bluuebunny/crossref_metadata_2025 huggingface dataset:
PriLive: privacy-preserving real-time filtering for next-generation sequencing
Authors: Loka Tobias P , Tausch Simon H , Dabrowski Piotr W , Radonić Aleksandar , Nitsche Andreas , Renard Bernhard Y
Published: March 2018

Motivation

In next-generation sequencing, re-identification of individuals and other privacy-breaching strategies can be applied even for anonymized data. This also holds true for applications in which human DNA is acquired as a by-product, e.g. for viral or metagenomic samples from a human host. Conventional data protection strategies including cryptography and post-hoc filtering are only appropriate for the final and processed sequencing data. This can result in an insufficient level of data protection and a considerable time delay in the further analysis workflow.

Results

We present PriLive, a novel tool for the automated removal of sensitive data while the sequencing machine is running. Thereby, human sequence information can be detected and removed before being completely produced. This facilitates the compliance with strict data protection regulations. The unique characteristic to cause almost no time delay for further analyses is also a clear benefit for applications other than data protection. Especially if the sequencing data are dominated by known background signals, PriLive considerably accelerates consequent analyses by having only fractions of input data. Besides these conceptual advantages, PriLive achieves filtering results at least as accurate as conventional post-hoc filtering tools.

Availability and implementation

PriLive is open-source software available at https://gitlab.com/rki_bioinformatics/PriLive.

Supplementary information

Supplementary data are available at Bioinformatics online.
Stakeholders’ conflicts and corporate assets: an institutional meta-complementarities approach
Authors: Landini Fabio , Pagano Ugo
Published: March 2018

In this paper, we argue that the relationship between shareholder conflicts and corporate assets can generate multiple equilibrium configurations that can be helpful to understand how corporate governance systems may change under different historical models of capitalism. These relationships can be modeled as ‘meta-complementarities’ existing among two different sets of institutional complementarity. The first institutional complementarity arises in realm of the conflicts among different stakeholders and generates multiple equilibria that define different systems of rights on corporate assets. The second institutional complementarity arises between corporate rights and assets. Dispersed shareholders and non-unionized workers are complementary organizational forms and generate a form of corporate governance interacting with complementary corporate assets. A similar set of institutional meta-complementarities characterizes the relation between concentrated ownership, unionized workers and corporate assets.
Transferring Patients From Methadone to Buprenorphine: The Feasibility and Evaluation of Practice Guidelines
Authors: Lintzeris Nicholas , Monds Lauren A. , Rivas Consuelo , Leung Stefanie , Dunlop Adrian , Newcombe David , Walters Carina , Galea Susanna , White Nancy , Montebello Mark , Demirkol Apo , Swanson Nicola , Ali Robert
Published: March 2018

Introduction and Aims:

Transfer from methadone to buprenorphine is problematic for many opioid-dependent patients, with limited documented evidence or practical clinical guidance, particularly for the range of methadone doses routinely prescribed for most patients (>50 mg). This study aimed to implement and evaluate recent national Australian guidelines for transferring patients from methadone to buprenorphine.

Design and Methods:

A multisite prospective cohort study. Participants were patients who transferred from methadone to buprenorphine-naloxone at 1 of 4 specialist addiction centers in Australia and New Zealand. Clinicians were trained in the guidelines, and medical records were reviewed to examine process (eg, transfer setting, doses, and guideline adherence) and safety (precipitated withdrawal) measures. Participants completed research interviews before and after transfer—assessing changes in substance use, health outcomes, and side effects.

Results:

In all, 33 participants underwent transfer, 9 from low methadone doses (<30 mg), 9 from medium doses (30–50 mg), and 15 from high doses (>50 mg). The majority of high-dose transfers occurred in inpatient settings. There was reasonable guideline adherence, and no complications identified in the low and medium-dose transfers. Three high-dose transfers (20%) experienced precipitated withdrawal, and 7/33 participants (21%) returned to methadone within 1 week of attempted transfer.

Discussions and Conclusions:

Transfer is feasible in outpatient settings for those transferring from methadone doses below 50 mg; however, inpatient settings and specialist supervision is recommended for higher-dose transfers. The Australian clinical guidelines appear safe and feasible, although further research is required to optimize high-dose transfer procedures.
Sex Specific Sacroiliac Joint Biomechanics During Standing Upright
Authors: Joukar Amin , Shah Anoli , Kiapour Ali , Vosoughi Ardalan Seyed , Duhon Bradley , Agarwal Anand K. , Elgafy Hossein , Ebraheim Nabil , Goel Vijay K.
Published: March 2018

Study Design.

The comparison of sacroiliac joint (SIJ) angular motions, pelvis ligaments strain, load sharing, and stress distribution across the joint for male and female spine-pelvis-femur models using finite element analysis.

Objective.

To quantify biomechanical parameters at SIJ for all motions for both male and female models.

Summary of Background Data.

SIJ has been recognized as a main source of pain in 13% to 30% of patients with low back pain. It is shown that the SIJ rotation and translation in different planes are not exceeding 2° to 3° and 2 mm, respectively. Due to limitation of in vivo and in vitro studies, it is difficult to quantify certain biomechanical parameters such as load-sharing and stress distribution across the joint. Finite element analysis is a useful tool which can be utilized to understand the biomechanics of the SIJ.

Methods.

The validated finite element models of a male and a female lumbar spine-pelvis-femur were developed from computer tomography (CT) scans. The models were used to simulate spine physiological motions. The range of motion, ligament strains, load sharing, and stress distribution across the left and right SIJs were compared between male and female models.

