bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Lived Experience of Gynecologic Cancer Survivors in Taiwan
Authors: Tsai Li-Yun , Wang Kung-Liahng , Liang Shu-Yuan , Tsai Jung-Mei , Tsay Shiow-Luan 
Published: October 2017

ABSTRACT

Background:
Although it is now possible to achieve permanent remission in a large percentage of gynecologic cancer (GC) cases, many GC patients in remission experience side effects or complications that influence their physical function and family relationships. Compared with other types of cancer patients, survivors of GC face greater challenges in terms of physical and psychological adaptations, and many of these do not receive sufficient assistance. An in-depth understanding of the lived experiences and demands of GC survivors is key to constructing comprehensive related healthcare services.

Purpose:
The aim of this study was to understand the lived experience of GC survivors in Taiwan to help their return to a healthy life.

Methods:
This was a phenomenological study. Twenty-three survivors of GC participated in semistructured interviews that were held in a private environment. The transcripts were based on synchronous recordings from the interviews. Giorgi’s phenomenology analysis was adopted for data analysis.

Results:
Three themes with six subthemes were extracted from the data, including (a) the inner struggle of living with cancer and recurrence: repeatedly exploring the causes of cancer and treatment and facing a fear of cancer recurrence, (b) the interpretation and adjustment to cancer treatment: filled with fluctuating physical and mental distress and working to adopt a different perspective, and (c) the long passage of finding a desirable lifestyle: adjusting to long-term coexistence with side effects and realizing the strength of society, body, and mind.

Conclusions/Implications for Practice:
The journey of rehabilitation for GC survivors is very long. The participants in this study faced different respective challenges during the diagnosis, treatment, and adjustment phases. Conventional disease-oriented medical care cannot satisfy the requirements of cancer patients because of patient-decentralized services. Our results indicate that GC survivors face diverse problems, both physically and mentally. Healthcare professionals should work to facilitate the psychological adjustment of cancer survivors and provide timely professional advice in combination with social resources. These results may serve as a reference for cancer care professionals who are navigating healthcare services.
Sensitivity of the Cogstate Test Battery for Detecting Prolonged Cognitive Alterations Stemming From Sport-Related Concussions
Authors: Sicard Veronik , Moore Robert D. , Ellemberg Dave 
Published: October 2017

Objective:
To determine if the Cogstate test battery contains the requisite sensitivity to detect prolonged cognitive alterations.

Methods:
One hundred twenty collegiate athletes (71 with a history of concussion; 49 controls) completed the Cogstate test battery, to which we added a 2-back condition. In addition to the Cogstate clinical (transformed variables), we analyzed the raw data.

Results:
The clinical variables failed to reveal any group differences. Further, although the raw data failed to reveal group differences for tasks measuring lower-level cognition, group differences were observed for accuracy on the 1- and 2-back tasks, which require multiple aspects of higher cognition. The overall classification accuracy was higher using the raw data than the clinical variables. The combined sensitivity of the 1- and 2-back task was moderate and specificity was high.

Conclusions:
These results suggest that using the raw scores over clinical variables increases the sensitivity of the test battery. Moreover, these results add another piece of evidence suggesting that concussive injuries are associated with subtle long-term alterations in aspects of higher cognition. Importantly, these deficits would have gone unobserved if we had relied solely on automated clinical variables. The current results further our scientific understanding of concussion and may be used to advance clinical practices.
Dual-Task Tandem Gait and Average Walking Speed in Healthy Collegiate Athletes
Authors: Howell David R. , Oldham Jessie R. , Meehan William P. , DiFabio Melissa S. , Buckley Thomas A. 
Published: October 2017

Objectives:
To (1) examine the association between a commonly used concussion test, tandem gait, in single/dual-task conditions with single-task and dual-task average walking speed, (2) characterize the prevalence of tandem gait false positives, and (3) develop a normative reference range of dual-task tandem gait times.

Design:
Cross-sectional study.

Setting:
Two NCAA collegiate athletic facilities.

Independent Variables:
Athletes completed the tandem gait test and a gait evaluation in single/dual-task conditions during a preseason examination.

Main Outcome Measures:
Associations between tandem gait times and average walking speeds were evaluated using multiple linear regression models. Various tandem gait test time pass/fail cutoffs were calculated to examine false-positive rates.

Results:
Among the 171 participants (103 men, 19.8 ± 1.2 years of age), dual-task tandem gait completion times were independently associated with dual-task average walking speed [β = −4.018; 95% confidence interval (CI), −7.153 to −0.883], but single-task associations were not found. Male gender was associated with faster tandem gait times in both single-task (β = −0.880, 95% CI, −1.731 to −0.029) and dual-task conditions (β = −2.225, 95% CI, −3.691 to −0.759). A pass/fail cutoff threshold of 14 seconds resulted in a 2% false-positive rate for single-task tandem gait, while it resulted in a 29% false-positive rate during dual-task tandem gait.

