bluuebunny/crossref_metadata_2025_split huggingface dataset:
Technique for Perforating a Prosthetic Liner to Expel Sweat
Authors: Caldwell Ryan , Fatone Stefania 
Published: May 2017

ABSTRACT

Introduction
Sweating and moisture buildup are caused by the insulative nature of prosthetic interface materials increasing the temperature of the residual limb. Hence, heat and sweating in the socket are among the most frequently reported problems that reduce quality of life for persons with amputation. The purpose of this technical note was to describe a simple, inexpensive technique for perforating a silicone prosthetic liner to expel sweat and enhance use of a lower-limb prosthesis.

Materials and Methods
A liner holder consisting of a towel and socks layered over a mandrel to mimic the distal liner shape was made to stabilize the liner during the perforation process. With the liner placed over the holder such that the exterior surface was exposed, a perforating roller was used to perforate the distal end of the liner. When the liner was inverted, the holes were visible all the way through to the inner surface of the liner.

Results
Expulsion of sweat through the perforations was demonstrated by pouring water into the liner, folding the proximal, open end of the liner to create a seal, and forcing water droplets to escape the perforations with some resistance. Additional evidence that water escaped was seen by the wet patches that formed on the exterior fabric of the perforated liner after active wear. One user with amputation described sweat being pumped out of the perforated liner into the socket and in some cases out of the socket through the air relief valve of the vacuum pump. Another user with amputation indicated that the perforations did not damage the skin and reduced slippage of the liner with respect to the limb.

Conclusions
Initial clinical experience with this technique suggested that expulsion of sweat occurred and user feedback indicated improved prosthesis use as a result. Current experience using this technique in clinical practice has been limited to silicone liners. The long-term effects of perforations on liner durability or limb health are not yet known.
Spinal and Pelvic Kinematics During Gait in People with Lower-Limb Amputation, with and without Low Back Pain: An Exploratory Study
Authors: Devan Hemakumar , Dillon Michael P. , Carman Allan B. , Hendrick Paul , Hale Leigh , Boocock Mark , Ribeiro Daniel Cury 
Published: May 2017

ABSTRACTIntroductionDespite the high prevalence of chronic low back pain (LBP) in people with lower-limb amputation, it is not clear whether there are differences in spinal and pelvic motion in individuals with and without LBP. This exploratory study aimed to describe the spinal and pelvic kinematics during gait in people with transfemoral amputation (TFA) and transtibial amputation (TTA), with and without LBP.MethodsEighteen participants with traumatic amputation (6 TFA, 12 TTA) were grouped according to their amputation level and presence (or absence) of LBP. Three-dimensional thoracic, lumbar, and pelvic kinematics during walking were reported to identify movement patterns that may be indicative of LBP.ResultsThe TFA-LBP group elevated the pelvis on the intact side and minimized lumbar lateral flexion to achieve the same trunk lateral flexion angle (Trendelenburg gait) as those with TFA-No LBP. Those with TFA-LBP kept the lumbar spine rotated toward the prosthetic limb throughout the gait cycle. There were no differences in the spinal and pelvic kinematics of people with TTA-LBP and TTA-No LBP.ConclusionsThis study provides preliminary evidence of differences in spinal and pelvic kinematics that may be associated with LBP in people with TFA.
Muscle metabolism
Authors: Tardif Nicolas , Grip Jonathan , Rooyackers Olav 
Published: May 2017

Purpose of review
To review the recent findings on metabolic derangements leading to loss of muscle mass and function.

Recent findings
Several recent studies investigated methods to assess muscle mass and function and its clinical relevance. These are also included. A few studies confirm that a low muscle mass is related to a worse outcome but also a compromised muscle function at discharge is related to long-term survival. A low quality of muscle assessed by the density of muscle from a computed tomography scan is related to mortality. For the metabolic derangements, a compromised handling of calcium is present in muscle of animal models and might be causing a decreased muscle function in patients. Transcriptomics analyses of muscle post-ICU indicated an upregulation of regenerative pathways, but still muscle mass is not recovering in most patients. This could be due to an impairment regenerative capacity due to satellite cells dysfunction.