Results.

Motions data at SIJs demonstrated that female model experienced 86% higher mobility in flexion, 264% in extension, 143% in left bending, and 228% in right bending compared with the male model. The stresses and loads on SIJs were higher on the female model compared with the male model. Female model ligaments underwent larger strains compared with the male model ligaments.

Conclusion.

Female SIJ had higher mobility, stresses, loads, and pelvis ligament strains compared with the male SIJ which led to higher stress across the joint, especially on the sacrum under identical loading conditions. This could be a possible reason for higher incidence of SIJ pain and pelvic stress fracture in females.

Level of Evidence: N/A.
Association of Early Myocardial Workload and Mortality Following Severe Traumatic Brain Injury*
Authors: Krishnamoorthy Vijay , Vavilala Monica S. , Chaikittisilpa Nophanan , Rivara Frederick P. , Temkin Nancy R. , Lele Abhijit V. , Gibbons Edward F. , Rowhani-Rahbar Ali
Published: March 2018

Objectives:

To examine the impact of early myocardial workload on in-hospital mortality following isolated severe traumatic brain injury.

Design:

Retrospective cohort study.

Setting:

Data from the National Trauma Databank, a multicenter trauma registry operated by the American College of Surgeons, from 2007 to 2014.

Patients:

Adult patients with isolated severe traumatic brain injury (defined as admission Glasgow Coma Scale < 8 and head Abbreviated Injury Score ≥ 4).

Interventions:

Admission rate-pressure product, categorized into five levels based on published low, normal, and submaximal human thresholds: less than 5,000; 5,000–9,999; 10,000–14,999; 15,000–19,999; and greater than 20,000.

Measurements and Main Results:

Data from 26,412 patients were analyzed. Most patients had a normal rate-pressure product (43%), 35% had elevated rate-pressure product, and 22% had depressed rate-pressure product at hospital admission. Compared with the normal rate-pressure product group, in-hospital mortality was 22 percentage points higher in the lowest rate-pressure product group (cumulative mortality, 50.2%; 95% CI, 43.6–56.9%) and 11 percentage points higher in the highest rate-pressure product group (cumulative mortality, 39.2%; 95% CI, 37.4–40.9%). The lowest rate-pressure product group was associated with a 50% increased risk of mortality, compared with the normal rate-pressure product group (adjusted relative risk, 1.50; 95% CI, 1.31–1.76%; p < 0.0001), and the highest rate-pressure product group was associated with a 25% increased risk of mortality, compared with the normal rate-pressure product group (adjusted relative risk, 1.25; 95% CI, 1.18–1.92%; p < 0.0001). This relationship was blunted with increasing age. Among patients with normotension, those with depressed and elevated rate-pressure products experienced increased mortality.

Conclusions:

Adults with severe traumatic brain injury experience heterogeneous myocardial workload profiles that have a “U-shaped” relationship with mortality, even in the presence of a normal blood pressure. Our findings are novel and suggest that cardiac performance is important following severe traumatic brain injury.
RBC Transfusion Practice in Pediatric Extracorporeal Membrane Oxygenation Support
Authors: Muszynski Jennifer A. , Reeder Ron W. , Hall Mark W. , Berg Robert A. , Shanley Thomas P. , Newth Christopher J. L. , Pollack Murray M. , Wessel David , Carcillo Joseph , Harrison Rick , Meert Kathleen L. , Dean J. Michael , Jenkins Tammara , Tamburro Robert F. , Dalton Heidi J.
Published: March 2018

Objectives:

To determine RBC transfusion practice and relationships between RBC transfusion volume and mortality in infants and children treated with extracorporeal membrane oxygenation.

Design:

Secondary analysis of a multicenter prospective observational study.

Setting:

Eight pediatric institutions within the Eunice Kennedy Shriver National Institute of Child Health and Human Development’s Collaborative Pediatric Critical Care Research Network.

Patients:

Patients age less than 19 years old treated with extracorporeal membrane oxygenation at a participating center.

Interventions:

None.

Measurements and Main Results:

Clinical data and target hemoglobin or hematocrit values (if set) were recorded daily by trained bedside extracorporeal membrane oxygenation specialists and research coordinators. Laboratory values, including hemoglobin and hematocrit, were recorded daily using the value obtained closest to 8:00 am. RBC transfusion was recorded as total daily volume in mL/kg. Multivariable logistic regression was used to determine the relationship between RBC transfusion volume and hospital mortality, accounting for potential confounders. Average goal hematocrits varied across the cohort with a range of 27.5–41.3%. Overall, actual average daily hematocrit was 36.8%, and average RBC transfusion volume was 29.4 mL/kg/d (17.4–49.7 mL/kg/d) on extracorporeal membrane oxygenation. On multivariable analysis, each additional 10 mL/kg/d of RBC transfusion volume was independently associated with a 9% increase in odds of hospital mortality (adjusted odds ratio, 1.09 [1.02–1.16]; p = 0.009).

Conclusions:

In this multicenter cohort of pediatric extracorporeal membrane oxygenation patients, daily hematocrit levels were maintained at normal or near-normal values and RBC transfusion burden was high. RBC transfusion volume was independently associated with odds of mortality. Future clinical studies to identify optimum RBC transfusion thresholds for pediatric extracorporeal membrane oxygenation are urgently needed.
Targeting Tumor Metabolism With Statins During Treatment for Advanced-stage Pancreatic Cancer
Authors: Iarrobino Nick A. , Gill Beant , Bernard Mark E. , Mishra Mark V. , Champ Colin E.
Published: March 2018

Introduction:

A growing body of preclinical data suggests that statins may exert potent antitumor effects, yet the interactions of these medications with standard therapies and clinical outcomes in this population is less clear. We assessed the impact of statin use on outcomes in patients with advanced-stage pancreatic adenocarcinoma undergoing various treatments.

