bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local protein solvation drives direct down-conversion in phycobiliprotein PC645 via incoherent vibronic transport
Authors: Blau Samuel M. , Bennett Doran I. G. , Kreisbeck Christoph , Scholes Gregory D. , Aspuru-Guzik Alán 
Published: March 2018

SignificanceTo harness sunlight for growth, plants and algae rapidly convey absorbed excitation energy from antennae pigments to a reaction center, where the excitations convert to chemical energy. In deep water environments, cryptophyte algae survive by using the molecular motion of phycobiliprotein antennae to funnel excitations to low-energy pigments. The mechanism of down-conversion in phycobiliproteins remains controversial: Could specific vibrations resonant with pigment energy gaps support coherence between excited states and thereby enhance the rate of transport by transient delocalization? Here, we demonstrate that down-conversion in a specific phycobiliprotein, PC645, is both incoherent and enhanced by a broad range of high-frequency vibrations. We suggest that a similar incoherent mechanism is appropriate across phycobiliproteins.
Interpreter-mediated drafting of written records in police interviews
Authors: Defrancq Bart , Verliefde Sofie 
Published: March 2018

Abstract
Text drafting is an essential component of many of the contexts in which interpreters are called in to ensure communication (Määttä 2015). As Komter (2006) shows, the drafting process itself can be considered a turn in the interaction. Interpreters involved in such contexts thus perform a communicative pas de quatre, crossing not only the language divide, but also the modal divide (oral vs. written). In this paper, we analyse how an interpreter in a Belgian police interview handles this complex task. It appears that she procedurally and declaratively recognises a written turn in the interaction and uses its authoritative voice to silence the witness by sight-translating the turn as it is being typed on the screen. In line with previous research on interpreters’ handling of dialogues (Hale 1997), the interpreter also shapes turns, including the written turn, to the needs of the addressees: upgrading the register properties of the interviewee’s talk and downgrading those of the written turn.
Understanding sequencing data as compositions: an outlook and review
Authors: Quinn Thomas P , Erb Ionas , Richardson Mark F , Crowley Tamsyn M 
Published: March 2018

AbstractMotivationAlthough seldom acknowledged explicitly, count data generated by sequencing platforms exist as compositions for which the abundance of each component (e.g. gene or transcript) is only coherently interpretable relative to other components within that sample. This property arises from the assay technology itself, whereby the number of counts recorded for each sample is constrained by an arbitrary total sum (i.e. library size). Consequently, sequencing data, as compositional data, exist in a non-Euclidean space that, without normalization or transformation, renders invalid many conventional analyses, including distance measures, correlation coefficients and multivariate statistical models.ResultsThe purpose of this review is to summarize the principles of compositional data analysis (CoDA), provide evidence for why sequencing data are compositional, discuss compositionally valid methods available for analyzing sequencing data, and highlight future directions with regard to this field of study.Supplementary informationSupplementary data are available at Bioinformatics online.
LSMM: a statistical approach to integrating functional annotations with genome-wide association studies
Authors: Ming Jingsi , Dai Mingwei , Cai Mingxuan , Wan Xiang , Liu Jin , Yang Can 
Published: March 2018

Abstract

Motivation
Thousands of risk variants underlying complex phenotypes (quantitative traits and diseases) have been identified in genome-wide association studies (GWAS). However, there are still two major challenges towards deepening our understanding of the genetic architectures of complex phenotypes. First, the majority of GWAS hits are in non-coding region and their biological interpretation is still unclear. Second, accumulating evidence from GWAS suggests the polygenicity of complex traits, i.e. a complex trait is often affected by many variants with small or moderate effects, whereas a large proportion of risk variants with small effects remain unknown.

Results
The availability of functional annotation data enables us to address the above challenges. In this study, we propose a latent sparse mixed model (LSMM) to integrate functional annotations with GWAS data. Not only does it increase the statistical power of identifying risk variants, but also offers more biological insights by detecting relevant functional annotations. To allow LSMM scalable to millions of variants and hundreds of functional annotations, we developed an efficient variational expectation-maximization algorithm for model parameter estimation and statistical inference. We first conducted comprehensive simulation studies to evaluate the performance of LSMM. Then we applied it to analyze 30 GWAS of complex phenotypes integrated with nine genic category annotations and 127 cell-type specific functional annotations from the Roadmap project. The results demonstrate that our method possesses more statistical power than conventional methods, and can help researchers achieve deeper understanding of genetic architecture of these complex phenotypes.