Summary
Muscle mass and function are related to outcome. New finding show that not only muscle mass but also muscle quality is important, that a compromised handling of calcium might be involved in muscle weakness and that regaining muscle could be compromised due to a defective regenerative capacity of satellite cells.
The Epidemiology of Hospital Death Following Pediatric Severe Sepsis: When, Why, and How Children With Sepsis Die*
Authors: Weiss Scott L. , Balamuth Fran , Hensley Josey , Fitzgerald Julie C. , Bush Jenny , Nadkarni Vinay M. , Thomas Neal J. , Hall Mark , Muszynski Jennifer 
Published: May 2017

Objective:
The epidemiology of in-hospital death after pediatric sepsis has not been well characterized. We investigated the timing, cause, mode, and attribution of death in children with severe sepsis, hypothesizing that refractory shock leading to early death is rare in the current era.

Design:
Retrospective observational study.

Setting:
Emergency departments and ICUs at two academic children’s hospitals.

Patients:
Seventy-nine patients less than 18 years old treated for severe sepsis/septic shock in 2012–2013 who died prior to hospital discharge.

Interventions:
None.

Measurements and Main Results:
Time to death from sepsis recognition, cause and mode of death, and attribution of death to sepsis were determined from medical records. Organ dysfunction was assessed via daily Pediatric Logistic Organ Dysfunction-2 scores for 7 days preceding death with an increase greater than or equal to 5 defined as worsening organ dysfunction. The median time to death was 8 days (interquartile range, 1–12 d) with 25%, 35%, and 49% of cumulative deaths within 1, 3, and 7 days of sepsis recognition, respectively. The most common cause of death was refractory shock (34%), then multiple organ dysfunction syndrome after shock recovery (27%), neurologic injury (19%), single-organ respiratory failure (9%), and nonseptic comorbidity (6%). Early deaths (≤ 3 d) were mostly due to refractory shock in young, previously healthy patients while multiple organ dysfunction syndrome predominated after 3 days. Mode of death was withdrawal in 72%, unsuccessful cardiopulmonary resuscitation in 22%, and irreversible loss of neurologic function in 6%. Ninety percent of deaths were attributable to acute or chronic manifestations of sepsis. Only 23% had a rise in Pediatric Logistic Organ Dysfunction-2 that indicated worsening organ dysfunction.

Conclusions:
Refractory shock remains a common cause of death in pediatric sepsis, especially for early deaths. Later deaths were mostly attributable to multiple organ dysfunction syndrome, neurologic, and respiratory failure after life-sustaining therapies were limited. A pattern of persistent, rather than worsening, organ dysfunction preceded most deaths.
Technical Feasibility of a Combined Noncontrast Magnetic Resonance Protocol for Preoperative Transcatheter Aortic Valve Replacement Evaluation
Authors: Cannaò Paola M. , Muscogiuri Giuseppe , Schoepf U. Joseph , De Cecco Carlo N. , Suranyi Pal , Lesslie Virginia W. , Piccini Davide , Giri Shivraman , Varga-Szemes Akos 
Published: May 2017

Purpose:
The aim of this study was to prospectively evaluate the technical feasibility of a noncontrast magnetic resonance angiography (MRA) protocol using investigational prototype self-navigated 3D (SN3D) radial whole-heart and quiescent-interval single-shot (QISS) pulse sequences regarding their potential in planning transcatheter aortic valve replacement (TAVR).

Materials and Methods:
Five patients (76±7 y) with severe aortic valve stenosis and prior computed tomographic angiography (CTA) for TAVR planning and 10 healthy volunteers (28±6 y) underwent noncontrast MRA on a 1.5 T system. A SN3D whole-heart acquisition was used to assess the aortic root anatomy. Evaluation of the aortoiliac access route was performed with both SN3D and QISS. Measurements were compared among SN3D, QISS, and CTA using a paired t test or 1-way analysis of variance. Image quality ratings and contrast-to-noise ratios (CNR) were analyzed using Mann-Whitney U tests. Interobserver agreement was evaluated using Cohen’s κ.

Results:
The combined SN3D and QISS protocol provided a 10.1±1.6-minute acquisition time. TAVR-relevant evaluation was technically feasible in healthy volunteers. All measurements showed good agreement with CTA in patients (all P>0.098). SN3D and QISS produced similar image quality both in volunteers and in patients (all P>0.122). There was no difference in qualitative ratings between MRA and CTA (all P>0.119). Interobserver agreement was good for MRA (κ=0.71 to 0.76) and excellent for CTA (κ=0.82 to 0.84). Thoracic SN3D provided a similar CNR compared with CTA (P=0.117). CTA yielded higher CNR in the abdominopelvic region compared with QISS (P=0.006).

