bluuebunny/crossref_metadata_2025_split huggingface dataset:
The European Registry for Patients with Mechanical Circulatory Support (EUROMACS): first EUROMACS Paediatric (Paedi-EUROMACS) report
Authors: de By Theo M M H , Schweiger Martin , Waheed Hina , Berger Felix , Hübler Michael , Özbaran Mustafa , Maruszewski Bohdan , Napoleone Carlo Pace , Loforte Antonio , Meyns Bart , Miera Oliver ,   Contributing clinicians, Antretter Herwig , Krachak Valeriya , Vanbelleghem Yves , Meyns Bart , Němec Petr , Netuka Ivan , Guihaire Julien , Sandica Eugen , Miera Oliver , Stiller Brigitte , Bodor Gabor , Amodeo Antonio , Iacovoni Attilio , Pace Napoleone Carlo , Loforte Antonio , Pya Yuri , Bogers Ad , Ramjankhan Faiz , Maruszewski Bodhan , Guereta Luis , Schweiger Martin , Carrel Thierry , Sezgin Atilla , Özbaran Mustafa , Pektok Erman 
Published: July 2018

Abstract

OBJECTIVES:
EUROMACS is a registry of the European Association for Cardio-Thoracic Surgery (EACTS) whose purpose is to gather clinical data related to durable mechanical circulatory support for scientific purposes and to publish annual reports. Because the treatment of children with end-stage heart failure has several significantly different characteristics than the treatment of adults, data and outcomes of interventions are analysed in this dedicated paediatric report.

METHODS:
Participating hospitals contributed pre-, peri- and long-term postoperative data on mechanical circulatory support implants to the registry. Data for all implants in paediatric patients (≤19 years of age) performed from 1 January 2000 to 31 December 2017 were analysed. This report includes updates of patient characteristics, implant frequency, outcome (including mortality rates, transplants and recovery rates) as well as adverse events.

RESULTS:
Twenty-five hospitals contributed 237 registered implants in 210 patients (81 ♀, 129 ♂) to the registry. The most frequent diagnosis was any form of cardiomyopathy (71.4%) followed by congenital heart disease (18.6%). Overall mean support time on a device was 11.6 months (±16.5 standard deviation). A total of 173 children (82.4%) survived to transplant, recovery or are ongoing; 37 patients (17.6%) died while on support within the observed follow-up time. At 12 months 38% of patients received transplants, 7% were weaned from their device and 15% died. At 24 months, 51% of patients received transplants, 17% died while on support, 22% were on a device and 9% were explanted due to myocardial recovery. The adverse events rate per 100 patient-months was 11.97 for device malfunction, 2.83 for major bleeding, 2.83 for major infection and 1.52 for neurological events within the first 3 months after implantation.

CONCLUSIONS:
The first paediatric EUROMACS report reveals a low transplant rate in European countries within the first 2 years of implantation compared to US data. The 1-year survival rate seems to be satisfactory. Device malfunction including pump chamber changes due to thrombosis was the most frequent adverse event.
A Longitudinal Study of the Association Between Persistent Pathogens and Incident Depression Among Older U.S. Latinos
Authors: Simanek Amanda M , Zheng Cheng , Yolken Robert , Haan Mary , Aiello Allison E 
Published: July 2018

Abstract
Depression is estimated to affect more than 6.5 million Americans 65 years of age and older and compared with non-Latino whites older U.S. Latinos have a greater incidence and severity of depression, warranting further investigation of novel risk factors for depression onset among this population. We used data on 771/1,789 individuals ≥60 years of age from the Sacramento Area Latino Study on Aging (1998–2008) who were tested for cytomegalovirus (CMV), herpes simplex virus, varicella zoster, Helicobacter pylori, Toxoplasma gondii, and C-reactive protein (CRP) and interleukin-6 (IL-6) level. Among those without elevated depressive symptoms at baseline, we examined the association between each pathogen, inflammatory markers and incident depression over up to nearly 10 years of follow-up using discrete-time logistic regression. We found that only CMV seropositivity was statistically significantly associated with increased odds of incident depression (odds ratio [OR]: 1.38, 95% confidence interval [CI]: 1.00–1.90) in the total sample as well as among women only (OR: 1.70, 95% CI: 1.01–2.86). These associations were not mediated by CRP or IL-6 levels. Our findings suggest that CMV seropositivity may serve as an important risk factor for the onset of depression among older U.S. Latinos, but act outside of inflammatory pathways.
Burden of Human Papillomavirus (HPV)-Related Cancers Attributable to HPVs 6/11/16/18/31/33/45/52 and 58
Authors: de Sanjosé Silvia , Serrano Beatriz , Tous Sara , Alejo Maria , Lloveras Belén , Quirós Beatriz , Clavero Omar , Vidal August , Ferrándiz-Pulido Carla , Pavón Miquel Ángel , Holzinger Dana , Halec Gordana , Tommasino Massimo , Quint Wim , Pawlita Michael , Muñoz Nubia , Bosch Francesc Xavier , Alemany Laia ,   RIS HPV TT, VVAP and Head and Neck study groups, Kulkarni Amit 
Published: July 2018

