bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radiation Therapy in HCC: What Data Exist and What Data Do We Need to Incorporate into Guidelines?
Authors: Xu Melody , Feng Mary 
Published: December 2018

AbstractHepatocellular carcinoma (HCC) is a complex and diverse disease, with choice of treatment dependent on a patient's disease burden, location of disease, underlying liver function, and performance status. While radiation therapy (RT) was historically omitted from treatment algorithms, immense technological advances over the past several decades have enabled introduction of RT as an effective and safe treatment option for patients with HCC. Growing prospective and retrospective evidence supports the use of RT, particularly stereotactic body radiotherapy (SBRT), for a wide range of indications in HCC from locally advanced unresectable disease to bridge therapy for liver transplant candidates. SBRT is associated with excellent local control, even for patients refractory to or ineligible for other forms of locoregional therapy. Treatment is well-tolerated and associated with low rates of severe toxicity. Randomized trials are needed to define the role of SBRT in HCC treatment relative to other established locoregional treatments.
Warum Daten sammeln sinnvoll ist
Authors: Behrendt Daniel 
Published: December 2018

ZusammenfassungModerne Informationstechnologie und Datenmanagementsysteme verändern die Arbeits- und Kommunikationsprozesse in der Pflege. Aber wie gelingt es,
Pflegeinformatik patienten- und praxisorientiert auszurichten? Ein Überblick.
Anleitung zum Glücklichsein
Authors: Ebner Markus 
Published: December 2018

ZusammenfassungSeit Ende der 90er Jahre erforscht die Positive Psychologie, was das Leben
erfolgreich und glücklich macht. Die Erkenntnisse nutzt auch das Führungsmodell
Positive Leadership, indem es diese in den Unternehmensalltag
überträgt.
Safe processing method and storage time threshold for consuming of powdered-infant formula based on total plate count test
Authors: Amelia S , Lubis NDA , Rozi MF , Nababan IFF 
Published: December 2018

Abstract
Powdered-infant formula (PIF) is theoretically suggested as a substitution for breast-milk. The presence of PIF has brought several problems related to its contamination, handling, and processing. Our study aimed to provide the evidence related to determine the safe processing method, between using hot water (HW) or boiled water (BW), and storage time threshold after PIF was left at room temperature for acertain period of time. We obtained PIF, cow milk-based, from supermarket and made it as suspension. Bacterial growth assessment was performedusing total plate agar, total plate count test, while several tests including the use of agar, blood and McConkey agar, and biochemical reactions were used to determine the bacterial species. We provided formula suspension in different amount of dilution (10−1, 102,103, and 10−4), furthermore observation of bacterial colonies for 3-8 hours was done. The study was carried out at Department of Microbiology, Faculty of Medicine, Universitas Sumatera Utara in October 2017. We obtained a significant number of bacterial colonies at the first time of observation in HW and using BW was safer than HW regardless of its nutritional value, based on total plate count tests. Meanwhile, safe storage time threshold for consuming after it was left at room temperature was no more than one hour. We identified Bacillus subtilis and Klebsiella sp. as contaminants during the observation. Thus, less contamination also reduces infection rate among infantsby performing appropriate handling.
Insights on protein thermal stability: a graph representation of molecular interactions
Authors: Miotto Mattia , Olimpieri Pier Paolo , Di Rienzo Lorenzo , Ambrosetti Francesco , Corsi Pietro , Lepore Rosalba , Tartaglia Gian Gaetano , Milanetti Edoardo 
Published: December 2018

AbstractMotivationUnderstanding the molecular mechanisms of thermal stability is a challenge in protein biology. Indeed, knowing the temperature at which proteins are stable has important theoretical implications, which are intimately linked with properties of the native fold, and a wide range of potential applications from drug design to the optimization of enzyme activity.ResultsHere, we present a novel graph-theoretical framework to assess thermal stability based on the structure without any a priori information. In this approach we describe proteins as energy-weighted graphs and compare them using ensembles of interaction networks. Investigating the position of specific interactions within the 3D native structure, we developed a parameter-free network descriptor that permits to distinguish thermostable and mesostable proteins with an accuracy of 76% and area under the receiver operating characteristic curve of 78%.Availability and implementationCode is available upon request to edoardo.milanetti@uniroma1.itSupplementary informationSupplementary data are available at Bioinformatics online.
Increasing the accuracy of protein loop structure prediction with evolutionary constraints
Authors: Marks Claire , Deane Charlotte M 
Published: December 2018