Availability and implementation
The LSMM software is available at https://github.com/mingjingsi/LSMM.

Supplementary information
Supplementary data are available at Bioinformatics online.
FaStore: a space-saving solution for raw sequencing data
Authors: Roguski Łukasz , Ochoa Idoia , Hernaez Mikel , Deorowicz Sebastian 
Published: March 2018

Abstract

Motivation
The affordability of DNA sequencing has led to the generation of unprecedented volumes of raw sequencing data. These data must be stored, processed and transmitted, which poses significant challenges. To facilitate this effort, we introduce FaStore, a specialized compressor for FASTQ files. FaStore does not use any reference sequences for compression and permits the user to choose from several lossy modes to improve the overall compression ratio, depending on the specific needs.

Results
FaStore in the lossless mode achieves a significant improvement in compression ratio with respect to previously proposed algorithms. We perform an analysis on the effect that the different lossy modes have on variant calling, the most widely used application for clinical decision making, especially important in the era of precision medicine. We show that lossy compression can offer significant compression gains, while preserving the essential genomic information and without affecting the variant calling performance.

Availability and implementation
FaStore can be downloaded from https://github.com/refresh-bio/FaStore.

Supplementary information
Supplementary data are available at Bioinformatics online.
Efficacy and Safety of Surgery for Mild Degenerative Cervical Myelopathy: Results of the AOSpine North America and International Prospective Multicenter Studies
Authors: Badhiwala Jetan H , Witiw Christopher D , Nassiri Farshad , Akbar Muhammad A , Mansouri Alireza , Wilson Jefferson R , Fehlings Michael G 
Published: March 2018

Abstract

BACKGROUND
There is controversy over the optimal treatment strategy for patients with mild degenerative cervical myelopathy (DCM).

OBJECTIVE
To evaluate the degree of impairment in baseline quality of life as compared to population norms, as well as functional, disability, and quality of life outcomes following surgery in a prospective cohort of mild DCM patients undergoing surgical decompression.

METHODS
We identified patients with mild DCM (modified Japanese Orthopaedic Association [mJOA] 15 to 17) enrolled in the prospective, multicenter AOSpine CSM-NA or CSM-I trials. Baseline quality of life Short Form-36 version 2 (SF-36v2) was compared to population norms by the standardized mean difference (SMD). Outcomes, including functional status (mJOA, Nurick grade), disability (NDI [Neck Disability Index]), and quality of life (SF-36v2), were evaluated at baseline and 6 mo, 1 yr, and 2 yr after surgery. Postoperative complications within 30 d of surgery were monitored.

RESULTS
One hundred ninety-three patients met eligibility criteria. Mean age was 52.4 yr. There were 67 females (34.7%). Patients had significant impairment in all domains of the SF-36v2 compared to population norms, greatest for Social Functioning (SMD –2.33), Physical Functioning (SMD –2.31), and Mental Health (SMD –2.30). A significant improvement in mean score from baseline to 2-yr follow-up was observed for all major outcome measures, including mJOA (0.87, P < .01), Nurick grade (–1.13, P < .01), NDI (–12.97, P < .01), and SF-36v2 Physical Component Summary (PCS) (5.75, P < .01) and Mental Component Summary (MCS) (6.93, P < .01). The rate of complication was low.

