bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaporation-induced foam stabilization in lubricating oils
Authors: Chandran Suja V. , Kar A. , Cates W. , Remmert S. M. , Savage P. D. , Fuller G. G. 
Published: July 2018

Significance
Mitigating lubricant foaming is of primary concern to lubricant manufacturers, as the control of deleterious foams is critical in high-performance applications. Facilitating the development of techniques to control foaming, the results from this research has identified that a special type of Marangoni flow driven by the differential evaporation of lubricant components plays a central role in promoting foaming in lubricant base oils. In addition, this research also shows that analyzing the stability of single bubbles can complement the foam stability data obtained from traditional bulk foam experiments. Hence, this paper provides physical insights into lubricant foaming and describes a convenient platform that lubricant manufacturers can use to develop better lubricants that are not susceptible to foaming.
Insights into bacterial lipoprotein trafficking from a structure of LolA bound to the LolC periplasmic domain
Authors: Kaplan Elise , Greene Nicholas P. , Crow Allister , Koronakis Vassilis 
Published: July 2018

Significance
The outer membrane of Gram-negative bacteria presents a selectively permeable barrier to the environment and is the first line of defense against antibiotics and other antimicrobial agents. Maintenance of the outer membrane relies on lipoproteins delivered by the LolABCDE system, making the Lol proteins attractive targets for the development of new antimicrobial compounds. During trafficking, lipoproteins are extracted from the cytoplasmic membrane by the LolCDE complex, transported across the periplasm by LolA, and integrated into the outer membrane by LolB. Here, we describe structural features underpinning the interaction between LolA and LolCDE. The structure of LolA bound to the periplasmic domain of LolC provides an arresting molecular snapshot of a key intermediate in the bacterial lipoprotein trafficking pathway.
A new assay to evaluate microvesicle plasmin generation capacity: validation in disease with fibrinolysis imbalance
Authors: Cointe Sylvie , Harti Souab Karim , Bouriche Tarik , Vallier Loris , Bonifay Amandine , Judicone Coralie , Robert Stéphane , Armand Romain , Poncelet Philippe , Albanese Jacques , Dignat‐George Françoise , Lacroix Romaric 
Published: July 2018

ABSTRACTAmong extracellular vesicles, leukocyte‐derived microvesicles (LMVs) have emerged as complex vesicular structures. Primarily identified as procoagulant entities, they were more recently ascribed to plasmin generation capacity (MV‐PGC). The objectives of this work were (1) to develop a new hybrid bio‐assay combining the specific isolation of LMVs and measurement of their PGC, and compare its performance to the original method based on centrifugation, (2) to validate MV‐PGC in septic shock, combining increased levels of LMVs and fibrinolytic imbalance. Using plasma sample spiked with LMVs featuring different levels of PGC, we demonstrated that CD15‐beads specifically extracted LMVs. The MV dependency of the test was demonstrated using electron microscopy, high speed centrifugation, nanofiltration and detergent‐mediated solubilization and the MV‐PGC specificity using plasmin‐specific inhibitors, or antibodies blocking elastase or uPA. Thanks to a reaction booster (ε‐ACA), we showed that the assay was more sensitive and reproducible than the original method. Moreover, it exhibited a good repeatability, inter‐operator and inter‐experiment reproducibility. The new immunomagnetic bio‐assay was further validated in patients with septic shock. As a result, we showed that MV‐PGC values were significantly lower in septic shock patients who died compared to patients who survived, both at inclusion and 24 h later (1.4 [0.8–3.0] vs 3.1 [1.7–18] A405 × 10−3/min, p = 0.02; 1.4 [1–1.6] vs 5.2 [2.2–16] A405 × 10−3/min, p = 0.004). Interestingly, combining both MV‐PGC and PAI‐1 in a ratio significantly improved the predictive value of PAI‐1. This strategy, a hybrid capture bioassay to specifically measure LMV‐PGC using for the first time, opens new perspectives for measuring subcellular fibrinolytic potential in clinical settings with fibrinolytic imbalance.
Dynamic compression schemes for graph coloring
Authors: Mustafa Harun , Schilken Ingo , Karasikov Mikhail , Eickhoff Carsten , Rätsch Gunnar , Kahles André 
Published: July 2018

Abstract

Motivation
Technological advancements in high-throughput DNA sequencing have led to an exponential growth of sequencing data being produced and stored as a byproduct of biomedical research. Despite its public availability, a majority of this data remains hard to query for the research community due to a lack of efficient data representation and indexing solutions. One of the available techniques to represent read data is a condensed form as an assembly graph. Such a representation contains all sequence information but does not store contextual information and metadata.

