bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimizing the Power to Identify the Genetic Basis of Complex Traits with Evolve and Resequence Studies
Authors: Vlachos Christos , Kofler Robert 
Published: August 2019

AbstractEvolve and resequence (E&R) studies are frequently used to dissect the genetic basis of quantitative traits. By subjecting a population to truncating selection for several generations and estimating the allele frequency differences between selected and nonselected populations using next-generation sequencing (NGS), the loci contributing to the selected trait may be identified. The role of different parameters, such as, the population size or the number of replicate populations has been examined in previous works. However, the influence of the selection regime, that is the strength of truncating selection during the experiment, remains little explored. Using whole genome, individual based forward simulations of E&R studies, we found that the power to identify the causative alleles may be maximized by gradually increasing the strength of truncating selection during the experiment. Notably, such an optimal selection regime comes at no or little additional cost in terms of sequencing effort and experimental time. Interestingly, we also found that a selection regime which optimizes the power to identify the causative loci is not necessarily identical to a regime that maximizes the phenotypic response. Finally, our simulations suggest that an E&R study with an optimized selection regime may have a higher power to identify the genetic basis of quantitative traits than a genome-wide association study, highlighting that E&R is a powerful approach for finding the loci underlying complex traits.
Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases
Authors: Priyam Anurag , Woodcroft Ben J , Rai Vivek , Moghul Ismail , Munagala Alekhya , Ter Filip , Chowdhary Hiten , Pieniak Iwo , Maynard Lawrence J , Gibbins Mark Anthony , Moon HongKee , Davis-Richardson Austin , Uludag Mahmut , Watson-Haigh Nathan S , Challis Richard , Nakamura Hiroyuki , Favreau Emeline , Gómez Esteban A , Pluskal Tomás , Leonard Guy , Rumpf Wolfgang , Wurm Yannick 
Published: August 2019

Abstract
Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver, a tool for running BLAST and visually inspecting BLAST results for biological interpretation. Sequenceserver uses simple algorithms to prevent potential analysis errors and provides flexible text-based and visual outputs to support researcher productivity. Our software can be rapidly installed for use by individuals or on shared servers.
SET8 prevents excessive DNA methylation by methylation-mediated degradation of UHRF1 and DNMT1
Authors: Zhang Huifang , Gao Qinqin , Tan Shuo , You Jia , Lyu Cong , Zhang Yunpeng , Han Mengmeng , Chen Zhaosu , Li Jialun , Wang Hailin , Liao Lujian , Qin Jun , Li Jiwen , Wong Jiemin 
Published: August 2019

Abstract
Faithful inheritance of DNA methylation across cell division requires DNMT1 and its accessory factor UHRF1. However, how this axis is regulated to ensure DNA methylation homeostasis remains poorly understood. Here we show that SET8, a cell-cycle-regulated protein methyltransferase, controls protein stability of both UHRF1 and DNMT1 through methylation-mediated, ubiquitin-dependent degradation and consequently prevents excessive DNA methylation. SET8 methylates UHRF1 at lysine 385 and this modification leads to ubiquitination and degradation of UHRF1. In contrast, LSD1 stabilizes both UHRF1 and DNMT1 by demethylation. Importantly, SET8 and LSD1 oppositely regulate global DNA methylation and do so most likely through regulating the level of UHRF1 than DNMT1. Finally, we show that UHRF1 downregulation in G2/M by SET8 has a role in suppressing DNMT1-mediated methylation on post-replicated DNA. Altogether, our study reveals a novel role of SET8 in promoting DNA methylation homeostasis and identifies UHRF1 as the hub for tuning DNA methylation through dynamic protein methylation.
Low daily MEWS scores as predictors of low-risk hospitalized patients
Authors: Mizrahi J , Kott J , Taub E , Goolsarran N 
Published: August 2019

Summary

Background
The Modified Early Warning System (MEWS) is a well-validated tool used by hospitals to identify patients at high risk for an adverse event to occur. However, there has been little evaluation into whether a low MEWS score can be predictive of patients with a low likelihood of an adverse event.

Aim
The present study aims to evaluate the MEWS score as a method of identifying patients at low risk for adverse events.