Materials and Methods:

After institutional review board approval, we conducted a retrospective-cohort study consisting of 303 newly diagnosed advanced-stage pancreatic adenocarcinoma patients to determine the impact of statin use on outcomes. Univariate and multivariable Cox proportional hazard regression models were utilized to estimate hazard ratios (HRs). Time-to-event was estimated using Kaplan-Meier survival analysis for overall survival, distant metastasis, and locoregional failure. Baseline and active statin usage were assessed and to mitigate risk of immortal time bias, subanalysis excluding patients with under 6 months of follow-up was conducted.

Results:

Both prior (P=0.021) and active (P=0.030) statin usage correlated with improved survival in this cohort. Surgery, chemoradiation, and statin use improved 2-year survival rates (84.1% vs. 55.0%; P<0.001). On multivariable analysis, statin exposure was associated with overall survival (HR, 0.662; P=0.027) and trended to significance for freedom from distant metastasis (HR, 0.577; P=0.060). Comorbid conditions were not significantly associated with outcomes.

Conclusions:

Statin use was associated with improved overall survival in advanced-stage pancreatic adenocarcinoma patients. This data supports previous findings in early-stage pancreatic adenocarcinoma and other cancer sites. To our knowledge this is the first report to examine the efficacy of statin use as a supplementary treatment option in advanced-stage pancreatic adenocarcinoma patients.
25-Hydroxyvitamin D (25(OH)D) and biomarkers of ovarian reserve
Authors: Jukic Anne Marie Z. , Baird Donna D. , Wilcox Allen J. , Weinberg Clarice R. , Steiner Anne Z.
Published: March 2018

Objective:

The aim of the study was to examine the associations between 25-hydroxyvitamin D (25(OH)D) and biomarkers of ovarian reserve in a large community-based sample of women.

Methods:

In 2010 to 2016, women aged 30 to 44 years without any known fertility problems were recruited from the Chapel Hill, NC area for a prospective time-to-pregnancy cohort study. At enrollment 561 women provided a blood sample that was used to measure 25(OH)D, anti-Müllerian hormone (AMH), follicle-stimulating hormone, and inhibin-B. Unadjusted associations were estimated with Spearman correlation coefficients. Multivariable linear regression was used to estimate associations of 25(OH)D with ovarian reserve biomarkers, after adjusting for age, race, body mass index, smoking history, and recent use of hormonal birth control.

Results:

The mean 25(OH)D was 36 ng/mL (SD = 11 ng/mL). 25(OH)D was not correlated with AMH, follicle-stimulating hormone, or inhibin-B (all r < 0.03). Multivariable results with continuous hormonal outcomes were also null. For dichotomous outcomes, there was a tendency for insufficient 25(OH)D (<30 ng/mL) to be associated with low AMH (<0.7 ng/mL) (odds ratio [95% CI]: 1.8 [0.9-4]).

Conclusions:

For the most part, 25(OH)D was not associated with ovarian reserve biomarkers in a group of women trying to become pregnant. We found some evidence that low 25(OH)D (<30 ng/mL) was associated with low AMH, but this should be confirmed in studies with a higher prevalence of low 25(OH)D.
Eliminating Preoperative Lymphoscintigraphy in Extremity Melanomas
Authors: McGregor Andrew , Pavri Sabrina N. , Kim Samuel , Xu Xiaolu , Narayan Deepak
Published: March 2018

Background:

Preoperative lymphoscintigraphy (LSG) is an imaging procedure routinely used to identify the draining nodal basin in melanomas. At our institute, we have traditionally performed preoperative LSG followed by intraoperative LSG for logistical and evaluative reasons. We sought to determine if preoperative LSG could be safely eliminated in the treatment of extremity melanomas, which exhibit consistent and predictable lymphatic drainage patterns.

Methods:

We reviewed the Yale Melanoma Registry 1308012545 for cutaneous extremity melanomas treated at our institution. From this registry, we calculated the incidence of atypical lymph node drainage patterns outside the axillary and inguinal regions. Based on these data, we eliminated preoperative LSG in 21 cases (8 upper extremities and 13 lower extremities). Additionally, we calculated the potential hospital charge reduction of forgoing preoperative LSG.

Results:

Upper and lower extremity melanomas treated at our institution exhibited atypical lymph node drainage at a rate of 3.4% and 2.0%, respectively. The sites of atypical drainage were to the epitrochlear and popliteal regions. In all 21 cases where preoperative LSG was eliminated, we were able to correctly identify the sentinel lymph node. The potential hospital charge reduction of forgoing preoperative LSG totaled $2,393.

Conclusions:

Preoperative LSG can be safely eliminated in the management of upper and lower extremity melanomas. Exceptions may be considered for primary lesions of the posterior calf, ankle, and heel as well as for patients with history of prior surgery or radiation. Forgoing preoperative LSG results in a hospital charge reduction of $2,393 and provides additional benefits to the patient. Ultimately, there is potential for significant charge reduction if applied across health care systems.
PRESERVATION OF THE FOVEAL FLAP IN MACULAR HOLE SURGERY
Authors: Lee Suhwan , Kim June-Gone
Published: March 2018

Purpose:

To investigate the impact of preserving the foveal flap on surgical outcomes of full-thickness macular hole (MH) with foveal flaps.

