bluuebunny/crossref_metadata_2025_split huggingface dataset:
KIR B donors improve the outcome for AML patients given reduced intensity conditioning and unrelated donor transplantation
Authors: Weisdorf Daniel , Cooley Sarah , Wang Tao , Trachtenberg Elizabeth , Vierra-Green Cynthia , Spellman Stephen , Sees Jennifer A. , Spahn Ashley , Vogel Jenny , Fehniger Todd A. , Woolfrey Ann E. , Devine Steven M. , Ross Maureen , Waller Edmund K. , Sobecks Ronald M. , McGuirk Joseph , Oran Betul , Farag Sherif S. , Shore Tsiporah , Van Besien Koen , Marsh Steven G. E. , Guethlein Lisbeth A. , Parham Peter , Miller Jeffrey S. 
Published: February 2020

Abstract
Natural killer (NK) cell recognition and killing of target cells are enhanced when inhibitory killer immunoglobulin-like receptors (KIR) are unable to engage their cognate HLA class I ligands. The genes of the KIR locus are organized into either KIR B haplotypes, containing 1 or more activating KIR genes or KIR A haplotypes, which lack those genes. Analysis of unrelated donor (URD) hematopoietic cell transplants (HCT), given to acute myeloid leukemia (AML) patients between 1988 and 2009, showed that KIR B haplotype donors were associated with better outcomes, primarily from relapse protection. Most of these transplants involved marrow grafts, fully myeloablative (MAC) preparative regimens, and significant HLA mismatch. Because the practice of HCT continues to evolve, with increasing use of reduced intensity conditioning (RIC), peripheral blood stem cell grafts, and better HLA match, we evaluated the impact of URD KIR genotype on HCT outcome for AML in the modern era (2010-2016). This analysis combined data from a prospective trial testing URD selection based on KIR genotypes (n = 243) with that from a larger contemporaneous cohort of transplants (n = 2419). We found that KIR B haplotype donors conferred a significantly reduced risk of leukemia relapse and improved disease-free survival after RIC, but not MAC HCT. All genes defining KIR B haplotypes were associated with relapse protection, which was significant only in transplant recipients expressing the C1 epitope of HLA-C. In the context of current HCT practice using RIC, selection of KIR B donors could reduce relapse and improve overall outcome for AML patients receiving an allogeneic HCT.
High-risk LCH in infants is serially transplantable in a xenograft model but responds durably to targeted therapy
Authors: Lee Lynn H. , Krupski Christa , Clark Jason , Wunderlich Mark , Lorsbach Robert B. , Grimley Michael S. , Burwinkel Matthew , Nelson Adam , Kumar Ashish R. 
Published: February 2020

Abstract
Langerhans cell histiocytosis (LCH) is a rare hematologic neoplasm characterized by a clonal proliferation of Langerhans-like cells. Genomic profiling has identified recurrent somatic activating mutations in the mitogen-activated protein kinase pathway, which are targetable by small-molecule inhibitors. However, key questions such as the curative potential of targeted therapy and the cell of origin remain unanswered. In this study, we describe clinical outcomes of a series of pediatric patients with multisystem BRAF V600E–mutant LCH, as well as the results of accompanying murine xenograft experiments. Four infants with LCH (range, 7-11 months at diagnosis) and secondary hemophagocytic lymphohistiocytosis were referred to our institution and subsequently treated with the BRAF V600E–specific inhibitor dabrafenib. All patients achieved complete clinical responses by 8 weeks of therapy, with remissions lasting a median of 36 months (range, 27-42 months). One infant successfully discontinued therapy long-term upon achieving a molecular response by real-time quantitative polymerase chain reaction (RT-qPCR). We further characterized the disease-propagating cell population in a subset of these patients by transplanting whole bone marrow into immunodeficient mice. Xenografted animals exhibited decreased survival with hematologic abnormalities, splenomegaly, and histiocytic infiltrates in the bone marrow resembling human disease. This process could also be secondarily transplanted, resulting in a comparable disease latency with similar histologic findings. These data further support the presence of a disease-initiating cell in the bone marrow compartment. We demonstrate that despite aggressive disease behavior in a xenograft model, these patients can achieve sustained clinical remissions with targeted monotherapy, with a select subset achieving molecular responses by RT-qPCR.
Prevalence and associated factors of diarrhea among under-five children in Debre Berhan town, Ethiopia 2018: a cross sectional study
Authors: Shine Sisay , Muhamud Sindew , Adanew Solomon , Demelash Alebachew , Abate Makda 
Published: February 2020

Abstract
Background
Diarrhea is responsible for 525,000 children under-five deaths and 1.7 billion cases globally and is the second leading cause of death among children under-five every year. It is a major public health problem in low income countries like Ethiopia. The main aim of this study was to assess the prevalence of diarrhea and associated risk factors among children under-five in Debre Berhan Town, Ethiopia.