Results
We present two new approaches for a compressed representation of a graph coloring: a lossless compression scheme based on a novel application of wavelet tries as well as a highly accurate lossy compression based on a set of Bloom filters. Both strategies retain a coloring even when adding to the underlying graph topology. We present construction and merge procedures for both methods and evaluate their performance on a wide range of different datasets. By dropping the requirement of a fully lossless compression and using the topological information of the underlying graph, we can reduce memory requirements by up to three orders of magnitude. Representing individual colors as independently stored modules, our approaches can be efficiently parallelized and provide strategies for dynamic use. These properties allow for an easy upscaling to the problem sizes common to the biomedical domain.

Availability and implementation
We provide prototype implementations in C++, summaries of our experiments as well as links to all datasets publicly at https://github.com/ratschlab/graph_annotation.

Supplementary information
Supplementary data are available at Bioinformatics online.
Random walk with restart on multiplex and heterogeneous biological networks
Authors: Valdeolivas Alberto , Tichit Laurent , Navarro Claire , Perrin Sophie , Odelin Gaëlle , Levy Nicolas , Cau Pierre , Remy Elisabeth , Baudot Anaïs 
Published: July 2018

Abstract

Motivation
Recent years have witnessed an exponential growth in the number of identified interactions between biological molecules. These interactions are usually represented as large and complex networks, calling for the development of appropriated tools to exploit the functional information they contain. Random walk with restart (RWR) is the state-of-the-art guilt-by-association approach. It explores the network vicinity of gene/protein seeds to study their functions, based on the premise that nodes related to similar functions tend to lie close to each other in the networks.

Results
In this study, we extended the RWR algorithm to multiplex and heterogeneous networks. The walk can now explore different layers of physical and functional interactions between genes and proteins, such as protein–protein interactions and co-expression associations. In addition, the walk can also jump to a network containing different sets of edges and nodes, such as phenotype similarities between diseases. We devised a leave-one-out cross-validation strategy to evaluate the algorithms abilities to predict disease-associated genes. We demonstrate the increased performances of the multiplex-heterogeneous RWR as compared to several random walks on monoplex or heterogeneous networks. Overall, our framework is able to leverage the different interaction sources to outperform current approaches. Finally, we applied the algorithm to predict candidate genes for the Wiedemann–Rautenstrauch syndrome, and to explore the network vicinity of the SHORT syndrome.

Availability and implementation
The source code is available on GitHub at: https://github.com/alberto-valdeolivas/RWR-MH. In addition, an R package is freely available through Bioconductor at: http://bioconductor.org/packages/RandomWalkRestartMH/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Translating the Lifestyle Interventions and Independence for Elders Clinical Trial to Older Adults in a Real-World Community-Based Setting
Authors: Reid Kieran F , Laussen Jonathan , Bhatia Karan , Englund Davis A , Kirn Dylan R , Price Lori Lyn , Manini Todd M , Liu Christine K , Kowaleski Christopher , Fielding Roger A 
Published: July 2018

Abstract

Background
The Lifestyle Interventions and Independence for Elders (LIFE) clinical trial demonstrated that a structured program of physical activity (PA) reduced mobility-disability in older adults by up to 28%. It remains unknown whether the benefits of LIFE PA can be translated to older adults at risk for mobility-disability in real-world community-based settings. To address this knowledge gap, we conducted the ENhancing independence using Group-based community interventions for healthy AGing in Elders (ENGAGE) pilot study and examined the safety, feasibility, and preliminary effectiveness of translating LIFE PA to a community-based senior center.