Design
Retrospective cohort study of 5676 patient days and analysis of associated MEWS scores, medical comorbidities and adverse events. The primary outcome was the association of average daily MEWS scores in those who had an adverse event compared with those who did not.

Results
Those with an average MEWS score of &gt;2 were over 9 times more likely to have an adverse event compared with those with an average MEWS score of 1–2, and over 15 times more likely to have an adverse event compared to those with an average MEWS score of &lt;1.

Conclusions
Our study shows that those with average daily MEWS scores &lt;2 are at a significantly lower likelihood of having an adverse event compared with a score of &gt;2, deeming them ‘low-risk patients’. Formal recognition of such patients can have major implications in a hospital setting, including more efficient resource allocation in hospitals and better patient satisfaction and safety by adjusting patient monitoring according to their individual risk profile.
Mathematics instructors’ awareness of accessibility barriers for disabled students
Authors: Cliffe Emma , Mac an Bhaird Ciarán , Ní Fhloinn Eabhnat , Trott Clare 
Published: August 2019

Abstract
In this paper, we discuss the results of a staff survey on accessibility barriers to participation and success for disabled students in higher education in the UK and Ireland. We focus on the range and complexity of student difficulties encountered by staff involved either in the lecturing of mathematics or the provision of Mathematics Learning Support. We report on the range of supports available to both staff and students in these situations and their varying levels of awareness and implementation of these supports. We close with a brief overview of how we intend to use the results of this survey to both increase awareness of existing appropriate supports and develop additional services to improve student accessibility.
Nurses’ Education, Confidence, and Competence in Appropriate Dressing Choice
Authors: Blackburn Joanna , Ousey Karen , Stephenson John 
Published: August 2019

ABSTRACT

BACKGROUND
Wound assessment and treatment are essential aspects of nursing care. Dressing-associated complications can delay wound healing, causing unnecessary patient distress. Despite evidence suggesting that dressings should be changed infrequently, there still remains a tendency for healthcare professionals to remove dressings regularly, increasing the risk of complications and the cost of wound care.

OBJECTIVE
To understand the experiences and current practices of tissue viability nurses (TVNs) involved in wound care and dressing wear time in the acute and community settings.

METHODS
This quality improvement project used a mixed-methods design. A retrospective audit was undertaken to establish nurse rationale for the renewal of foam dressings on patients with acute/chronic wounds. Semistructured qualitative interviews were conducted with registered TVNs (n = 12) working in acute and community care settings and focused on their experiences with all dressing types.

MAIN RESULTS
The analysis identified several key themes, including Training and Education (including the subthemes of TVN Experience and TVN Training), Knowledge and Information, Lack of Confidence (including the subthemes Reasons for Dressing Change and Ritualistic Practice), and Dressing Choice.

CONCLUSIONS
Fundamental changes in staff attitudes and beliefs about dressing wear time are essential to optimizing dressing performance and increasing patient quality of care. Flexible community services that are reflective of the needs of the service are central to changing practice and increasing dressing wear time in these settings.
Depot Medroxyprogesterone Acetate, Oral Contraceptive, Intrauterine Device Use, and Fracture Risk
Authors: Raine-Bennett Tina , Chandra Malini , Armstrong Mary Anne , Alexeeff Stacey , Lo Joan C. 
Published: August 2019

OBJECTIVE:
To assess fracture risk among women with depot medroxyprogesterone acetate (DMPA), oral contraceptive pill (OCP), and intrauterine device (IUD) use.

METHODS:
A retrospective cohort study of 308,876 women age 12–45 years who initiated DMPA, combined or progestin-only OCPs, and copper and levonorgestrel IUDs from 2005 to 2015. Cumulative DMPA, OCP, and IUD use was assessed. Time since last DMPA injection was quantified as recent (within 2 years) and past (more than 2 years ago). Crude fracture rate was estimated using a Poisson distribution. Unadjusted and adjusted hazard ratios (HRs) were estimated using cox proportional hazards models.

