bluuebunny/crossref_metadata_2025 huggingface dataset:
Creatively Improving Care Delivery
Authors: Boyle Brendan M. , Hill Ivor
Published: December 2016

The medical community has been challenged to improve upon deficiencies in the delivery of patient care. Quality improvement methods are therefore increasingly used in everyday clinical practice. As demonstrated in this review, creative and impactful improvement projects within pediatric gastroenterology can be successfully achieved as either multicenter projects or single‐center efforts. Through our willingness to accept the challenge to improve, practitioners within the pediatric gastroenterology community have become leaders in using quality improvement to change practice and improve clinical outcomes.
Predictors of Suboptimal Follow-up in Pediatric Cancer Survivors
Authors: May Leana , Schwartz David D. , Frugé Ernest , Laufman Larry , Holm Suzanne , Kamdar Kala , Harris Lynnette , Brackett Julienne , Unal Sule , Tanyildiz Gulsah , Bryant Rosalind , Suzawa Hilary , Dreyer Zoann , Okcu M. Fatih
Published: December 2016

Attendance to follow-up care after completion of cancer treatment is an understudied area. We examined demographic, clinical, and socioeconomic predictors of follow-up by pediatric cancer patients at a large center in 442 newly diagnosed patients using multivariable logistic regression analyses. Patients who did not return to clinic for at least 1000 days were considered lost to follow-up. Two hundred forty-two (54.8%) patients were lost. In multivariable analyses, the following variables were independent predictors of being lost to follow-up: treatment with surgery alone (odds ratio [OR]=6.7; 95% confidence interval [CI], 3.1-14.9), older age at diagnosis (reference, 0 to 4; ages, 5 to 9: OR=1.8, 95% CI, 1.1-3; ages, 10 to 14: OR=3.3; CI, 1.8-6.1; and ages, 15 and above: OR=4.8; CI, 2.1-11.7), lack of history of stem cell transplantation (OR=2, 95% CI, 1.04-3.7) and lack of insurance (OR=3.4; CI, 1.2-9.2). Hispanic patients had the best follow-up rates (53.7%) compared to whites and blacks (P=0.03). Attendance to long-term follow-up care is suboptimal in childhood cancer survivors. Predictors that were associated with nonattendance can be used to design targeted interventions to improve follow-up care for survivors of pediatric cancer.
Management of Pregnancy in Women Who Have Undergone Bariatric Surgery
Authors: Dolin Cara , Ude Welcome Akuezunkpa O. , Caughey Aaron B.
Published: December 2016

Importance

As the problem of obesity continues to grow, more patients are choosing to undergo bariatric surgery to lose weight and treat comorbidities, such as diabetes. Of the more than 200,000 procedures performed each year, 80% are in women, many of reproductive age. Taking care of a pregnant woman who has undergone bariatric surgery requires understanding of the risks, the need for additional surveillance, and the limitations of our knowledge about how bariatric surgery affects pregnancy.

Objective

The aims of this study were to review the current literature on bariatric surgery and pregnancy and summarize the important evidence to help the obstetrician care for a pregnant woman after bariatric surgery.

Evidence Acquisition

Evidence for this review was acquired using PubMed.

Conclusions

Pregnancy after bariatric surgery is safe and may be associated with improved pregnancy outcomes; however, more research is needed to better understand how to manage pregnant women with a history of bariatric surgery.

Relevance

Obstetricians will increasingly be caring for women who have undergone bariatric surgery and subsequently become pregnant.

Target Audience

Obstetricians and gynecologists, family physicians.

Learning Objectives

After participating this activity, the learner should be better able to understand the indications for bariatric surgery and how different types of bariatric procedures change gastrointestinal physiology and nutrient metabolism; appropriately counsel patients about the risks and benefits of pregnancy after bariatric surgery; and understand the importance of monitoring nutritional status and supplementation in pregnancies after bariatric surgery.
Effect of Vaginal Estrogen on Pessary Use
Authors: Dessie Sybil G. , Armstrong Katherine , Modest Anna M. , Hacker Michele R. , Hota Lekha S.
Published: December 2016

(Abstracted from Int Urogynecol J 2016;27:1423–1429)

A simple, noninvasive, treatment option for patients with pelvic organ prolapse (POP) or stress urinary incontinence is the pessary. Serious adverse effects associated with its use, such as fistula development, fecal impaction, or hydronephrosis, are rare and almost always result from neglected pessary care.
Stress and Burnout Among Gynecologic Oncologists: A Society Of Gynecologic Oncology Evidence-Based Review and Recommendations
Authors: Cass Ilana , Duska Linda R. , Blank Stephanie V. , Cheng Georgina , duPont Nefertiti C. , Frederick Peter J. , Hill Emily K. , Matthews Carolyn M. , Pua Tarah L. , Rath Kellie S. , Ruskin Rachel , Thaker Premal H. , Berchuck Andrew , Gostout Bobbie S. , Kushner David M. , Fowler Jeff M.
Published: December 2016

(Abstracted from Gynecol Oncol 2016;143:421–427)

