bluuebunny/crossref_metadata_2025_split huggingface dataset:
VARUS: sampling complementary RNA reads from the sequence read archive
Authors: Stanke Mario , Bruhn Willy , Becker Felix , Hoff Katharina J. 
Published: November 2019

Abstract

Background
Vast amounts of next generation sequencing RNA data has been deposited in archives, accompanying very diverse original studies. The data is readily available also for other purposes such as genome annotation or transcriptome assembly. However, selecting a subset of available experiments, sequencing runs and reads for this purpose is a nontrivial task and complicated by the inhomogeneity of the data.

Results
This article presents the software VARUS that selects, downloads and aligns reads from NCBI’s Sequence Read Archive, given only the species’ binomial name and genome. VARUS automatically chooses runs from among all archived runs to randomly select subsets of reads. The objective of its online algorithm is to cover a large number of transcripts adequately when network bandwidth and computing resources are limited. For most tested species VARUS achieved both a higher sensitivity and specificity with a lower number of downloaded reads than when runs were manually selected. At the example of twelve eukaryotic genomes, we show that RNA-Seq that was sampled with VARUS is well-suited for fully-automatic genome annotation with BRAKER.

Conclusions
With VARUS, genome annotation can be automatized to the extent that not even the selection and quality control of RNA-Seq has to be done manually. This introduces the possibility to have fully automatized genome annotation loops over potentially many species without incurring a loss of accuracy over a manually supervised annotation process.
Hooked on you: shape of attachment structures in cymothoid isopods reflects parasitic strategy
Authors: Baillie Charles , Welicky Rachel L. , Hadfield Kerry A. , Smit Nico J. , Mariani Stefano , D. Beck Robin M. 
Published: November 2019

Abstract

Background
Parasite attachment structures are critical traits that influence effective host exploitation and survival. Morphology of attachment structures can reinforce host specificity and niche specialisation, or even enable host switching. Therefore, it is important to understand the determinants of variation in attachment structures. Cymothoid isopods are striking ectoparasites of fishes that include the infamous ‘tongue-biters.’ They are known to parasitise hosts in one of four qualitatively distinct anatomical regions. Here, we quantify variation in cymothoid attachment structures — hook-like appendages called dactyli — and test whether differences in dactylus shape are correlated with parasite mode (where they attach), allometry, or both, using multivariate ordinary least squares regression. We also assess the influence of shared ancestry on shape using a molecular phylogeny to weight our models using phylogenetic generalised least squares regression.

Results
We find clear differences in shape between externally-attaching and internally-attaching cymothoids but also between anterior and posterior dactyli across various species with the same attachment mode. Allometric effects are significant for anterior but not posterior dactyli. Mouth-attaching species show greater shape variability than gill- and mouth-attaching species. We find no evidence that there are clade-specific patterns of association between parasite mode and dactylus shape.

Conclusions
Parasite mode appears to be the main driver of attachment morphology. This likely reflects several components of parasite ecology including feeding and functional demands of attachment in different microhabitats. Geometric morphometric approaches to the quantification of shape variation of simple structures is an effective tool that provides new insights into the evolvability of parasite attachment.
The dating of thrombus organization in cases of pulmonary embolism: an autopsy study
Authors: Mansueto Gelsomina , Costa Dario , Capasso Emanuele , Varavallo Federica , Brunitto Giuseppina , Caserta Rosanna , Esposito Salvatore , Niola Massimo , Sardu Celestino , Marfella Raffaele , Napoli Claudio , Paternoster Mariano 
Published: November 2019

Abstract

Background
Pulmonary embolism (PE) is associated to high mortality rate worldwide. However, the diagnosis of PE often results inaccurate. Many cases of PE are incorrectly diagnosed or missed and they are often associated to sudden unexpected death (SUD). In forensic practice, it is important to establish the time of thrombus formation in order to determine the precise moment of death. The autopsy remains the gold standard method for the identification of death cause allowing the determination of discrepancies between clinical and autopsy diagnoses. The aim of our study was to verify the morphological and histological criteria of fatal cases of PE and evaluate the dating of thrombus formation considering 5 ranges of time.

Methods
Pulmonary vessels sections were collected from January 2010 to December 2017. Sections of thrombus sampling were stained with hematoxylin and eosin. The content of infiltrated cells, fibroblasts and collagen fibers were scored using a semi-quantitative three-point scale of range values.

