcomes (better sanitation and clean cooking fuel) can prevent a further deterioration of children’s health in Honduras.