Burnout in physicians is a significant problem in all fields of medicine. A 2008 survey of members of the American College of Surgeons (ACS) and a 2014 survey of members of the Society of Gynecologic Oncology (SGO) reported that physician burnout occurs in 32% to 40% of gynecologic oncologists and surgeons This article describes the risk factors responsible for burnout in gynecologic oncologists and other physicians and the consequences of burnout and explores potential solutions.
A Randomized Controlled Trial of Intramuscular Versus Vaginal Progesterone for the Prevention of Recurrent Preterm Birth
Authors: Elimian Andrew , Smith Katie , Williams Marvin , Knudtson Eric , Goodman Jean R. , Escobedo Marilyn B.
Published: December 2016

(Abstracted from Int J Gynecol Obstet 2016;134:169–172)

Preterm birth (PTB) is responsible for most of the neonatal deaths that occur in the absence of congenital anomalies. It is also a major cause of long-term disabilities, including cerebral palsy, blindness, and deafness in childhood.
Increased Immunoglobulin G4-positive Plasma Cells in Lymphadenoma of the Salivary Gland: An Immunohistochemical Comparison Among Lymphoepithelial Lesions
Authors: Kim Jiyoon , Song Joon Seon , Roh Jong-Lyel , Choi Seung-Ho , Nam Soon Yuhl , Kim Sang Yoon , Cho Kyung-Ja
Published: December 2016

Background:

Lymphadenoma (LA) of the salivary gland, nonsebaceous type, is an uncommon benign lymphoepithelial neoplasm. The histogenesis of the lymphoid component of LA is under debate as in Warthin’s tumor. A recent study has described immunoglobulin (Ig) class switching to IgG4 in a subset of Warthin’s tumors. The aim of this study is to evaluate IgG4 status of LA and presume the role of IgG4 status in pathogenesis of LA.

Materials and Methods:

The distribution of IgG-positive and IgG4-positive cells was compared by immunohistochemistry among 15 lymphoepithelial lesions of the salivary gland (8 LAs, 3 lymphoepithelial carcinomas, and 4 lymphoepithelial cysts). Epstein-Barr virus in situ hybridization was also performed.

Results:

IgG-positive and IgG4-positive plasma cells were observed in all cases, but to a remarkable degree (IgG4>100/hpf) in 2 of 8 LAs. The IgG4 plasma cells in LA were distributed in interfollicular areas and in the vicinity of epithelial nests. Among all cases, the mean number of IgG4 plasma cells was not correlated with the presence of germinal centers (12/15) or Epstein-Barr virus positivity (2/15).

Conclusions:

Increased IgG4 plasma cells in LA suggest involvement of an immune reaction in the pathogenesis of LA similar to Warthin’s tumor.
Expression of CAS/CSE1L, the Cellular Apoptosis Susceptibility Protein, Correlates With Neoplastic Progression in Barrett’s Esophagus
Authors: Jiang Kun , Neill Kevin , Cowden Daniel , Klapman Jason , Eschrich Steven , Pimiento José , Malafa Mokenge P. , Coppola Domenico
Published: December 2016

Background:

Identifying the molecular switch responsible for the neoplastic progression of Barrett’s esophagus (BE) and initiation of adenocarcinoma (ADC) is clinically essential and it will have a profound impact on patient diagnosis, prognosis, and treatment. The cellular apoptosis susceptibility gene CAS/CSE1L is overexpressed in various cancers, including a rare report on esophageal ADC; however, its expression in BE neoplasia has not been addressed.

Materials and Methods:

We investigated the expression of the CAS/CSE1L protein immunohistochemically in 56 esophageal resection specimens for ADC arising in BE. For each specimen, a full representative section of the invasive ADC was selected to include, when possible, BE, low-grade dysplasia (LGD) and high-grade dysplasia (HGD). Samples were stained for CAS/CSE1L expression using a rabbit polyclonal antibody recognizing the N-terminus of human CAS/CSE1L. Protein expression levels were measured using the Allred semiquantitative scoring system. The data were evaluated using χ2 statistical analysis. Gene expression Omnibus was queried for CAS/CSE1L and BE neoplasia.

Results:

We found minimal to absent CAS/CSE1L in all BE tissue samples; however, CAS/CSE1L was upregulated in 60% of LGD and overexpressed in HGD and ADC. The results were statistically significant (P<0.05). The localization of CAS/CSE1L protein was nuclear in BE; it became nuclear and cytoplasmic in LGD and HGD, and predominantly cytoplasmic in ADC. A similar progressive increase was observed for CAS/CSE1L gene expression.

Conclusion:

These findings show changes in CAS/CSE1L during BE progression. CAS/CSE1L may represent a potential marker for dysplasia/carcinoma.
A Serous Peritoneal Cancer Revealing Itself With Double Breast Cancer Metastases in 2 Different Periods
Authors: Beksac Kemal , Irkkan Cigdem , Argun Guldeniz , Cetin Bahadir
Published: December 2016

A 72-year-old woman presented with a mass on the right axilla. This was thought to be an occult breast cancer case, and the patient was treated with modified radical mastectomy, followed by hormonotherapy. Two years later she presented with incarcerated umbilical hernia. Pathology revealed Sister Mary Joseph’s nodule inside the hernia sac. Further evaluation revealed that the primary tumor was papillary serous carcinoma of the peritoneal surface. The patient received adjuvant chemotherapy. Two years later the metastatic tumor was located on the other breast. The disease progressed gradually, and the patient eventually died from disseminated disease. This case is extraordinary in that it first presented with axillary metastasis without abdominal involvement and then later metastasized to the other breast after a long disease-free period.
In-Flight Injuries Involving Children on Commercial Airline Flights
Authors: Alves Paulo M. , Nerwich Neil , Rotta Alexandre T.
Published: December 2016

Background

More than 3 billion passengers are transported every year on commercial airline flights worldwide, many of whom are children. The incidence of in-flight medical events (IFMEs) affecting children is largely unknown. This study seeks to characterize pediatric IFMEs, with particular focus on in-flight injuries (IFIs).