Abstract

Motivation
Accurate prediction of loop structures remains challenging. This is especially true for long loops where the large conformational space and limited coverage of experimentally determined structures often leads to low accuracy. Co-evolutionary contact predictors, which provide information about the proximity of pairs of residues, have been used to improve whole-protein models generated through de novo techniques. Here we investigate whether these evolutionary constraints can enhance the prediction of long loop structures.

Results
As a first stage, we assess the accuracy of predicted contacts that involve loop regions. We find that these are less accurate than contacts in general. We also observe that some incorrectly predicted contacts can be identified as they are never satisfied in any of our generated loop conformations. We examined two different strategies for incorporating contacts, and on a test set of long loops (10 residues or more), both approaches improve the accuracy of prediction. For a set of 135 loops, contacts were predicted and hence our methods were applicable in 97 cases. Both strategies result in an increase in the proportion of near-native decoys in the ensemble, leading to more accurate predictions and in some cases improving the root-mean-square deviation of the final model by more than 3 Å.

Supplementary information
Supplementary data are available at Bioinformatics online.
Prot-SpaM: fast alignment-free phylogeny reconstruction based on whole-proteome sequences
Authors: Leimeister Chris-Andre , Schellhorn Jendrik , Dörrer Svenja , Gerth Michael , Bleidorn Christoph , Morgenstern Burkhard 
Published: December 2018

Abstract
Word-based or ‘alignment-free' sequence comparison has become an active research area in bioinformatics. While previous word-frequency approaches calculated rough measures of sequence similarity or dissimilarity, some new alignment-free methods are able to accurately estimate phylogenetic distances between genomic sequences. One of these approaches is Filtered Spaced Word Matches. Here, we extend this approach to estimate evolutionary distances between complete or incomplete proteomes; our implementation of this approach is called Prot-SpaM. We compare the performance of Prot-SpaM to other alignment-free methods on simulated sequences and on various groups of eukaryotic and prokaryotic taxa. Prot-SpaM can be used to calculate high-quality phylogenetic trees for dozens of whole-proteome sequences in a matter of seconds or minutes and often outperforms other alignment-free approaches. The source code of our software is available through Github: https://github.com/jschellh/ProtSpaM.
Mental Health Navigation – a Model
Authors: Knesek Gerald , Hemphill Thomas 
Published: December 2018

Summary
The need for mental health care services is a growing concern around the world. This article proposes a conceptual model for the role a mental health care navigator to meet the growing needs of consumers who are seeking greater access to fragmented and confusing mental health care services. This conceptual model proposes integrating mental health into primary care with a more patient-centered approach to the care of the whole person. This approach is congruent with The Ottawa Charter for Health Promotion Charter calling for the reorienting of health services focusing on the total needs of the individual as a whole person. Although USA focused, the model has potential for sharing across countries to build capacity for mental health care in other countries around the world. The conceptual model focuses on matching consumer mental health care needs with the correct mental health care services. This would ensure that patients get the appropriate mental health care services while allowing the primary care physician to maintain the role of coordinator of care for all of the patient’s health care needs. The main intent of the model is to stimulate discussion and exploration around the role of a proposed mental health care navigator that can lead to creating models reflecting local need and adaptation. Successful models can lead to collaborative discussion encouraging capacity building in other countries. The authors maintain that coordination of health care, including mental, medical and surgical care, is the best approach to controlling costs and ensuring the health of the whole person.
Pregnancy Choices and the Role of Ultrasound Viewing
Authors: York Ashley B. , Bagwell Laurie L. 
Published: December 2018