Methods:

We retrospectively reviewed patients with Stages 2 and 3 idiopathic MH, who underwent pars plana vitrectomy by a single surgeon at Asan Medical Center from November 2011 to November 2016. In the study group, we included eyes with MH and a foveal flap on preoperative spectral domain optical coherence tomography and successfully preserved the flap during surgery. The control group included eyes with MH and an operculum in the posterior vitreous plane on preoperative optical coherence tomography. We compared the anatomical and functional surgical outcomes between these groups.

Results:

Postoperative mean best-corrected visual acuity at the last visit was 20/25 and 20/33 in the study (9 eyes) and control (23 eyes) groups, respectively. The study group showed a significantly better postoperative best-corrected visual acuity (P < 0.05). Restoration of both the external limiting membrane and ellipsoid zone, as assessed by spectral domain optical coherence tomography, was achieved in 9 (100%) and 15 (65.2%) eyes of the study and control groups, respectively.

Conclusion:

Preserving the foveal flap might improve both functional and anatomical outcomes of vitrectomy for MHs with a foveal flap.
SIGNIFICANCE OF PREOPERATIVE EXTERNAL LIMITING MEMBRANE HEIGHT ON VISUAL PROGNOSIS IN PATIENTS UNDERGOING MACULAR HOLE SURGERY
Authors: Geenen Caspar , Murphy Declan C. , Sandinha Maria T. , Rees Jon , Steel David H. W.
Published: March 2018

Purpose:

To investigate the association between the vertical elevation of the external limiting membrane (ELM) and visual outcome in patients undergoing surgery for idiopathic full-thickness macular hole.

Methods:

Retrospective observational study of a consecutive cohort of patients undergoing vitrectomy to treat macular hole. The greatest vertical height of the central ELM above the retinal pigment epithelium (ELM height) was measured on spectral domain optical coherence tomography preoperatively. The relationship of ELM height to other preoperative and postoperative variables, including macular hole width and height, and visual acuity was analyzed.

Results:

Data from 91 eyes of 91 patients who had undergone successful hole closure were included. The mean ELM height was 220 μm (range 100–394). There were significant correlations between the ELM height and the diameter of the hole, hole height, and worsening preoperative visual acuity. For holes less than 400 μm in width, better postoperative visual acuity was significantly predicted by a lower ELM height.

Conclusion:

The ELM height varies widely in idiopathic macular hole. It is higher in eyes where the hole is wider and also when the hole itself is higher. For holes of less than 400 μm in width, a lower ELM height is a strong independent predictor of a good postoperative outcome.
Relative Rise of Serum IgG4 Levels After Steroid Therapy for Autoimmune Pancreatitis Predicts the Likelihood of Relapse
Authors: Suzuki Daisuke , Shimizu Kyoko , Tokushige Katsutoshi
Published: March 2018

Objectives

Serum IgG4 level is a useful diagnostic marker of autoimmune pancreatitis (AIP); however, it is difficult to predict relapse. We investigated whether a change in serum IgG4 is predictive of AIP relapse during maintenance therapy.

Methods

Seventy-three patients with AIP treated with steroids were divided into 3 groups according to their initial serum IgG4 levels: level 1 group (>2-fold upper limit), level 2 group (1- to 2-fold upper limit), and a normal group. The relapse rate and the prevalence of extrapancreatic lesions were compared between the 3 groups. The correlation between the relative rise of serum IgG4 levels and relapse during maintenance therapy was analyzed.

Results

There were no differences in serum IgG4 levels in the presence or absence of relapse. The average number of extrapancreatic lesions was 1.02, 0.47, and 0.27 in level 1, level 2, and the normal group, respectively. The relative rise of serum IgG4 levels after steroid therapy was significantly higher in relapse than in nonrelapse cases. The area under the receiver operating characteristic curve of the relative rise of IgG4 levels for discriminating between the relapse and the nonrelapse cases was 0.85.

Conclusions

The relative rise of serum IgG4 levels after steroid therapy may provide an indication of relapse.
Impact of Antibiotic-Resistant Bacterial and Fungal Infections in Outcome of Acute Pancreatitis
Authors: Moka Praneeth , Goswami Pooja , Kapil Arti , Xess Immaculata , Sreenivas Vishnubhatla , Saraya Anoop
Published: March 2018

Objectives

The knowledge about pathogens and their antibiotic susceptibility patterns is essential to select an appropriate antibiotic.

Methods

We investigated the microbiological profile in pancreatic and extrapancreatic infections, and antibiotic sensitivity pattern in patients with acute pancreatitis.

Results

Of 556 patients with acute pancreatitis, only 189 developed bacterial infection; however, bacteremia was present in 42 patients (7.6%). Culture-proven infected pancreatic necrotic collection was present in 161 patients (29%). Escherichia coli and Klebsiella pneumoniae were the most common organisms. Among the bacterial infection cohort, 164 patients developed multidrug-resistant bacterial infection. Infection with multidrug-resistant bacteria, especially at multiple sites, increased mortality. Nearly 50% of patients (n = 94) acquired extremely drug-resistant bacterial infection at some time and emerged as key reason for prolonged hospital and intensive care unit stay. Colistin resistance and tigecycline resistance were documented in 2.1% and 17.2% of the specimens at admission and in 4.6% and 21% of specimens during the hospital stay. Of 556 patients, 102 patients developed fungal infection and 28 patients had only fungal infection without bacterial infection.