Methods

We reviewed the records of all IFMEs from January 2009 to January 2014 involving children treated in consultation with a ground-based medical support center providing medical support to commercial airlines.

Results

Among 114 222 IFMEs, we identified 12 226 (10.7%) cases involving children. In-flight medical events commonly involved gastrointestinal (35.4%), infectious (20.3%), neurological (12.2%), allergic (8.6%), and respiratory (6.3%) conditions. In addition, 400 cases (3.3%) of IFMEs involved IFIs. Subjects who sustained IFIs were younger than those involved in other medical events (3 [1–8] vs 7 [3–14] y, respectively), and lap infants were overrepresented (35.8% of IFIs vs 15.9% of other medical events). Examples of IFIs included burns, contusions, and lacerations from falls in unrestrained lap infants; fallen objects from the overhead bin; and trauma to extremities by the service cart or aisle traffic.

Conclusions

Pediatric IFIs are relatively infrequent given the total passenger traffic but are not negligible. Unrestrained lap children are prone to IFIs, particularly during meal service or turbulence, but not only then. Children occupying aisle seats are vulnerable to injury from fallen objects, aisle traffic, and burns from mishandled hot items. The possible protection from using in-flight child restraints might extend beyond takeoff and landing operations or during turbulence.
Leisure Participation Patterns of Children With Movement Impairments in New Zealand
Authors: Kanagasabai Parimala S. , Mulligan Hilda , Mirfin-Veitch Brigit , Hale Leigh A.
Published: December 2016

Purpose:

To investigate the leisure participation patterns of children with movement impairments in New Zealand.

Methods:

A cross-sectional survey was conducted with children with movement impairments aged 6 to 12 years using the Children's Assessment of Participation and Enjoyment questionnaire. Descriptive statistics were used to analyze the data.

Results:

Children participated in an average of 57.3% of activities, with a greater number and frequency of recreational, social, and self-improvement activities as compared with skill-based and physical activities. Children performed nearly 50% of activities with family and 13% of activities with friends. Approximately 50% of activities were performed at home and 50% of activities were performed outside the home.

Conclusions:

Children with movement impairments participated in diverse leisure activities. However, reduced involvement in physical activities needs further investigation to identify the actual level of physical exertion, barriers faced, and how increased opportunities for regular physical activity could be instigated.
Power-Up: Exploration and Play in a Novel Modified Ride-On Car for Standing
Authors: Logan Samuel W. , Lobo Michele A. , Feldner Heather A. , Schreiber Melynda , MacDonald Megan , Winden Haylee N. , Stoner Tracy , Galloway James Cole
Published: December 2016

Purpose:

The purpose of this study was to compare the physical activity and play behaviors of preschoolers without disabilities and 1 preschooler with physical disability.

Methods:

Participants were 42 preschoolers without disabilities and 1 preschooler with physical disability (Child A). Child A used either crutches or a modified ride-on car while in the gymnasium and playground.

Results:

In the gymnasium, Child A engaged in less solitary play and more parallel play while using the modified ride-on car compared with crutches. On the playground, Child A engaged in more sitting and less running while using crutches compared with preschoolers without disabilities. On the playground, Child A engaged in more peer interaction and less teacher interaction when using the modified ride-on car compared with crutches.

Conclusions:

For children with disabilities who may use assistive devices, clinicians, families, and teachers are encouraged to embrace a “right device, right time, right place” approach.
A Child With a Burn-Related Foot and Ankle Contracture Treated With Multiple Modalities
Authors: Yelvington Miranda , Scoggins Michelle , White Leslie
Published: December 2016

Purpose:

The presence of hypertrophic scars, which cross lower extremity joints, can often result in decreased range of motion, limitations in functional mobility, and gait deviations. This article reviews a case and describes a multimodal treatment approach.

Summary of Key Points:

A 6-year-old girl developed aggressive hypertrophic scars following a burn injury. A multimodal treatment approach, including splinting, elastomers, and physical therapy, was developed.

Conclusions:

Rapid improvements were demonstrated in measured objective outcomes.

Recommendations for Clinical Practice:

Early multimodal intervention, in addition to range of motion, stretching, massage, and compression garments, is recommended when treating hypertrophic scars. This case suggests that further study into a multimodal treatment approach may be beneficial to develop a standardized protocol for more efficient scar management.
Implementation of Antiretroviral Therapy for Life in Pregnant/Breastfeeding HIV+ Women (Option B+) Alongside Rollout and Changing Guidelines for ART Initiation in Rural Zimbabwe: The Lablite Project Experience
Authors: Ford Deborah , Muzambi Margaret , Nkhata Misheck J. , Abongomera George , Joseph Sarah , Ndlovu Makosonke , Mabugu Travor , Grundy Caroline , Chan Adrienne K. , Cataldo Fabian , Kityo Cissy , Seeley Janet , Katabira Elly , Gilks Charles F. , Reid Andrew , Hakim James , Gibb Diana M. ,   the Lablite Team
Published: December 2016

Background:

Lifelong antiretroviral therapy (ART) for pregnant and breastfeeding women (Option B+) was rolled out in Zimbabwe from 2014, with simultaneous raising of the CD4 treatment threshold to 500 cells per cubic millimeter in nonpregnant/breastfeeding adults and children 5 years and over.