Methods
A community-based cross-sectional study was conducted in 420 parent or caretaker/children pairs in Debre Berhan town between 13 and 18 April 2018. A multi-stage sampling strategy was used to select the study participants. Data were collected using pre-tested and structured questionnaires. Data were entered in Epi-info computer software version 3.5.1 and exported to SPSS Window Version-16 for analysis. Adjusted odds ratio with 95% confidence intervals were used to assess the level of significance.

Results
The two week prevalence of diarrhea among children under-five was 16.4% (69/351). Children aged 7–11 months (adjusted odds ratio (AOR): 4.2, 95% confidence interval (CI): 1.2–15.3), being the second-born child (AOR: 3.9, 95%CI: 1.8–8.5), not vaccinated against rotavirus (AOR: 10.3, 95%CI: 3.2–91.3) and feeding children by hand (AOR: 2.5, 95%CI: 1.1–6.1) were significant predictors of diarrhea.

Conclusions
This study revealed that the two weeks period prevalence of diarrhea among children under-five years was 16.4%. Education programs on the importance of vaccination against rotavirus, increasing breast feeding frequency with complementary food after six months and the critical points of hand washing are recommended.
Randomized controlled trials for comparison of laparoscopic versus conventional open catheter placement in peritoneal dialysis patients: a meta-analysis
Authors: Sun Mei-Lan , Zhang Yong , Wang Bo , Ma Te-An , Jiang Hong , Hu Shou-Liang , Zhang Piao , Tuo Yan-Hong 
Published: February 2020

Abstract
Background
The application of laparoscopic catheterization technology in peritoneal dialysis (PD) patients has recently increased. However, the advantages and disadvantages of laparoscopic versus conventional open PD catheter placement are still controversial. The aim of this meta-analysis is to assess the complications of catheterization in PD patients and to provide a reference for choosing a PD-catheter placement technique in the clinic.

Methods
We searched numerous databases, including Embase, PubMed, CNKI and the Cochrane Library, for published randomized controlled trials (RCTs).

Results
Eight relevant studies (n = 646) were included in the meta-analysis. The pooled results showed a lower incidence of catheter migration (OR: 0.42, 95% CI: 0.19 to 0.90, P: 0.03) and catheter removal (OR: 0.41, 95% CI: 0.21 to 0.79, P: 0.008) but a higher incidence of bleeding (OR: 3.25, 95% CI: 1.18 to 8.97, P: 0.02) with a laparoscopic approach than with a conventional approach. There was no significant difference in the incidence of omentum adhesion (OR: 0.32, 95% CI: 0.05 to 2.10, P: 0.24), hernia (OR: 0.38, 95% CI: 0.09 to 1.68, P: 0.20), leakage (OR: 0.69, 95% CI: 0.38 to 1.26, P: 0.23), intestinal obstruction (OR: 0.96, 95% CI: 0.48 to 1.91, P: 0.90) or perforation (OR: 0.95, 95% CI: 0.06 to 15.42, P: 0.97). The statistical analysis showed no significant difference in early (OR: 0.44, 95% CI: 0.15 to 1.33, P: 0.15), late (OR: 0.89, 95% CI: 0.41 to 1.90, P: 0.76) or total (OR: 0.68, 95% CI: 0.42 to 1.12, P: 0.13) peritonitis infections between the 2 groups, and there are no no significant difference in early (OR: 0.39, 95% CI: 0.06 to 2.36, P: 0.30), late (OR: 1.35, 95% CI: 0.78 to 2.33, P: 0.16) or total (OR: 1.20, 95% CI: 0.71 to 2.02, P: 0.17) tunnel or exit-site infections between the 2 groups.