Results
The 30 autopsies included 19 males (63.3%) and 11 females (36.7%) with an average age of 64.5 ± 12.3 years. The time intervals were as follows: early (≤1 h), recent (> 1 h to 24 h), recent-medium (> 24 h to 48 h), medium (> 48 h to 72 h) and old (> 72 h). In the first hour, we histologically observed the presence of platelet aggregation by immunofluorescence method for factor VIII and fibrinogen. The presence of lymphocytes has been identified from recent thrombus (> 1 h to 24 h) and the fibroblast cells were peripherally located in vascular tissue between 48 and 72 h, whereas they resulted central and copious after 72 h.

Conclusions
After a macroscopic observation and a good sampling traditional histology, it is important to identify the time of thrombus formation. We identified histologically a range of time in the physiopathology of the thrombus (early, recent, recent-medium, medium, old), allowing to determine the dating of thrombus formation and the exact time of death.

Clinical trial number
NCT03887819.

Trial registration
The trial registry is Cliniclatrials.gov, with the unique identifying number NCT03887819. The date of registration was 03/23/2019 and it was “Retrospectively registered”.
Rapidly declining trend of signet ring cell cancer of the stomach may parallel the infection rate of Helicobacter pylori
Authors: Ohyama Hiroshi , Yoshimura Dai , Hirotsu Yosuke , Amemiya Kenji , Amano Hiroyuki , Miura Yuko , Ashizawa Hiroshi , Nakagomi Keiko , Takaoka Shinya , Hosoda Kenji , Suzuki Yoji , Oyama Toshio , Hada Masao , Kojima Yuichiro , Mochizuki Hitoshi , Omata Masao 
Published: November 2019

AbstractBackgroundStudies indicate that gastric cancer (GC) incidence has decreased, whereas signet ring cell carcinoma (SRC) incidence has increased. However, recent trends in GC incidence are unclear. We used our hospital cancer registry to evaluate the changes in the incidence of GC, SRC, and non-SRC (NSRC) over time in comparison to changes in theH. pyloriinfection rates over time.MethodsWe identified 2532 patients with GC enrolled in our registry between January 2007 and December 2018 and statistically analyzed SRC and NSRC incidence. TheH. pyloriinfection rate in patients with SRC was determined by serum anti-H. pyloriantibody testing, urea breath test, biopsy specimen culture, and immunohistochemical analysis (IHC) of gastric tissue. Additionally, genomic detection ofH. pyloriwas performed in SRCs by extracting DNA from formalin-fixed paraffin-embedded gastric tissue and targeting 16S ribosomal RNA ofH. pylori.ResultsOverall, 211 patients had SRC (8.3%). Compared with patients with NSRC, those with SRC were younger (P <  0.001) and more likely to be female (P <  0.001). Time series analysis using an autoregressive integrated moving average model revealed a significant decrease in SRC (P <  0.001) incidence; NSRC incidence showed no decline. There was no difference inH. pyloriinfection prevalence between the SRC and NSRC groups. IHC and genomic methods detectedH. pyloriin 30 of 37 (81.1%) SRCs.ConclusionsReduction inH. pyloriinfection prevalence may be associated with the decrease in the incidence of SRC, which was higher than that of NSRC.
Case report of congenital asplenia presenting with Haemophilus influenzae type a (Hia) sepsis: an emerging pediatric infection in Minnesota
Authors: Albrecht Tiffany , Poss Kristina , Issaranggoon Na Ayuthaya Satja , Triden Lori , Schleiss Katherine L. , Schleiss Mark R. 
Published: November 2019

Abstract

Background
In the pre-vaccine era, invasive disease with Haemophilus influenzae, type b (Hib) commonly presented with osteoarticular involvement. Haemophilus influenzae, type a (Hia) sepsis is a rare but emerging problem in recent years. Here, we report a case of sepsis with concomitant osteoarthritis due to Hia that was the presenting infectious disease manifestation of isolated asplenia in a young child. This unique observation adds to our understanding of sepsis and asplenia in children.