Conclusions

Colistin and tigecycline are best reserved as last-resort antibiotics. Fungal infection was found to be associated with increased mortality, median hospital stay, and intensive care unit stay.
Early Endoscopic Retrograde Cholangiopancreatography Versus Conservative Treatment in Patients With Acute Biliary Pancreatitis
Authors: Coutinho Lara M. de A. , Bernardo Wanderley M. , Rocha Rodrigo S. , Marinho Fabio R. , Delgado Aureo , Moura Eduardo T.H. , Matuguma Sergio E. , Chaves Dalton , Franzini Tomazo A.P. , Sakai Paulo , de Moura Eduardo G.H.
Published: March 2018

Objectives

The aim of the study was to evaluate the role of early endoscopic retrograde cholangiopancreatography (ERCP) in the treatment of acute biliary pancreatitis, in comparison with conservative treatment.

Methods

Systematic review via databases (MEDLINE [PubMed], Latin-American and Caribbean Health Sciences Literature database, Embase, Cochrane Central, and the [Brazilian] Regional Library of Medicine) is conducted. We analyzed 10 randomized controlled trials (1091 patients). Outcomes were the following: local and systemic adverse events; acute cholangitis; death; length of hospital stay; cost; abdominal pain; and time to a reduction in body temperature. For the meta-analysis, we used risk difference (RD) and mean with standard deviation as measures of variability.

Results

There was a statistically significant difference between the patients submitted to ERCP in terms of the following: local adverse events (RD, 0.74; 95% confidence interval [CI], 0.55–0.99), time to pain relief and time to a reduction in axillary temperature (RD, −5.01; 95% CI, −6.98 to −3.04, and RD, −1.70; 95 CI%, −2.33 to −1.08, respectively). Patients undergoing ERCP spent less time in hospital (RD, −11.04; 95% CI, −15.15 to −6.93). Cost was lower in the group treated with ERCP.

Conclusions

Early ERCP decreases local adverse events, shortening the time to pain relief, to a reduction in axillary temperature, hospital stays, and cost in patients with acute biliary pancreatitis.
Endoscopic Retrograde Cholangiopancreatography Decreases All-Cause and Pancreatitis Readmissions in Patients With Acute Gallstone Pancreatitis Who Do Not Undergo Cholecystectomy
Authors: Qayed Emad , Shah Rushikesh , Haddad Yara K.
Published: March 2018

Objectives

Cholecystectomy is the definitive management of gallstone pancreatitis (GSP). The benefit of endoscopic retrograde cholangiopancreatography (ERCP) in patients who do not undergo cholecystectomy remains unclear. This study aims to evaluate the effect of ERCP on all-cause and pancreatitis readmissions in GSP.

Methods

Adult hospitalizations for GSP in the 2010–2014 National Readmissions Database were divided into the following 3 groups: (1) no cholecystectomy nor ERCP, (2) no cholecystectomy with ERCP, and (3) cholecystectomy group. A multivariable Cox model was used to compare the 60-day readmission rates controlling for significant confounders.

Results

There were 153,480 GSP admissions, 29.2% did not undergo cholecystectomy or ERCP, 12.0 % underwent ERCP only, and 58.8% had cholecystectomy. In the no cholecystectomy group, ERCP was associated with lower all-cause readmissions (adjusted hazard ratio, 0.80; 95% confidence interval, 0.76–0.83; P < 0.0001) and pancreatitis readmissions rate (adjusted hazard ratio, 0.51; 95% confidence interval, 0.47–0.55; P < 0.0001) compared with no ERCP. The protective effect of ERCP remained significant in severe pancreatitis. Cholecystectomy had the strongest protective effect against readmissions.

Conclusions

In this large, nationally representative sample, ERCP was associated with reduced readmissions in patients with GSP who did not undergo cholecystectomy. Although cholecystectomy remains the most important intervention to prevent readmissions, these results support performing ERCP in patients unfit for surgery.
A Prospective Evaluation of a Multisite Cryptococcal Screening and Treatment Program in HIV Clinics in Uganda
Authors: Nalintya Elizabeth , Meya David B. , Lofgren Sarah , Huppler Hullsiek Kathy , Boulware David R. , Rajasingham Radha
Published: March 2018

Background:

Cryptococcus is a leading cause of AIDS-related mortality. Cryptococcal antigen (CrAg) is detectable in blood before meningitis onset and predicts death. CrAg screening among those with advanced HIV, and treatment of those CrAg+ with fluconazole, has demonstrated survival benefit. However, implementation and widespread uptake have been slow outside clinical trials.

Methods:

We designed a CrAg screening program for routine care that incorporated intensive education and training of clinic staff. We evaluated programmatic implementation, including time to initiation of fluconazole, time to initiation of antiretroviral therapy, and 6-month clinical outcomes.

Results:

Between December 2015 and January 2017, 1440 persons were screened at 11 HIV clinics in Kampala, and CRAG+ prevalence was 6.5% (n = 94/1440) among adults with a CD4 <100 cells/µL. Of those CrAg+, 7 of 94 persons (7%) died or were lost before further clinic evaluation. Fifty-three persons (56%) were asymptomatic and had 6-month survival of 87% (46/53). Of CrAg+ persons, 28% (26/94) were symptomatic at the time of clinic return. Most had confirmed cryptococcal meningitis, and 54% (14/26) of the symptomatic CrAg+ persons were dead or lost at 6 months. Of the 7 symptomatic persons who declined lumbar puncture for further evaluation, all were dead or lost by 6 months.