Conclusion
Laparoscopic catheterization and conventional open catheter placement in PD patients have unique advantages, but laparoscopic PD catheterization may be superior to conventional open catheter placement. However, this conclusion needs to be confirmed with further large-sample-size, multi-centre, high-quality RCTs.
A case report of an unusual non-mucinous papillary variant of CPAM type 1 with KRAS mutations
Authors: Koopman Timco , Rottier Bart L. , ter Elst Arja , Timens Wim 
Published: February 2020

Abstract
Background
congenital pulmonary airway malformation (CPAM) is the most frequent congenital lung disorder. CPAM type 1 is the most common subtype, typically having a cystic radiological and histological appearance. Mucinous clusters in CPAM type 1 have been identified as premalignant precursors for mucinous adenocarcinoma. These mucinous adenocarcinomas and the mucinous clusters in CPAM commonly harbor a specific KRAS mutation.

Case presentation
we present a case of a 6-weeks-old girl with CPAM type 1 where evaluation after lobectomy revealed a highly unusual complex non-mucinous papillary architecture in all cystic parts, in which both mucinous clusters and non-mucinous papillary areas harbored the known KRAS mutation.

Conclusions
we found that a KRAS mutation thought to be premalignant in mucinous clusters only, was also present in the other cyst lining epithelial cells of this unusual non-mucinous papillary variant of CPAM type 1, warranting clinical follow-up because of uncertain malignant potential.
Hierarchical structural component model for pathway analysis of common variants
Authors: Jiang Nan , Lee Sungyoung , Park Taesung 
Published: February 2020

Abstract
Background
Genome-wide association studies (GWAS) have been widely used to identify phenotype-related genetic variants using many statistical methods, such as logistic and linear regression. However, GWAS-identified SNPs, as identified with stringent statistical significance, explain just a small portion of the overall estimated genetic heritability. To address this ‘missing heritability’ issue, gene- and pathway-based analysis, and biological mechanisms, have been used for many GWAS studies. However, many of these methods often neglect the correlation between genes and between pathways.

Methods
We constructed a hierarchical component model that considers correlations both between genes and between pathways. Based on this model, we propose a novel pathway analysis method for GWAS datasets, Hierarchical structural Component Model for Pathway analysis of Common vAriants (HisCoM-PCA). HisCoM-PCA first summarizes the common variants of each gene, first at the gene-level, and then analyzes all pathways simultaneously by ridge-type penalization of both the gene and pathway effects on the phenotype. Statistical significance of the gene and pathway coefficients can be examined by permutation tests.

Results
Using the simulation data set of Genetic Analysis Workshop 17 (GAW17), for both binary and continuous phenotypes, we showed that HisCoM-PCA well-controlled type I error, and had a higher empirical power compared to several other methods. In addition, we applied our method to a SNP chip dataset of KARE for four human physiologic traits: (1) type 2 diabetes; (2) hypertension; (3) systolic blood pressure; and (4) diastolic blood pressure. Those results showed that HisCoM-PCA could successfully identify signal pathways with superior statistical and biological significance.

Conclusions
Our approach has the advantage of providing an intuitive biological interpretation for associations between common variants and phenotypes, via pathway information, potentially addressing the missing heritability conundrum.
DeepTRIAGE: interpretable and individualised biomarker scores using attention mechanism for the classification of breast cancer sub-types
Authors: Beykikhoshk Adham , Quinn Thomas P. , Lee Samuel C. , Tran Truyen , Venkatesh Svetha 
Published: February 2020

Abstract
Background
Breast cancer is a collection of multiple tissue pathologies, each with a distinct molecular signature that correlates with patient prognosis and response to therapy. Accurately differentiating between breast cancer sub-types is an important part of clinical decision-making. Although this problem has been addressed using machine learning methods in the past, there remains unexplained heterogeneity within the established sub-types that cannot be resolved by the commonly used classification algorithms.

Methods
In this paper, we propose a novel deep learning architecture, called (Deep learning for the TRactable Individualised Analysis of Gene Expression), which uses an attention mechanism to obtain personalised biomarker scores that describe how important each gene is in predicting the cancer sub-type for each sample. We then perform a principal component analysis of these biomarker scores to visualise the sample heterogeneity, and use a linear model to test whether the major principal axes associate with known clinical phenotypes.

Results
Our model not only classifies cancer sub-types with good accuracy, but simultaneously assigns each patient their own set of interpretable and individualised biomarker scores. These personalised scores describe how important each feature is in the classification of any patient, and can be analysed post-hoc to generate new hypotheses about latent heterogeneity.