Conclusions:
A noncontrast MRA protocol combining SN3D and QISS acquisitions for the assessment of cardiac and vascular access route anatomy has technical feasibility for TAVR planning.
Lung Density and Pulmonary Artery Diameter are Predictors of Pulmonary Hypertension in Systemic Sclerosis
Authors: Bakker Margreet E. , Ninaber Maarten K. , Stolk Jan , Kroft Lucia J.M. , Schouffoer Anne A. , de Vries Bouwstra Jeska K. , van Wijngaarden Suzanne E. , Stoel Berend C. 
Published: May 2017

Purpose:The aim was to evaluate computed tomography (CT)-measured pulmonary artery diameter (PAD) and lung density as predictors of pulmonary hypertension (PH) in subjects with systemic sclerosis (SSc). We compared these PAD values with normal values and between SSc subgroups with PH and/or interstitial lung disease (ILD). We investigated whether PAD predicts PH and whether lung densitometry, by using the 85th percentile density value (Perc85) as a measure for ILD, can predict PH.Materials and Methods:PAD and Perc85 were measured in axial CT scans and compared between 54 SSc and 76 control subjects. Four SSc subgroups were defined on the basis of PH (systolic PA pressure ≥35 mm Hg) and/or ILD (fibrosis score ≥7): PH−/ILD−, PH−/ILD+, PH+/ILD−, and PH+/ILD+. The association of PAD with age, body mass index, Perc85, lung function, and hemodynamic measures was investigated using univariate correlation along with the predictive value of these measures with respect to PH.Results:PAD in SSc was larger than that in controls (30.1±4.9 vs. 26.9±2.7 mm,P<0.001). PH+ patients showed increased PAD compared with PH− patients (34.2±4.2 vs. 28.6±4.3 mm,P<0.001), where PH+/ILD+ subjects showed the widest diameter (34.6±4.1 mm). In SSc patients, hemodynamic measures, age, body mass index, Perc85, and lung function correlated with PAD. PAD was best explained by Perc85, together with age (R2=0.358). PAD best predicted PH (AUC, 0.877;P<0.001), and PAD≥30.7 mm showed 80% sensitivity and 87% specificity. Perc85 also predicted PH (AUC, 0.733;P=0.024).Conclusions:In subjects with SSc, lung density and PAD are CT markers, each with predictive value for PH.
Surgeon Experience and Medicare Expenditures for Laparoscopic Compared to Open Colectomy
Authors: Sheetz Kyle H. , Ibrahim Andrew M. , Regenbogen Scott E. , Dimick Justin B. 
Published: May 2017

Objective:
To quantify the extent to which payments for laparoscopic and open colectomy are influenced by a surgeon's experience with laparoscopy.

Background:
Numerous studies suggest that healthcare costs for laparoscopic colectomy are lower than open surgery. None have assessed the importance of surgeon experience on the relative financial benefits of laparoscopy.

Methods:
We conducted a study of 182,852 national Medicare beneficiaries undergoing laparoscopic or open colectomy between 2010 and 2012. Using instrumental variable methods to account for selection bias, we compared Medicare payments for laparoscopic and open colectomy. We stratified our analysis by surgeons’ annual experience with laparoscopic colectomy to determine the influence of provider experience on payments.

Results:
In the fully adjusted analysis, average episode payments per patient were $2640 [95% confidence interval (CI) −$4091 to −$1189] lower with the laparoscopic approach versus open. Surgeons in the highest quartile of laparoscopic experience demonstrated an average payment savings of $5456 per patient (CI −$7918 to −$2994) in their laparoscopic versus open cases. Among surgeons in the lowest quartile of laparoscopic experience, there was, however, no difference between laparoscopic and open cases (difference: $954, 95% CI −$731 to $2639). Differences in payments were explained by differences in complications rates. Both groups had similar rates of complications for open procedures (least experience, 21%, most experience, 21%; P = 0.45), but differed significantly on rates of complications for laparoscopic cases (least experience, 28%, most experience, 15%; P < 0.01).

Conclusions:
This population-based study demonstrates that differences in payments between laparoscopic and open colectomy are influenced by surgeon experience. The laparoscopic approach does not reduce payments for patients whose surgeons have limited experience with the procedure.
Distinct pattern of epigenetic DNA modification in leukocytes from patients with colorectal carcinoma and individuals with precancerous conditions, benign adenoma and inflammatory bowel disease – a link to oxidative stress
Authors: Starczak Marta , Zarakowska Ewelina , Modrzejewska Martyna , Dziaman Tomasz , Szpila Anna , Linowiecka Kinga , Guz Jolanta , Szpotan Justyna , Gawronski Maciej , Labejszo Anna , Liebert Ariel , Banaszkiewicz Zbigniew , Klopocka Maria , Foksinski Marek , Gackowski Daniel , Olinski Ryszard 
Published: May 2017