Abstract

Background
Many countries, mainly high- and upper-middle income, have implemented human papillomavirus (HPV) vaccination programs, with 47 million women receiving the full course of vaccine (three doses) in 2014. To evaluate the potential impact of HPV vaccines in the reduction of HPV-related disease, we aimed to estimate the HPV type distribution and burden of anogenital and head and neck cancers attributable to HPV types (HPVs 16/18/31/33/45/52/58/6/11) included in currently licensed HPV vaccines.

Methods
In all, 18 247 formalin-fixed paraffin-embedded specimens were retrieved from 50 countries. HPV DNA detection and typing were performed with the SPF-10 PCR/DEIA/LiPA25 system. With the exception of cervical cancer, HPV DNA-positive samples were additionally subjected to HPV E6*I mRNA detection and/or p16INK4a immunohistochemistry. For cervical cancer, estimates were based on HPV DNA, whereas for other sites, estimates were based on HPV DNA, E6*I mRNA, and p16INK4a biomarkers.

Results
The addition of HPVs 31/33/45/52/58 to HPVs 16/18/6/11 in the nonavalent HPV vaccine could prevent almost 90% of cervical cancer cases worldwide. For other sites, the nonavalent HPV vaccine could prevent 22.8% of vulvar, 24.5% of penile, 60.7% of vaginal, 79.0% of anal cancers, 21.3% of oropharyngeal, 4.0% of oral cavity, and 2.7% of laryngeal cancer cases.

Conclusions
Our estimations suggest a potential impact of the nonavalent HPV vaccine in reducing around 90% of cervical cancer cases and a global reduction of 50% of all the cases at HPV-related cancer sites.
Gut Microbiota and Clinical Features Distinguish Colonization With Klebsiella pneumoniae Carbapenemase-Producing Klebsiella pneumoniae at the Time of Admission to a Long-term Acute Care Hospital
Authors: Seekatz Anna M , Bassis Christine M , Fogg Louis , Moore Nicholas M , Rhee Yoona , Lolans Karen , Weinstein Robert A , Lin Michael Y , Young Vincent B , Hayden Mary K ,   Centers for Disease Control and Prevention Epicenters Program
Published: July 2018

AbstractBackgroundIdentification of gut microbiota features associated with antibiotic-resistant bacterial colonization may reveal new infection prevention targets.MethodsWe conducted a matched, case–control study of long-term acute care hospital (LTACH) patients to identify gut microbiota and clinical features associated with colonization by Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae (KPC-Kp), an urgent antibiotic resistance threat. Fecal or rectal swab specimens were collected and tested for KPC-Kp; 16S rRNA gene-based sequencing was performed. Comparisons were made between cases and controls in calibration and validation subsamples using microbiota similarity indices, logistic regression, and unit-weighted predictive models.ResultsCase (n = 32) and control (n = 99) patients had distinct fecal microbiota communities, but neither microbiota diversity nor inherent clustering into community types distinguished case and control specimens. Comparison of differentially abundant operational taxonomic units (OTUs) revealed 1 OTU associated with case status in both calibration (n = 51) and validation (n = 80) subsamples that matched the canonical KPC-Kp strain ST258. Permutation analysis using the presence or absence of OTUs and hierarchical logistic regression identified 2 OTUs (belonging to genus Desulfovibrio and family Ruminococcaceae) associated with KPC-Kp colonization. Among clinical variables, the presence of a decubitus ulcer alone was independently and consistently associated with case status. Combining the presence of the OTUs Desulfovibrio and Ruminococcaceae with decubitus ulcer increased the likelihood of KPC-Kp colonization to &gt;38% in a unit-weighted predictive model.ConclusionsWe identified microbiota and clinical features that distinguished KPC-Kp gut colonization in LTACH patients, a population particularly susceptible to KPC-Kp infection. These features may warrant further investigation as markers of risk for KPC-Kp colonization.
LAMOST J221750.59+210437.2: A new member of carbon-enhanced extremely metal-poor stars with excesses of Mg and Si
Authors: Aoki Wako , Matsuno Tadafumi , Honda Satoshi , Ishigaki Miho N , Li Haining , Suda Takuma , Kumar Yerra Bharat 
Published: July 2018