Methods:

Lablite is an implementation project in Zimbabwe, Malawi, and Uganda evaluating ART rollout. Routine patient-level data were collected for 6 months before and 12 months after Option B+ rollout at a district hospital and 3 primary care facilities in Zimbabwe (2 with outreach ART and 1 with no ART provision before Option B+).

Results:

Between September 2013 and February 2015, there were 1686 ART initiations in the 4 facilities: 91% adults and 9% children younger than 15 years. In the 3 facilities with established ART, initiations rose from 300 during 6 months before Option B+ to 869 (2.9-fold) and 463 (1.5-fold), respectively, 0–6 months and 6–12 months after Option B+. Post-Option B+, an estimated 43% of pregnant/breastfeeding women needed ART for their own health, based on World Health Organization stage 3/4 or CD4 ≤350 per cubic millimeter (64% for CD4 ≤500). Seventy-four men (22%) and 123 nonpregnant/breastfeeding women (34%) initiated ART with CD4 >350 after the CD4 threshold increase. Estimated 12-month retention on ART was 79% (69%–87%) in Option B+ women (significantly lower in younger women, P = 0.01) versus 93% (91%–95%) in other adults (difference P < 0.001).

Conclusions:

There were increased ART initiations in all patient groups after implementation of World Health Organization 2013 guidelines. Retention of Option B+ women was poorer than retention of other adults; younger women require attention because they are more likely to disengage from care.
Managing nonalcoholic fatty liver disease in patients living with HIV
Authors: Tafesh Zaid H. , Verna Elizabeth C.
Published: December 2016

Purpose of review

Nonalcoholic fatty liver disease (NAFLD) is common among patients living with HIV and may lead to liver-related morbidity and mortality.

Recent findings

The prevalence of NAFLD among patients with HIV is increasingly well described due to new noninvasive techniques to quantify hepatic steatosis and fibrosis. Patients with HIV may be at increased risk of disease progression, though high-quality natural history studies are not available. The high rates of metabolic syndrome, dyslipidemia and insulin resistance may partially account for this excess risk, though the impact of HIV itself, antiretroviral medications and dysregulation of the gut–liver axis likely play important roles. Treatment of NAFLD in patients with HIV is poorly studied. Current recommendations include diet and lifestyle modifications, HIV viral suppression and limitation of hepatotoxic medications as possible. In addition, there are a large number of novel medications now in clinical trials designed to target the accumulation of hepatic fat, oxidative stress, inflammation and/or fibrosis, which will revolutionize this field.

Although additional work is needed to understand the natural history of NAFLD in patients with HIV and identify those at highest risk, novel treatment approaches are now being tested in this population. We may soon have effective treatments to combat this epidemic.
Hepatic Kaposi Sarcoma Revisited
Authors: Chen Frank , Gulati Mittul , Tchelepi Hisham
Published: December 2016

Hepatic Kaposi sarcoma (KS) is the most commonly seen hepatic neoplasm in patients with acquired immunodeficiency syndrome (AIDS), found in 34% of patients in an autopsy series. However, the incidence of hepatic KS has significantly declined since the advent of highly active antiretroviral therapy and is not as commonly seen on imaging. We present a case of hepatic KS in a patient with AIDS, which was initially mistaken for hepatic abscesses on computed tomography. We discuss the computed tomography, grayscale ultrasound, and contrast-enhanced ultrasound appearance of hepatic KS and how to distinguish this hepatic neoplasm from other common hepatic lesions seen in patients with AIDS.
Striatal Dopamine Transporter Modulation After Rotigotine: Results From a Pilot Single-Photon Emission Computed Tomography Study in a Group of Early Stage Parkinson Disease Patients
Authors: Rossi Carlo , Genovesi Dario , Marzullo Paolo , Giorgetti Assuero , Filidei Elena , Corsini Giovanni Umberto , Bonuccelli Ubaldo , Ceravolo Roberto
Published: December 2016

Introduction

Several in vitro data have reported negative interference by dopamine-agonists on the expression of dopamine transporter (DAT), whereas the majority of imaging studies have shown that neither L-dopa nor dopamine-agonists interfere with DAT availability. As yet, there are no in vivo studies on DAT expression after treatment with rotigotine.

Methods

We evaluated presynaptic nigrostriatal function in 8 patients with de novo Parkinson disease (age, 59 ± 6.2 years; male/female sex, 5/3) using 123-I- N-ω-fluoropropyl-2-β-carbomethoxy-3-β-(4-iodophenyl)nortropane (FP-CIT) single-photon emission computed tomography before and after 3 months of treatment with rotigotine (mean dose, 7.75 ± 1.98 mg). For data analysis, specific (left and right caudate, left and right putamen) to nonspecific (occipital cortex) binding ratios, putamen-to-caudate ratios, and asymmetry indices were calculated.

Results

After rotigotine, motor symptoms improved in all patients (Unified Parkinson Disease Rating Scale III mean score, 11.88 ± 2.59 vs 7.63 ± 1.92 on therapy; P = 0.0022). Striatal FP-CIT levels showed a significant improvement in every patient at the follow-up scan. Comparisons between before and after treatment in the whole group revealed a significant improvement in FP-CIT uptake in both caudate and putamen (P < 0.001 in each nucleus). Putamen-to-caudate ratio and asymmetry indices did not show any significant difference before and after treatment.

