bluuebunny/crossref_metadata_2025_split huggingface dataset:
Donor pretreatment and machine perfusion: current views
Authors: O’Neill Stephen , Oniscu Gabriel C. 
Published: December 2019

Purpose of review
To summarise recently published studies of donor pretreatment and machine perfusion strategies in kidney transplantation.

Recent findings
The sparsity of donor pretreatment trials has resulted in the re-analysis of already existing data, and RCTs are urgently needed to reinvigorate this aspect of donor research. Uncontrolled donation after circulatory death kidney transplantation has the highest risk of delayed graft function and graft failure, and recent studies have reported that normothermic regional perfusion improves graft function and survival in this setting. Hypothermic machine perfusion reduces delayed graft function following deceased donor kidney transplantation across donor types but unanswered questions still remain regarding its use. The use of oxygenated hypothermic machine perfusion appears to improve graft function in controlled donation after circulatory death mediated by a reduction in acute rejection. Ex-situ normothermic perfusion is emerging and while technically challenging it may facilitate the delivery of pretreatments.

Summary
RCTs are urgently needed to reinvigorate research into donor pretreatment and to establish the place of specific preservation techniques in deceased donor kidney transplantation.
Should living donor liver transplant selection be subject to the same restrictions as deceased donor transplant?
Authors: Kwon Yong K. , Etesami Kambiz , Genyk Yuri 
Published: December 2019

Purpose of review
In the United States, most of the liver allografts come from deceased donors, and our current liver recipient selection process is heavily centered on the ethical principle of utility to maximize the net benefit to the liver recipient community as a group rather than individuals due to the organ scarcity. Although living donor liver transplantation contributes less than 5% of total liver transplant in the United States, these living donor recipients are being subjected to the same selection process designed to benefit the group as a whole rather than the individuals. We would like to examine if these recipients who have living donors should be subjected to the same selection process.

Recent findings
There are several disease processes where liver transplantation is the only curative option, and recent studies have shown clear survival benefits with liver transplantation.

Summary
For those who have living donors, different selection criteria based on their specific disease, not based on the principle of utilization should be used to evaluate their candidacy.
Health Impacts of Early Complementary Food Introduction Between Formula‐fed and Breastfed Infants
Authors: Rippey Phyllis L.F. , Aravena Fabiola , Nyonator John Paul 
Published: December 2019

ABSTRACTBackground:Global health agencies agree that infants should not be fed complementary foods before 4 to 6 months of age. However, given the World Health Organization (WHO) definition of complementary food as “anything other than breast milk,” little is known about the relative risks of formula compared with other complementary foods on infant health. This article aims to fill this gap in the literature, by assessing how differences in the timing of the introduction of nonformula complementary food between breastfed and formula‐fed infants impacts infant health.Methods:Eight health outcomes by complementary food introduction, breast‐feeding, formula feeding, and mixed feeding (breastfed and formula‐fed) were predicted using logistic regression with generalized estimating equations on the newborn through 6‐month waves of the Infant Feeding Practices Study II (IFPS‐II).Results:Complementary foods increased the likelihood for all health risks measured. Given greater prevalence of early complementary food introduction among formula‐fed infants, most health differences between breast‐feeding groups shift to nonsignificance in full models, with the exception of higher rates of hard stool and cough/wheeze among formula‐fed and mixed‐fed infants but lower rates of diarrhea (LO = −0.577; 95% confidence interval [CI] = −1.074 to 0.080) and runny nose or cold (LO = −3.19; 95% CI = −0.552 to −0.086) for mixed‐fed than breastfed infants.Conclusions:Our results confirm health benefits of exclusive breast‐feeding and that the introduction of complementary foods before 4 to 6 months poses a greater risk to infant health than does formula. Greater attention to the early introduction of complementary foods is needed in research and clinical practice.
Effect of Definitions of Acute Gastroenteritis Episodes Using Symptom Diaries in Paediatric Cohorts
Authors: Mihala Gabor , Grimwood Keith , Morley Carla , Lambert Stephen B. , Ware Robert S. 
Published: December 2019