ABSTRACT:
Limited research exists on the impact of ultrasound use in abortion or pregnancy clinic settings, to assist women in decision-making regarding their pregnancy. A retrospective chart review study was conducted at a pregnancy resource center to examine the impact of ultrasound viewing on a woman's decision to continue her pregnancy. During a 1-year period, intention to terminate pregnancy was reduced from 44 cases to 14 cases after viewing the ultrasound. Nursing implications include understanding the value of ultrasound viewing among pregnant women considering abortion.
Navigating Nursing Transitions
Authors: Bouws Melissa , Weeda Janet 
Published: December 2018

ABSTRACT:
Novice nurses and those new to academic leadership roles may question their career choice when fulfillment and joy are elusive. Resolving these questions often means revisiting the vocation and calling that led nurses to the profession. The authors describe how support from others and gratitude, as well as spiritual awareness, contribute to job satisfaction; a case study illustrates the journey from novice to career-satisfied professional nurse.
Google Glass for Remote Surgical Tele-proctoring in Low- and Middle-income Countries: A Feasibility Study from Mozambique
Authors: McCullough Meghan C. , Kulber Louie , Sammons Patrick , Santos Pedro , Kulber David A. 
Published: December 2018

Background:
Untreated surgical conditions account for one-third of the total global burden of disease, and a lack of trained providers is a significant contributor to the paucity of surgical care in low- and middle-income countries (LMICs). Wearable technology with real-time tele-proctoring has been demonstrated in high-resource settings to be an innovative method of advancing surgical education and connecting providers, but application to LMICs has not been well-described.

Methods:
Google Glass with live-stream capability was utilized to facilitate tele-proctoring between a surgeon in Mozambique and a reconstructive surgeon in the United States over a 6-month period. At the completion of the pilot period, a survey was administered regarding the acceptability of the image quality as well as the overall educational benefit of the technology in different surgical contexts.

Results:
Twelve surgical procedures were remotely proctored using the technology. No complications were experienced in any patients. Both participants reported moderate visual impairment due to image distortion and light over-exposure. Video-stream latency and connection disruption were also cited as limitations. Overall, both participants reported that the technology was highly useful as training tool in both the intraoperative and perioperative setting.

Conclusions:
Our experience in Mozambique demonstrates the feasibility of wearable technology to enhance the reach and availability of specialty surgical training in LMICs. Despite shortcomings in the technology and logistical challenges inherent to international collaborations, this educational model holds promise for connecting surgeons across the globe and introducing expanded access to education and mentorship in areas with limited opportunities for surgical trainees.
Can Robotic-Assisted Surgery Overcome the Risk of Mortality in Cardiac Reoperation?
Authors: Kitahara Hiroto , Wehman Brody , Balkhy Husam H. 
Published: December 2018

Objective A robotic-assisted approach potentially has many advantages for cardiac reoperation, which include sternum-sparing and three-dimensional visualization leading to precise adhesiolysis and excellent exposure in a limited field. Methods We retrospectively reviewed our patients undergoing robotic cardiac reoperation (redo group) from July 2013 to April 2017 at our institution and compared with our patients undergoing standard robotic surgery (nonredo group). In the reoperative cases, a thoracoscope was inserted through a 5-mm port placed away from the previous scar. Another 5-mm port was inserted under direct vision to make space for one or two robotic arms, and further precise dissection was performed robotically. Results A total of 486 patients underwent robotic-assisted cardiac surgery. There were 36 patients who had one or more previous cardiac surgeries (42 surgeries). Although the mean operative and cardiopulmonary bypass time were longer in the redo group (median = 351 minutes vs. 289 minutes and 219 minutes vs. 178 minutes, P < 0.05, respectively), cardiac arrest time was similar between two groups. The redo group had a higher incidence of postoperative prolonged ventilation (16.7% vs. 6.9%, P = 0.046) and pneumonia (11.1% vs. 0.2%, P < 0.001). The 30-day mortality was 2.8% (1/36) in the redo group and similar to that in the nonredo group (1.3%, P = 0.419). Conclusions Robotic cardiac reoperation is feasible with acceptable clinical outcomes including a low mortality rate similar to standard robotic surgery in our hands. Robotic assistance may have the potential to minimize morbidity and mortality.
Rigorous surveillance is necessary for high confidence in end-of-outbreak declarations for Ebola and other infectious diseases
Authors: Thompson Robin N. , Morgan Oliver W. , Jalava Katri 
Published: December 2018