Discussion

Although the study population was small, we found DAT overexpression after chronic treatment with rotigotine, presumably related to its pharmacological profile. The DAT upregulation by rotigotine in an opposite direction with respect to early Parkinson disease compensatory mechanisms might reduce the risk of dyskinesia, but it could imply less motor benefit because of less stimulation by the dopamine itself on dopaminergic receptors.
Efficacy of the Treatments Used in Multiple Sclerosis: From Meta-analysis to Number Needed to Treat
Authors: García-Ruiz Antonio J. , Izquierdo-Ayuso Guillermo , Navarro-Mascarell Guillermo , Montesinos-Gálvez Ana C. , Martos-Crespo Francisco , Jódar-Sánchez Francisco , Correa Manuel , García-Agua Soler Nuria
Published: December 2016

Objectives

The aim of this study was to analyze the efficacy of drugs used in relapsing-remitting multiple sclerosis, first- and second-line drugs, using the number needed to treat (NNT) as a measure of efficacy.

Methods

Data from randomized clinical trials were analyzed for 3 categories of clinical efficacy outcomes: relapse, change in Expanded Disability Status Scale, and number of new lesions in magnetic resonance imaging. Meta-analysis results are expressed as odds ratios.

Results

The global odds ratio was 0.41 (95% confidence interval [CI], 0.34–0.49). For analyzed clinical outcomes, the odds ratio was less for second-line drugs (odds ratio, 2.0). For all studied clinical conditions, in the control group, 47 of 100 patients do not get benefits, compared with 25 (95% CI, 18–32 patients) of 100 for the active treatment group. The NNT was 5 patients (95% CI, 4–7 patients). For the proportion of patients free of relapses, in the control group, 56 of 100 patients had a relapse at 2 years, compared with 37 of 100 patients in the treatment group, with an NNT of 6 patients (95% CI, 5–8 patients).

Conclusions

Active treatments produced statistically significant improvements compared with placebo.
Incidental Learning: A Brief, Valid Measure of Memory Based on the WAIS–IV Vocabulary and Similarities Subtests
Authors: Spencer Robert J. , Reckow Jaclyn , Drag Lauren L. , Bieliauskas Linas A.
Published: December 2016

Objective:

We assessed the validity of a brief incidental learning measure based on the Similarities and Vocabulary subtests of the Wechsler Adult Intelligence Scale–Fourth Edition (WAIS–IV).

Background:

Most neuropsychological assessments for memory require intentional learning, but incidental learning occurs without explicit instruction. Incidental memory tests such as the WAIS–III Symbol Digit Coding subtest have existed for many years, but few memory studies have used a semantically processed incidental learning model.

Methods:

We conducted a retrospective analysis of 37 veterans with traumatic brain injury, referred for outpatient neuropsychological testing at a Veterans Affairs hospital. As part of their evaluation, the participants completed the incidental learning tasks. We compared their incidental learning performance to their performance on traditional memory measures.

Results:

Incidental learning scores correlated strongly with scores on the California Verbal Learning Test–Second Edition (CVLT–II) and Brief Visuospatial Memory Test–Revised (BVMT–R). After we conducted a partial correlation that controlled for the effects of age, incidental learning correlated significantly with the CVLT–II Immediate Free Recall, CVLT–II Short-Delay Recall, CVLT–II Long-Delay Recall, and CVLT–II Yes/No Recognition Hits, and with the BVMT–R Delayed Recall and BVMT–R Recognition Discrimination Index.

Conclusions:

Our incidental learning procedures derived from subtests of the WAIS–IV Edition are an efficient and valid way of measuring memory. These tasks add minimally to testing time and capitalize on the semantic encoding that is inherent in completing the Similarities and Vocabulary subtests.
On expert curation and sustainability: UniProtKB/Swiss-Prot as a case study
Authors: Poux Sylvain , Arighi Cecilia N. , Magrane Michele , Bateman Alex , Wei Chih-Hsuan , Lu Zhiyong , Boutet Emmanuel , Bye-A-Jee Hema , Famiglietti Maria Livia , Roechert Bernd ,   The UniProt Consortium
Published: December 2016

MOTIVATION

Biological knowledgebases, such as UniProtKB/Swiss-Prot, constitute an essential component of daily scientific research by offering distilled, summarized, and computable knowledge extracted from the literature by expert curators. While knowledgebases play an increasingly important role in the scientific community, the question of their sustainability is raised due to the growth of biomedical literature.

RESULTS

By using UniProtKB/Swiss-Prot as a case study, we address this question by using different literature triage approaches. With the assistance of the PubTator text-mining tool, we tagged more than 10,000 articles to assess the ratio of papers relevant for curation. We first show that curators read and evaluate many more papers than they curate, and that measuring the number of curated publications is insufficient to provide a complete picture. We show that a large fraction of published papers found in PubMed is not relevant for curation in UniProtKB/Swiss-Prot and demonstrate that, despite appearances, expert curation is sustainable.

AVAILABILITY

UniProt is freely available athttp://www.uniprot.org/.

