bluuebunny/crossref_metadata_2025_split huggingface dataset:
SigMod: an exact and efficient method to identify a strongly interconnected disease-associated module in a gene network
Authors: Liu Yuanlong , Brossard Myriam , Roqueiro Damian , Margaritte-Jeannin Patricia , Sarnowski Chloé , Bouzigon Emmanuelle , Demenais Florence 
Published: January 2017

Abstract

Motivation
Apart from single marker-based tests classically used in genome-wide association studies (GWAS), network-assisted analysis has become a promising approach to identify a set of genes associated with disease. To date, most network-assisted methods aim at finding genes connected in a background network, whatever the density or strength of their connections. This can hamper the findings as sparse connections are non-robust against noise from either the GWAS results or the network resource.

Results
We present SigMod, a novel and efficient method integrating GWAS results and gene network to identify a strongly interconnected gene module enriched in high association signals. Our method is formulated as a binary quadratic optimization problem, which can be solved exactly through graph min-cut algorithms. Compared to existing methods, SigMod has several desirable properties: (i) edge weights quantifying confidence of connections between genes are taken into account, (ii) the selection path can be computed rapidly, (iii) the identified gene module is strongly interconnected, hence includes genes of high functional relevance, and (iv) the method is robust against noise from either the GWAS results or the network resource. We applied SigMod to both simulated and real data. It was found to outperform state-of-the-art network-assisted methods in identifying disease-associated genes. When SigMod was applied to childhood-onset asthma GWAS results, it successfully identified a gene module enriched in consistently high association signals and made of functionally related genes that are biologically relevant for asthma.

Availability and implementation
An R package SigMod is available at: https://github.com/YuanlongLiu/SigMod

Supplementary information
Supplementary data are available at Bioinformatics online.
Posterior Wall Osteotomy of the Acetabulum to Access Incarcerated Marginal Impaction
Authors: Schroeder Amanda J. , Avilucea Frank R. , Archdeacon Michael T. 
Published: January 2017

Summary:
Marginal impaction of the acetabulum is typically accessible through fracture planes specific to the nature of the injury. Infrequently, however, incarcerated marginal impaction or free osteochondral fragments are not accessible through these existing fracture planes. As such, alternative methods to access these articular pieces must be considered to ensure adequate reduction. We describe an osteotomy of the posterior wall to access incarcerated fragments and marginal impaction of the acetabulum, enabling concentric articular reduction.
Sexual activity and function assessment in middle-aged Chinese women using the female sexual function index
Authors: Zhang Caiyun , Cui Liping , Zhang Lizhi , Shi Chang , Zang Hong 
Published: January 2017

Abstract

Objective:
To assess sexual activity, sexual function, and their correlation with vaginal maturation status among middle-aged Chinese women.

Methods:
A cross-sectional study with comparisons across age groups was carried out. In all, 120 women aged 45 to 60 years were recruited into three groups: 45 to 50 (youngest group), 51 to 55 (intermediate group), and 56 to 60 years old (eldest group). Sexual function was assessed through the Female Sexual Function Index (FSFI); vaginal maturation status was determined through the Vaginal Maturation Index (VMI) and pH value. Sexual activity was recorded with self-administered questionnaires.

Results:
Low sexual frequency was present in a higher proportion of women, but sexual distress was identified within a lower proportion of women in the eldest group. The total FSFI score was significantly lower in the eldest group than in the youngest and intermediate groups (P < 0.01 and 0.05, respectively); however, the domain score of sexual desire, arousal, and satisfaction was lower in the eldest group than in the youngest group (P < 0.01, 0.05, and 0.05) only. The domain score for lubrication was lower in the eldest group than in both the youngest and intermediate groups (P < 0.01 and 0.05), and the pain score was lower in both the intermediate and eldest groups than in the youngest group (P < 0.01 and 0.05). A lower VMI (P < 0.001) and a higher pH value (P < 0.01) were observed in the eldest group, compared with the youngest group. Moreover, VMI was positively correlated with the total FSFI score, the domain score for sexual desire, and lubrication (r = 0.26, 0.25, 0.34; P < 0.05, 0.05, 0.01), but the opposite associations were demonstrated for pH value (r = −0.47, −0.37, −0.38; P < 0.01, respectively), especially with vaginal pain (r = −0.44, P < 0.01).

