bluuebunny/crossref_metadata_2025 huggingface dataset:
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

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.
Nurse Executives Wearing 2 Hats as Strategic Leaders
Authors: Boston-Fleischhauer Carol
Published: January 2017

Disruptions in healthcare are challenging nurse leaders to develop innovative care delivery strategies and make the space for nursing practice innovation at the point of care or service. These functions are interdependent and require strong nursing leadership to challenge the status quo thinking of our colleagues. The ultimate goal of disruptive innovation is to ensure that care innovations are aligned with changing consumer and payer expectations, while ensuring safety, reliability, and cost-effectiveness.
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.
Theory of Constraints
Authors: Pawlak Roberta
Published: January 2017

Demand for nurses is influenced by many factors. Labor statistics and health services literature reveal current and predicted supply gaps in meeting this demand. One strategy in response can be drawn from manufacturing industries. This column suggests the application of the Theory of Constraints in efforts to relieve bottlenecks in producing and retaining nurse labor.
Interobserver Agreement in Endometrial Carcinoma Histotype Diagnosis Varies Depending on The Cancer Genome Atlas (TCGA)-based Molecular Subgroup
Authors: Hoang Lien N. , Kinloch Mary A. , Leo Joyce M. , Grondin Katherine , Lee Cheng-Han , Ewanowich Carol , Köbel Martin , Cheng Angela , Talhouk Aline , McConechy Melissa , Huntsman David G. , McAlpine Jessica N. , Soslow Robert A. , Gilks C. Blake
Published: January 2017

The Cancer Genome Atlas recently identified a genomic-based molecular classification of endometrial carcinomas, with 4 molecular categories: (1) ultramutated (polymerase epsilon [POLE] mutated), (2) hypermutated (microsatellite instability), (3) copy number abnormalities-low, and (4) copy number abnormalities-high. Two studies have since proposed models to classify endometrial carcinomas into 4 molecular subgroups, modeled after The Cancer Genome Atlas, using simplified and more clinically applicable surrogate methodologies. In our study, 151 endometrial carcinomas were molecularly categorized using sequencing for the exonuclease domain mutations (EDM) of POLE, and immunohistochemistry for p53 and mismatch repair (MMR) proteins. This separated cases into 1 of 4 groups: (1) POLE EDM, (2) MMR-D, (3) p53 wildtype (p53 wt), or (4) p53 abnormal (p53 abn). Seven gynecologic pathologists were asked to assign each case to one of the following categories: grade 1 to 2 endometrioid carcinoma (EC), grade 3 EC, mucinous, serous carcinoma (SC), clear cell, dedifferentiated, carcinosarcoma, mixed, and other. Consensus diagnosis among all 7 pathologists was highest in the p53 wt group (37/41, 90%), lowest in the p53 abn group (14/36, 39%), and intermediate in the POLE EDM (22/34, 65%) and MMR-D groups (23/40, 58%). Although the majority of p53 wt endometrial carcinomas are grade 1 to 2 EC (sensitivity: 90%), fewer than half of grade 1 to 2 EC fell into the p53 wt category (positive predictive value: 42%). Pure SC almost always resided in the p53 abn group (positive predictive value: 96%), but it was insensitive as a marker of p53 abn (sensitivity 64%) and the reproducibility of diagnosing SC was suboptimal. The limitations in the precise histologic classification of endometrial carcinomas highlights the importance of an ancillary molecular-based classification scheme.
Steatohepatitis-like Changes in Focal Nodular Hyperplasia, A Finding to Distinguish From Steatohepatitic Variant of Hepatocellular Carcinoma
Authors: Deniz Kemal , Moreira Roger K. , Yeh Matthew M. , Ferrell Linda D.
Published: January 2017