CONTACT

sylvain.poux@sib.swiss
Miniature diamond anvils for X-ray Raman scattering spectroscopy experiments at high pressure
Authors: Petitgirard Sylvain , Spiekermann Georg , Weis Christopher , Sahle Christoph , Sternemann Christian , Wilke Max
Published: December 2016

X-ray Raman scattering (XRS) spectroscopy is an inelastic scattering method that uses hard X-rays of the order of 10 keV to measure energy-loss spectra at absorption edges of light elements (Si, Mg, Oetc.), with an energy resolution below 1 eV. The high-energy X-rays employed with this technique can penetrate thick or dense sample containers such as the diamond anvils employed in high-pressure cells. Here, we describe the use of custom-made conical miniature diamond anvils of less than 500 µm thickness which allow pressure generation of up to 70 GPa. This set-up overcomes the limitations of the XRS technique in very high-pressure measurements (>10 GPa) by drastically improving the signal-to-noise ratio. The conical shape of the base of the diamonds gives a 70° opening angle, enabling measurements in both low- and high-angle scattering geometry. This reduction of the diamond thickness to one-third of the classical diamond anvils considerably lowers the attenuation of the incoming and the scattered beams and thus enhances the signal-to-noise ratio significantly. A further improvement of the signal-to-background ratio is obtained by a recess of ∼20 µm that is milled in the culet of the miniature anvils. This recess increases the sample scattering volume by a factor of three at a pressure of 60 GPa. Examples of X-ray Raman spectra collected at the OK-edge and SiL-edge in SiO2glass at high pressures up to 47 GPa demonstrate the significant improvement and potential for spectroscopic studies of low-Zelements at high pressure.
Crystal structure of truncated human coatomer protein complex subunit ζ1 (Copζ1)
Authors: Lunev Sergey , Semmelink Marije F. W. , Xian Jia Ling , Ma Kai Yu , Leenders Anna J. A. , Dömling Alexander S. S. , Shtutman Michael , Groves Matthew R.
Published: December 2016

The majority of modern anticancer approaches target DNA/protein targets involved in tumour-cell proliferation. Such approaches have a major drawback, as nonproliferating cancer cells remain unaffected and may cause relapse or remission. Human coatomer protein complex I (COPI) subunit ζ (Copζ), a component of the coat protein involved in cell apoptosis and intracellular trafficking, has recently been proposed as a potential anticancer drug target. Previous studies have shown that two different isoforms of the Copζ subunit exist in mammalian cells. While normal cells express both Copζ1 and Copζ2 isoforms, various types of tumour cells display a loss of Copζ2 expression and rely solely on Copζ1 for growth and survival. Subsequent knockdown of Copζ1 results in specific inhibition of both proliferating and dormant tumour-cell populations, with no adverse growth effects on normal cells. Therefore, a Copζ1-targeting therapy was proposed to bypass the problem of dormant cancer cells that are resistant to conventional antiproliferative drugs, which is the major cause of tumour relapse. In order to aid in structure-based inhibitor design, a crystal structure is required. In this article, the recombinant expression, purification, crystallization and crystal structure of Copζ1, as well as the expression and purification of Copζ2, are reported.
Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core
Authors: Montemayor Eric J. , Didychuk Allison L. , Liao Honghong , Hu Panzhou , Brow David A. , Butcher Samuel E.
Published: December 2016

U6 small nuclear RNA (snRNA) is a key component of the active site of the spliceosome, a large ribonucleoprotein complex that catalyzes the splicing of precursor messenger RNA. Prior to its incorporation into the spliceosome, U6 is bound by the protein Prp24, which facilitates unwinding of the U6 internal stem-loop (ISL) so that it can pair with U4 snRNA. A previously reported crystal structure of the `core' of the U6 small nuclear ribonucleoprotein (snRNP) contained an ISL-stabilized A62G mutant of U6 bound to all four RNA-recognition motif (RRM) domains of Prp24 [Montemayoret al.(2014),Nature Struct. Mol. Biol.21, 544–551]. The structure revealed a novel topology containing interlocked rings of protein and RNA that was not predicted by prior biochemical and genetic data. Here, the crystal structure of the U6 snRNP core with a wild-type ISL is reported. This complex crystallized in a new space group, apparently owing in part to the presence of an intramolecular cross-link in RRM1 that was not observed in the previously reported U6-A62G structure. The structure exhibits the same protein–RNA interface and maintains the unique interlocked topology. However, the orientation of the wild-type ISL is altered relative to the A62G mutant structure, suggesting inherent structural dynamics that may facilitate its pairing with U4. Consistent with their similar architectures in the crystalline state, the wild-type and A62G variants of U6 exhibit similar Prp24-binding affinities and electrophoretic mobilities when analyzed by gel-shift assay.
Structural studies of substrate and product complexes of 5-aminolaevulinic acid dehydratase from humans,Escherichia coliand the hyperthermophilePyrobaculum calidifontis
Authors: Mills-Davies N. , Butler D. , Norton E. , Thompson D. , Sarwar M. , Guo J. , Gill R. , Azim N. , Coker A. , Wood S. P. , Erskine P. T. , Coates L. , Cooper J. B. , Rashid N. , Akhtar M. , Shoolingin-Jordan P. M.
Published: December 2016