Conclusions:
Among middle-aged Chinese women, sexual desire is lower in 56 to 60-year-old women, compared with those aged 45 to 55 years, whereas vaginal dryness and dyspareunia become more prevalent with age. Importantly, sexual function is associated with vaginal maturation status in women at midlife.
A Comparison of Dry Eye Diagnostic Tests Between Symptomatic and Asymptomatic Age-Matched Females
Authors: Ngo William , Srinivasan Sruthi , Jones Lyndon 
Published: January 2017

Purpose:
To quantify the strength of association of dry eye (DE) symptoms to DE diagnostic tests in age-matched females.

Methods:
Twenty females with DE symptoms (Ocular Surface Disease Index, OSDI, ≥13) were age-matched with 20 females without DE symptoms (OSDI<13) in this cross-sectional study. Noninvasive tear breakup time (NIBUT), ocular staining, meibum quality, number of obstructed meibomian glands (MGs), lid wiper epitheliopathy, Marx line placement, eyelid margin score, Schirmer test, meibography, and visual acuity were assessed in both groups.

Results:
Twenty participant pairs completed the study. The age (median/interquartile range [IQR]) of the symptomatic group was 60/15 and the asymptomatic group was 62/15. The tests (median/IQR, P value) that were significantly different between the symptomatic group and the asymptomatic group were OSDI (35.4/35.4 vs. 3.1/6.7, P<0.01), NIBUT (2.1/0.7 sec vs. 3.0/3.0 sec, P=0.01), meibum quality (3.0/0.0 grade units vs. 2.0/1.0 grade units, P<0.01), number of obstructed MGs (7.0/2.0 glands vs. 5.0/4.8 glands, P<0.01), and ocular staining (5.5/3.8 grade units vs. 0.5/1.0 grade units, P<0.01). The tests (area under curve, [AUC], odds ratio [OR]) that were most strongly associated with DE symptoms were ocular staining (0.93, 5.0), number of obstructed MGs (0.79, 2.6), meibum quality (0.76, 2.4), and NIBUT (0.74, 3.2) (all P<0.05). There was no significant difference between the two groups for the other DE tests (all P>0.05), and similarly, no significant association to DE symptoms (all P>0.05).

Conclusion:
The diagnostic tests most strongly associated with DE symptoms in older women were ocular staining, meibum quality, number of obstructed MGs, and tear film stability.
Microarchitecture of Schlemm Canal Before and After Selective Laser Trabeculoplasty in Enhanced Depth Imaging Optical Coherence Tomography
Authors: Skaat Alon , Rosman Michael S. , Chien Jason L. , Ghassibi Mark P. , Liebmann Jeffrey M. , Ritch Robert , Park Sung Chul 
Published: January 2017

Purpose:
To characterize the in vivo effect of selective laser trabeculoplasty (SLT) on the Schlemm canal (SC) in eyes with primary open-angle glaucoma (POAG).

Materials and Methods:
Eighty-one serial horizontal enhanced depth imaging optical coherence tomograph B-scans (interval between B-scans, ∼35 μm) of the nasal corneoscleral limbus were obtained before and 4 weeks after SLT. Fifty B-scans in the overlapping regions before and after SLT were selected for analysis based on the structures of aqueous and blood vessels as landmarks. The SC cross-sectional area (CSA) was measured in each selected B-scan and averaged to generate the mean SC CSA of the eye. SC volume in the overlapping region was calculated using commercially available 3-dimensional reconstruction software. The mean SC CSA and SC volume were compared between pre-SLT and post-SLT B-scans. Correlation analysis was performed between SC CSA changes and intraocular pressure (IOP) changes.

Results:
Thirteen POAG eyes (13 patients) were included for analysis (mean age, 68.2±9.2 y). After SLT, the mean IOP was reduced from 19.8±7.6 to 14.4±3.8 mm Hg (P=0.003); the mean SC CSA increased by 8%, from 2478±550 to 2682±598 μm2 (P=0.029); and the mean SC volume increased from 4,304,592±954,777 to 4,658,250±1,039,956 μm3 (P=0.029). Increase in SC CSA had a significant positive correlation with IOP reduction after SLT (P=0.023, R=0.622).

