bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy of Tensed and Straight Free Jejunum Transfer for the Reduction of Postoperative Dysphagia
Authors: Tachibana Satsuki , Miyamoto Shimpei , Goto Takahiro , Ishida Katsuhiro , Iida Takuya , Okazaki Mutsumi , Yoshida Sei , Nomura Shogo , Hayashi Ryuichi , Sakuraba Minoru 
Published: December 2017

Background:
Free jejunal transfer (FJT) is a standard method of reconstruction after total pharyngo-laryngo-cervical esophagectomy (TPLE) in patients with advanced head and neck cancer. However, it is related to various degrees of postoperative swallowing dysfunction. This study aimed to assess whether the tensed and straight FJT method results in a reduced rate of postoperative dysphagia compared with historical controls.

Methods:
Patients who were undergoing FJT after TPLE for squamous cell carcinoma of the hypopharynx or cervical esophagus were enrolled. The primary endpoint was the rate of not developing dysphagia within 6 months of the surgery, and we compared this value with that obtained from historical data of patients who underwent FJT. The secondary endpoint was the rate of developing surgical complications.

Results:
Although 128 patients were registered between August 2012 and July 2015, 7 were excluded based on the exclusion criteria. Of the remaining 121 patients, FJT with the craniocaudally tensed and straight method was performed in all patients. The rate of not developing dysphagia and its 95% confidence interval (CI) were 66.1% and 57.0–74.5%, respectively. The lower limit of the CI was higher than the prespecified threshold value of 50.0%. The rate of developing complications of total necrosis of the jejunum was 3.3%, cervical infection was 9.9%, and major anastomotic leakage was 4.1%.

Conclusions:
Our findings revealed that the proportion of postoperative dysphagia decreased in patients who underwent tensed and straight FJT. This method may become the standard surgical method in reconstruction of defects after TPLE.
Myelofibrosis‐Related Anemia
Authors: Naymagon Leonard , Mascarenhas John 
Published: December 2017

AbstractMyelofibrosis (MF) is a clonal hematopoietic stem cell disorder characterized by pathological myeloproliferation and aberrant cytokine production resulting in progressive fibrosis, inflammation, and functional compromise of the bone marrow niche. Patients with MF develop splenomegaly (due to extramedullary hematopoiesis), hypercatabolic symptoms (due to overexpression of inflammatory cytokines), and anemia (due to bone marrow failure and splenic sequestration). MF remains curable only with allogeneic hematopoietic stem cell transplantation (ASCT), a therapy that few MF patients are deemed fit to undergo. The goals of treatment are thus often palliative. The approval of the JAK inhibitor ruxolitinib has done much to address the burden of splenomegaly and constitutional symptoms of patients with MF; however, therapy‐related anemia is often an anticipated downside. Anemia thus remains a challenge in the management of MF and represents a major unmet need. Intractable anemia depresses quality of life, portends poor outcomes, and can act to restrict access to palliative JAK inhibition in some patients. While therapies for MF‐related anemia do exist, they are limited in their efficacy, durability, and tolerability. Therapies currently in development promise improved anemia‐specific outcomes; however, are still early in the pathway to regulatory approval and regular clinical use. In this review, we will discuss established and emerging treatments for MF‐related anemia. We will give particular attention to developmental therapies which herald significant progress in the understanding and management of MF‐related anemia.
Cost Analysis of a Student-Run, Free Physical Therapy Clinic
Authors: Stickler Kellie , Sabus Carla , Denney Linda 
Published: December 2017

Introduction.
Within many physical therapy education programs, service learning is essential to student development and often complements the institutional priorities of serving the community. Service learning experiences vary from local, institution-hosted clinics to international experiences. Although the benefits of service learning to the students and community have been widely reported, it is also important to appreciate the cost to implement and support a service learning clinic within an academic department. The purpose of this study was to determine the cost of running a student-run free physical therapy clinic for estimated labor costs calculated as wage opportunity cost, quantify equipment and infrastructure cost per patient, estimate facility cost, and derive an estimated cost of care delivery per patient.