Conclusions:
Average walking speed and dual-task tandem gait represent objective measures that are useful in concussion management. While a single-task tandem gait cutoff of 14 seconds seems appropriate for males, adjustments may be necessary based on sex and alternate pass/fail criteria may be appropriate for dual-task tandem gait.
Patient Experience-based Value Sets
Authors: Pickard A. Simon , Hung Yu-Ting , Lin Fang-Ju , Lee Todd A. 
Published: October 2017

Background:
Although societal preference weights are desirable to inform resource-allocation decision-making, patient experienced health state-based value sets can be useful for clinical decision-making, but context may matter.

Objective:
To estimate EQ-5D value sets using visual analog scale (VAS) ratings for patients undergoing knee replacement surgery and compare the estimates before and after surgery.

Methods:
We used the Patient Reported Outcome Measures data collected by the UK National Health Service on patients undergoing knee replacement from 2009 to 2012. Generalized least squares regression models were used to derive value sets based on the EQ-5D-3 level using a development sample before and after surgery, and model performance was examined using a validation sample.

Results:
A total of 90,450 preoperative and postoperative valuations were included. For preoperative valuations, the largest decrement in VAS values was associated with the dimension of anxiety/depression, followed by self-care, mobility, usual activities, and pain/discomfort. However, pain/discomfort had a greater impact on VAS value decrement in postoperative valuations. Compared with preoperative health problems, postsurgical health problems were associated with larger value decrements, with significant differences in several levels and dimensions, including level 2 of mobility, level 2/3 of usual activities, level 3 of pain/discomfort, and level 3 of anxiety/depression. Similar results were observed across subgroups stratified by age and sex.

Conclusions:
Findings suggest patient experience-based value sets are not stable (ie, context such as timing matters). However, the knowledge that lower values are assigned to health states postsurgery compared with presurgery may be useful for the patient-doctor decision-making process.
Form, Function, and Esthetics in Prosthetically Rehabilitated Maxillary Defects
Authors: Mittal Manish , Sharma Rohit , Kalra Ashish , Sharma Parvinder 
Published: October 2017

Purpose:
Patients with maxillofacial defects secondary to the removal of benign and malignant pathologies of midface have a profound impact on quality of life. The aim of this study was to collect and analyze the data pertaining to 4 designs of obturator by assessment of the patient with obturator functioning scale (OFS)

Materials and Methods:
This retrospective analysis included all the patients who underwent prosthetic rehabilitation of maxillary defects using 4 different types (conventional, cast partial, hollow bulb, and magnet retained) of obturators from 2009 to 2016 with minimum 1 year of follow up. Demographics, number, size, location, type of pathology, postmorbid dentition, and the treatment rendered were recorded. Obturator functioning scale was used to subjectively assess the patient satisfaction.

Results:
The mean score on OFS was 5.67 (standard deviation: 1.8). There was a fair and statistical improvement in chewing/eating, speech clarity in public/on phone, swallowing of foods and liquids, pronunciation of words, and social interaction (P < 0.05). The outcome was best in magnet retained followed by cast partial group. The least outcome was in conventional obturator group.

Conclusion:
Obturators of different designs do play an important role in rehabilitation of maxillary defects with a satisfactory outcome.
Thyroglossal Duct Cyst at the Base of Tongue: The Emerging Role of Transoral Endoscopic-Assisted Surgery
Authors: Turri-Zanoni Mario , Battaglia Paolo , Castelnuovo Paolo 
Published: October 2017

Abstract
Cystic lesions involving the tongue base are rare, generally presenting in pediatric patients, and they may encompass different pathologies such as ranula, lingual ectopic thyroid, thyroglossal duct cyst (TDC), dysontogenetic cysts, benign, and malignant tumors.
This paper describes the case of a 19-year-old girl with phonation impairment and mild dysphagia due to limited tongue protrusion and movements. Radiologic examinations revealed a bulky cystic lesion at the base of tongue with displacement of extrinsic lingual muscles. A minimally invasive transoral removal of the mass was performed under the assistance of the endoscopic system. The histopathologic analysis confirmed the diagnosis of intralingual TDC. After 2 years of clinical and radiologic follow-up, no recurrence of disease was observed and the patient is completely asymptomatic.
The present experience suggests that the endoscopic-assisted transoral removal of intralingual TDC can be proposed as a safe and effective procedure, alternative to traditional transcervical surgery as well as to transoral robotic surgery, leading to very appealing cosmetic results and encouraging functional outcomes in terms of phonation and swallowing. Preoperative radiologic examinations should be performed for an accurate diagnosis and appropriate selection of patients.
A Bioinformatics Pipeline for Whole Exome Sequencing: Overview of the Processing and Steps from Raw Data to Downstream Analysis
Authors: Meena Narendra , Mathur Praveen , Medicherla Krishna Mohan , Suravajhala Prashanth 
Published: October 2017