ABSTRACTEstimates of acute gastroenteritis (AGE) burden are difficult to compare between studies because of inconsistent definitions describing this illness. AGE definitions used in prospective, community‐based childhood cohort studies were identified by searching databases for studies that collected daily observations of AGE symptoms. Disease definitions and refractory periods were extracted. Data from the Australian community‐based Observational Research in Childhood Infectious Diseases birth cohort were used to calculate AGE incidence and duration using identified AGE definitions, and the World Health Organization definition for diarrhoea. Eight distinct AGE definitions were identified. All included loose stools and 7 included vomiting as symptoms. The refractory period separating episodes ranged from 1 to 21 days. When applied to the Observational Research in Childhood Infectious Diseases dataset, AGE incidence ranged from 0.8 to 2.6 episodes per child‐year‐at‐risk, a 3‐fold relative difference. Direct comparisons of rates from different cohorts can only be undertaken if a standard definition for AGE is adopted.
Blending Evidence-Based Practice and Lean Six Sigma Methodology to Reduce Hospital-Acquired Pressure Injuries in a Progressive Care Unit
Authors: Gallo Ana-Maria , Doyle Rochelle Anne Catahay , Beckman Jennifer , Lizarraga Cabiria G. 
Published: December 2019

Background:
Hospital-acquired pressure injuries (HAPIs) continue to challenge acute care facilities. Best practice to reduce HAPI includes assessment, documentation, positioning, and treatment.

Local Problem:
In spite of using evidence-based practices, the hospital's gastrointestinal/genitourinary progressive care unit had more HAPIs each month than the other units in the hospital.

Methods:
A combination of Lean Six Sigma and evidence-based practice was used to decrease HAPIs.

Interventions:
The T3 program (turn, touch, and tidy) was developed to address the areas of concern identified in the root cause analysis.

Results:
HAPIs were reduced from 22 in the previous 2 quarters to zero for 3 consecutive quarters with a cost avoidance to $379 767.

Conclusions:
The successful implementation of the T3 program was the result of blending Lean Six Sigma and evidence-based practice.
Assessment of the Cost-Effectiveness of a Brief Video Intervention for Sexually Transmitted Disease Prevention
Authors: Williams Austin M. , Gift Thomas L. , O'Donnell Lydia N. , Rietmeijer Cornelis A. , Malotte C. Kevin , Margolis Andrew D. , Warner Lee 
Published: December 2019

Background
Cost-effective, scalable interventions are needed to address high rates of sexually transmitted diseases (STDs) in the United States. Safe in the City, a 23-minute video intervention designed for STD clinic waiting rooms, effectively reduced new infections among STD clinic clients. A cost-effectiveness analysis of this type of intervention could inform whether it should be replicated.

Methods
The cost-effectiveness of a brief video intervention was calculated under a baseline scenario in which this type of intervention was expanded to a larger patient population. Alternative scenarios included expanding the intervention over a longer period or to more clinics, including HIV prevention benefits, and operating the intervention part time. Program costs, net costs per STD case averted, and the discounted net cost of the intervention were calculated from a health sector perspective across the scenarios. Monte Carlo simulations were used to calculate 95% confidence intervals surrounding the cost-effectiveness measures.

Results
The net cost per case averted was $75 in the baseline scenario. The net cost of the intervention was $108,015, and most of the alternative scenarios found that the intervention was cost saving compared with usual care.

Conclusions
Single session, video-based interventions can be highly cost effective when implemented at scale. Updated video-based interventions that account for the changing STD landscape in the United States could play an important role in addressing the recent increases in infections.
Facial Asymmetry in Unilateral Duane Retraction Syndrome
Authors: Akbari Mohamad Reza , Khorrami-Nejad Masoud , Aghazadeh Amiri Mohamad , Akbarzadeh Baghban Alireza , Khosravi Bahram , Nourizad Sima 
Published: December 2019