AbstractThe World Health Organization considers an Ebola outbreak to have ended once 42 days have passed since the last possible exposure to a confirmed case. Benefits of a quick end-of-outbreak declaration, such as reductions in trade/travel restrictions, must be balanced against the chance of flare-ups from undetected residual cases. We show how epidemiological modelling can be used to estimate the surveillance level required for decision-makers to be confident that an outbreak is over. Results from a simple model characterising an Ebola outbreak suggest that a surveillance sensitivity (i.e. case reporting percentage) of 79% is necessary for 95% confidence that an outbreak is over after 42 days without symptomatic cases. With weaker surveillance, unrecognised transmission may still occur: if the surveillance sensitivity is only 40%, then 62 days must be waited for 95% certainty. By quantifying the certainty in end-of-outbreak declarations, public health decision-makers can plan and communicate more effectively.
Activation of intracellular transport by relieving KIF1C autoinhibition
Authors: Siddiqui Nida , Bachmann Alice , Zwetsloot Alexander James , Hussain Hamdi , Roth Daniel , Kaverina Irina , Straube Anne 
Published: December 2018

AbstractThe kinesin-3 KIF1C is a fast organelle transporter implicated in the transport of dense core vesicles in neurons and the delivery of integrins to cell adhesions. Here we report the mechanisms of autoinhibition and release that control the activity of KIF1C. We show that the microtubule binding surface of KIF1C motor domain interacts with its stalk and that these autoinhibitory interactions are released upon binding of protein tyrosine phosphatase PTPN21. The FERM domain of PTPN21 stimulates dense core vesicle transport in primary hippocampal neurons and rescues integrin trafficking in KIF1C-depleted cells. In vitro, human full-length KIF1C is a processive, plus-end directed motor. Its landing rate onto microtubules increases in the presence of either PTPN21 FERM domain or the cargo adapter Hook3 that binds the same region of KIF1C tail. This autoinhibition release mechanism allows cargo-activated transport and might enable motors to participate in bidirectional cargo transport without undertaking a tug-of-war.
Influence of multiple hypothesis testing on reproducibility in neuroimaging research
Authors: Puoliväli Tuomas , Palva Satu , Palva J. Matias 
Published: December 2018

AbstractBackgroundReproducibility of research findings has been recently questioned in many fields of science, including psychology and neurosciences. One factor influencing reproducibility is the simultaneous testing of multiple hypotheses, which increases the number of false positive findings unless the p-values are carefully corrected. While this multiple testing problem is well known and has been studied for decades, it continues to be both a theoretical and practical problem.New MethodHere we assess the reproducibility of research involving multiple-testing corrected for family-wise error rate (FWER) or false discovery rate (FDR) by techniques based on random field theory (RFT), cluster-mass based permutation testing, adaptive FDR, and several classical methods. We also investigate the performance of these methods under two different models.ResultsWe found that permutation testing is the most powerful method among the considered approaches to multiple testing, and that grouping hypotheses based on prior knowledge can improve power. We also found that emphasizing primary and follow-up studies equally produced most reproducible outcomes.Comparison with Existing Method(s)We have extended the use of two-group and separate-classes models for analyzing reproducibility and provide a new open-source software “MultiPy” for multiple hypothesis testing.ConclusionsOur results suggest that performing strict corrections for multiple testing is not sufficient to improve reproducibility of neuroimaging experiments. The methods are freely available as a Python toolkit “MultiPy” and we aim this study to help in improving statistical data analysis practices and to assist in conducting power and reproducibility analyses for new experiments.
Anacapa Toolkit: an environmental DNA toolkit for processing multilocus metabarcode datasets
Authors: Curd Emily E. , Gold Zack , Kandlikar Gaurav S , Gomer Jesse , Ogden Max , O’Connell Taylor , Pipes Lenore , Schweizer Teia , Rabichow Laura , Lin Meixi , Shi Baochen , Barber Paul , Kraft Nathan , Wayne Robert , Meyer Rachel S. 
Published: December 2018