AbstractRecent advances in next generation sequencing (NGS) technologies have given an impetus to find causality for rare genetic disorders. Since 2005 and aftermath of the human genome project, efforts have been made to understand the rare variants of genetic disorders. Benchmarking the bioinformatics pipeline for whole exome sequencing (WES) has always been a challenge. In this protocol, we discuss detailed steps from quality check to analysis of the variants using a WES pipeline comparing them with reposited public NGS data and survey different techniques, algorithms and software tools used during each step. We observed that variant calling performed on exome and whole genome datasets have different metrics generated when compared to variant callers, GATK and VarScan with different parameters. Furthermore, we found that VarScan with strict parameters could recover 80-85% of high quality GATK SNPs with decreased sensitivity from NGS data. We believe our protocol in the form of pipeline can be used by researchers interested in performing WES analysis for genetic diseases and by large any clinical phenotypes.
Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case
Authors: dos Reis Mario , Gunnell Gregg F. , Barba-Montoya José , Wilkins Alex , Yang Ziheng , Yoder Anne D. 
Published: October 2017

AbstractPrimates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the K-Pg boundary and the timing of diversification of the main crown groups remain controversial. Here we analysed a dataset of 372 taxa (367 Primates and 5 outgroups, 61 thousand base pairs) that includes nine complete primate genomes (3.4 million base pairs). We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (auto-correlated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the auto-correlated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene.
Comprehensive skin microbiome analysis reveals the uniqueness of human-associated microbial communities among the class Mammalia
Authors: Ross Ashley A. , Müller Kirsten , Weese J. Scott , Neufeld Josh D. 
Published: October 2017

AbstractSkin is the largest organ of the body and represents the primary physical barrier between mammals and their external environment. The objective of this research was to generate a skin microbiota baseline for members of the class Mammalia, testing the effects of host species, geographic location, body region, and biological sex. The back, torso, and inner thigh regions of 177 non-human mammals were collected to include representatives from 38 species and 10 mammalian orders. Animals were collected from local farms, zoos, households, and the wild. All samples were amplified using the V3-V4 16S rRNA gene region and sequenced using a MiSeq (Illumina). For reference, previously published skin microbiome data from 20 human participants, sampled using an identical protocol to the non-human mammals, were included in the analysis. Human skin was significantly less diverse than all other mammalian orders and the factor most strongly associated with community variation for all samples was whether the host was a human. Within non-human samples, host taxonomic order was the most significant factor influencing the skin community, followed by the geographic location of the habitat. By comparing the congruence between known host phylogeny and microbial community dendrograms, we observed that Artiodactyla (even-toed ungulates) and Perissodactyla (odd-toed ungulates) had significant congruence, providing first evidence of phylosymbiosis between skin communities and their hosts.SignificanceSkin forms a critical protective barrier between a mammal and its external environment. Baseline data on the mammalian skin microbiome is crucial for making informed decisions related to veterinary research and biodiversity conservation strategies, in addition to providing insight into mammalian evolutionary history. To our knowledge, this study represents the largest mammalian skin microbiota project to date. These findings demonstrate that human skin is distinct, not only from other Primates, but from all 10 mammalian orders sampled. Using phylosymbiosis analysis, we provide the first evidence that co-evolution may be occurring between skin communities and their mammalian hosts, which warrants more in-depth future studies of the relationships between mammals and their skin microbiota.
InfoTrim: A DNA Read Quality Trimmer Using Entropy
Authors: Porter Jacob , Zhang Liqing 
Published: October 2017

AbstractBiological DNA reads are often trimmed before mapping, genome assembly, and other tasks to improve the quality of the results. Biological sequence complexity relates to alignment quality as low complexity regions can align poorly. There are many read trimmers, but many do not use sequence complexity for trimming. Alignment of reads generated from whole genome bisulfite sequencing is especially challenging since bisulfite treated reads tend to reduce sequence complexity. InfoTrim, a new read trimmer, was created to explore these issues. It is evaluated against five other trimmers using four read mappers on real and simulated bisulfite treated DNA data. InfoTrim produces reasonable results consistent with other trimmers.
Tandem repeats contribute to coding sequence variation in bumblebees (Hymenoptera: Apidae)
Authors: Zhao Xiaomeng , Su Long , Schaack Sarah , Sadd Ben M. , Sun Cheng 
Published: October 2017