Methods.
This retrospective study reviewed patient charts and clinic data from a student-run free clinic between January 2013 and December 2014. Both total outgoing cost and potential total cost were determined for this study. The total outgoing cost was determined by calculating equipment cost and cost of liability insurance. The potential total cost was determined by calculating volunteer hours, facility cost, and outgoing clinic costs.

Results.
In the 2-year study period, the clinic incurred a potential total cost of $68,405.40. However, the total outgoing cost of the clinic was $1,993.23 for 253 patient visits, which gives the clinic an average cost per visit of $7.64.

Discussion/Conclusion.
This study demonstrates the feasibility of a student-run, free physical therapy clinic through monetized gain for the community while enhancing students' skills. Furthermore, this study demonstrates a method to capture quantifiable monetary cost and benefit to program stakeholders and the community.
Impact of New Medications and $4 Generic Programs on Overactive Bladder Treatment Among Older Adults in the United States, 2000–2015
Authors: Kinlaw Alan C. , Jonsson Funk Michele , Conover Mitchell M. , Pate Virginia , Markland Alayne D. , Wu Jennifer M. 
Published: December 2017

Background:
Despite several new medications being Food and Drug Administration-approved for overactive bladder (OAB) and new prescription drug payment programs, there are limited population-based data regarding OAB medication use among older adults.

Objectives:
To examine: (1) impacts of new medications and $4 generic programs on time trends for OAB-related medication dispensing for older adults in the United States; (2) differences by age and sex; and (3) temporal changes in OAB-related medication payments.

Methods:
Using Truven Health Analytics’ Medicare Supplemental Database (2000–2015), we analyzed OAB-related medication claims for 9,477,061 Medigap beneficiaries age 65–104. We estimated dispensing rates (per 1000 person-months), assessed dispensing trends using interrupted time-series methods, compared dispensing rates by age and sex, and summarized payment trends.

Results:
From 2000 to 2015, 771,609 individuals filled 13,863,998 OAB-related prescriptions. During 2000–2007, 3 new extended-release medications became available (tolterodine, darifenacin, solifenacin), leading to increases in overall OAB-related dispensing rates by 19.1 (99% confidence interval, 17.0–21.2), a 92% increase since 2000; overall rates remained stable during 2008–2015. By 2015, the most common medications were oxybutynin (38%), solifenacin (20%), tolterodine (19%), and mirabegron (12%). Dispensing rates peaked at age 90 (rate, 53.4; 99% confidence interval, 53.1–53.7). Women had higher rates than men at all ages (average ratewomen−ratemen, 22.0). The gap between upper and lower percentiles of medication payments widened between 2008–2015; by 2015, 25% of reimbursed dispensed prescriptions had total payments exceeding $250.

Conclusions:
Medication-specific dispensing rates for OAB changed when new alternatives became available. Recent changes in utilization and cost of OAB medications have implications for clinical guidelines, pharmacoepidemiologic studies, and payment policies.
In vitro study of dentin hypersensitivity treated by whitlockite glass-ceramics
Authors: Juraski Amanda C. 
Published: December 2017

AbstractThe aim of this study is to evaluate the potential of a bioactive glass based on the 3CaO.P2O5-SiO2MgO-system and its glassceramics containing whitlockite on the remineralization of dentin as a possible treatment to dentin hypersensitivity. For that, 40 third molar human teeth were artificially demineralized and randomly distributed in 4 groups (n = 10): G1 - Negative Control (no treatment), G2 - Positive Control (treated by Bioglass® 45S5), G3 – BG (treated by bioactive glass based on 3CaO.P2O5-SiO2-MgOsystem), and G4 – BGC (treated by bioactive whitlockite glass-ceramics). After treatment, the samples were emerged in artificial saliva and stored for 7 days in a controlled temperature of 37ºC. After that, scanning electron microscopy (SEM) and atomic force microscopy (AFM) was used to evaluate samples morphology. The analysis confirmed the formation of hydroxyapatite on the surface of all the biomaterials studied, that in the dentine specimens treated by bioactive glass and whitlockite glas-ceramic most of the dentinal tubules were completely occluded.
Confidence modulates exploration and exploitation in value-based learning
Authors: Boldt Annika , Blundell Charles , De Martino Benedetto 
Published: December 2017