A number of X-ray analyses of an enzyme involved in a key early stage of tetrapyrrole biosynthesis are reported. Two structures of human 5-aminolaevulinate dehydratase (ALAD), native and recombinant, have been determined at 2.8 Å resolution, showing that the enzyme adopts an octameric quaternary structure in accord with previously published analyses of the enzyme from a range of other species. However, this is in contrast to the finding that a disease-related F12L mutant of the human enzyme uniquely forms hexamers [Breiniget al.(2003),Nature Struct. Biol.10, 757–763]. Monomers of all ALADs adopt the TIM-barrel fold; the subunit conformation that assembles into the octamer includes the N-terminal tail of one monomer curled around the (α/β)8barrel of a neighbouring monomer. Both crystal forms of the human enzyme possess two monomers per asymmetric unit, termedAandB. In the native enzyme there are a number of distinct structural differences between theAandBmonomers, with the latter exhibiting greater disorder in a number of loop regions and in the active site. In contrast, the second monomer of the recombinant enzyme appears to be better defined and the active site of both monomers clearly possesses a zinc ion which is bound by three conserved cysteine residues. In native human ALAD, theAmonomer also has a ligand resembling the substrate ALA which is covalently bound by a Schiff base to one of the active-site lysines (Lys252) and is held in place by an ordered active-site loop. In contrast, these features of the active-site structure are disordered or absent in theBsubunit of the native human enzyme. The octameric structure of the zinc-dependent ALAD from the hyperthermophilePyrobaculum calidifontisis also reported at a somewhat lower resolution of 3.5 Å. Finally, the details are presented of a high-resolution structure of theEscherichia coliALAD enzyme co-crystallized with a noncovalently bound moiety of the product, porphobilinogen (PBG). This structure reveals that the pyrrole side-chain amino group is datively bound to the active-site zinc ion and that the PBG carboxylates interact with the enzymeviahydrogen bonds and salt bridges with invariant residues. A number of hydrogen-bond interactions that were previously observed in the structure of yeast ALAD with a cyclic intermediate resembling the product PBG appear to be weaker in the new structure, suggesting that these interactions are only optimal in the transition state.
The employability skills of business graduates in Syria
Authors: Ayoubi Rami M. , Alzarif Kahla , Khalifa Bayan
Published: December 2016

Purpose

The purpose of this paper is to compare the desired employability skills of business graduates in Syria from the perspective of both higher education policymakers and employers in the private sector.

Design/methodology/approach

Interviews were conducted with 12 higher education policymakers and managers from the business sector. Content analysis was utilized to analyse the content of the interviews and the strategic priorities of the higher education sector in Syria.

Findings

Results revealed that although higher education policymakers focus more on societal, public and thinking skills for business graduates, the business sector focusses more on individual, private and practical skills. Accordingly, a comparative tool that aligns the two perspectives was developed in the study. The tool, based on the contradicting employability skills, identified four types of business graduates: leader, collective, technical and trainee.

Research limitations/implications

The study is limited by data collected before the current political instability in Syria in 2012. The data were collected only from official documents and interviews with policymakers and employers. Students were not part of the study.

Practical implications

The managerial tool developed at the end of the study will help both policymakers and the private sector to statistically allocate business graduates for better planning. The study provides recommendations to the different stakeholders in the higher education sector in Syria.

Originality/value

Although the majority of the previous literature raises the voices of the business sector, this study is one of the first studies that aligns the discrepant perspectives of the higher education and business sectors. The managerial tool developed in the study is original and usable by policymakers and the business sector, and it is subject to further development.
Building a better workforce
Authors: Douglas-Lenders Rachel Claire , Holland Peter Jeffrey , Allen Belinda
Published: December 2016

Purpose

The purpose of this paper is to examine the impact of experiential simulation-based learning of employee self-efficacy.

Design/methodology/approach

The research approach is an exploratory case study of a group of trainees from the same organisation. Using a quasi-experiment, one group, pre-test-post-test design (Tharenou et al., 2007), a questionnaire with validated scales at Time 1 (T1) prior to training and Time (T2) three months after training were used. All scales had been validated by the researchers and had acceptable levels of reliability. In addition interviews are undertaken with the participants immediately at the end of the programme.

Findings

The research found strong evidence of the positive impact of the training on skills transfer to the workplace with support from supervisors as key criteria.

Research limitations/implications

There remains a need for additional studies with larger and more diverse samples and studies which incorporate control groups into their design.

Practical implications

This study provided support for the transfer of knowledge using simulation-based training and advances our limited knowledge and understanding of simulation-based training as a form of experiential (management) learning and development.

Originality/value

This is the first study to undertake a longitudinal analysis of the impact on self-efficacy in the workplace and as such adds to the research in this field.
Identifying crucial sustainability assessment criteria for container seaports
Authors: Lu Chin-Shan , Shang Kuo-Chung , Lin Chi-Chang
Published: December 2016

Purpose

The purpose of this study is to identify crucial sustainability assessment criteria in the context of international port sector.

Design/methodology/approach

Data collection was based on a questionnaire survey from 135 managers and supervisors at major international ports in Taiwan, including Keelung, Taichung and Kaohsiung. A confirmatory factor analysis was conducted to identify crucial sustainability assessment criteria at ports.

Findings

A total of 31 important sustainable assessment criteria were adapted from previous studies in terms of environmental, economic and social issues. Results revealed that social issues with respect to staff job security and safety were ranked as the most important sustainability assessment criteria, followed by environmental protection when handling cargo, facilitation of economic activities, port traffic accidents prevention and cargo handled safely and effectively. In contrary, respondents revealed their less importance in the criteria, namely, mitigating light influence on neighboring residents, considering the arrangement of vehicles when constructing port transportation system, avoiding using unpolluted land in port area and hiring minority groups and consulting interests groups when making port projects. Four sustainability assessment dimensions were identified, namely, environmental material, economic issue, environmental practices and social concerns.