RESULTS:
Thirteen percent of women used DMPA, 78.6% combined OCPs, 17.4% progestin-only OCPs, and 26.2% IUDs; 29.5% used more than one method. There were 7,659 fractures in 1,391,251 person-years (5.5/1,000 person-years [95% CI 5.4–5.6]). The fracture rate for women with any DMPA use was 6.6 (95% CI 6.1–7.2) and 7.8 (95% CI 6.0–10.0) for women with recent use and more than 2 years of cumulative use. Women who had recent use with 2 years or less, or more than 2 years of cumulative use had higher fracture risk compared with women who had no DMPA use and used other methods (adjusted HR 1.15 [95% CI 1.01–1.31] and 1.42 [95% CI 1.10–1.83], respectively). Fracture risk was not increased in women with past DMPA use. Women who had more than 2 years cumulative use of combined OCPs and women with any progestin-only OCP use had lower fracture risk compared with women who did not use OCPs and used other methods (adjusted HR 0.85 [95% CI 0.76–0.96] and 0.88 [95% CI 0.80–0.97], respectively).

CONCLUSION:
Use of DMPA beyond 2 years should not be considered an absolute contraindication. Although DMPA use was associated with slightly increased fracture risk compared with other methods, the absolute risk of fracture was small and was not observed after discontinuation.
Sensitivity and Specificity of B-Type Natriuretic Peptide in Diagnosing Heart Failure in Pregnancy
Authors: Malhamé Isabelle , Hurlburt Heather , Larson Lucia , Poppas Athena , Nau Christopher , Bourjeily Ghada , Mehta Niharika 
Published: August 2019

OBJECTIVE:
To evaluate the performance of B-type natriuretic peptide as a diagnostic tool for heart failure in pregnant or postpartum women with singleton gestations.

METHODS:
We conducted a retrospective study of diagnostic accuracy. We identified pregnant and postpartum women with B-type natriuretic peptide and echocardiography performed at an obstetric teaching hospital from 2007 to 2018. Women with known cardiac disease or multiple gestation were excluded. A panel of two cardiovascular disease experts, blinded to B-type natriuretic peptide values, determined the diagnosis of heart failure by consensus. Their judgement was based on detailed clinical features and parameters at the time of presentation with suspected heart failure. Where consensus could not be reached, differences were adjudicated by a third expert. A receiver operating characteristic curve estimated the sensitivity, specificity, positive likelihood ratio, and negative likelihood ratio of B-type natriuretic peptide at various thresholds.

RESULTS:
In total, 22 pregnant and 38 postpartum women were included in the cohort. Average age was 32±6.8 years. The most common clinical features at the time of presentation with suspected heart failure included preeclampsia (33/60, 55%), dyspnea (50/60, 83%), chest discomfort (34/60, 58%), and bilateral lower extremity edema (32/60, 53%). In total, 39 (65%) women had heart failure. The median B-type natriuretic peptide level was 326 pg/mL (interquartile range 200.5–390.5) in women with heart failure, as compared with 75.5 pg/mL (interquartile range 19–245) in women without heart failure (P<.01). The estimated optimal B-type natriuretic peptide cutoff was 111 (95% CI 78–291) pg/mL. Using this threshold, 45 (75%) women had an elevated B-type natriuretic peptide, which yielded a 95% sensitivity (95% CI 83–99), 62% specificity (95% CI 38–82), a positive likelihood ratio of 2.5 (95% CI 1.4–4.3), and a negative likelihood ratio of 0.1 (95% CI 0.0–0.3) for heart failure.

CONCLUSIONS:
B-type natriuretic peptide is a useful clinical tool to evaluate pregnant and postpartum women with suspected heart failure.
Health Care Provider Adherence to Surgical Guidelines for Risk-Reducing Salpingo-Oophorectomy
Authors: Wilhite Annelise M. , Oestreich Makinna C. , Olson Megan , Bedell Sabrina M. , Westenberg Danielle , Bangdiwala Ananta , Ikramuddin Salman , Sanchez-Avila Monica , Madoff Robert D. , Khalifa Mahmoud A. , Erickson Britt K. 
Published: August 2019

OBJECTIVE:
To evaluate health care provider adherence to the surgical protocol endorsed by the National Comprehensive Cancer Network and the American College of Obstetricians and Gynecologists at the time of risk-reducing salpingo-oophorectomy and compare adherence between gynecologic oncologists and obstetrician–gynecologists (ob-gyns).