Abstract
We report on the elemental abundances of the carbon-enhanced metal-poor (CEMP) star J2217+2104, discovered through our metal-poor star survey with LAMOST and Subaru. This object is a red giant and has extremely low Fe abundance ([Fe/H] = −4.0) and very large enhancement of C, N, and O with excesses of Na, Mg, Al, and Si. This star is a new example of a small group of such CEMP stars identified by previous studies. We find a very similar abundance pattern for O–Zn in this class of objects that shows enhancement of elements up to Si and normal abundance of Ca and Fe-group elements. Whereas the C/N ratio is different among these stars, the (C + N)/O ratio is similar. This suggests that similar abundance ratios of C were also yielded, relative to O–Zn in progenitors, and was later affected by the CN-cycle. By contrast, the heavy neutron-capture elements Sr and Ba are deficient in J2217+2104, compared to the four objects in this class previously studied. This indicates that the neutron-capture process in the early Galaxy, presumably the r-process, has no direct connection to the phenomenon that has formed such CEMP stars. Comparisons of the abundance pattern that are well determined for such CEMP stars with those of supernova nucleosynthesis models constrain the progenitor mass to be about 25 M⊙, which is not particularly different from the typical mass of progenitors expected for extremely metal-poor stars in general.
Blood Procalcitonin Levels and Duration of Antibiotics in Neonatal Sepsis
Authors: Mathur N B , Behera Bijaylaxmi 
Published: July 2018

Abstract

Objective
To determine the time to normalization of procalcitonin (PCT) levels and duration of antibiotics in neonatal sepsis.

Methods
A prospective observational study design was used. The participants included were neonates with sepsis. The primary outcome measure was time to normalization of PCT levels and duration of antibiotics following clinical resolution.

Results
Time to normalization of PCT levels was 9.6 ± 4.2 days in neonates with septic shock, 6.2 ± 2.5 days in neonates without shock, 9.6 ± 3.1 days in neonates with culture-positive sepsis and 6.4 ± 3.1 days in neonates with culture-negative sepsis. Time to normalization of PCT levels according to the stage of systemic inflammatory response syndrome was 5.8 ± 2.8 days in neonates with sepsis, 6.1 ± 3.1 days in those with sepsis syndrome, 6.3 ± 3.3 days in those with early septic shock and 9.4 ± 3.6 days in those with multiorgan dysfunction syndrome. There was no morbidity and mortality in any neonate in the 4-week follow-up.

Conclusion
The duration of antibiotics can be determined by observing the time to normalization of PCT following clinical resolution of sepsis.
Transient elastography can stratify patients with Child–Pugh A cirrhosis according to risk of early decompensation
Authors: Dillon Audrey , Galvin Zita , Sultan Alyshah A. , Harman David , Guha Indra N. , Stewart Stephen 
Published: July 2018

Background
Compensated cirrhosis has a variable prognosis depending on stage. There are currently no straightforward and robust tools in clinical practice to predict decompensation in Child–Pugh A cirrhosis. We set out to determine whether transient elastography (TE) could be used across liver disease aetiologies to determine risk of decompensation.

Patients and methods
Participants were enrolled at two sites (Dublin and Nottingham) and followed up for a minimum of 2 years. The primary outcome of the study was liver decompensation, defined as the development of overt hepatic encephalopathy or ascites or presentation with bleeding varices. All patients received a TE examination to measure liver stiffness measurement (LSM) and had routine blood measurements taken at the baseline visit and on each subsequent visit.

Results
In 259 participants, the overall rate of liver-related outcome was 31 per 1000 person-years (95% confidence interval: 19–47 per 1000 person-years). Of the total population, 6 and 11% developed a liver-related outcome within 2 and 4 years of follow-up, respectively. There were no events in the population with a LSM less than 21 kPa. A LSM of more than 35 kPa was associated with a decompensation risk of 39% at 4 years. For each unit increase in the LSM above 20 kPa, the risk of liver-related outcome increased by 6% (hazard ratio=1.06; 95% confidence interval: 1.04–1.82) after adjusting for age, sex Mayo End Liver Disease Score, cohort source and aetiology.