Conclusions
We apply the framework to classify the gene expression signatures of luminal A and luminal B breast cancer sub-types, and illustrate its use for genes as well as the GO and KEGG gene sets. Using , we calculate personalised biomarker scores that describe the most important features for classifying an individual patient as luminal A or luminal B. In doing so, simultaneously reveals heterogeneity within the luminal A biomarker scores that significantly associate with tumour stage, placing all luminal samples along a continuum of severity.
Discovery of inflammatory bowel disease-associated miRNAs using a novel bipartite clustering approach
Authors: Altaf-Ul-Amin Md. , Karim Mohammad Bozlul , Hu Pingzhao , ONO Naoaki , Kanaya Shigehiko 
Published: February 2020

Abstract
Background
Multidimensional data mining from an integrated environment of different data sources is frequently performed in computational system biology. The molecular mechanism from the analysis of a complex network of gene-miRNA can aid to diagnosis and treatment of associated diseases.

Methods
In this work, we mainly focus on finding inflammatory bowel disease (IBD) associated microRNAs (miRNAs) by biclustering the miRNA-target interactions aided by known IBD risk genes and their associated miRNAs collected from several sources. We rank different miRNAs by attributing to the dataset size and connectivity of IBD associated genes in the miRNA regulatory modules from biclusters. We search the association of some top-ranking miRNAs to IBD related diseases. We also search the network of discovered miRNAs to different diseases and evaluate the similarity of those diseases to IBD.

Results
According to different literature, our results show the significance of top-ranking miRNA to IBD or related diseases. The ratio analysis supports our ranking method where the top 20 miRNA has approximately tenfold attachment to IBD genes. From disease-associated miRNA network analysis we found that 71% of different diseases attached to those miRNAs show more than 0.75 similarity scores to IBD.

Conclusion
We successfully identify some miRNAs related to IBD where the scoring formula and disease-associated network analysis show the significance of our method. This method can be a promising approach for isolating miRNAs for similar types of diseases.
Identification of DNA N6-methyladenine sites by integration of sequence features
Authors: Wang Hao-Tian , Xiao Fu-Hui , Li Gong-Hua , Kong Qing-Peng 
Published: February 2020

Abstract
Background
An increasing number of nucleic acid modifications have been profiled with the development of sequencing technologies. DNA N6-methyladenine (6mA), which is a prevalent epigenetic modification, plays important roles in a series of biological processes. So far, identification of DNA 6mA relies primarily on time-consuming and expensive experimental approaches. However, in silico methods can be implemented to conduct preliminary screening to save experimental resources and time, especially given the rapid accumulation of sequencing data.

Results
In this study, we constructed a 6mA predictor, p6mA, from a series of sequence-based features, including physicochemical properties, position-specific triple-nucleotide propensity (PSTNP), and electron–ion interaction pseudopotential (EIIP). We performed maximum relevance maximum distance (MRMD) analysis to select key features and used the Extreme Gradient Boosting (XGBoost) algorithm to build our predictor. Results demonstrated that p6mA outperformed other existing predictors using different datasets.

Conclusions
p6mA can predict the methylation status of DNA adenines, using only sequence files. It may be used as a tool to help the study of 6mA distribution pattern. Users can download it from https://github.com/Konglab404/p6mA.
Crohn’s disease: failure of a proprietary fluorescent in situ hybridization assay to detect M. avium subspecies paratuberculosis in archived frozen intestine from patients with Crohn’s disease.
Authors: Greenstein Robert J. , Su Liya , Fam Peter S. , Gurland Brooke , Endres Paul , Brown Sheldon T. 
Published: February 2020

Abstract
Objectives
Although controversial, there is increasing concern that Crohn’s disease may be a zoonotic infectious disease consequent to a mycobacterial infection. The most plausible candidate is M. avium subspecies paratuberculosis (MAP) that is unequivocally responsible for Johne’s disease in ruminants. The purpose of this study was to evaluate a proprietary (Affymetrix™ RNA view®) fluorescent in situ hybridization (FISH) assay for MAP RNA. Non-identifiable intestine from patients with documented Crohn’s disease was assayed according to the manufacturer’s instructions and with suggested modifications. Probes were custom designed for MAP and human β-actin (as the eukaryotic housekeeping gene) from published genomes.