Conclusions:
SLT expands SC in POAG patients and even more so with greater IOP reduction after SLT. Post-SLT expansion of SC may be due to increased trabecular aqueous outflow, IOP decrease, or structural changes in trabecular meshwork resulting from SLT.
Skin Necrosis After Implantation With the BAHA Attract: A Case Report and Review of the Literature
Authors: Chen Stephanie Y. , Mancuso Dean , Lalwani Anil K. 
Published: January 2017

Objective:
The bone-anchored hearing aid (BAHA) Attract is a transcutaneous bone conduction hearing aid that uses magnetic coupling to enable sound conduction. We report the first case of skin necrosis associated with the BAHA Attract and perform a literature review of soft tissue complications related to the device.

Patient:
A single patient who was found to develop skin necrosis 2 weeks after being fitted for the BAHA Attract speech processor.

Intervention:
After the patient developed skin necrosis from the device, she was advised to immediately discontinue use of the Attract to allow complete wound healing, upon which the Attract was successfully converted to a percutaneous BAHA.

Main Outcome and Results:
We monitored for the development of skin complications from the BAHA Attract. The patient's immediate postoperative course was unremarkable and she was fitted with a speech processor of M5 magnet strength at 1 month postoperatively. After 1 week of use, she reported discomfort and was advised to downgrade to an M4 magnet; however, she continued to use the M5 and the following week was found to have developed skin necrosis around the device.

Conclusion:
Despite the infrequency of skin necrosis related to the BAHA Attract, it must be considered in counseling and managing candidates for the device.
Meaningful Use of Electronic Health Records by Outpatient Physicians and Readmissions of Medicare Fee-for-Service Beneficiaries
Authors: Unruh Mark A. , Jung Hye-Young , Vest Joshua R. , Casalino Lawrence P. , Kaushal Rainu 
Published: January 2017

Background:
Nearly one-fifth of hospitalized Medicare fee-for-service beneficiaries are readmitted within 30 days. Participation in the Meaningful Use initiative among outpatient physicians may reduce readmissions.

Objective:
To evaluate the impact of outpatient physicians’ participation in Meaningful Use on readmissions.

Subjects and Research Design:
The study population included 90,774 Medicare fee-for-service beneficiaries from New York State (2010–2012). We compared changes in the adjusted odds of readmission for patients of physicians who participated in Meaningful Use—stage 1, before and after attestation as meaningful users, with concurrent patients of matched control physicians who used paper records or electronic health records without Meaningful Use participation. Three secondary analyses were conducted: (1) limited to patients with 3+ Elixhauser comorbidities; (2) limited to patients with conditions used by Medicare to penalize hospitals with high readmission rates (acute myocardial infarction, congestive heart failure, and pneumonia); and (3) using only patients of physicians with electronic health records who were not meaningful users as the controls.

Main Outcome:
Thirty-day readmission.

Results:
Patients of Meaningful Use physicians had 6% lower odds of readmission compared with patients of physicians who were not meaningful users, but the estimate was not statistically significant (odds ratio: 0.94, 95% confidence interval, 0.88–1.01). Estimated odds ratios from secondary analyses were broadly consistent with our primary analysis.

Conclusions:
Physician participation in Meaningful Use was not associated with reduced readmissions. Additional studies are warranted to see if readmissions decline in future stages of Meaningful Use where more emphasis is placed on health information exchange and outcomes.
A Qualitative Study of Factors Facilitating Clinical Nurse Engagement in Emergency Department Catheter-Associated Urinary Tract Infection Prevention
Authors: Carter Eileen J. , Pallin Daniel J. , Mandel Leslie , Sinnette Corine , Schuur Jeremiah D. 
Published: January 2017

OBJECTIVE:
The aim of this study was to explore the actions of nurse leaders that facilitated clinical nurses' active involvement in emergency department (ED) catheter-associated urinary tract infection (CAUTI) prevention programs.

BACKGROUND:
Hospitals face increasing financial pressures to reduce CAUTI. Urinary catheters, often inserted in the ED, expose patients to CAUTI risk. Nurses are the principal champions of ED CAUTI prevention programs.