Case presentation
A five-year-old girl developed acute Hia bacteremia and sepsis. The patient developed arthritis shortly after onset of septic shock. Arthrocentesis was culture-negative, but given the difficulty differentiating between septic and reactive arthritis, prolonged antibiotic administration was provided for presumed osteoarticular infection, and the patient had an uneventful recovery. The finding of Howell-Jolly bodies on blood smear at the time of presentation prompted an evaluation that revealed isolated congenital asplenia. Evaluation for known genetic causes of asplenia was unrevealing. Investigation by the Minnesota Department of Health revealed an emergence of Hia infections over the past 5 years, particularly in children with an American Indian background.

Conclusions
Hia is an important pathogen in the differential diagnosis of invasive bacterial infections in children and shares overlap in clinical presentation and pathogenesis with Hib. Invasive Hia disease can be a presenting manifestation of asplenia in children. Hia is an emerging pathogen in American Indian children.
Prevalence of self-reported mental disorders in pregnancy and associations with adverse neonatal outcomes: a population-based cross-sectional study
Authors: Mongan David , Lynch Janine , Hanna Donncha , Shannon Ciaran , Hamilton Shona , Potter Claire , Gorman Colin , McCambridge Orlagh , Morrow Rachel , Mulholland Ciaran 
Published: November 2019

Abstract

Background
Mental disorders in pregnancy are common causes of morbidity and mortality with associated risks of adverse neonatal outcomes. Our aims were to evaluate the prevalence of self-reported mental disorders in women presenting to maternity services and to determine the association between history of self-reported maternal mental disorder and adverse neonatal outcomes.

Methods
Data on all singleton pregnancies known to maternity services in Northern Ireland over the period 2010 to 2015 were extracted from the Northern Ireland Maternity System (NIMATS), including frequency data for number of pregnancies where the mother reported a history of mental disorder. Odds ratios were derived from logistic regression analyses to determine the associations between self-reported maternal mental disorder and preterm birth, low infant birth weight and APGAR scores.

Results
In total, 140,569 singleton pregnancies were registered using NIMATS over this period. In 18.9% of these pregnancies, the mother reported a history of at least one mental disorder. After adjustment for potential confounding factors, significant associations were demonstrated between self-reported maternal mental disorder and preterm birth (odds ratio [OR] 1.31, 95% confidence interval [CI] 1.25–1.37), low infant birth weight (OR 1.29, 95% CI 1.21–1.38) and APGAR score < 7 at 1 min (OR 1.14, 95% CI 1.10–1.19) and 5 min (OR 1.23, 95% CI 1.12 to 1.34).

Conclusions
These findings emphasise the critical importance of routine enquiry regarding psychiatric history when women present to maternity services and the impact of maternal mental illnesses upon outcomes for their infants.
Potential genetic modifiers for somatic EGFR mutation in lung cancer: a meta-analysis and literature review
Authors: Cheng Yue I. , Gan Yun Cui , Liu Dan , Davies Michael P. A. , Li Wei Min , Field John K. 
Published: November 2019

Abstract

Background
Accumulating evidence indicates inherited risk in the aetiology of lung cancer, although smoking exposure is the major attributing factor. Family history is a simple substitute for inherited susceptibility. Previous studies have shown some possible yet conflicting links between family history of cancer and EGFR mutation in lung cancer. As EGFR-mutated lung cancer favours female, never-smoker, adenocarcinoma and Asians, it may be argued that there may be some underlying genetic modifiers responsible for the pathogenesis of EGFR mutation.

Methods
We searched four databases for all original articles on family history of malignancy and EGFR mutation status in lung cancer published up to July 2018. We performed a meta-analysis by using a random-effects model and odds ratio estimates. Heterogeneity and sensitivity were also investigated. Then we conducted a second literature research to curate case reports of familial lung cancers who studied both germline cancer predisposing genes and their somatic EGFR mutation status; and explored the possible links between cancer predisposing genes and EGFR mutation.

Results
Eleven studies have been included in the meta-analysis. There is a significantly higher likelihood of EGFR mutation in lung cancer patients with family history of cancer than their counterparts without family history, preferentially in Asians (OR = 1.35[1.06–1.71], P = 0.01), those diagnosed with adenocarcinomas ((OR = 1.47[1.14–1.89], P = 0.003) and those with lung cancer-affected relatives (first and second-degree: OR = 1.53[1.18–1.99], P = 0.001; first-degree: OR = 1.76[1.36–2.28, P < 0.0001]). Familial lung cancers more likely have concurrent EGFR mutations along with mutations in their germline cancer predisposition genes including EGFR T790 M, BRCA2 and TP53. Certain mechanisms may contribute to the combination preferences between inherited mutations and somatic ones.