Steatohepatitis-like change has not been described in focal nodular hyperplasia (FNH). Steatohepatitis-like change in FNH may show overlapping features with steatohepatitic variant of hepatocellular carcinoma (HCC). This problem can be compounded if seen in FNH with widened cell plates or hepatocyte rosettes, other features that can also be seen in HCC. This study examined steatotic FNHs for the frequency of steatohepatitis-like change, especially in the setting of FNH with rosettes and/or widened cell plates. Thirty-three resection specimens of steatotic FNH from 3 institutions were evaluated for degree of steatosis, background liver steatosis, ductular reaction, and lymphocytic infiltrate, as well as presence of thick fibrous bands, thick-walled vessels, ballooned hepatocytes, Mallory-Denk bodies, dilated sinusoids, hepatocyte rosettes, and thick hepatic plates. Steatosis was distributed along fibrous septa as well as diffusely throughout the FNH. Steatohepatitis-like changes were focally present in 54% (18 cases). Thick plates>3 cells were focally found in 14 cases (42%); rosettes were common (70%). All cases showed at least 2 of the histologic features highly suggestive for the diagnosis of FNH such as thick bands of fibrosis, thick-walled vessels and/or ductular reaction and the typical map-like pattern of glutamine synthetase immunostaining. More than half of fatty FNH examined for this study had features of at least focal steatohepatitis-like changes. This finding should not be confused with steatohepatitic variant of HCC. Common typical features of FNH including thick-walled vessels, ductular reaction and thick fibrous bands are helpful for discrimination of FNH from HCC.
Transdifferentiation of Neuroendocrine Cells
Authors: Sergeant Camille , Jublanc Christel , Leclercq Delphine , Boch Anne-Laure , Bielle Franck , Raverot Gerald , Daly Adrian F. , Trouillas Jacqueline , Villa Chiara
Published: January 2017

Gangliocytomas are rare and benign neuronal cell tumors, mostly found in the hypothalamic and sellar regions. Their histogenesis is still the subject of discussions. Herein we present a unique case of a pituitary gangliocytoma associated with a prolactinoma and a corticotroph adenoma in a patient affected by MEN1. The histologic study revealed shared features between adenomatous and neuronal cells, supporting the etiological hypothesis of a common origin or a phenomenon of transdifferentiation. Furthermore, gangliocytoma could be a new tumor related to MEN1. The clinical and histologic observations are discussed and the literature on the topic is reviewed.
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

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

Introduction

In 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.

Methods

The 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.

Results

All (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.

Conclusions

An 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’.
Origins and demonstrations of electrons with orbital angular momentum
Authors: McMorran Benjamin J. , Agrawal Amit , Ercius Peter A. , Grillo Vincenzo , Herzing Andrew A. , Harvey Tyler R. , Linck Martin , Pierce Jordan S.
Published: January 2017

The surprising message of Allen
et al.
(Allen
et al.
1992
Phys. Rev. A
45
, 8185 (
doi:10.1103/PhysRevA.45.8185
)) was that photons could possess orbital angular momentum in free space, which subsequently launched advancements in optical manipulation, microscopy, quantum optics, communications, many more fields. It has recently been shown that this result also applies to quantum mechanical wave functions describing massive particles (matter waves). This article discusses how electron wave functions can be imprinted with quantized phase vortices in analogous ways to twisted light, demonstrating that charged particles with non-zero rest mass can possess orbital angular momentum in free space. With Allen
et al.
as a bridge, connections are made between this recent work in electron vortex wave functions and much earlier works, extending a 175 year old tradition in matter wave vortices.