METHODS:
This was a qualitative analysis from a multisite, comparative case study project. A total of 52 interviews and 9 focus groups were analyzed across 6 enrolled EDs. Using a conventional content analysis, members of the research team coded data and developed site summaries to describe themes that had emerged across transcripts. Subsequently, all codes and site summaries were reviewed to identify the actions of nurse leaders that facilitated clinical nurses' engagement in CAUTI prevention efforts.

RESULTS:
Nurse leaders were the principal champions of CAUTI prevention programs and successfully engaged clinical nurses in CAUTI prevention efforts by (1) reframing urinary catheters as a source of potential patient harm; (2) empowering clinical nurses to identify and address CAUTI improvement opportunities; (3) fostering a culture of teamwork, which facilitated interdisciplinary communication around urinary catheter appropriateness and alternatives; and (4) holding clinical nurses accountable for CAUTI process and outcome measures.

CONCLUSIONS:
The prevention of CAUTI is an important opportunity for nurse leaders to engage clinical nurses in meaningful improvement efforts. Clinical nurses are best positioned to examine urinary catheter insertion workflow and to suggest improvements in avoiding use and improving placement and maintenance. To engage clinical nurses in CAUTI prevention, nurse leaders should focus on how urinary catheters expose patients to potential harm, involve nurses in designing and implementing practice changes, and provide local data to show the impact of nursing practices on patient outcomes.
Evidence-Based Practice and Job-Related Nurse Outcomes at Magnet®-Aspiring, Magnet-Conforming, and Non-Magnet University Hospitals in Finland
Authors: Saunders Hannele , Vehviläinen-Julkunen Katri 
Published: January 2017

OBJECTIVE:
The aim of this study was to compare nurses’ evidence-based practice (EBP) beliefs, EBP knowledge, and nurse workforce outcomes between Magnet®-aspiring, Magnet-conforming, and non-Magnet university hospitals in Finland.

BACKGROUND:
The effect of Magnet designation on EBP and nursing workforce outcomes is well studied where Magnet hospitals exist. Less is known about it in countries where hospitals are embarking upon the initial Magnet journey.

METHODS:
A descriptive cross-sectional national survey was conducted at Finnish university hospitals with a convenience sample (n = 943) of practicing nurses. Data were analyzed using descriptive and inferential statistics.

RESULTS:
Although nurses’ EBP beliefs were favorable and they were satisfied with their jobs, they reported low levels of EBP knowledge. Statistically significant differences were found between hospitals’ Magnet journey status and nurses’ levels of perceived EBP knowledge.

CONCLUSIONS:
Although nurses believed in the value of EBP and were satisfied with and likely to stay in their jobs and in nursing, they lacked the EBP knowledge required for integrating best evidence into clinical care.
Cell Phone Calls in the Operating Theater and Staff Distractions: An Observational Study
Authors: Avidan Alexander , Yacobi Galel , Weissman Charles , Levin Phillip D. 
Published: January 2017

Objectives
Cell phones are the primary communication tool in our institution. There are no restrictions on their use in the operating rooms. The goal of this study was to evaluate the extent of cell phone use in the operating rooms during elective surgery and to evaluate whether they cause staff distractions.

Methods
The following data on cell phone use were recorded anonymously: number of incoming and outgoing cell phone calls, duration of cell phone calls and their content (patient related, work related, private), who was distracted by the cell phone calls, and duration of distractions.

Results
We made observations during 52 surgeries. There were 205 cell phone calls, 197 (96.1%; median, 3 per surgery; interquartile range, 2–5) incoming and 8 (3.9%) outgoing. Incoming calls were answered on 110 (55.8%) of 197 (median, 2; interquartile range, 1–3) occasions. The mean duration of incoming calls (64 ± 40 seconds) was shorter than those of the outgoing calls (137 ± 242 seconds, P < 0.001). During 29 (14.7%) of 197 incoming calls, 30 staff distractions occurred. Distractions were caused mainly for surgeons talking on their cell phones (24/30, 80.0%). The mean duration of the distractions was 43.6 ± 22.3 seconds. During all 8 outgoing calls, no other staff members were distracted.