AbstractTandem repeats (TRs) are highly dynamic regions of the genome. Mutations at these loci represent a significant source of genetic variation and can facilitate rapid adaptation. Bumblebees are important pollinating insects occupying a wide range of habitats. However, to date, molecular mechanisms underlying the potential adaptation of bumblebees to diverse habitats are largely unknown. In the present study, we investigate how TRs contribute to genetic variation in bumblebees, thus potentially facilitating adaptation. We identified 26,595 TRs in the buff-tailed bumblebee (Bombus terrestris) genome, 66.7% of which reside in genic regions. We also compared TRs found inB. terrestriswith those present in the whole genome sequence of a congener,B. impatiens. We found that a total of 1,137 TRs were variable in length between the two sequenced bumblebee species, and further analysis reveals that 101 of them are located within coding regions. The 101 TRs were responsible for coding sequence variation and corresponded to protein sequence length variation between the two bumblebee species. The variability of identified TRs in coding regions between bumblebees was confirmed by PCR amplification of a subset of loci. Functional classification of bumblebee genes where coding sequences include variable-length TRs suggests that a majority of these genes are related to transcriptional regulation. Our results show that TRs contribute to coding sequence variation in bumblebees and TRs may facilitate the adaptation of bumblebees through diversifying proteins involved in controlling gene expression.
Angiogenesis inhibiting capacity of Basella rubra and Syszygium cumini fruit extracts using chorioallantoic membrane assay
Authors: Galang Hannah Paula G. , Medina Milton Norman D. , Castillo Pedrito M. 
Published: October 2017

ABSTRACTAngiogenesis is a physiological process of new blood vessel development from pre-existing capillaries. This process is also the main qualification for tumor growth and plays a vital role in tumor invasion and metastasis. Nevertheless, angiogenesis inhibitors can be used to impede abnormal blood vessel growth. The study was conducted to assess angiogenesis inhibiting potential of B. rubra (Alugbati) and S. cumini (Lumboy) fruit extracts as cell mass growth retardants using Chorioallantoic Membrane (CAM) Assay in Anas platyrhyncho (common Duck) embryo. The treatments were individually compared to Retinol palmitate as positive control and 0.9% sterilized normal saline solution as negative control. Data were gathered and analyzed using Analysis of Variance (ANOVA) and Least Significant Difference (LSD) to test for the significant anti-angiogenic activity and pair-wise comparison among the treatments respectively using a p-value of less than 0.01. Analysis showed that there is no significant difference between the fruit extracts and positive control while a significant difference between the fruit extracts and negative control was observed. Both treatments showed very good anti-angiogenic effect with average scores of 1.33 and 1.67 respectively compared to the positive control with a scoring averaging of 1.78. Furthermore, toxicity test is recommended for both treatments.
Quantitativein vivoevaluation of the reverse β-oxidation pathway for fatty acid production inSaccharomyces cerevisiae
Authors: Teixeira Paulo Gonçalves , Siewers Verena , Nielsen Jens 
Published: October 2017

AbstractProduction of fatty acids using engineeredSaccharomyces cerevisiaecells is a challenging task in part due to low efficiency of the native fatty acid biosynthesis pathway. One option for improving production efficiency relies on exploring alternative fatty acid production pathways with either improved kinetics, thermodynamics or yield properties.In this work, we explored the reverse β-oxidation pathway as an alternative pathway for free fatty acid production. Different gene combinations and analysis methods were tested for assessing pathway efficiency when expressed in the yeastSaccharomyces cerevisiae. Even though different alternatives were tested, quantitative analysis showed no improvement or major change in fatty acid production of the tested strains in our conditions. This lack of improvement suggests that the tested pathway designs and constructs are either nonfunctional in the tested conditions or the resulting strains lack a metabolic driving force that is needed for a functional pathway.We conclude that expression of the reverse β-oxidation pathway inS. cerevisiaeposes many challenges when compared to expression in bacterial systems. These factors gravely hinder development efforts and success rate for producing fatty acids through this pathway.
Multiscale dynamics and information flow in a data-driven model of the primary motor cortex microcircuit
Authors: Dura-Bernal Salvador , Neymotin Samuel A , Suter Benjamin A , Shepherd Gordon M G , Lytton William W 
Published: October 2017

AbstractWe developed a biophysically detailed multiscale model of mouse primary motor cortex (M1) with over 10,000 neurons and 35 million synapses. We focused on intratelencephalic (IT) and pyramidal-tract (PT) neurons of layer 5 (L5), which were modeled at high multicompartment resolution. Wiring densities were based on prior detailed measures from mouse slice, and depended on cell class and cortical depth at sublaminar resolution. Prominent phase-amplitude-coupled delta and gamma activity emerged from the network. Spectral Granger causality analysis revealed the dynamics of information flow through populations at different frequencies. Stimulation of motor vs sensory long-range inputs to M1 demonstrated distinct intra- and inter-laminar dynamics and PT output. Manipulating PTIhaltered PT activity, supporting the hypothesis thatIhneuromodulation is involved in translating motor planning into execution. Our model sheds light on the multiscale dynamics of cell-type-specific M1 circuits and how connectivity relates to dynamics.