Conclusion:

All asymptomatic CrAg+ persons identified by our screening program who returned to clinic, initated fluconazole and antiretroviral therapy in a timely manner. Despite this, 27% of CrAg+ (asymptomatic and symptomatic) identified on routine screening were dead or lost to follow-up at 6 months, even with preemptive therapy for those asymptomatic, and standard amphotericin-based treatment for meningitis.
Relationship Between Health-Related Quality of Life and Patient Acceptable Symptom State With Disease Activity and Functional Status in Patients With Ankylosing Spondylitis in Thailand
Authors: Chiowchanwisawakit Praveena , Thaweeratthakul Phakhamon , Wattanamongkolsil Luksame , Srinonprasert Varalak , Koolvisoot Ajchara , Muangchan Chayawee , Nilganuwong Surasak , Arromdee Emvalee , Katchamart Wanruchada
Published: March 2018

Objective

This study aimed to identify factors associated with EuroQoL–5 Dimensions, 5 Levels and Patient Acceptable Symptom State (PASS) and health utility (HU) in Thai patients with ankylosing spondylitis (AS).

Methods

This was a cross-sectional study of consecutive AS patients visiting Siriraj Hospital between May 31, 2012, and March 31, 2016. Demographic data and outcomes related to HU (Thai version of EuroQoL–5 Dimensions, 5 Levels), disease activity (Bath Ankylosing Spondylitis Disease Activity Index, Ankylosing Spondylitis Disease Activity Score–erythrocyte sedimentation rate or Ankylosing Spondylitis Disease Activity Score–C-reactive protein, number of tender and swollen joints, and enthesitis), and functional status (Bath Ankylosing Spondylitis Functional Index and Health Assessment Questionnaire) were collected. Regression analysis was used to explore factors associated with each EuroQOL–5 Dimensions (EQ-5D) domain, HU, and PASS.

Results

Among 119 AS patients, the mean age was 40.4 years; 61.3% were male. The mean EQ-5D was 0.75. In univariate analysis, lower disease activity and less impaired function were significantly associated with higher HU and not to mild problems in each EQ-5D domain. In multivariate regression analysis, Bath Ankylosing Spondylitis Disease Activity Index, C-reactive protein, and Health Assessment Questionnaire adjusting for age explained 77.4% of the HU variance. Patients answering yes to PASS were significantly older, had higher HU, and lower disease activity compared with those answering no to PASS. Usual activity and pain problems were importantly related to PASS after adjusting for other domains and age.

Conclusions

Disease activity and functional status in AS patients were significant factors related to HU and PASS. To improve quality of life, treatment goals should be achieving remission, improving function, and controlling pain.
LAP-VEGaS Practice Guidelines for Reporting of Educational Videos in Laparoscopic Surgery
Authors: Celentano Valerio , Smart Neil , McGrath John , Cahill Ronan A. , Spinelli Antonino , Obermair Andreas , Hasegawa Hirotoshi , Lal Pawanindra , Almoudaris Alex M. , Hitchins Charlotte R. , Pellino Gianluca , Browning Matthew G. , Ishida Takashi , Luvisetto Federico , Cingiloglu Pinar , Gash Katherine , Harries Rhiannon , Harji Deena , Di Candido Francesca , Cassinotti Elisa , McDermott Frank D. , Berry James E. A. , Battersby Nick J. , Platt Esther , Campain Nicholas J. , Keeler Barrie D. , Boni Luigi , Gupta Sharmila , Griffith John P. , Acheson Austin G. , Cecil Tom D. , Coleman Mark G.
Published: March 2018

Objective:

Consensus statement by an international multispecialty trainers and trainees expert committee on guidelines for reporting of educational videos in laparoscopic surgery.

Summary of Background Data:

Instructive laparoscopy videos with appropriate exposition could be ideal for initial training in laparoscopic surgery, but there are no guidelines for video annotation or procedural educational and safety evaluation.

Methods:

Delphi questionnaire of 45 statements prepared by a steering group and voted on over 2 rounds by committee members using an electronic survey tool. Committee selection design included representative surgical training experts worldwide across different laparoscopic specialties, including general surgery, lower and upper gastrointestinal surgery, gynecology and urology, and a proportion of aligned surgical trainees.

Results:

All 33 committee members completed both the first and the second round of the Delphi questionnaire related to 7 major domains: Video Introduction/Authors’ information; Patient Details; Procedure Description; Procedure Outcome; Associated Educational Content; Peer Review; and Use in Educational Curriculae. The 17 statements that did not reach at least 80% agreement after the first round were revised and returned into the second round. The committee consensus approved 37 statements to at least an 82% agreement.

Conclusion:

Consensus guidelines on how to report laparoscopic surgery videos for educational purposes have been developed. We anticipate that following our guidelines could help to improve video quality.

These reporting guidelines may be useful as a standard for reviewing videos submitted for publication or conference presentation.
A Telephone Call to Decrease Patient Anxiety Before Urodynamic Testing: A Randomized Controlled Trial
Authors: Warda Hussein , Hacker Michele R. , Haviland Miriam J. , Hota Lekha S.
Published: March 2018

Objective

The aim of this study was to determine if a telephone call before undergoing urodynamic study (UDS) would decrease test-related anxiety compared with standard care.

Methods

We performed a randomized controlled trial at a single practice from April 2016 to June 2017. Patients at least 18 years old with lower urinary tract dysfunction and undergoing UDS for the first time were eligible. All participants received standard counseling; participants randomized to the intervention group also received a telephone call before their UDS appointment to answer any questions regarding their upcoming test. All participants completed surveys before and after testing to assess anxiety, preparedness, and satisfaction. The primary outcome was anxiety level immediately before UDS. Secondary outcomes included self-reported patient preparedness, pain, and satisfaction with counseling. Data were compared using χ2, Fisher exact, and Wilcoxon rank sum tests.