Conclusion
The number of cell phone calls in the operating rooms during elective surgery was lower than expected and caused short-lived distractions mainly to the operating surgeons. We recommend that operating surgeons turn off their cell phones before surgery.
Adenofibroma in the Uterine Cervix Manifesting as Multilocular Cystic Lesions
Authors: Ra Joon Chul , Park Sung Bin , Lee Jong Beum , Han Byoung Hee , Lee Young Ho , Hong Sung Ran 
Published: January 2017

Abstract
Uterine cervical adenofibroma, a very rare benign neoplasm, has rarely been reported in imaging features in the English literature. Herein, we describe a case of uterine cervical adenofibroma that was depicted as a multilocular cystic lesion with enhanced solid portions.
An Innovative Approach
Authors: Hellier Susan D. , Ramponi Denise R. , Wrynn Alexander , Garofalo Stephanie 
Published: January 2017

IntroductionIn response to the growing body of evidence that simulation is a satisfactory way to instruct procedural skills, we developed an innovative model to teach common gynecologic procedures such as cervical cancer screening, cervical polyp removal, intrauterine device removal, and endometrial biopsy. The objectives of this study were to describe the construction of the model and to assess participants' satisfaction and confidence in applying the learning objectives to their clinical practice.MethodsThe researchers created the model with reusable and readily available materials. During a hands-on skills workshop, practicing clinicians performed simulated cervical cancer screening, endocervical polyp removal, intrauterine device removal, and an endometrial biopsy on a low-fidelity gynecologic model. Using convenience sampling, each participant completed a survey designed to measure satisfaction with the workshop and self-confidence in their newly acquired skills.ResultsAll (N = 30,100%) of the participants agreed at the “agree” or “strongly agree” level that the gynecologic skills workshop using lecture and a hands-on model was a satisfying and self-confidence–building experience.ConclusionsAn easily reproducible and reusable gynecologic procedure simulator was highly rated as a means of teaching common primary care gynecologic procedures. The simulated model provided an opportunity for hands-on skills learning for clinicians who wish to expand their gynecologic procedure skill set.
Photokinetic analysis of the forces and torques exerted by optical tweezers carrying angular momentum
Authors: Yevick Aaron , Evans Daniel J. , Grier David G. 
Published: January 2017

The theory of photokinetic effects expresses the forces and torques exerted by a beam of light in terms of experimentally accessible amplitude and phase profiles. We use this formalism to develop an intuitive explanation for the performance of optical tweezers operating in the Rayleigh regime, including effects arising from the influence of light’s angular momentum. First-order dipole contributions reveal how a focused beam can trap small objects, and what features limit the trap’s stability. The first-order force separates naturally into a conservative intensity-gradient term that forms a trap and a non-conservative solenoidal term that drives the system out of thermodynamic equilibrium. Neither term depends on the light’s polarization; light’s spin angular momentum plays no role at dipole order. Polarization-dependent effects, such as trap-strength anisotropy and spin-curl forces, are captured by the second-order dipole-interference contribution to the photokinetic force. The photokinetic expansion thus illuminates how light’s angular momentum can be harnessed for optical micromanipulation, even in the most basic optical traps.
This article is part of the themed issue ‘Optical orbital angular momentum’.
Orbital angular momentum light in microscopy
Authors: Ritsch-Marte Monika 
Published: January 2017

Light with a helical phase has had an impact on optical imaging, pushing the limits of resolution or sensitivity. Here, special emphasis will be given to classical light microscopy of phase samples and to Fourier filtering techniques with a helical phase profile, such as the spiral phase contrast technique in its many variants and areas of application.
This article is part of the themed issue ‘Optical orbital angular momentum’.
Swings and roundabouts: optical Poincaré spheres for polarization and Gaussian beams
Authors: Dennis M. R. , Alonso M. A. 
Published: January 2017

The connection between Poincaré spheres for polarization and Gaussian beams is explored, focusing on the interpretation of elliptic polarization in terms of the isotropic two-dimensional harmonic oscillator in Hamiltonian mechanics, its canonical quantization and semiclassical interpretation. This leads to the interpretation of structured Gaussian modes, the Hermite–Gaussian, Laguerre–Gaussian and generalized Hermite–Laguerre–Gaussian modes as eigenfunctions of operators corresponding to the classical constants of motion of the two-dimensional oscillator, which acquire an extra significance as families of classical ellipses upon semiclassical quantization.
This article is part of the themed issue ‘Optical orbital angular momentum’.