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’.
Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software
Authors: Sczyrba Alexander , Hofmann Peter , Belmann Peter , Koslicki David , Janssen Stefan , Dröge Johannes , Gregor Ivan , Majda Stephan , Fiedler Jessika , Dahms Eik , Bremges Andreas , Fritz Adrian , Garrido-Oter Ruben , Jørgensen Tue Sparholt , Shapiro Nicole , Blood Philip D. , Gurevich Alexey , Bai Yang , Turaev Dmitrij , DeMaere Matthew Z. , Chikhi Rayan , Nagarajan Niranjan , Quince Christopher , Meyer Fernando , Balvoit Monika , Hansen Lars Hestbjerg , Sørensen Søren J. , Chia Burton K. H. , Denis Bertrand , Froula Jeff L. , Wang Zhong , Egan Robert , Kang Dongwan Don , Cook Jeffrey J. , Deltel Charles , Beckstette Michael , Lemaitre Claire , Peterlongo Pierre , Rizk Guillaume , Lavenier Dominique , Wu Yu-Wei , Singer Steven W. , Jain Chirag , Strous Marc , Klingenberg Heiner , Meinicke Peter , Barton Michael , Lingner Thomas , Lin Hsin-Hung , Liao Yu-Chieh , Silva Genivaldo Gueiros Z. , Cuevas Daniel A. , Edwards Robert A. , Saha Surya , Piro Vitor C. , Renard Bernhard Y. , Pop Mihai , Klenk Hans-Peter , Göker Markus , Kyrpides Nikos C. , Woyke Tanja , Vorholt Julia A. , Schulze-Lefert Paul , Rubin Edward M. , Darling Aaron E. , Rattei Thomas , McHardy Alice C.
Published: January 2017

In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation metrics complicates proper performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on datasets of unprecedented complexity and realism. Benchmark metagenomes were generated from ~700 newly sequenced microorganisms and ~600 novel viruses and plasmids, including genomes with varying degrees of relatedness to each other and to publicly available ones and representing common experimental setups. Across all datasets, assembly and genome binning programs performed well for species represented by individual genomes, while performance was substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below the family level. Parameter settings substantially impacted performances, underscoring the importance of program reproducibility. While highlighting current challenges in computational metagenomics, the CAMI results provide a roadmap for software selection to answer specific research questions.
Automatic classification of diatoms of Merja fouarate
Authors: Chahboune Nouzha , Mehdi Mohamed , Douira Allal
Published: January 2017

RESUME

Objective:

This work consists of developing an automatic method of form analysis and classification of diatoms through processing of scanned images. The fundamental objective is to determine to what extent two diatoms are similar from the images stored in a database, and to conclude to what classes they belong. To do so, a comparison is made between a manual identification and an automatic identification, based on the ultimate points and the Freeman Chain Code.
Reliability of multigrain indexing for orthorhombic polycrystals above 1 Mbar: application to MgSiO3 post-perovskite
Authors: Langrand Christopher , Hilairet Nadège , Nisr Carole , Roskosz Mathieu , Ribárik Gábor , Vaughan Gavin B. M. , Merkel Sébastien
Published: January 2017

This paper describes a methodology for characterizing the orientation and position of grains of an orthorhombic polycrystalline material at high pressure in a diamond anvil cell. The applicability and resolution of the method are validated by simulations and tested on an experimental data set collected on MgSiO3 post-perovskite at 135 GPa. In the simulations, ∼95% of the grains can be indexed successfully with ∼80% of the peaks assigned. The best theoretical average resolutions in grain orientation and position are 0.02° and 1.4 µm, respectively. The indexing of experimental data leads to 159 grains of post-perovskite with 30% of the diffraction peaks assigned with a 0.2–0.4° resolution in grain orientation. The resolution in grain location is not sufficient for in situ analysis of spatial relationships at high pressure. The grain orientations are well resolved and sufficient for following processes such as plastic deformation or phase transformation. The paper also explores the effect of the indexing parameters and of experimental constraints such as rotation range and step on the validity of the results, setting a basis for optimized experiments.
SUePDF: a program to obtain quantitative pair distribution functions from electron diffraction data
Authors: Tran Dung Trung , Svensson Gunnar , Tai Cheuk-Wai
Published: January 2017