Results

One hundred two participants were included in this as-treated analysis: 52 in the intervention group and 50 in the standard care group. The 2 groups were similar in age, ethnicity, and the proportion seeking additional information before testing. There were no statistically significant differences between groups with respect to overall anxiety, anxiety regarding specific elements of the test, or anticipated pain (all P ≥ 0.19). Participant satisfaction with pre-UDS counseling was significantly higher in the intervention group (80.8%) compared with the standard care group (54.0%; P = 0.002).

Conclusions

Our study showed that a telephone call before undergoing UDS did not decrease anxiety compared with standard care; however, the telephone call was associated with higher satisfaction with pre-UDS counseling.
A Scoping Study of Psychosocial Factors in Women Diagnosed With and/or Treated for Pelvic Organ Prolapse
Authors: Touza Kaitlin K. , Rand Kevin L. , Carpenter Janet S. , Chen Chen X. , Heit Michael H.
Published: March 2018

Objective

Pelvic organ prolapse (POP) is prevalent and can impact women's physical and psychosocial health. To develop interventions that support this population, an understanding of the state of research on psychosocial factors related to POP is essential. We conducted a scoping study focused on the psychosocial experience of women with POP. The purpose of this review was to (1) inventory and describe the current state of knowledge of the psychosocial experience of women with POP, (2) identify gaps in knowledge, and (3) identify targets for future research.

Method

Electronic databases PsycINFO, PubMed, EMBASE, and CINAHL were searched through November 1, 2017.

Results

Of 524 titles reviewed, 103 articles met all inclusion criteria. Articles were grouped by the disease period (ie, prediagnosis, diagnosis/preintervention, intervention, follow-up, and mixed) and psychosocial factors. Most articles (n = 73) focused on women undergoing intervention. Articles focusing on the preintervention period was the next largest category (n = 14). Follow-up after intervention (n = 8) and samples of mixed disease periods (n = 7) were less common. One article focused on women before diagnosis. Articles focused on quality of life (QOL; n = 79), sexual function (n = 51), satisfaction (n = 16), body image (n = 13), psychological distress (n = 4), and knowledge (n = 3).

Conclusions

Research on the psychosocial experience of POP has largely focused on changes in QOL and sexual function. Future research should target emotional experience of women with POP; relationships among QOL, psychological distress, body image, and sexual function; and psychosocial factors related to treatment outcomes.
Stability of nonlinear waves and patterns and related topics
Authors: Ghazaryan Anna , Lafortune Stephane , Manukian Vahagn
Published: March 2018

Periodic and localized travelling waves such as wave trains, pulses, fronts and patterns of more complex structure often occur in natural and experimentally built systems. In mathematics, these objects are realized as solutions of nonlinear partial differential equations. The existence, dynamic properties and bifurcations of those solutions are of interest. In particular, their stability is important for applications, as the waves that are observable are usually stable. When the waves are unstable, further investigation is warranted of the way the instability is exhibited, i.e. the nature of the instability, and also coherent structures that appear as a result of an instability of travelling waves. A variety of analytical, numerical and hybrid techniques are used to study travelling waves and their properties.

This article is part of the theme issue ‘Stability of nonlinear waves and patterns and related topics’.
A novel prophage identified in strains from Salmonella enterica serovar Enteritidis is a phylogenetic signature of the lineage ST-1974
Authors: D'Alessandro Bruno , Pérez Escanda Victoria , Balestrazzi Lucía , Iriarte Andrés , Pickard Derek , Yim Lucía , Chabalgoity José Alejandro , Betancor Laura
Published: March 2018

Salmonella enterica serovar Enteritidis is a major agent of foodborne diseases worldwide. In Uruguay, this serovar was almost negligible until the mid 1990s but since then it has become the most prevalent. Previously, we characterized a collection of strains isolated from 1988 to 2005 and found that the two oldest strains were the most genetically divergent. In order to further characterize these strains, we sequenced and annotated eight genomes including those of the two oldest isolates. We report on the identification and characterization of a novel 44 kbp Salmonella prophage found exclusively in these two genomes. Sequence analysis reveals that the prophage is a mosaic, with homologous regions in different Salmonella prophages. It contains 60 coding sequences, including two genes, gogB and sseK3, involved in virulence and modulation of host immune response. Analysis of serovar Enteritidis genomes available in public databases confirmed that this prophage is absent in most of them, with the exception of a group of 154 genomes. All 154 strains carrying this prophage belong to the same sequence type (ST-1974), suggesting that its acquisition occurred in a common ancestor. We tested this by phylogenetic analysis of 203 genomes representative of the intraserovar diversity. The ST-1974 forms a distinctive monophyletic lineage, and the newly described prophage is a phylogenetic signature of this lineage that could be used as a molecular marker. The phylogenetic analysis also shows that the major ST (ST-11) is polyphyletic and might have given rise to almost all other STs, including ST-1974.
The UBR-1 Ubiquitin Ligase Regulates Glutamate Metabolism to Generate Coordinated Motor Pattern inC. elegans
Authors: Chitturi Jyothsna , Hung Wesley , Abdel Rahman Anas M. , Wu Min , Lim Maria A. , Calarco John , Baran Renee , Huang Xun , Dennis James W. , Zhen Mei
Published: March 2018

UBR1 is an E3 ubiquitin ligase best known for its ability to target protein degradation by the N-end rule. The physiological functions of UBR family proteins, however, remain not fully understood. We found that the functional loss ofC. elegansUBR-1 leads to a specific motor deficit: when adult animals generate reversal movements, A-class motor neurons exhibit synchronized activation, preventing body bending. This motor deficit is rescued by removing GOT-1, a transaminase that converts aspartate to glutamate. Both UBR-1 and GOT-1 are expressed and critically required in premotor interneurons of the reversal motor circuit to regulate the motor pattern.ubr-1andgot-1mutants exhibit elevated and decreased glutamate level, respectively. These results raise an intriguing possibility that UBR proteins regulate glutamate metabolism, which is critical for neuronal development and signaling.