Methods
Forty older adults with severe lower extremity functional limitations (age: 76.9 ± 7.3 years; body mass index: 32.7 ± 8 kg/m2; 85% female; short physical performance battery score: 6.3 ± 2.2) were randomized to 24 weeks of PA or a health education control intervention.

Results
Community-based PA was safe (serious adverse events: PA vs health education, 0:2; nonserious adverse events: PA vs health education, 3:1) and participants successfully adhered to the PA intervention (65.2%). Compared to health education, PA participants who attended ≥25% of scheduled visits had meaningful and sustained short physical performance battery improvements at follow-up (between group short physical performance battery score differences: ~0.7 units).

Conclusions
ENGAGE has demonstrated the preliminary safety, feasibility, and effectiveness of LIFE PA in a real-world community-based setting. Larger-scale translational studies are needed to further disseminate the benefits of LIFE PA to vulnerable older adults in a variety of community-based settings.
Working Channel Endoscopic Interlaminar Microdiscectomy: 2-Dimensional Operative Video
Authors: Kolcun John Paul G , Wang Michael Y 
Published: July 2018

Abstract
This video demonstrates a working channel interlaminar microdiscectomy performed in a patient with significant back and leg pain due to a persistent disc herniation. We describe this technique in detail, describing the endoscopic anatomy and illustrating key steps to safely perform this operation. Due to the limited soft tissue destruction required to access the disc space with this approach, the patient was able to leave the hospital on the day of surgery, and required no pain medication by short-term follow-up a few weeks postoperatively.
All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.
The patient gave direct consent for the use of the endoscopic footage and associated information from this surgery for the making of this video.
Randomized factorial experiment of components of the SmokeFree Baby smartphone application to aid smoking cessation in pregnancy
Authors: Tombor Ildiko , Beard Emma , Brown Jamie , Shahab Lion , Michie Susan , West Robert 
Published: July 2018

Abstract
Smartphone applications (apps) might be able to reach pregnant smokers who do not engage with face-to-face support. However, we do not know how far pregnant smokers will engage with smoking cessation apps or what components are likely to be effective. This study aimed to assess pregnant smokers’ engagement with the SmokeFree Baby app (v1) and to assess the short-term efficacy of selected components (“modules”) for smoking abstinence. Positive outcomes would provide a basis for further development and evaluation. SmokeFree Baby was developed drawing on behavior change theories and relevant evidence. Pregnant smokers (18+) who were interested in quitting and set a quit date were recruited. Following multiphase optimization development principles, participants (N = 565) were randomly allocated to one of 32 (2 × 2 × 2 × 2 × 2) experimental groups in a full factorial design to evaluate five modules (each in minimal and full version: identity, health information, stress management, face-to-face support, and behavioral substitution). Measures of engagement included duration and frequency of engagement with the app. Smoking abstinence was measured by self-reported number of smoke-free days up to 4 weeks from the quit date. Participants engaged with the app for a mean of 4.5 days (SD = 8.5) and logged in a mean of 2.9 times (SD = 3.1). Main effects of the modules on the number of smoke-free days were not statistically significant (identity: p = .782, health information: p = .905, stress management: p = .103, face-to-face support: p = .397, behavioral substitution: p = .945). Despite systematic development and usability testing, engagement with SmokeFree Baby (v1) was low and the app did not appear to increase smoking abstinence during pregnancy.
AFLIBERCEPT FOR PERSISTENT DIABETIC MACULAR EDEMA
Authors: Bahrami Bobak , Hong Thomas , Schlub Timothy E. , Chang Andrew A. 
Published: July 2018

Purpose:
To evaluate functional and anatomical outcomes after a switch from intravitreal bevacizumab to aflibercept in patients with persistent diabetic macular edema.

Methods:
Prospective, single-arm, open-label clinical trial of patients with persistent diabetic macular edema, despite previous treatment with bevacizumab. Five loading doses of intravitreal aflibercept were administered every 4 weeks with subsequent injections administered every 8 weeks. Patients were reviewed every 4 weeks, and best-corrected visual acuity and central macular thickness were recorded. Primary outcome measures included change in central macular thickness and best-corrected visual acuity at week 48 compared with baseline. Paired t-tests were used to assess change between baseline and follow-up visits.