Results
Repetitively, false positive signal was observed in our “No-Probe” negative control. Attempts were made to correct this according to the manufacturer’s suggestions (by modifying wash solutions, using recommended hydrochloric acid titration and different fluorescent filters). None prevented false positive signal in the “No-Probe” control. It is concluded that when performed according to manufactures instruction and with multiple variations on the manufactures recommended suggestions to correct for false positive signal, that the Affymetrix™ RNA view® cannot be used to detect MAP in pre-frozen resected intestine of humans with Crohn’s disease.
Bactericidal activity of hexylresorcinol lozenges against oropharyngeal organisms associated with acute sore throat
Authors: Matthews Derek , Adegoke Oluwajoba , Shephard Adrian 
Published: February 2020

Abstract
Objective
For the majority of people with acute sore throat, over-the-counter treatments represent the primary option for symptomatic relief. This study evaluated the in vitro bactericidal activity of lozenges containing the antiseptic hexylresorcinol against five bacteria associated with acute sore throat: Staphylococcus aureus, Streptococcus pyogenes, Moraxella catarrhalis, Haemophilus influenzae and Fusobacterium necrophorum.

Results
Hexylresorcinol 2.4 mg lozenges were dissolved into 5 mL of artificial saliva medium. Inoculum cultures were prepared in triplicate for each test organism to give an approximate population of 108 colony-forming units (cfu)/mL. Bactericidal activity was measured by log reduction in cfu. Greater than 3log10 reductions in cfu were observed at 1 min after dissolved hexylresorcinol lozenges were added to S. aureus (log10 reduction cfu/mL ± standard deviation, 3.3 ± 0.2), M. catarrhalis (4.7 ± 0.4), H. influenzae (5.8 ± 0.4) and F. necrophorum (4.5 ± 0.2) and by 5 min for S. pyogenes (4.3 ± 0.4). Hexylresorcinol lozenges achieved a > 99.9% reduction in cfu against all tested organisms within 5 min, which is consistent with the duration for a lozenge to dissolve in the mouth. In conclusion, in vitro data indicate that hexylresorcinol lozenges offer rapid bactericidal activity against organisms implicated in acute sore throat.
16S rRNA sequence data of Bombyx mori gut bacteriome after spermidine supplementation
Authors: Rajan Resma , Chunduri Alekhya Rani , Lima Anugata , Mamillapalli Anitha 
Published: February 2020

Abstract
Objectives
The silkworm Bombyx mori (B. mori) is an important domesticated lepidopteran model for basic and applied research. They produce silk fibres that have great economic value. The gut microbiome plays an important role in the growth of organisms. Spermidine (Spd) is shown to be important for the growth of all living cells. The effect of spermidine feeding on the gut microbiome of 5th instar B. mori larvae was checked. The B. mori gut samples from control and spermidine fed larvae were subjected to next-generation sequencing analysis to unravel changes in the bacterial community upon spermidine supplementation.

Data description
The changes in gut bacteriota after spermidine feeding is not studied before. B. mori larvae were divided into two groups of 50 worms each and were fed with normal mulberry leaves and mulberry leaves fortified with 50 µM spermidine. The gut tissues were isolated aseptically and total genomic DNA was extracted, 16S rRNA region amplified and sequenced using Illumina platform. The spermidine fed gut samples were shown to have abundance and diversity of the phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria.
Tuning high flow concurrency for MPTCP in data center networks
Authors: Huang Jiawei , Li Weihe , Li Qi , Zhang Tao , Dong Pingping , Wang Jianxin 
Published: February 2020

AbstractIn the data center networks, multipath transmission control protocol(MPTCP) uses multiple subflows to balance traffic over parallel paths and achieve high throughput. Despite much recent progress in improving MPTCP performance in data center, how to adjust the number of subflows according to network status has remained elusive. In this paper, we reveal theoretically and empirically that controlling the number of concurrent subflows is very important in reducing flow completion time (FCT) under network dynamic. We further propose a novel design called MPTCP_OPN, which adaptively adjusts the number of concurrent subflows according to the real-time network state and flexibly shifts traffic from congested paths to mitigate the high tail latency. Experimental results show that MPTCP_OPN effectively reduces the timeout probability caused by full window loss and flow completion time by up to 50% compared with MPTCP protocol.