AbstractUncertainty is ubiquitous in cognitive processing, which is why agents require a precise handle on how to deal with the noise inherent in their mental operations. Previous research suggests that people possess a remarkable ability to track and report uncertainty, often in the form of confidence judgments. Here, we argue that humans use uncertainty inherent in their representations of value beliefs to arbitrate between exploration and exploitation. Such uncertainty is reflected in explicit confidence judgments. Using a novel variant of a multi-armed bandit paradigm, we studied how beliefs were formed and how uncertainty in the encoding of these value beliefs (belief confidence) evolved over time. We found that people used uncertainty to arbitrate between exploration and exploitation, reflected in a higher tendency towards exploration when their confidence in their value representations was low. We furthermore found that value uncertainty can be linked to frameworks of metacognition in decision making in two ways. First, belief confidence drives decision confidence—that is people’s evaluation of their own choices. Second, individuals with higher metacognitive insight into their choices were also better at tracing the uncertainty in their environment. Together, these findings argue that such uncertainty representations play a key role in the context of cognitive control.
False discovery rate estimation and heterobifunctional cross-linkers
Authors: Fischer Lutz , Rappsilber Juri 
Published: December 2017

AbstractFalse discovery rate (FDR) estimation is a cornerstone of proteomics that has recently been adapted to cross-linking/mass spectrometry. Here we demonstrate that heterobifunctional cross-linkers, while theoretically different from homobifunctional cross-linkers, need not be considered separately in practice. We develop and then evaluate the impact of applying a correct FDR formula for use of heterobifunctional cross-linkers and conclude that there are minimal practical advantages. Hence a single formula can be applied to data generated from the many different non-cleavable cross-linkers.
Endogenous tagging reveals differential regulation of Ca2+channels at single AZs during presynaptic homeostatic potentiation and depression
Authors: Gratz Scott J. , Goel Pragya , Bruckner Joseph J. , Hernandez Roberto X. , Khateeb Karam , Macleod Gregory T. , Dickman Dion , O’Connor-Giles Kate M. 
Published: December 2017

AbstractNeurons communicate through Ca2+-dependent neurotransmitter release at presynaptic active zones (AZs). Neurotransmitter release properties play a key role in defining information flow in circuits and are tuned during multiple forms of plasticity. Despite their central role in determining neurotransmitter release properties, little is known about how Ca2+channel levels are modulated to calibrate synaptic function. We used CRISPR to tag theDrosophilaCaV2 Ca2+ channel Cacophony (Cac) and investigated the regulation of endogenous Ca2+channels during homeostatic plasticity in males in which all endogenous Cac channels are tagged. We found that heterogeneously distributed Cac is highly predictive of neurotransmitter release probability at individual AZs and differentially regulated during opposing forms of presynaptic homeostatic plasticity. Specifically, Cac levels at AZ are increased during chronic and acute presynaptic homeostatic potentiation (PHP), and live imaging during acute expression of PHP reveals proportional Ca2+channel accumulation across heterogeneous AZs. In contrast, endogenous Cac levels do not change during presynaptic homeostatic depression (PHD), implying that the reported reduction in Ca2+influx during PHD is achieved through functional adaptions to pre-existing Ca2+channels. Thus, distinct mechanisms bi-directionally modulate presynaptic Ca2+levels to maintain stable synaptic strength in response to diverse challenges, with Ca2+channel abundance providing a rapidly tunable substrate for potentiating neurotransmitter release over both acute and chronic timescales.
bcGST - an interactive bias-correction method to identify over-represented gene-sets in boutique arrays
Authors: Wang Kevin YX , Menzies Alexander M , Silva Ines P , Wilmott James S , Yan Yibing , Wongchenko Matthew , Kefford Richard F , Scolyer Richard A , Long Georgina V , Tarr Garth , Mueller Samuel , Yang Jean YH 
Published: December 2017