SIGNIFICANCEThe overall objective of this study was to evaluate facial asymmetry in patients with unilateral Duane retraction syndrome (DRS). The results showed a high frequency of facial asymmetry parameters of the opposite side of head turn in unilateral DRS patients.PURPOSEThe purposes of this study were to evaluate the characteristics of facial asymmetry in unilateral exotropic and esotropic DRS and to compare the findings with orthotropic subjects.METHODSThis cross-sectional comparative case series study was performed in 44 consecutive patients with head turn caused by DRS and 44 orthotropic subjects from 2016 to 2019. Four pictures were taken from the patients' faces. The first and second pictures were taken when patients had head turn and when the head was completely straight for calculating the facial angle and relative facial size, respectively. The third and fourth pictures were taken when the head was positioned downward (to compare the size of the cheek) and upward (to evaluate nose asymmetry).RESULTSThe mean ± SD age of DRS patients and orthotropic subjects was 16.23 ± 9.92 and 20.68 ± 11.82 years, respectively. The frequency of facial asymmetry and all facial parameters (cheek compression, nasal tip and columella deviation, and compression of one of the nostrils) was significantly higher in DRS patients compared with orthotropic subjects (P< .001). In DRS patients with facial asymmetry, columella and nasal tip deviation (P= .006) and cheek and face compression (P= .03) were significantly more prevalent in the opposite direction of head turn. In the DRS group, the mean ± SD age of the patients with and without facial asymmetry was 17.37 ± 9.76 and 7.40 ± 6.54 years, respectively (P= .02).CONCLUSIONSThe frequency of facial asymmetry and all facial parameters was significantly higher in DRS patients compared with orthotropic subjects. In unilateral DRS patients, the face was more commonly affected on the opposite side of head turn.
Contrast Energy and Contour Interaction
Authors: Bedell Harold E. , Siderov John , Pluháček František 
Published: December 2019

SIGNIFICANCE
Contour interaction describes an impairment of visual acuity produced by nearby flanking features, which exerts a significant impact in many clinical tests of visual acuity. Our results indicate that the magnitude of interaction depends either on the flanker contrast energy (i.e., the product of flanker contrast and width) or the flanker contrast alone, depending on the contrast energy of the flankers.

PURPOSE
The discrimination of acuity targets is impaired by the presence of nearby flanking contours, a phenomenon known as contour interaction.

METHODS
In this study, we measured percent correct identification for threshold size, high-contrast Sloan letters at the fovea and at 5° in the inferior visual field for different combinations of flanking-bar width, and Weber contrast corresponding to specific fixed values of contrast energy (width × contrast, in %-min arc).

RESULTS
For flanking bars with low-contrast energy, contour interaction exhibited no systematic dependence on the flanking-bar width. However, when the flanking bars had higher contrast energy, narrower high-contrast bars produced significantly greater contour interaction than wider bars of lower contrast.

CONCLUSIONS
The results are consistent with the interpretation that contour interaction depends primarily on the contrast energy of flanking contours when their contrast energy is low. As the contrast energy of the flanking contours increases, the magnitude of contour interaction depends on the flanker contrast. For high-contrast flanking contours, the magnitude of contour interaction saturates when the width of the flanking contours is approximately 20% of letter size.
Towards establishing internal validity for correlated gene expression measures in imaging genomics of functional networks: why distance corrections and external face validity alone fall short. Reply to “Distance is not everything in imaging genomics of functional networks: reply to a commentary on Correlated gene expression supports synchronous activity in brain networks”
Authors: Pantazatos Spiro P. , Schmidt Mike 
Published: December 2019