Conclusions
Potential genetic modifiers may contribute to somatic EGFR mutation in lung cancer, although current data is limited. Further studies on this topic are needed, which may help to unveil lung carcinogenesis pathways. However, caution is warranted in data interpretation due to limited cases available for the current study.
Nebulized hypertonic saline 3% for 1 versus 3 days in hospitalized bronchiolitis: a blinded non-inferiority randomized controlled trial
Authors: Beal Gaëlle , Barbier Catherine , Thoret Sophie , Rubio Amandine , Bonnet Mathilde , Mazet Roseline , Ego Anne , Pin Isabelle 
Published: November 2019

Abstract

Background
The use and optimal duration of treatment with nebulized hypertonic saline (HS) in infants hospitalized for acute bronchiolitis is unclear. The objective was to compare the efficacy of 1 versus 3 days of nebulized 3% HS at 72 h of treatment. We conducted a blinded non-inferiority randomized controlled trial including infants aged less than 12 months old, hospitalized for a moderate bronchiolitis.

Methods
Nebulisations of 3% HS for 1 day were followed by either the continuation of 3% HS (HS3d group) or switched to 0.9% normal isotonic saline (HS1d group) for 2 days Randomization was performed according to a predefined list with a 1:1 ratio, obtained with a random generator number with blocks.. Main outcome was mean Wang clinical severity score (CSS) after 72 h of treatment.

Results
One hundred sixteen infants (HS1d n = 59 and HS3d n = 57), were included over two epidemic seasons from 2014 to 2016, but recruitement did not reach the planned sample size. The difference for the Wang CSS score in the HS3d vs HS1d group was 0.71 [IC 90% 0.1; 1.3], above the precluded value of 0.4 set in the protocol defining the non-inferiority of shorter treatment duration. Clinical remission was more rapidly obtained in the HS3d than in HS1d (2.3 ± 1.6 vs 2.9 ± 1.4 days, p = 0.04), with a non-significant tendency for less need of nutritional support and supplemental oxygen in HS3d group. Clinical worsening and treatment intolerance were similar in the 2 groups.

Conclusions
Despite being underpowered, results seem not to be in favour of reducing the duration of nebulised HS treatment from 3 to 1 day in acute moderate bronchiolitis.

Trial registration
Clinical trials NCT 02538458, October 2014.
Predictors of professional help-seeking for emotional problems in Afghan and Iraqi refugees in Australia: findings from the Building a New Life in Australia Database
Authors: Slewa-Younan Shameran , Rioseco Pilar , Guajardo Maria Gabriela Uribe , Mond Jonathan 
Published: November 2019

Abstract

Background
Refugees are particularly vulnerable to poor mental health outcomes due to exposure to pre migration trauma and post migration stressors. Research has demonstrated evidence to suggest that the professional help-seeking among refugee groups is low or problematic. This study seeks to examine help-seeking for emotional problems in two large samples of Iraqi and Afghan refugees in Australia.

Methods
This study uses data from two waves of the Building a New Life in Australia, the longitudinal study of Humanitarian migrants. The data was collected face-to-face between 2013 and 2016, among humanitarian migrants. All participants held a permanent protection visa and had arrived in Australia or been granted their visa between period of May to December 2013. The study sample included 1288 participants born in Iraq and Afghanistan (aged 15 and over). In the Wave 3 interview (2015–2016) participants reported on professional help received to deal with emotional problems.

Results
Approximately 36 and 37% of the Iraqi and Afghan groups respectively, reported seeking help for emotional problems. Within the Iraqi group, associations between mental health status, namely general psychological distress and PTSD and help-seeking were found but this was not present in the Afghan group, where age seemed to play a role in help-seeking. Frequency of help received was low with approximately 47% of the Iraqi and 57% of the Afghan groups reporting having received help 5 times or less in the last 12 months.