AbstractMotivation: Gene annotation and pathway databases such as Gene Ontology and Kyoto Encyclopedia of Genes and Genomes are important tools in Gene Set Test (GST) that describe gene biological functions and associated pathways. GST aims to establish an association relationship between a gene set of interest and an annotation. Importantly, GST tests for over-representation of genes in an annotation term. One implicit assumption of GST is that the gene expression platform captures the complete or a very large proportion of the genome. However, this assumption is neither satisfied for the increasingly popular boutique array nor the custom designed gene expression profiling platform. Specifically, conventional GST is no longer appropriate due to the gene set selection bias induced during the construction of these platforms.Results: We propose bcGST, a bias-corrected Gene Set Test by introducing bias correction terms in the contingency table needed for calculating the Fisher’s Exact Test (FET). The adjustment method works by estimating the proportion of genes captured on the array with respect to the genome in order to assist filtration of annotation terms that would otherwise be falsely included or excluded. We illustrate the practicality of bcGST and its stability through multiple differential gene expression analyses in melanoma and TCGA cancer studies.Availability: The bcGST method is made available as a Shiny web application at http://shiny.maths.usyd.edu.au/bcGST/Contact:kevin.wang@sydney.edu.au
MSAC: Compression of multiple sequence alignment files
Authors: Deorowicz Sebastian , Walczyszyn Joanna , Debudaj-Grabysz Agnieszka 
Published: December 2017

AbstractMotivationBioinformatics databases grow rapidly and achieve values hardly to imagine a decade ago. Among numerous bioinformatics processes generating hundreds of GB is multiple sequence alignments of protein families. Its largest database, i.e., Pfam, consumes 40–230 GB, depending of the variant. Storage and transfer of such massive data has become a challenge.ResultsWe propose a novel compression algorithm, MSAC (Multiple Sequence Alignment Compressor), designed especially for aligned data. It is based on a generalisation of the positional Burrows–Wheeler transform for non-binary alphabets. MSAC handles FASTA, as well as Stockholm files. It offers up to six times better compression ratio than other commonly used compressors, i.e., gzip. Performed experiments resulted in an analysis of the influence of a protein family size on the compression ratio.AvailabilityMSAC is available for free at https://github.com/refresh-bio/msac and http://sun.aei.polsl.pl/REFRESH/msac.Contactsebastian.deorowicz@polsl.plSupplementary materialSupplementary data are available at the publisher Web site.
Whisper: Read sorting allows robust mapping of sequencing data
Authors: Deorowicz Sebastian , Debudaj-Grabysz Agnieszka , Gudyś Adam , Grabowski Szymon 
Published: December 2017

AbstractMotivationMapping reads to a reference genome is often the first step in a sequencing data analysis pipeline. Mistakes made at this computationally challenging stage cannot be recovered easily.ResultsWe present Whisper, an accurate and high-performant mapping tool, based on the idea of sorting reads and then mapping them against suffix arrays for the reference genome and its reverse complement. Employing task and data parallelism as well as storing temporary data on disk result in superior time efficiency at reasonable memory requirements. Whisper excels at large NGS read collections, in particular Illumina reads with typical WGS coverage. The experiments with real data indicate that our solution works in about 15% of the time needed by the well-known Bowtie2 and BWA-MEM tools at a comparable accuracy (validated in variant calling pipeline).AvailabilityWhisper is available for free from https://github.com/refresh-bio/Whisper or http://sun.aei.polsl.pl/REFRESH/Whisper/Contactsebastian.deorowicz@polsl.plSupplementary informationSupplementary data are available at publisher Web site.
Decoding the gene co-expression network underlying the ability of Gevuina avellana Mol. to live in diverse light conditions
Authors: Ostria-Gallardo E , Ranjan A , Ichihashi Y , Corcuera LJ , Sinha NR 
Published: December 2017