CONCLUSION
Mild DCM is associated with significant impairment in quality of life. Surgery results in significant gains in functional status, level of disability, and quality of life.
Applied Pediatric Math: Bridging the Gap Between Theory and Practice for a Diverse Group of Learners
Authors: Murphy Glenn , Murphy Jackie 
Published: March 2018

Abstract
A gap exists between didactic theory and clinical practice when nursing students learn clinical calculations. Educators can provide innovative classroom teaching methods using practical mathematics to decrease this gap. In the simulation lab, students complete weight-based calculations and then administer medications as part of medication skills stations. Math assessments in the psychomotor domain promote application of didactic math content. Implementing math assessments that include a hands-on component facilitates the students’ abilities to take math out of the classroom and apply it in clinical practice, enabling the educator to minimize disparities found when students have different mathematics backgrounds.
Alcohol and Drug Screening, Brief Intervention, and Referral to Treatment (SBIRT) Training and Implementation: Perspectives from 4 Health Professions
Authors: Wamsley Maria , Satterfield Jason M. , Curtis Alexa , Lundgren Lena , Satre Derek D. 
Published: March 2018

Objectives:
Screening, Brief Intervention, and Referral to Treatment (SBIRT) can effectively identify and address substance misuse and substance use disorders (SUDs), and can be delivered by a range of trained health professionals. Yet, barriers remain to effective training and implementation of SBIRT in health and social service settings, and models of interprofessional collaboration in SBIRT delivery are underdeveloped.

Methods:
We reviewed current literature regarding SBIRT effectiveness, training, and implementation by physicians, nurses, psychologists, and social workers. An SBIRT expert and representative from each health profession synthesized literature and training experiences to inform the development of interprofessional training and collaborative implementation strategies.

Results:
Each of the health professions involved in SBIRT training and implementation have strengths and weaknesses that influence how SBIRT is taught, learned, and delivered. Some of these are specific to the components of SBIRT, for example, screening versus brief intervention, whereas others depend on profession-driven competencies, for example, motivational interviewing. Professional organizations have encouraged a range of tailored SBIRT training initiatives, but true interprofessional training and the implementation of collaborative, team-based care are largely unrealized.

Conclusions:
SBIRT can be a valuable approach to screening and treatment for SUDs when delivered by a range of healthcare professionals. A more nuanced understanding of the assumptions and characteristics of each profession, informed by the emerging field of implementation science, may shape more effective training curricula and highlight interprofessional models of SBIRT delivery that maximize the strengths of each profession.
Variability Analysis of Manual and Computer-Assisted Preoperative Thoracic Pedicle Screw Placement Planning
Authors: Knez Dejan , Mohar Janez , Cirman Robert J. , Likar Boštjan , Pernuš Franjo , Vrtovec Tomaž 
Published: March 2018

Study Design.
A comparison among preoperative pedicle screw placement plans, obtained from computed tomography (CT) images manually by two spine surgeons and automatically by a computer-assisted method.

Objective.
To analyze and compare the manual and computer-assisted approach to pedicle screw placement planning in terms of the inter- and intraobserver variability.

Summary of Background Data.
Several methods for computer-assisted pedicle screw placement planning have been proposed; however, a systematic variability analysis against manual planning has not been performed yet.

Methods.
For 256 pedicle screws, preoperative placement plans were determined manually by two experienced spine surgeons, each independently performing two sets of measurements by using a dedicated software for surgery planning. For the same 256 pedicle screws, preoperative placement plans were also obtained automatically by a computer-assisted method that was based on modeling of the vertebral structures in 3D, which were used to determine the pedicle screw size and insertion trajectory by maximizing its fastening strength through the underlying bone mineral density.

Results.
A total of 1024 manually (2 observers × 2 sets × 256 screws) and 256 automatically (1 computer-assisted method × 256 screws) determined preoperative pedicle screw placement plans were obtained and compared in terms of the inter- and intraobserver variability. A large difference was observed for the pedicle screw sagittal inclination that was, in terms of the mean absolute difference and the corresponding standard deviation, equal to 18.3° ± 7.6° and 12.3° ± 6.5°, respectively for the intraobserver variability of the second observer and for the interobserver variability between the first observer and the computer-assisted method.

Conclusion.
The interobserver variability among the observers and the computer-assisted method is within the intraobserver variability of each observer, which indicates on the potential use of the computer-assisted approach as a useful tool for spine surgery that can be adapted according to the preferences of the surgeon.