Conclusions
Findings from this study provide clear directions on areas where culturally tailored mental health promotion programs should target in these two refugee communities. Further, the differences in help-seeking behaviour of these communities should be noted by both clinicians and policy makers as efforts to provide culturally responsive mental health services.
The effectiveness, suitability, and sustainability of non-pharmacological methods of managing pain in community-dwelling older adults: a systematic review
Authors: Tang Shuk Kwan , Tse Mimi Mun Yee , Leung Sau Fong , Fotis Theofanis 
Published: November 2019

Abstract

Background
Pain is common in older adults. To maintain their quality of life and promote healthy ageing in the community, it is important to lower their pain levels. Pharmacological pain management has been shown to be effective in older adults. However, as drugs can have various side effects, non-pharmacological pain management is preferred for community-dwelling older adults. This systematic review evaluates the effectiveness, suitability, and sustainability of non-pharmacological pain management interventions for community-dwelling older adults.

Methods
Five databases, namely, CINHAL, Journals@Ovid, Medline, PsycInfo, and PubMed, were searched for articles. The criteria for inclusion were: full-text articles published in English from 2005 to February 2019 on randomized controlled trials, with chronic non-cancer pain as the primary outcome, in which pain was rated by intensity, using non-pharmacological interventions, and with participants over 65 years old, community-dwelling, and mentally competent. A quality appraisal using the Jadad Scale was conducted on the included articles.

Results
Ten articles were included. The mean age of the older adults was from 66.75 to 76. The interventions covered were acupressure, acupuncture, guided imagery, qigong, periosteal stimulation, and Tai Chi. The pain intensities of the participants decreased after the implementation of the intervention. The net changes in pain intensity ranged from − 3.13 to − 0.65 on a zero to ten numeric rating scale, in which zero indicates no pain and ten represents the worst pain.

Conclusions
Non-pharmacological methods of managing pain were effective in lowering pain levels in community-dwelling older adults, and can be promoted widely in the community.
Time to poor treatment outcome and its predictors among drug-resistant tuberculosis patients on second-line anti-tuberculosis treatment in Amhara region, Ethiopia: retrospective cohort study
Authors: Ketema Daniel Bekele , Muchie Kindie Fentahun , Andargie Asrat Atsedeweyn 
Published: November 2019

Abstract

Background
Treatment of drug-resistant tuberculosis is often more complex and toxic with longer treatment time and poor treatment outcomes including treatment failure or death. Monitoring drug-resistant tuberculosis therapy including early identification of prognostic factors and close monitoring of body weight in resource-limited settings is crucial to ensure successful treatment. Therefore, this study was conducted to assess time to poor treatment outcome which is defined as the proportion of all patients who died or failed treatment and its predictors among drug-resistant tuberculosis patients on second-line anti-tuberculosis treatment in Amhara region, Ethiopia.

Methods
A retrospective cohort study was conducted on all patients who started drug-resistant tuberculosis therapy from September 1, 2010 through December 31, 2017, at the University of Gondar Comprehensive Specialized Hospital, Boru-Meda Hospital, and Debre-Markos Referral Hospital in Amhara Region, Ethiopia. Data were entered using Epi-data Version 3.1 and analyzed using R version 3.41 software. The survival time was estimated using Kaplan-Meier survival curve and the survival time between different categorical variables were compared using the log rank test. Event time ratio with 95% confidence interval (CI) and p-value less than 0.05 were used to measure the strength of association and to declare statistically significant predictors respectively.

Results
A total of 508 patients with a median age of 28.5 [IQR: 22–40] years were included in this study. The overall cumulative survival probability of patients at the end of 24 months was 79% [95% CI,75,84%]. Rate of body weight change [Adjusted time ratio (ATR) = 5; 95% CI: 3.2, 7.7], secondary and above level of education [ATR = 2.3;95% CI:1.2,2.9], being non-anemic [ATR = 2.8,95% CI:1.2,3.8], being non-diabetic [ATR = 3.4;95% CI:1.3,8.8], without clinical complications [ATR = 7.6;95% CI:4.2,13.9], HIV negative [ATR = 1. 94:95% CI:1.35,2.35] and residing in rural [ATR = 0.51,95% CI:0.30,0.86] were predictors of time to poor treatment outcomes.

Conclusion
The survival rate of tuberculosis patients was higher at end of follow up relative to other studies. However, poor treatment outcome was higher in early phase of therapy. Educational level, rural residence, HIV/AIDS, diabetes mellitus, previous treatment, clinical complication, rate of body weight change and smoking history were significant predictors of time to poor treatment outcome. Therefore, intervention programs should focus on the identified factors to improve survival time of drug-resistant tuberculosis patients.