Results:
At baseline, 43 eyes from 43 patients were recruited with a median (interquartile range) of 12 (7–24) previous intravitreal anti–vascular endothelial growth factor injections over a period of 18 (8–34) months. Mean ± SD central macular thickness reduced by 59 ± 114 μm (P = 0.002), and best-corrected visual acuity improved by 3.9 ± 7.0 letters (P = 0.001) after 48 weeks in the 41 patients who completed the trial. Best-corrected visual acuity improvements were more marked in patients who gained ≥5 letters after the first injection (8.9 ± 5.7 vs. 1.8 ± 6.5 letter gain at 48 weeks, P = 0.002), a difference which remained significant after regression analysis with baseline best-corrected visual acuity . Vision gains and central macular thickness reduction were similar in 9 fellow eyes eligible for inclusion being concurrently treated for diabetic macular edema with bevacizumab.

Conclusion:
Intravitreal aflibercept was effective in improving anatomical and visual outcomes among patients with an incomplete response to intravitreal bevacizumab with 48 weeks of follow-up. Patients with a good early response subsequent to switching had a better improvement in vision at 48 weeks.
ANATOMICAL AND FUNCTIONAL TESTING IN DIABETIC PATIENTS WITHOUT RETINOPATHY
Authors: Meshi Amit , Chen Kevin C. , You Qi Sheng , Dans Kunny , Lin Tiezhu , Bartsch Dirk-Uwe , Cheng Lingyun , Amador-Patarroyo Manuel J. , Muftuoglu Ilkay Kilic , Gomez Maria L. , Nudleman Eric , Freeman William R. 
Published: July 2018

Purpose:
To assess early retinal microvascular and functional changes in diabetic patients without clinical evidence of diabetic retinopathy with optical coherence tomography angiography and central visual analyzer.

Methods:
This was an observational case–control study of diabetic patients without diabetic retinopathy and nondiabetic controls. Patients underwent optical coherence tomography angiography imaging and visual acuity testing using the central visual analyzer. The foveal avascular zone area and the capillary density in the superficial and deep capillary plexuses were measured manually by a masked grader.

Results:
Sixty eyes from 35 diabetic patients were included in the study group, and 45 eyes from 31 nondiabetic patients were included in the control group. The foveal avascular zone area was not significantly different between the diabetic group and controls (both P > 0.05). The mean capillary density in the deep capillary plexus was significantly lower in diabetic eyes compared with control eyes (P = 0.04). The mean visual acuity in all central visual analyzer modules was significantly decreased in diabetic patients compared with controls (all P < 0.05).

Conclusion:
Optical coherence tomography angiography was able to detect retinal microvascular changes in the deep capillary plexus, and the central visual analyzer showed signs of decreased visual acuity under conditions simulating suboptimal contrast and glare in diabetic patients without diabetic retinopathy.
TRANSCORNEAL SUTURELESS SILICONE OIL REMOVAL USING 23-GAUGE TROCAR SYSTEM IN APHAKIA
Authors: Sayman Muslubas Isil , Hocaoglu Mumin , Ersoz Mehmet Giray , Arf Serra , Karacorlu Murat 
Published: July 2018

Purpose:
To describe transcorneal sutureless silicone oil removal using 23-gauge trocars as an alternative surgical technique in an aphakic eye.

Methods:
We retrospectively evaluated the management of a 50-year-old male patient who had a history of bilateral congenital cataract removal at the age of 5 and developed rhegmatogenous retinal detachment. A 3-port 23-gauge pars plana vitrectomy, removal of the vitreous up to the vitreous base, 60° temporal retinotomy, and anterior flap retinectomy were performed. Silicone oil (1,000 cSt) was selected as a tamponading agent. The patients underwent active silicone oil removal at subsequent surgery 2 months after the initial vitrectomy.

Results:
The silicone oil was successfully extracted from the aphakic eye by using transcorneal 23-gauge trocars. No suture was needed at the corneal wound sites. There were no intraoperative or postoperative complications.