Research limitations/implications

The research findings indicated that economic issue was deemed as the most important dimension of sustainability assessment criteria from a port operator’s perspective, followed by environmental practices, social concerns and environmental material. Practical implications for port sustainability assessment were discussed in this research.

Originality/value

Although a majority of previous studies on sustainability assessment have been discussed, there is still a lack of investigation of sustainability assessment in the context of port sector. This study not only develops sustainability assessment attributes but also highlights the important criteria of sustainability assessment. Further, this study identified four crucial sustainability assessment factors, which provide helpful information for port corporations to identify important criteria and policy of sustainability assessment.
Risks in emerging markets: logistics services in the Mediterranean region
Authors: Moslemi Amir , Hilmola Olli-Pekka , Vilko Jyri
Published: December 2016

Purpose

This study aims to explore and analyzes the risk factors in container shipping and logistics services using a dual perspective. The authors gather data not only from logistics service companies but also from their most important customers.

Design/methodology/approach

In this research, the authors used case study methodology (interviews and surveys) to examine risk factors that are related to one another within the interaction between logistics service companies and their customers in the emerging markets of the Mediterranean region (Turkey, Algeria, Tunisia and Libya).

Findings

The findings show the most important risk factors and compare them using a dual perspective. Customers identify additional risks and estimate their consequences as wider. Interestingly, oil price change plays a dual role because a price increase could be beneficial to the region; at the same time, however, the competitiveness of shipping would decrease. In both response groups, risk likelihood and risk consequence have a positive and statistically significant correlation.

Research limitations/implications

The findings of the study are limited to one shipping/logistics service company. On a global scale, the company is medium-sized; however, in terms of Northern Europe, it is an important player. Extending its service portfolio to the Mediterranean region is an important step.

Practical implications

In emerging markets, risks go hand in hand with profitability, and companies need to apply extensive risk analysis and mitigation strategies to survive.

Social implications

The southern Mediterranean region is showing some signs of economy recovery. Efficient, robust supply chains are in demand to support sustainable growth.

Originality/value

Using a case study approach in supply chain risk management in shipping is rather rare; this work is ground-breaking in that it uses dual perspective in the analysis.
Performing the EU referendum: A view from afar
Authors: Moeran Brian
Published: December 2016

This editorial makes use of the EU Referendum to discuss the presence of magic in contemporary societies. It analysis magic in terms of magicians, magical representations, and magical rites – as originally expounded by Malinowski and Mauss – and argues that magic is to be found not only in political activities, but also in the worlds of finance, medicine, law, media, and various forms of cultural production.
Magical formulae for market futures: Tales from the World Economic Forum meeting in Davos
Authors: Garsten Christina , Sörbom Adrienne
Published: December 2016

Markets are often portrayed as being organized by way of rationalized knowledge, objective reasoning, and the fluctuations of demand and supply. In parallel, and often mixed with this modality of knowledge, magical beliefs and practices are prevalent. Business leaders, management consultants, and financial advisors are often savvy in the art of creatively blending the ‘objective facts’ of markets with magical formulae, rites, and imaginaries of the future. This article looks at the World Economic Forum's yearly Davos meeting as a large‐scale ritual that engages senior executives of global corporations, top‐level politicians, and civil society leaders to contribute to the overall aim of ‘improving the world’. The Davos gathering has become a vital part of the business calendar, just as much for the intensity of its networking as for the declarations of action from the speakers’ podiums. The presentations and performances in Davos work as ‘technologies of enchantment’ in Gell's (1992) sense, instilling a sense of agency onto participants. The ritual also contributes towards securing the acquiescence of individuals and organizations in a transnational network of politico‐economic intentionalities. By invoking global and regional challenges and risks, discussing possible scenarios and solutions, presenters invoke a sense of urgency and contribute to the articulation of global ‘problems’ and ‘solutions’. It is proposed that the magic of Davos resides to a large extent in the ritualized form of interaction and the technologies of enchantment through which it is set up.
Exploring Evergreening: Insights from Two Medicines
Authors: Moir Hazel V. J.
Published: December 2016

Litigated pharmaceutical patents are a valuable source of data on how much inventiveness is required for a patent grant and what are the costs of patents. Although innovation is central to economic growth and the competitiveness of firms, there are few data about either the cost of granted patents or the quantum of inventiveness required for a patent. Two cases of litigated pharmaceutical patents allow investigation of two types of secondary ‘evergreening’ patents—new formulations and closely related chemical variants. Both lead to higher Pharmaceutical Benefits Scheme outlays, and in some cases, these can be substantial. There are clear policy implications.
Markets, Monopolies and Moguls: The Relationship between Inequality and Competition
Authors: Leigh Andrew , Triggs Adam
Published: December 2016

Analysing private market research data, we estimate the degree of market concentration across 481 industries in the Australian economy. On average, the largest four firms control 36 per cent of the market. Some industries are considerably more concentrated. In department stores, newspapers, banking, health insurance, supermarkets, domestic airlines, Internet service providers, baby food and beer, the biggest four firms control more than 80 per cent of the market. We suggest ways in which high market concentration may increase inequality and discuss some policy ideas to address the problem.