Level of Evidence: 3
One-Year Outcomes in Patients With Acute Respiratory Distress Syndrome Enrolled in a Randomized Clinical Trial of Helmet Versus Facemask Noninvasive Ventilation
Authors: Patel Bhakti K. , Wolfe Krysta S. , MacKenzie Erica L. , Salem Dhafer , Esbrook Cheryl L. , Pawlik Amy J. , Stulberg Megan , Kemple Crystal , Teele Megan , Zeleny Erin , Macleod Julia , Pohlman Anne S. , Hall Jesse B. , Kress John P. 
Published: March 2018

Objectives:
Many survivors of acute respiratory distress syndrome have poor long-term outcomes possibly due to supportive care practices during “invasive” mechanical ventilation. Helmet noninvasive ventilation in acute respiratory distress syndrome may reduce intubation rates; however, it is unknown if avoiding intubation with helmet noninvasive ventilation alters the consequences of surviving acute respiratory distress syndrome.

Design:
Long-term follow-up data from a previously published randomized controlled trial.

Patients:
Adults patients with acute respiratory distress syndrome enrolled in a previously published clinical trial.

Setting:
Adult ICU.

Intervention:
None.

Measurements and Main Results:
The primary outcome was functional independence at 1 year after hospital discharge defined as independence in activities of daily living and ambulation. At 1 year, patients were surveyed to assess for functional independence, survival, and number of institution-free days, defined as days alive spent living at home. The presence of ICU-acquired weakness and functional independence was also assessed by a blinded therapist on hospital discharge. On hospital discharge, there was a greater prevalence of ICU-acquired weakness (79.5% vs 38.6%; p = 0.0002) and less functional independence (15.4% vs 50%; p = 0.001) in the facemask group. One-year follow-up data were collected for 81 of 83 patients (97.6%). One-year mortality was higher in the facemask group (69.2% vs 43.2%; p = 0.017). At 1 year, patients in the helmet group were more likely to be functionally independent (40.9% vs 15.4%; p = 0.015) and had more institution-free days (median, 268.5 [0–354] vs 0 [0–323]; p = 0.017).

Conclusions:
Poor functional recovery after invasive mechanical ventilation for acute respiratory distress syndrome is common. Helmet noninvasive ventilation may be the first intervention that mitigates the long-term complications that plague survivors of acute respiratory distress syndrome managed with noninvasive ventilation.
Modified Pfannenstiel Open Approach as an Alternative to Laparoscopic Total Proctocolectomy and IPAA: Comparison of Short- and Long-term Outcomes and Quality of Life
Authors: Duraes Leonardo C. , Schroeder Destiny A. , Dietz David W. 
Published: March 2018

BACKGROUND:
A laparoscopic approach to total proctocolectomy with IPAA has been suggested to have better short-term outcomes and cosmesis, whereas open surgery by midline incision may result in shorter operative times. We hypothesized that a modified Pfannenstiel open approach would combine the advantages of both techniques.

OBJECTIVE:
The purpose of this study was to compare outcomes of open total proctocolectomy with IPAA using a modified Pfannenstiel incision versus those following the laparoscopic approach.

DESIGN:
This was a retrospective study comparing patients submitted to open IPAA using modified Pfannenstiel incision versus laparoscopy from 1998 to 2014.

SETTINGS:
The study was conducted at a high-volume tertiary referral center.

PATIENTS:
Among 1275 patients, 119 patients underwent the laparoscopic approach and 33 underwent the modified Pfannenstiel approach.

MAIN OUTCOME MEASURES:
Short- and long-term outcomes were evaluated, and quality-of-life questionnaires were assessed.

RESULTS:
Patients who underwent the modified Pfannenstiel approach were younger, more often women, and had lower BMI and ASA classification compared with those who underwent laparoscopy. Surgical time was lower in Pfannenstiel, and no difference was observed in length of hospital stay. No difference was observed in postoperative complications, pouch failure rate, or quality of life. Patients were then matched 1:1 by diagnosis, sex, age (±5 y) and BMI (±5 kg/m2). The Pfannenstiel approach still had a shorter surgical time. No difference was observed in the length of hospital stay, complications, pouch failure, or quality of life. In long-term follow-up, pouchitis symptoms occurred more frequently in Pfannenstiel (mean follow-up = 7.3 y), and seepage was more frequently observed in the laparoscopy group (mean follow-up = 4.2 y). These differences were not observed in matched patients.

LIMITATIONS:
The study was limited by its retrospective design and inherent selection bias.