SUePDFis a graphical user interface program written in MATLAB to achieve quantitative pair distribution functions (PDFs) from electron diffraction data. The program facilitates structural studies of amorphous materials and small nanoparticles using electron diffraction data from transmission electron microscopes. It is based on the physics of electron scattering as well as the total scattering methodology. A method of background modeling is introduced to treat the intensity tail of the direct beam, inelastic scattering and incoherent multiple scattering. Kinematical electron scattering intensity is scaled using the electron scattering factors. The PDFs obtained after Fourier transforms are normalized with respect to number density, nanoparticle form factor and the non-negativity of probability density.SUePDFis distributed as free software for academic users.
How many water molecules are detected in X-ray protein crystal structures?
Authors: Gnesi Marco , Carugo Oliviero
Published: January 2017

The positions of several water molecules can be determined in protein crystallography, either buried in internal cavities or at the protein surface. It is important to be able to estimate the expected number of these water molecules to facilitate crystal structure determination. Here, a multiple Poisson regression model implemented on nearly 10 000 protein crystal structures shows that the number of detectable water molecules depends on eight variables: crystallographic resolution, R factor, percentage of solvent in the crystal, average B factor of the protein atoms, percentage of amino acid residues in loops, average solvent-accessible surface area of the amino acid residues, grand average of hydropathy of the protein(s) in the asymmetric unit and normalized number of heteroatoms that are not water molecules. Furthermore, a secondary analysis tested the effect of different software packages. Given the values of these eight variables, it is possible to compute the expected number of water molecules detectable in electron-density maps with reasonable accuracy (as suggested by an external validation of the model).
Crystal structure of caesium dihydrogen citrate from laboratory X-ray powder diffraction data and DFT comparison
Authors: Rammohan Alagappa , Kaduk James A.
Published: January 2017

The crystal structure of caesium dihydrogen citrate, Cs+·H2C6H5O7−, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The coordination polyhedra of the nine-coordinate Cs+cations share edges to form chains along thea-axis. These chains are linked by corners along thec-axis. The un-ionized carboxylic acid groups form two different types of hydrogen bonds; one forms a helical chain along thec-axis, and the other is discrete. The hydroxy group participates in both intra- and intermolecular hydrogen bonds.
Developing organizations: a system of enquiry, action and learning
Authors: Graham Wayne
Published: January 2017

Purpose

This paper aims to demonstrate the applicability of an action learning model to improve organizational outcomes.

Design/methodology/approach

This paper extends previous work by applying the system of enquiry, action and learning (SEAL) model using an action research methodology to a small business operating in the health services industry.

Findings

The SEAL model is a useful approach to introduce small business practitioners to the principles of organizational development (OD).

Research limitations/implications

The application is limited to one small business, and subsequent studies could apply the model to more organizations that operate in industries other than health services.

Practical implications

Business owners from this study and previous studies have found the model to be useful in the improvement of organizational outcomes.

Originality/value

The SEAL model is a simplified model that introduces principles of OD and has provided value to the business owners of this study.
Developing your career: harnessing the power of the internet for “digital career management”
Authors: Hooley Tristram
Published: January 2017

Purpose

This paper aims to discuss the role of the internet in framing individual’s career building. It argues that the 7 Cs of digital career literacy offer a useful framework for those working in learning and development in organizations. Every individual needs to engage with the internet when thinking about how to manage and future-proof their careers. Learning and development (L&D) professionals can support employees to harness the power of the internet and learn how to make use of the new opportunities of “digital career management”.

Design/methodology/approach

This paper highlights steps that every individual needs to take for “digital career management” and pulls out the role of L&D professionals in addressing the developing internet context.

Findings

Sets out “7 C’s” for proactively managing a “digital career profile”.

Originality/value

The internet has shifted the context for career building and learning how to maximize the opportunities now offered is the central task for anyone wishing to carve out their future careers.
University students in the workplace strategies for successful industry placement experiences
Authors: Burdett Jane , Barker Sandy
Published: January 2017

Purpose

Increasing numbers of university students in USA, UK and Australia are undertaking industry placements to gain workplace experience. However, outcomes are not always as expected. This paper aims to identify challenges for universities and host organizations in delivering quality student industry placement and presents strategies to achieve successful learning outcomes.