AbstractThe primary claim of the Richiardi et. al. 2015 Science article1is that a measure of correlated gene expression, significant strength fraction (SSF), is related to resting state fMRI (rsfMRI) networks. However, there is still debate about this claim and whether spatial proximity, in the form of contiguous clusters, accounts entirely, or only partially, for SSF2,3. Here, thirteen distributed networks were simulated by combining 34 contiguous clusters randomly placed throughout cortex, with resulting edge distance distributions similar to rsfMRI networks. Cluster size was modulated (6-15mm radius) to test its influence on SSF false positive rate (SSF-FPR) among the simulated ‘noise’ networks. The contribution of rsfMRI networks on SSF-FPR was examined by comparing simulations using: 1) all cortical samples 2) all samples with non-rsfMRI cluster centers and 3) only non-rsfMRI samples. Results show that SSF-FPR is influenced only by cluster size (r>0.9, p<0.001), not by rsfMRI samples. Simulations using 14mm radius clusters most resembled rsfMRI networks. When thresholding at p<10-4, the SSF-FPR was 0.47. Genes that maximize SF have highglobalspatial autocorrelation. In conclusion, SSF is unrelated to rsfMRI networks. The main conclusion of Richiardi et. al. 2015 is based on a finding that is ∼50% likely to be a false positive, not less than 0.01% as originally reported in the article1. We discuss why distance corrections alone and external face validity are insufficient to establish a trustworthy relationship between correlated gene expression measures and rsfMRI networks, and propose more rigorous approaches to preclude common pitfalls in related studies.
An evolution-based high-fidelity method of epistasis measurement: theory and application to influenza
Authors: Pedruzzi Gabriele , Rouzine Igor M. 
Published: December 2019

AbstractLinkage effects in a multi-locus population strongly influence its evolution. The models based on the traveling wave approach enable us to predict the speed of evolution and the statistics of phylogeny. However, predicting the evolution of specific sites and pairs of sites in the multi-locus context remains a mathematical challenge. In particular, the effects of epistasis, the interaction of gene regions contributing to phenotype, is difficult both to predict theoretically and detect experimentally in sequence data. A large number of false interactions arise from stochastic linkage effects and indirect interactions, which mask true interactions. Here we develop a method to filter out false-positive interactions. We start by demonstrating that the averaging of the two-way haplotype frequencies over a multiple independent populations is necessary but not sufficient, because it still leaves high numbers of false interactions. To compensate for this residual stochastic noise, we develop a triple-way haplotype method isolating true interactions. The fidelity of the method is confirmed using simulated genetic sequences evolved with a known epistatic network. The method is then applied to a large database sequences of neurominidase protein of influenza A H1N1 obtained from various geographic locations to infer the epistatic network responsible for the difference between the pre-pandemic virus and the pandemic strain of 2009. These results present a simple and reliable technique to measure site-site interactions from sequence data.Author’s summaryInteraction of genomic sites creating “fitness landscape” is very important for predicting the escape of viruses from drugs and immune response and for passing through fitness valleys. Many efforts have been invested into measuring these interactions from DNA sequence sets. Unfortunately, reproducibility of the results remains low, due partly to a very small fraction of interaction pairs, and partly to stochastic noise intrinsic for evolution masking true interactions. Here we propose a method based on analysis of genetic sequences at three genomic sites to clean stochastic linkage and apply it to influenza virus sequence data.
A Holistic Analysis of the Intestinal Stem Cell Niche Network
Authors: Hansen Darrick M. , Giles Paloma Ivon Meneses , He Xi C. , Chen Shiyuan , Paulson Ariel , Dekaney Christopher M. , Wang Jennifer , Hu Deqing , Venkatraman Aparna , Kim Woosook , Kaddis John , Olack Barbara J. , Dunn James C.Y. , Kuo Calvin , Henning Susan , Hanash Alan M. , Houchen Courtney W. , Lynch John , Martin Martin G. , Niland Joyce C. , Stelzner Matthias , Wong Melissa , Wang Timothy C. , Yu Jian , Yan Kelley , Li Linheng 
Published: December 2019