Conclusion
The risk of liver decompensation increased with increasing LSM in mixed aetiology compensated cirrhosis. LSM may be used to risk stratify patients, potentially reassure patients with low scores, and select patients with higher scores for experimental therapeutic studies with acceptable timelines.
Additional role of liver stiffness measurement in stratifying residual hepatocellular carcinoma risk predicted by serum biomarkers in chronic hepatitis B patients under antiviral therapy
Authors: Song Byeong G. , Sinn Dong H. , Chi Sangah , Kim Kyunga , Kang Wonseok , Gwak Geum-Youn , Paik Yong-Han , Choi Moon S. , Lee Joon H. , Koh Kwang C. , Paik Seung W. 
Published: July 2018

Background
The risk of hepatocellular carcinoma (HCC) remains among patients who are treated with antiviral therapy (AVT). The degree of liver fibrosis has been suggested as an important biomarker to stratify the risk of developing HCC. We tested whether liver stiffness (LS) measured using transient elastography is useful over two noninvasive serum biomarkers of fibrosis [the aspartate aminotransferase to platelet ratio index (APRI) and fibrosis-4 (FIB-4)].

Patients and methods
A retrospective cohort of 1014 CHB patients who were under AVT with nucleos(t)ide analogs for at least a year was analyzed. The risk of HCC development according to serum biomarkers (APRI and FIB-4) and LS was compared.

Results
The HCC risk was higher for those with a higher degree of liver fibrosis, as estimated by the LS, APRI, and FIB-4. When the two serum biomarkers were used to group the patients, the 3-year HCC incidence rates were 7.3, 3.0, and 1.3% for both high APRI (≥0.5) and FIB-4 (≥1.45) scores, either a high APRI or FIB-4 score, and both low APRI and FIB-4 scores, respectively (P<0.001). Among the 758 patients with discordant or both low APRI and FIB-4 scores, the LS value was high (>6) for a significant proportion of the patients (39.9%). The HCC risk was significantly different according to the LS value (3-year HCC incidence rate of 1.1, 2.0, and 6.8% for LS <6, 6–9, and >9, respectively, P<0.001).

Conclusion
Among CHB patients under AVT, LS could stratify risk for HCC, including patients with discordant or both low APRI and FIB-4 score. This finding indicates that LS measurement plays an additional role over the serum biomarkers in stratifying the residual risk of HCC.
Epidemiology of Disease and Mortality From a PICU in Mozambique*
Authors: Punchak Maria , Hall Kaitlin , Seni Amir , Buck W. Chris , DeUgarte Daniel A. , Hartford Emily , Kelly Robert B. , Muando Valéria I. 
Published: July 2018

Objectives:
Delivery of pediatric critical care in low-income countries is limited by a lack of infrastructure, resources, and providers. Few studies have analyzed the epidemiology of disease associated with a PICU in a low-income country. The aim of this study was to document the primary diagnoses and the associated mortality rates of patients presenting to a tertiary PICU in Mozambique in order to formulate quality improvement projects through an international academic partnership. We hypothesized that the PICU mortality rate would be high and that sepsis would be a common cause of death.

Design:
Retrospective, observational study.

Setting:
Tertiary academic PICU.

Patients:
All admitted PICU patients.

Interventions:
All available data collection forms containing demographic and clinical data of patients admitted to the PICU at Hospital Central de Maputo, Mozambique from January 2013 to December 2013 were analyzed retrospectively.

Measurements and Main Results:
The patient median age was 2 years (57% male). The most common primary diagnoses were malaria (22%), sepsis (18%), respiratory tract infections (12%), and trauma (6%). The mortality rate was 25%. Mortality rates were highest among patients with sepsis (59%), encephalopathy (56%), noninfectious CNS pathologies (33%), neoplastic diseases (33%), meningitis/encephalitis (29%), burns (26%), and cardiovascular pathologies (26%). The median length of PICU stay was 2 days. HIV exposure/infection had a nonstatistically significant association with mortality. Patients admitted for burns had the highest median length of PICU stay (4 d). Most trauma admissions were male (75%), and approximately half of all trauma admissions had an associated head injury (55%).