Design/methodology/approach

The reflections, evaluation and feedback data received from stakeholders, namely, university students, host organizations and faculty mentors in a large Australian university were used to formulate strategies.

Findings

Lessons learned from the authors’ experience in industry placement programs over 5 years with 180 students in 127 organizations indicate that careful planning and management of placements is needed to achieve successful learning outcomes.

Research limitations/implications

Further research into the application of these strategies in other universities would be valuable.

Practical implications

Lessons learned and recommendations offered provide strategies to assist in planning and management of industry placements.

Originality/value

Given the growing popularity of work experience in university programs, this should be of interest to faculty and organizations.
Essential Oils Against Pathogen and Spoilage Microorganisms of Fruit Juices: Use of Versatile Antimicrobial Delivery Systems
Authors: Trinetta Valentina , Morgan Mark T. , Coupland John N. , Yucel Umut
Published: January 2017

Essential oils (EO) are increasingly used as natural antimicrobial compounds, however the effect of delivery system to enhance their antimicrobial activity has not been widely studied. Limonene (0 to 10 μL/mL) was added to microbial suspensions (∼105 CFU/mL) of selected foodborne pathogens (Listeria monocytogenes Scott A, Salmonella enterica Typhimurium, Escherichia coli and Staphylococcus aureus), and spoilage microorganisms (Lactobacillus plantarum, Saccharomyces cerevisiae, and Candida albicans). S. aureus was found to be the most sensitive foodborne pathogen while Salmonella enterica showed continued growth under all concentrations. Stable nanoemulsions and solid lipid nanoparticles (SLN) (d ∼ 170 nm) were prepared using an alkane carrier oil (n‐tetradecane and n‐eicosane, respectively). Interfacial effects and homogenous distribution of limonene in nanoemulsions improved its (8 and 12 μL/mL) antimicrobial effect against S. aureus. Higher aqueous concentrations as a result of expulsion from SLN further enhanced the antimicrobial activity pronounced at higher limonene concentrations. Therefore, our findings confirm that the emulsion‐based delivery systems are able to effectively distribute limonene inside a microbial suspension to improve its antimicrobial activity.
Formation and Characterization of Green Tea Extract Loaded Liposomes
Authors: Dag Damla , Oztop Mecit Halil
Published: January 2017

Green tea extract was encapsulated into liposomes to enhance bioavailability and stability of catechins by protecting their functional properties simultaneously. Encapsulation was achieved by dispersing 1% (w/v) soy lecithin through high pressure homogenization (microfluidization) and ultrasonication. Effects of homogenization type and pH of the dispersing medium on the physical properties and stability of the liposomes during 1‐mo storage period were investigated. Mean particle size, total phenolic content by Folin–Ciocalteu method and antioxidant activity by 2‐diphenyl‐1‐picrylhydrazyl radical scavenging and ferric reducing‐antioxidant power methods, and transmission electron microscopy (TEM) experiments were conducted for characterization. Green tea extract loaded liposomes prepared by microfluidization in distilled water were determined as the most stable system which demostrated no significant difference (P > 0.05) on mean particle size, total phenolic content, and antioxidant activity between the first and final day of 1‐mo storage time. Additionally, uniform size and shape in TEM images supported the results.
Fish and Invertebrate Flow‐Biology Relationships to Support the Determination of Ecological Flows for North Carolina
Authors: Phelan Jennifer , Cuffney Tom , Patterson Lauren , Eddy Michele , Dykes Robert , Pearsall Sam , Goudreau Chris , Mead Jim , Tarver Fred
Published: January 2017