AbstractA characteristic feature of malignant cells, including colorectal cancer cells, is a profound decrease in level of 5-hydroxymethylcytosine, product of 5-methylcytosine oxidation by TET enzymes. This study included four groups of subjects: healthy controls, and patients with inflammatory bowel disease (IBD), benign polyps and colorectal cancer. Patients from all groups presented with significantly lower levels of 5-methylcytosine and 5-hydroxymethylcytosine than the controls. A similar tendency was also observed for 5-hydroxymethyluracil level. Patients with IBD showed the highest levels of 5-formylcytosine and 8-oxo-7,8-dihydro-2’-deoxyguanosine of all study subjects, and individuals with colorectal cancer presented with the lowest concentrations of vitamin C and A. Expressions of TET1 and TET2 turned out to be the highest in IBD group. To the best of our knowledge, this is the first study to show that healthy subjects, individuals with precancerous conditions and colorectal cancerpatients present with distinct specific patterns of epigenetic modifications in leukocyte DNA.
Static and dynamic DNA loops form AP-1 bound activation hubs during macrophage development
Authors: Phanstiel Douglas H. , Van Bortle Kevin , Spacek Damek , Hess Gaelen T. , Shamim Muhammad Saad , Machol Ido , Love Michael I. , Aiden Erez Lieberman , Bassik Michael C. , Snyder Michael P. 
Published: May 2017

SUMMARYThe three-dimensional arrangement of the human genome comprises a complex network of structural and regulatory chromatin loops important for coordinating changes in transcription during human development. To better understand the mechanisms underlying context-specific 3D chromatin structure and transcription during cellular differentiation, we generated comprehensive in situ Hi-C maps of DNA loops during human monocyte-to-macrophage differentiation. We demonstrate that dynamic looping events are regulatory rather than structural in nature and uncover widespread coordination of dynamic enhancer activity at preformed and acquired DNA loops. Enhancer-bound loop formation and enhancer-activation of preformed loops represent two distinct modes of regulation that together form multi-loop activation hubs at key macrophage genes. Activation hubs connect 3.4 enhancers per promoter and exhibit a strong enrichment for Activator Protein 1 (AP-1) binding events, suggesting multi-loop activation hubs driven by cell-type specific transcription factors may represent an important class of regulatory chromatin structures for the spatiotemporal control of transcription.HIGHLIGHTSHigh resolution and high sensitivity of loop detection via deeply sequenced in situ Hi-C experiments during monocyte to macrophage differentiation (> 10 billion total reads)Multi-loop interaction communities identified surrounding key macrophage genes.Multi-loop communities connect dynamic enhancers through both static and newly acquired DNA loops, forming hubs of activationMacrophage activation hubs are enriched for AP-1 bound long-range enhancer interactions, suggesting cell-type specific TFs drive changes in 3D structure and transcription through regulatory DNA loops
Characterizing the structure-function relationship of a naturally-occurring RNA thermometer
Authors: Meyer Sarai , Lucks Julius B. 
Published: May 2017

AbstractA wide number of bacteria have been found to govern virulence and heat shock responses using temperature-sensing RNAs known as RNA thermometers. A prime example is theagsAthermometer known to regulate the production of the AgsA heat shock protein inSalmonella entericausing a “fourU” structural motif. Using the SHAPE-Seq RNA structure-probing methodin vivoandin vitro, we found that the regulator functions by a subtle shift in equilibrium RNA structure populations that lead to a partial melting of the helix containing the ribosome binding site. We also demonstrate that ribosome binding to theagsAmRNA causes changes to the thermometer structure that appear to facilitate thermometer helix unwinding. These results demonstrate how subtle RNA structural changes can govern gene expression and illuminate the function of an important bacterial regulatory motif.
Pheno4J: a gene to phenotype graph database
Authors: Mughal Sajid , Moghul Ismail , Yu Jing , Clark Tristan , Gregory David S , Pontikos Nikolas 
Published: May 2017