Conclusions:
Infectious disease and trauma were highly represented in this Mozambican PICU, and overall mortality was high compared with high-income countries. With this knowledge, targeted collaborative projects in Mozambique can now be created and modified. Further research is needed to monitor the potential benefits of such interventions.
Assembly of Mb-size genome segments from linked read sequencing of CRISPR DNA targets
Authors: Shin GiWon , Greer Stephanie U. , Xia Li C. , Lee HoJoon , Zhou Jun , Boles T. Christian , Ji Hanlee P. 
Published: July 2018

ABSTRACTWe developed a targeted sequencing method for intact high molecular weight (HMW) DNA targets as large as 0.2 Mb. This process uses HMW DNA isolated from intact cells, custom designed Cas9-guide RNA complexes to generate 0.1 – 0.2 Mb DNA targets, electrophoretic isolation of the DNA targets and sequencing with barcode linked reads. We used alignment methods as well as local assembly of the target regions to identify haplotypes and structural variants (SVs) across multi-Megabase genomic regions. To demonstrate the performance of this approach, we designed three assays that covered a 0.2 Mb region surrounding the BRCA1 gene, a set of 40 overlapping 0.2 Mb targets covering the entire 4-Mb MHC locus, and 18 well-characterized structural variants. Using the highly characterized NA12878 genome, we achieved on-target coverage of more than 50X, while overall whole genome coverage was approximately 4X. We generated haplotypes that completely covered each targeted locus, with a maximum size of 4 Mb (for the MHC region). This method detected structural variants such as deletions and inversions with determination of the exact breakpoints and genotypes. Even breakpoints inside highly homologous segmental duplications are precisely determined with our high-quality assemblies. Overall, this is a new method to sequence large DNA segments.
A chromosome scale assembly of the model desiccation tolerant grass Oropetium thomaeum
Authors: VanBuren Robert , Wai Ching Man , Keilwagen Jens , Pardo Jeremy 
Published: July 2018

AbstractOropetium thomaeum is an emerging model for desiccation tolerance and genome size evolution in grasses. A high-quality draft genome of Oropetium was recently sequenced, but the lack of a chromosome scale assembly has hindered comparative analyses and downstream functional genomics. Here, we reassembled Oropetium, and anchored the genome into ten chromosomes using Hi-C based chromatin interactions. A combination of high-resolution RNAseq data and homology-based gene prediction identified thousands of new, conserved gene models that were absent from the V1 assembly. This includes thousands of new genes with high expression across a desiccation timecourse. The sorghum and Oropetium genomes have a surprising degree of chromosome-level collinearity, and several chromosome pairs have near perfect synteny. Other chromosomes are collinear in the gene rich chromosome arms but have experienced pericentric translocations. Together, these resources will be useful for the grass comparative genomic community and further establish Oropetium as a model resurrection plant.
Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data
Authors: Lin Chieh , Bar-Joseph Ziv 
Published: July 2018

AbstractMotivationMethods for reconstructing developmental trajectories from time series single cell RNA-Seq (scRNA-Seq) data can be largely divided into two categories. The first, often referred to as pseudotime ordering methods, are deterministic and rely on dimensionality reduction followed by an ordering step. The second learns a probabilistic branching model to represent the developmental process. While both types have been successful, each suffers from shortcomings that can impact their accuracy.ResultsWe developed a new method based on continuous state HMMs (CSHMMs) for representing and modeling time series scRNA-Seq data. We define the CSHMM model and provide efficient learning and inference algorithms which allow the method to determine both the structure of the branching process and the assignment of cells to these branches. Analyzing several developmental single cell datasets we show that the CSHMM method accurately infers branching topology and correctly and continuously assign cells to paths, improving upon prior methods proposed for this task. Analysis of genes based on the continuous cell assignment identifies known and novel markers for different cell types.AvailabilitySoftware and Supporting website:www.andrew.cmu.edu/user/chiehll/CSHMM/Contactzivbj@cs.cmu.eduSupplementary informationSupplementary data are available atBioinformaticsonline.
Batch Effect Removal via Batch-Free Encoding
Authors: Shaham Uri 
Published: July 2018

AbstractBiological measurements often contain systematic errors, also known as “batch effects”, which may invalidate downstream analysis when not handled correctly. The problem of removing batch effects is of major importance in the biological community. Despite recent advances in this direction via deep learning techniques, most current methods may not fully preserve the true biological patterns the data contains. In this work we propose a deep learning approach for batch effect removal. The crux of our approach is learning a batch-free encoding of the data, representing its intrinsic biological properties, but not batch effects. In addition, we also encode the systematic factors through a decoding mechanism and require accurate reconstruction of the data. Altogether, this allows us to fully preserve the true biological patterns represented in the data. Experimental results are reported on data obtained from two high throughput technologies, mass cytometry and single-cell RNA-seq. Beyond good performance on training data, we also observe that our system performs well on test data obtained from new patients, which was not available at training time. Our method is easy to handle, a publicly available code can be found at https://github.com/ushaham/BatchEffectRemoval2018.