Abstract1. Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable, and non-invasive. Longstanding needs of the eDNA community are modular informatics tools, comprehensive and customizable reference databases, flexibility across high-throughput sequencing platforms, fast multilocus metabarcode processing, and accurate taxonomic assignment. As bioinformatics tools continue to improve, addressing each of these demands within a single bioinformatics toolkit is becoming a reality.2. We present the modular metabarcode sequence toolkit Anacapa (https://github.com/limey-bean/Anacapa/), which addresses the above needs, allowing users to build comprehensive reference databases and assign taxonomy to raw multilocus metabarcode sequence data A novel aspect of Anacapa is our database building module, Creating Reference libraries Using eXisting tools (CRUX), which generates comprehensive reference databases for specific user-defined metabarcode loci. The Quality Control and Dereplication module sorts and processes multiple metabarcode loci and processes merged, unmerged and unpaired reads maximizing recovered diversity. Followed by amplicon sequence variants (ASVs) detection using DADA2. The Anacapa Classifier module aligns these ASVs to CRUX-generated reference databases using Bowtie2. Taxonomy is assigned to ASVs with confidence scores using a Bayesian Lowest Common Ancestor (BLCA) method. The Anacapa Toolkit also includes an R package, ranacapa, for automated results exploration through standard biodiversity statistical analysis.3. We performed a series of benchmarking tests to verify that the Anacapa Toolkit generates comprehensive reference databases that capture wide taxonomic diversity and that it can assign high-quality taxonomy to both MiSeq-length and Hi-Seq length sequence data. We demonstrate the value of the Anacapa Toolkit to assigning taxonomy to eDNA sequences from seawater samples from southern California including capability of this tool kit to process multilocus metabarcoding data.4. The Anacapa Toolkit broadens the exploration of eDNA and assists in biodiversity assessment and management by generating metabarcode specific databases, processing multilocus data, retaining all read types, and expanding non-traditional eDNA targets. Anacapa software and source code are open and available in a virtual container to ease installation.
Counter-stimuli Inhibit GRPR Neurons via GABAergic Signaling in the Spinal Cord
Authors: Bardoni Rita , Barry Devin M. , Li Hui , Shen Kai-Feng , Jeffry Joseph , Yang Qianyi , Comitato Antonella , Li Yun-Qing , Chen Zhou-Feng 
Published: December 2018

AbstractA myriad of counter-stimuli, including algogens and cooling, could inhibit itch sensation; however, the underlying molecular and neural mechanisms remain poorly understood. Here, we show that the spinal neurons expressing gastrin releasing peptide receptor (GRPR) primarily comprise excitatory interneurons that receive direct and indirect inputs from C and Aδ fibers and form contacts with projection neurons expressing the neurokinin 1 receptor (NK1R). Optical or chemogenetic activation of GRPR neurons evokes itch behavior that is partly dependent on NK1R activation. Importantly, we show that noxious or cooling counter-stimuli inhibit the activity of GRPR neurons via GABAergic signaling. By contrast, capsaicin, which could evoke a mix of itch and pain sensations, could exert both excitatory and inhibitory effects on GRPR neurons. These data strengthen the role of GRPR neurons as a key circuit for itch transmission and illustrate a spinal mechanism whereby counter-stimuli inhibit itch by suppressing the function of GRPR neurons.HighlightsActivation of GRPR neurons evokes itch and is dependent upon NK1R activationGRPR neurons receive both direct and indirect inputs from C/Aδ fibersCounter-stimuli inhibit GRPR neurons via GABAergic signalingIncreased excitability of GRPR neurons in chronic itch condition