METHODS:
In this multicenter retrospective cohort study, women were included if they had a pathogenic BRCA mutation and underwent risk-reducing salpingo-oophorectomy between 2011 and 2017. Adherence was defined as completing all of the following: collection of washings, complete resection of the fallopian tube, and performing the Sectioning and Extensively Examining the Fimbriated End (SEE-FIM) pathologic protocol.

RESULTS:
Of 290 patients who met inclusion criteria, 160 patients were treated by 18 gynecologic oncologists and 130 patients by 75 ob-gyns. Surgery was performed at 10 different hospitals throughout a single metropolitan area. Demographic and clinical characteristics were similar between groups. Overall, 199 cases (69%) were adherent to the surgical protocol. Gynecologic oncologists were more than twice as likely to fully adhere to the full surgical protocol as ob-gyns (91% vs 41%, P<.01). Specifically, gynecologic oncologists were more likely to resect the entire tube (99% vs 95%, P=.03), to have followed the SEE-FIM protocol (98% vs 82%, P<.01), and collect washings (94% vs 49%, P<.01). Complication rates did not differ between groups. Occult neoplasia was diagnosed in 11 patients (3.8%). The incidence of occult neoplasia was 6.3% in gynecologic oncology patients and 0.8% in obstetrics and gynecology patients (P=.03).

CONCLUSION:
Despite clear surgical guidelines, only two thirds of all health care providers were fully adherent to guidelines. Gynecologic oncologists were more likely to follow surgical guidelines compared with general ob-gyns and more likely to diagnose occult neoplasia despite similar patient populations. Rates of risk-reducing surgery will likely continue to increase as genetic testing becomes more widespread, highlighting the importance of health care provider education for this procedure. Centralized care or referral to subspecialists for risk-reducing salpingo-oophorectomy may be warranted.
Practice Patterns in the Management of Primary Pterygium: A Survey Study
Authors: Graue-Hernandez Enrique O. , Córdoba Andrea , Jimenez-Corona Aida , Ramirez-Miranda Arturo , Navas Alejandro , Serna-Ojeda Juan C. , Mannis Mark J. 
Published: August 2019

Purpose:
To characterize cornea specialists’ current practice preferences in the management of primary pterygium.

Methods:
A 25-item survey regarding indications for surgery, surgical technique, use of adjuvant therapy, type and duration of postoperative therapy, and treatment of early recurrences was designed and sent to members of the Cornea Society through the kera-net listserv.

Results:
In total, 199 cornea specialists completed the questionnaire. More than 90% considered that surgery should be performed when there is proximity of the pterygium to the visual axis, pain or redness, eye movement restriction, or induction of astigmatism. Cosmesis was considered as an indication by 41.7% of the participants. The most frequent technique for pterygium excision was complete resection including the base and a moderate quantity of Tenon capsule followed by autologous conjunctival or limbal-conjunctival graft. The preferred graft fixation method in this survey was fibrin glue (61.2%). Most respondents reported a recurrence rate of less than 5% and no use of adjuvant agents to prevent recurrence. When early recurrence did occur, the preferred agents were corticosteroids.

Conclusions:
This study reflects the preferences of cornea experts regarding primary pterygium treatment and may serve as a guide for the management of this pathology.
Outcomes of Extended Infusion Cefepime in Pediatric Patients
Authors: Beauchamp Lauren C. , Nichols Kristen R. , Knoderer Chad A. 
Published: August 2019

Background
Extended infusions of cefepime optimize pharmacokinetic and pharmacodynamic parameters and improve clinical outcomes in adults with gram-negative infections, but there are no similar studies in children. The objective of this study was to compare clinical outcomes in children receiving extended and traditional infusion cefepime.

Methods
This was a retrospective cohort study of patients aged 31 days to 17 years receiving extended or traditional infusion cefepime for at least 48 hours for a susceptible gram-negative bacteremia at a tertiary care children's hospital. The primary outcome was a composite clinical outcome comprised of infection-related mortality within 14 days of antibiotic initiation, bacteremic relapse within 30 days of culture clearance, and treatment failure.