AbstractSummaryEfficient storage and querying of large amounts of genetic and phenotypic data is crucial to contemporary clinical genetic research. This introduces computational challenges for classical relational databases, due to the sparsity and sheer volume of the data. Our Java based solution loads annotated genetic variants and well phenotyped patients into a graph database to allow fast efficient storage and querying of large volumes of structured genetic and phenotypic data. This abstracts technical problems away and lets researchers focus on the science rather than the implementation. We have also developed an accompanying webserver with end-points to facilitate querying of the database.Availability and ImplementationThe Java code and python code is available athttps://github.com/phenopolis/pheno4iContactn.pontikos@ucl.ac.uk
Native KCC2 interactome reveals PACSIN1 as a critical regulator of synaptic inhibition
Authors: Mahadevan Vivek , Khademullah C. Sahara , Dargaei Zahra , Chevrier Jonah , Uvarov Pavel , Kwan Julian , Bagshaw Richard D. , Pawson Tony , Emili Andrew , DeKoninck Yves , Anggono Victor , Airaksinen Matti S. , Woodin Melanie A. 
Published: May 2017

AbstractKCC2 is a neuron-specific K+-Cl−cotransporter essential for establishing the Cl−gradient required for hyperpolarizing inhibition. KCC2 is highly localized to excitatory synapses where it regulates spine morphogenesis and AMPA receptor confinement. Aberrant KCC2 function contributes to numerous human neurological disorders including epilepsy and neuropathic pain. Using unbiased functional proteomics, we identified the KCC2-interactome in the mouse brain to determine KCC2-protein interactions that regulate KCC2 function. Our analysis revealed that KCC2 interacts with a diverse set of proteins, and its most predominant interactors play important roles in postsynaptic receptor recycling. The most abundant KCC2 interactor is a neuronal endocytic regulatory protein termed PACSIN1 (SYNDAPIN1). We verified the PACSIN1-KCC2 interaction biochemically and demonstrated that shRNA knockdown of PACSIN1 in hippocampal neurons significantly increases KCC2 expression and hyperpolarizes the reversal potential for Cl−. Overall, our global native-KCC2 interactome and subsequent characterization revealed PACSIN1 as a novel and potent negative regulator of KCC2.
Mosaic chromosomal aneuploidy detection by sequencing (MAD-seq)
Authors: Kong Yu , Berko Esther R. , Marcketta Anthony , Maqbool Shahina B. , Simões-Pires Claudia A. , Kronn David F. , Ye Kenny Q. , Suzuki Masako , Auton Adam , Greally John M. 
Published: May 2017

ABSTRACTCurrent approaches to detect and characterize mosaic chromosomal aneuploidy are limited by sensitivity, efficiency, cost or the need to culture cells. We describe a combination of a new sequencing-based assay and a novel analytical approach that allows low levels of mosaicism for chromosomal aneuploidy to be detected, assigned to a meiotic or mitotic origin, and quantified as a proportion of the cells in the sample. We show results from a multi-ethnic assay design that is suitable for populations of diverse racial and ethnic origins, and how theMADSEQanalytical approach applied to exome sequencing data reveals unrecognized aneuploidy in 1000 Genomes samples and cell lines from public repositories. We have made the assay design and analytical software open for unrestricted use, with the goal that it can be applied in clinical samples to allow new insights into the unrecognized prevalence of mosaic chromosomal aneuploidy and its phenotypic associations.
Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets
Authors: Zhou Xiaofan , Shen Xingxing , Hittinger Chris Todd , Rokas Antonis 
Published: May 2017

AbstractPhylogenetics has witnessed dramatic increases in the sizes of data matrices assembled to resolve branches of the tree of life, motivating the development of programs for fast, yet accurate, inference. For example, several different fast programs have been developed in the very popular maximum likelihood framework, including RAxML/ExaML, PhyML, IQ-TREE, and FastTree. Although these four programs are widely used, a systematic evaluation and comparison of their performance using empirical genome-scale data matrices has so far been lacking. To address this question, we evaluated these four programs on 19 empirical phylogenomic data sets from diverse animal, plant, and fungal lineages with respect to likelihood maximization, tree topology, and computational speed. For single-gene tree inference, we found that the more exhaustive and slower strategies (ten searches per alignment) outperformed faster strategies (one tree search per alignment) using RAxML, PhyML, or IQ-TREE. Interestingly, single-gene trees inferred by the three programs yielded comparable coalescent-based species tree estimations. For concatenation–based species tree inference, IQ-TREE consistently achieved the best-observed likelihoods for all data sets, and RAxML/ExaML was a close second. In contrast, PhyML often failed to complete concatenation-based analyses, whereas FastTree was the fastest but generated lower likelihood values and more dissimilar tree topologies in both types of analyses. Finally, data matrix properties, such as the number of taxa and the strength of phylogenetic signal, sometimes substantially influenced the relative performance of the programs. Our results provide real-world gene and species tree phylogenetic inference benchmarks to inform the design and execution of large-scale phylogenomic data analyses.