Conclusion:
Transcorneal silicone oil removal using 23-gauge trocars can be performed easily with today's modern vitreoretinal surgery systems as an alternative treatment modality.
MULTIMODAL IMAGING IN DIDANOSINE RETINOPATHY
Authors: Shifera Amde Selassie , Singh Mandeep 
Published: July 2018

Purpose:
To present the multimodal retinal imaging findings in didanosine retinopathy in a patient who presented 6.5 years after stopping the use of didanosine and to highlight the absence of progression during a 1.5-year follow-up.

Methods:
Case report involving clinical examination, fundus photography, fundus autofluorescence, fluorescein angiography, optical coherence tomography, Goldmann kinetic perimetry, and full-field electroretinography.

Results:
A 52-year-old patient presented with bilateral retinopathy 6.5 years after stopping didanosine having used the medication for 8.5 years. Fundus examination showed a ring-shaped zone of atrophy of the retinal pigment epithelium involving the midperiphery. On autofluorescence imaging, there was diffuse hypoautofluorescence involving the midperipheral retina in both eyes. On fluorescein angiography, there was a granular mottled pattern of diffuse hyperfluorescence in the midperiphery in both eyes, with baring of the large choroidal vessels in some areas. On Goldmann kinetic perimetry, both eyes showed marked constriction of the isopter to the I4e stimulus, and there was a temporal scotoma to the III4e target in both eyes. Full-field electroretinography showed generalized rod and cone photoreceptor dysfunction in both eyes. During a follow-up for 1.5 years, there was no evidence of progression.

Conclusion:
Patients who have used didanosine should be evaluated for the presence of retinopathy, which involves the midperipheral retina.
Long-term pain relief in canine osteoarthritis by a single intra-articular injection of resiniferatoxin, a potent TRPV1 agonist
Authors: Iadarola Michael J. , Sapio Matthew R. , Raithel Stephen J. , Mannes Andrew J. , Brown Dorothy Cimino 
Published: July 2018

Abstract
The translational potential of analgesic approaches emerging from basic research can be augmented by client-owned dog trials. We report on a peripheral interventional approach that uses intra-articular injection of the ultrapotent TRPV1 agonist resiniferatoxin (RTX) to produce a selective long-term chemoinactivation of nociceptive primary afferent nerve endings for pain control in naturally occurring canine osteoarthritis. A single injection of 10 µg of RTX, produced suppression of pain, improvement in gait, weight bearing, and improvement in the dog's activities of daily living lasting 4 months or longer. Two to 3 years after the injection, there are no alterations to suggest that removal of inflammatory pain caused accelerated joint degeneration (Charcot joint) in any of the dogs. To amplify the effective use of canine subjects in translational analgesia research, we report a high-quality canine dorsal root ganglion transcriptome. Some targets for analgesia are highly conserved both in protein sequence and level of expression within a target tissue while others diverge substantially from the human. This knowledge is especially important for development of analgesics aimed at peripheral molecular targets and provides a template for informed translational research. The peripheral site of action, long duration of analgesia, apparent safety, and retention of coordination, all resulting from a single dose suggest that intra-articular RTX may be an effective intervention for osteoarthritis pain with few or no side effects and lead to an improved quality of life.
Prevention of hospital-acquired pneumonia
Authors: Lyons Patrick G. , Kollef Marin H. 
Published: July 2018

Purpose of review
Hospital-acquired pneumonia (HAP) is the leading cause of death from hospital-acquired infection. Little work has been done on strategies for prevention of HAP. This review aims to describe potential HAP prevention strategies and the evidence supporting them. Oral care and aspiration precautions may attenuate some risk for HAP. Oral and digestive decontamination with antibiotics may be effective but could increase risk for resistant organisms. Other preventive measures, including isolation practices, remain theoretical or experimental.

Recent findings
Hospital-acquired pneumonia occurs because of pharyngeal colonization with pathogenic organisms and subsequent aspiration of these pathogens.

Summary
Most potential HAP prevention strategies remain unproven.