Results
Sixty-seven patients were included; 21 (31.3%) received extended infusion, and 46 (68.7%) received traditional infusion. Extended infusion patients were older and larger than traditional infusion patients with a median (interquartile range) age of 7 (0.8–11.5) years versus 0.5 (0.2–2) years (P = 0.05) and weight of 23.7 (8.2–44.2) kg versus 6.2 (2.4–13.1) kg (P < 0.05). The most common pathogens within the extended infusion group were Enterobacter cloacae (23.8%) and Klebsiella oxytoca (23.8%), whereas Escherichia coli was the most common within the traditional infusion group (28.2%). There was no difference in minimum inhibitory concentrations, as the most common minimum inhibitory concentrations were less than or equal to 1 μg/mL in both extended (95.2%) and traditional infusion (87.0%) (P = nonsignificant). The primary outcome occurred in 2 extended (9.5%) and 3 traditional infusion patients (6.5%) (P = nonsignificant).

Conclusions
Clinical outcomes were similar with extended and traditional infusion cefepime in this cohort of children with susceptible gram-negative bacteremia.
Relationship Between Nostril, Nasal Valve and Minimal Cross-Sectional Area in Functional Upper Airway
Authors: Fariña Rodrigo , González Andrea , Toledo Ximena , Villanueva Rodrigo , Martínez Benjamín , Pérez Hernán 
Published: August 2019

Purpose:
To propose a three-dimensional cephalometric analysis of upper airway (UA) related to its functionality, defining normal reference values in healthy individuals and the relationship between nostril, nasal valve, and minimal cross-sectional area (MCS) in functional upper airway.

Materials and Methods:
The UAs of 20 Class I patients were analyzed with CBCT using Nemoceph 3D-OS and HOROS software, determining linear distances, volumes and cross-sectional areas, including MCS.

Results:
MCS was mostly located in the middle-upper oropharynx and high hypopharynx. MCS showed moderate correlation with the area of both nares (BNA) (r = 0.60, P = 0.004) and high correlation with the area of both internal nasal valves (BNV) (r = 0.66, P = 0.0016). BNA and BNV showed a moderate correlation (r = 0.445, P = 0.049). A total upper airway (TUA) and functional upper airway (FUA) volumes were established. TUA and FUA showed the strongest statistical correlation (r = 0.82, P = 0.00). A paired samples t test compared the measurement as absolute values of MCS with BNA (t = 0.781, P = 0.44), with BNV (t = −0.12, P = 0.90); and BNA with BNV (t = −0.76, P = 0.45), showed no significant differences.

Conclusions:
A functional cephalometric analysis of the UA with stable parameters in cervical spine and normal reference values has been proposed. BNA and BNV could be used as reference to establish the MCS compatible with respiratory health.
An Analysis of Association Between Nasal Bone Morphology and Sinonasal Anatomical Variations
Authors: Kuzucu Ihsan , Parlak Selcuk , Baklaci Deniz , Guler Ismail , Sakalli Cemal , Mendi Ahmet Bokebatur , Kum Rauf Oguzhan , Ozcan Muge 
Published: August 2019

Abstract
The goal of this study was to investigate the association between various sinonasal anatomical variations and the morphological features of lateral nasal bone, using paranasal computerized tomography (PNCT) sections. Two hundred and fifty patients who underwent a PNCT scan because of a prediagnosis of nasal septum deviation or sinusitis were included in the study. For each patient, presence of the following anatomical variations was determined on CT sections: length and thickness of nasal bone, thickness of intermediate nasal bone, pneumatized middle turbinate, paradox middle turbinate, Agger nasi cell, Haller cell, Onodi cell, supraorbital cell, pneumatized uncinate process, and nasal septal deviation. The effect of each anatomical variation on the length and thickness of the lateral nasal bone was investigated. The patients with bilateral pneumatized middle turbinate and the patients with bilateral Agger nasi cell had a thinner lateral nasal bone both on the right and the left sides compared to those without. The patients with bilateral Onodi cell and Agger nasi cell had a longer lateral nasal bone both on the right and the left sides compared to those without. The nasal bone thickness was significantly thicker on the deviation side than the contralateral nasal bone. The nasal bone length was significantly longer on the side of the septum deviation. In this study, we found that sex, presence of Agger nasi and Onodi cells, pneumatization of middle turbinate, and direction of nasal septal deviation influenced the morphology of the nasal bone. For successful nasal surgery, careful examination of preoperative anatomical variations is very important.