SummaryAlthough many studies into the intestinal stem cell (ISC) niche have been carried out, they have focused on the role of a single cell type or molecular signal. However, no holistic comparisons of the predominant cell types and signals present within the intestinal mucosa have been conducted to date. We utilize bulk RNA sequencing to profile 20 different mucosal cell types covering four major cell categories: epithelial, stromal, endothelial and immune. We further examined the stromal signaling environment using scRNAseq to provide a more comprehensive view of the signaling microenvironment within the intestinal mucosa. We identified the primary signals for the major ISC regulatory pathways and their respective cellular sources. Our analysis suggests that a ‘niche network’ exists, with no single cell type being responsible for ISC self-renewal, proliferation, or differentiation; rather, each cell type within the network carries out specific functions in a highly cooperative and coordinated manner.
AnthOligo: Automating the design of oligonucleotides for capture/enrichment technologies
Authors: Jayaraman Pushkala , Mosbruger Timothy , Hu Taishan , Tairis Nikolaos G , Wu Chao , Clark Peter M , D’Arcy Monica , Ferriola Deborah , Mackiewicz Katarzyna , Gai Xiaowu , Monos Dimitrios , Sarmady Mahdi 
Published: December 2019

AbstractSummaryA number of methods have been devised to address the need for targeted genomic resequencing. One of these methods, Region-specific extraction (RSE) of DNA is characterized by the capture of long DNA fragments (15-20 kb) by magnetic beads, after enzymatic extension of oligonucleotides hybridized to selected genomic regions. Facilitating the selection of the most optimal capture oligos targeting a region of interest, satisfying the properties of temperature (Tm) and entropy (ΔG), while minimizing the formation of primer dimers in a pooled experiment is therefore necessary. Manual design and selection of oligos becomes an extremely arduous task complicated by factors such as length of the target region and number of targeted regions. Here we describe, AnthOligo, a web-based application developed to optimally automate the process of generation of oligo sequences to be used for the targeting and capturing the continuum of large and complex genomic regions. Apart from generating oligos for RSE, this program may have wider applications in the design of customizable internal oligos to be used as baits for gene panel analysis or even probes for large-scale comparative genomic hybridization (CGH) array processes.Implementation and AvailabilityThe application written in Java8 and run on Tomcat9 is a lightweight Java Spring MVC framework that provides the user with a simple interface to upload an input file in BED format and customize parameters for each task. A Redis-likeMapReduceframework is implemented to run sub-tasks in parallel to optimize time and system resources alongside a ‘task-queuing’ system that runs submitted jobs as a server-side background daemon. The task of probe design in AnthOligo commences when a user uploads an input file and concludes with the generation of a result-set containing an optimal set of region-specific oligos.AnthOligo is currently available as a public web application with URL:http://antholigo.chop.edu.
Impact of temperature onLegionella pneumophila, its protozoan host cells, and the microbial diversity of the biofilm community of a pilot cooling tower
Authors: Paniagua Adriana Torres , Paranjape Kiran , Hu Mengqi , Bédard Émilie , Faucher Sébastien 
Published: December 2019

ABSTRACTLegionella pneumophila (Lp)is a waterborne bacterium known for causing Legionnaires’ Disease, a severe pneumonia. Cooling towers are a major source of outbreaks, since they provide ideal conditions forLpgrowth and produce aerosols. In such systems,Lptypically grow inside protozoan hosts. Several abiotic factors such as water temperature, pipe material and disinfection regime affect the colonization of cooling towers byLp.The local physical and biological factors promoting the growth ofLpin water systems and its spatial distribution are not well understood. Therefore, we built a lab-scale cooling tower to study the dynamics ofLpcolonization in relationship to the resident microbiota and spatial distribution. The pilot was filled with water from an operating cooling tower harboring low levels ofLp. It was seeded withVermamoeba vermiformis, a natural host ofLp, and then inoculated withLp.After 92 days of operation, the pilot was disassembled, the water was collected, and biofilm was extracted from the pipes. The microbiome was studied using16S rRNAand18S rRNAgenes amplicon sequencing. The communities of the water and of the biofilm were highly dissimilar. The relative abundance ofLegionellain water samples reached up to 11% whereas abundance in the biofilm was extremely low (≤0.5 %). In contrast, the host cells were mainly present in the biofilm. This suggest thatLpgrows in host cells associated with biofilm and is then released back into the water following host cell lysis. In addition, water temperature shaped the bacterial and eukaryotic community of the biofilm, indicating that different parts of the systems may have different effects onLegionellagrowth.