Author Summary

Ubiquitin-mediated protein degradation is central to diverse biological processes. The selection of substrates for degradation is carried out by the E3 ubiquitin ligases, which target specific groups of proteins for ubiquitination. The human genome encodes hundreds of E3 ligases; many exhibit sequence conservation across animal species, including one such ligase called UBR1. Patients carrying mutations inUBR1exhibit severe systemic defects, but the biology behinds UBR1’s physiological function remains elusive. Here we found that theC. elegansUBR-1 regulates glutamate level. When UBR-1 is defective,C. elegansexhibits increased glutamate; this leads to synchronization of motor neuron activity, hence defective locomotion when animals reach adulthood. UBR1-mediated glutamate metabolism may contribute to the physiological defects ofUBR1mutations.
crsra: A package for Cleaning and Analyzing Coursera Research Export Data
Authors: Hadavand Aboozar , Leek Jeffrey
Published: March 2018

Due to the fundamental differences between traditional education and Massive Open Online Courses (MOOCs) and the ever-increasing popularity of MOOCs more research is needed to under- stand current and future trends in education. Although research in the field has rapidly grown in recent years, one of the main challenges facing researchers remains to be the complexity and messiness of the data. Therefore, it is imperative to provide tools that pave the way for more research on the new subject of MOOCs. This paper introduces a package called crsra based on the statistical software R to help clean and analyze massive loads of data provided by Coursera. The advantages of the package are as follows: a) faster loading and organizing data for analysis, b) an efficient method for combining data from multiple courses and even across institutions, and c) provision of a set of functions for analyzing student behaviors.
The contribution of parent-to-offspring transmission of telomeres to the heritability of telomere length in humans
Authors: Delgado Dayana A. , Zhang Chenan , Demanelis Kathryn , Chen Lin S. , Gao Jianjun , Roy Shantanu , Shinkle Justin , Sabarinathan Mekala , Argos Maria , Tong Lin , Ahmed Alauddin , Islam Tariqul , Rakibuz-Zaman Muhammad , Sarwar Golam , Shahriar Hasan , Rahman Mahfuzar , Yunus Muhammad , Doherty Jennifer A. , Jasmine Farzana , Kibriya Muhammad G. , Ahsan Habibul , Pierce Brandon L.
Published: March 2018

Leukocyte telomere length (LTL) is a heritable trait with two potential sources of heritability (h2): inherited variation in non-telomeric regions (e.g., SNPs that influence telomere maintenance) and variability in the lengths of telomeres in gametes that produce offspring zygotes (i.e., “direct” inheritance). Prior studies of LTL h2have not attempted to disentangle these two sources. Here, we use a novel approach for detecting the direct inheritance of telomeres by studying the association between identity-by-descent (IBD) sharing at chromosome ends and phenotypic similarity in LTL. We measured genome-wide SNPs and LTL for a sample of 5,069 Bangladeshi adults with substantial relatedness. For each of the 7,254 relative pairs identified, we used SNPs near the telomeres to estimate the number of chromosome ends shared IBD, a proxy for the number of telomeres shared IBD (Tshared). We then estimated the association between Tsharedand the squared pairwise difference in LTL ((ΔLTL)2) within various classes of relatives (siblings, avuncular, cousins, and distant), adjusting for overall genetic relatedness (ϕ). The association between Tsharedand (ΔLTL)2was inverse among all relative pair types. In a meta-analysis including all relative pairs (ϕ >0.05), the association between Tsharedand (ΔLTL)2(P=0.002) was stronger than the association between ϕ and (ΔLTL)2(P=0.45). Our results provide strong evidence that telomere length (TL) in parental germ cells impacts TL in offspring cells and contributes to LTL h2despite telomere “reprogramming” during embryonic development. Applying our method to larger studies will enable robust estimation of LTL h2attributable to direction transmission.
Accelerometry data in health research: challenges and opportunities
Authors: Karas Marta , Bai Jiawei , Strączkiewicz Marcin , Harezlak Jaroslaw , Glynn Nancy W. , Harris Tamara , Zipunnikov Vadim , Crainiceanu Ciprian , Urbanek Jacek K.
Published: March 2018

Wearable accelerometers provide detailed, objective, and continu-ous measurements of physical activity (PA). Recent advances in technology and the decreasing cost of wearable devices led to an explosion in the popula-rity of wearable technology in health research. An ever increasing number of studies collect high-throughput, sub-second level raw acceleration data. In this paper we discuss problems related to the collection and analysis of raw acce-lerometry data and provide insights into potential solutions. In particular, we describe the size and complexity of the data, the within- and between-subject variability and the effects of sensor location on the body. We also provide a short tutorial for dealing with sampling frequency, device calibration, data labeling and multiple PA monitors synchronization. We illustrate these po-ints using the Developmental Epidemiological Cohort Study (DECOS), which collected raw accelerometry data on individuals both in a controlled and the free-living environment.