A method was developed to characterize fish and invertebrate responses to flow alteration in the state of North Carolina. This method involved using 80th percentile linear quantile regressions to relate six flow metrics to the diversity of riffle‐run fish and benthic Ephemeroptera, Plecoptera, and Trichoptera (EPT) richness. All twelve flow‐biology relationships were found to be significant, with both benthos and fish showing negative responses to ecodeficits and reductions in flow. The responses of benthic richness to reduced flows were consistent and generally greater than that of fish diversity. However, the riffle‐run fish guild showed the greatest reductions in diversity in response to summer ecodeficits. The directional consistency and differential seasonal sensitivities of fish and invertebrates to reductions in flow highlight the need to consider seasonality when managing flows. In addition, all relationships were linear, and therefore do not provide clear thresholds to support ecological flow determinations and flow prescriptions to prevent the degradation of fish and invertebrate communities in North Carolina rivers and streams. A method of setting ecological flows based on the magnitude of change in biological condition that is acceptable to society is explored.
Sofosbuvir‐based treatment regimens: real life results of 14 409 chronic HCV genotype 4 patients in Egypt
Authors: Elsharkawy A. , Fouad R. , El Akel W. , El Raziky M. , Hassany M. , Shiha G. , Said M. , Motawea I. , El Demerdash T. , Seif S. , Gaballah A. , El Shazly Y. , Makhlouf M. A. M. , Waked I. , Abdelaziz A. O. , Yosry A. , El Serafy M. , Thursz M. , Doss W. , Esmat G.
Published: January 2017

Background

Chronic hepatitis C virus infection is one of the most important health problems in Egypt. The Ministry of Health's National Treatment Programme introduced sofosbuvir‐based therapy in October 2014.

Aim

To assess the clinical effectiveness and predictors of response to SOF‐based treatment regimens, either dual therapy, with SOF/ribavirin (RBV) for 6 months or triple therapy with SOF/peg‐IFN‐alfa‐2a/RBV for 3 months, in a cohort of patients treated in National Treatment Programme affiliated centres in Egypt.

Methods

Between October 2014 and end of 2014, patients who were eligible for treatment were classified according to their eligibility for interferon therapy: Group 1 (interferon eligible) were treated with triple therapy for 12 weeks and Group 2 (interferon ineligible) were treated with dual therapy for 24 weeks. Difficult to treat patients included those with F3‐F4 on Metavir score, Fib‐4 >3.25, albumin ≤3.5, total Bilirubin >1.2 mg/dL, INR >1.2 and platelet count <150 000 mm3.

Results

Twelve weeks post‐treatment data were available on 14 409 patients; 8742 in group 1 and 5667 in group 2. In group 1, the sustained virological response at week 12 (SVR12) was 94% and in group 2 the SVR12 was 78.7%. Multivariate logistic regression analysis in which treatment failure is the dependent variable was done. Male gender, being a difficult to treat patient and previous interferon therapy were significant predictors of nonresponse in both treatment groups.

Conclusion

Results of sofosbuvir‐based therapies in Egypt achieved similar rates of SVR12 as seen in phase III efficacy studies.
Application of solvent dye in the field of biodiesel preservation
Authors: de Souza Ana Caroline Dias , Comin Marina , de Oliveira Luiz Henrique , Silva Cinthia Aparecida de Andrade , Muzzi Rozanna Marques , Fiorucci Antonio Rogério , Caires Anderson Rodrigues Lima , Trindade Magno Aparecido Gonçalves
Published: January 2017

In this study, biodiesel (OSRB) from degummed oilseed radish oil (OSR) was obtained by transesterification, and the effect on its thermal stability of a binary compound containing a conventional antioxidant and a solvent dye was evaluated. A combination of the traditional antioxidant tert‐butylhydroquinone (TBHQ) and a solvent dye, so‐called CI Solvent Blue 35 (SB‐35), was prepared and incorporated into OSR and OSRB prior to analysis. The acid value, peroxide value, and induction period were measured, and it was found that TBHQ and SB‐35 were highly effective in stabilising OSR and OSRB when used in combination. The TBHQ/SB‐35 blend had strong antioxidation activity, even at very low concentrations, when compared with the addition of the individual compounds. In summary, the results showed that a TBHQ/SB‐35 blend may be successfully used as an alternative additive for improving oil and biodiesel preservation.