SummaryGevuina avellana Mol. (Proteaceae) is a typical tree from the South American temperate rainforest. Although this species mostly regenerates in shaded understories, it exhibits an exceptional ecological breadth, being able to live under a wide range of light conditions. Here we studied the genetic basis regulating physiological acclimation of the photosynthetic responses of G. avellana under contrasting light conditions.We analyzed carbon assimilation and light energy used for photochemical process in plants acclimated to contrasting light conditions. Also, we used a transcriptional profile of leaf primordia from G. avellana saplings growing under different light environments to identify the gene co-expression network underpinning photosynthetic performance and light-related processes.The photosynthetic parameters revealed optimal performance regardless of light conditions. Strikingly, the mechanism involved in dissipation of excess light energy showed no significant differences between high and low-light acclimated plants. The gene co-expression network defined a community structure consistent with the photochemical responses, including genes involved mainly in assembly and functioning of photosystems, photoprotection, and retrograde signaling.Our ecophysiological genomics approach provides an understanding of the molecular regulatory mechanisms that allows this tree to have an optimal balance between photochemical, photoprotective and antioxidant performance in the diverse light habitats it encounters in nature.
Scaling of G1 duration with population doubling time by a cyclin inSaccharomyces cerevisiae
Authors: Blank Heidi M. , Callahan Michelle , Pistikopoulos Ioannis P.E. , Polymenis Aggeliki O. , Polymenis Michael 
Published: December 2017

ABSTRACTThe longer cells stay in particular phases of the cell cycle, the longer it will take these cell populations to increase. However, the above qualitative description has very little predictive value, unless it can be codified mathematically. A quantitative relation that defines the population doubling time (Td) as a function of the time eukaryotic cells spend in specific cell cycle phases would be instrumental for estimating rates of cell proliferation and for evaluating introduced perturbations. Here, we show that in human cells the length of the G1 phase (TG1) regressed on Tdwith a slope of ≈0.75, while in the yeastSaccharomyces cerevisiaethe slope was slightly smaller, at ≈0.60. On the other hand, cell size was not strongly associated with Tdor TG1in cell cultures that were proliferating at different rates. Furthermore, we show that levels of the yeast G1 cyclin Cln3p were positively associated with rates of cell proliferation over a broad range, at least in part through translational control mediated by a short uORF in theCLN3transcript. Cln3p was also necessary for the proper scaling between TG1and Td. In contrast, yeast lacking the Whi5p transcriptional repressor maintained the scaling between TG1and Td. These data reveal fundamental scaling relations between the duration of eukaryotic cell cycle phases and rates of cell proliferation, point to the necessary role of Cln3p in these relations in yeast and provide a mechanistic basis linking Cln3p levels to proliferation rates and the scaling of G1 with doubling time.
A new recommendation system on the basis of consumer initiative decision based on an associative classification approach
Authors: Yin Chengxin , Guo Yan , Yang Jianguo , Ren Xiaoting 
Published: December 2017

Purpose
The purpose of this paper is to improve the customer satisfaction by offering online personalized recommendation system.

Design/methodology/approach
By employing an innovative associative classification method, this paper is able to predict a customer’s pleasure during the online while-recommending process. Consumers can make an active decision to recommended products. Based on customer’s characteristics, a product will be recommended to the potential buyer if the model predicts that he/she will click to view the product. That is, he/she is satisfied with the recommended product. Finally, the feasibility of the proposed recommendation system is validated through a Taobao shop.

Findings
The results of the experimental study clearly show that the online personalized recommendation system maximizes the customer’s satisfaction during the online while-recommending process based on an innovative associative classification method on the basis of consumer initiative decision.

Originality/value
Conventionally, customers are considered as passive recipients of the recommendation system. However, customers are tired of the recommendation system, and they can do nothing sometimes. This paper designs a new recommendation system on the basis of consumer initiative decision. The proposed recommendation system maximizes the customer’s satisfaction during the online while-recommending process.