CONCLUSIONS:
The modified Pfannenstiel approach provides equivalent short- and long-term outcomes and similar quality of life compared with laparoscopy but with a significantly shorter operative time. The modified Pfannenstiel approach to total proctocolectomy with IPAA may be the most efficient method in selected patients. See Video Abstract at http://links.lww.com/DCR/A562.
Factors associated with knowledge about menopause and hormone therapy in middle-aged Brazilian women: a population-based household survey
Authors: de Arruda Amaral Isabel C.G. , Baccaro Luiz F. , Lui-Filho Jeffrey F. , Osis Maria J.D. , Pedro Adriana O. , Costa-Paiva Lúcia 
Published: March 2018

Abstract

Objectives:
The aim of the study was to evaluate knowledge about menopause and hormone therapy (HT) among middle-aged Brazilian women and identify the factors associated with the level of knowledge.

Methods:
A cross-sectional study was conducted with 749 women aged 45 to 60 years, residing in the Metropolitan Region of Campinas, Brazil. The dependent variable was knowledge about menopause and HT evaluated using a numerical score based on the answers given to three questions that had several response options. The independent variables were sociodemographic characteristics, personal habits, and health conditions. Statistical analysis was carried out by Mann–Whitney, Kruskal–Wallis, and a generalized linear model.

Results:
The mean age was 52.5 (±4.4) years. Most of the women were postmenopausal (68%) and 19.5% had a history of current or previous use of HT. The final score for knowledge about menopause ranged from +1 to +11, with a mean of 4.59 (±1.86) and a median of 4. Women with higher levels of schooling (coefficient = 0.64, P < 0.001); with higher socioeconomic status (coefficient = 0.47, P < 0.002); with vaginal dryness (coefficient = 0.47, P = 0.003); who consumed alcohol (coefficient = 0.61, P = 0.006); who use or had ever used any type of treatment to counteract menopausal symptoms (coefficient = 0.41, P = 0.008); with anxiety (coefficient = 0.35, P = 0.037); and with depression (coefficient = 0.31, P = 0.043) possessed greater knowledge about menopause and HT. Women with a higher number (≥3) of vaginal deliveries (coefficient = −0.61, P < 0.001) and a higher body mass index (coefficient = −0.02, P = 0.046) possessed less knowledge about menopause and HT.

Conclusions:
The knowledge about menopause and HT demonstrated by the interviewees was low and possibly related to the time of exposure to qualified information.
Cellular Proliferation and Migration of Human Pterygium Cells: Mitomycin Versus Small-Molecule Inhibitors
Authors: Cao Di , Chu Wai Kit , Ng Tsz Kin , Yip Yolanda W.Y. , Young Alvin L. , Pang Chi Pui , Jhanji Vishal 
Published: March 2018

Purpose:
Nutlin is a drug that has been reported to activate p53 in various cell lines. We aim to study the effects of Nutlin in pterygium and compare the effects of Nutlin and mitomycin C (MMC) in pterygium cell lines.

Methods:
Pterygium samples (n = 3) were collected during surgical excision. Normal conjunctival tissues (n = 3) were collected from another quadrant of the same eye. Cell lines were established, and cells from passages 2 to 5 were used. Pterygium and conjunctival cells were treated with different doses of Nutlin and MMC. Cell proliferation and cell migration were measured.

Results:
Cell proliferation was reduced by 39-fold after treatment with 50 μM Nutlin. Cell migration was inhibited with increasing dosages of Nutlin (95% and 28% after treating with 2 and 50 μM Nutlin, respectively). Compared with MMC, Nutlin induced more pterygium cell death and less conjunctival cell death at low doses. At 50% lethal dose for pterygium cells, 95% of conjunctival cells survived after Nutlin treatment, whereas only 63% of conjunctival cells survived after MMC treatment. p21 expression was not detectable in MMC-treated pterygium cells but was detectable after Nutlin treatment.

Conclusions:
In our study, MMC induced cell death in pterygium and conjunctival cell lines, whereas Nutlin had a targeted impact on pterygium cells. Our results implied that MMC inhibited both pterygium cell proliferation and migration through an apoptosis-independent pathway.