bluuebunny/crossref_metadata_2025_split huggingface dataset:
A natural upper bound to the accuracy of predicting protein stability changes upon mutations
Authors: Montanucci Ludovica , Martelli Pier Luigi , Ben-Tal Nir , Fariselli Piero 
Published: October 2018

Abstract

Motivation
Accurate prediction of protein stability changes upon single-site variations (ΔΔG) is important for protein design, as well as for our understanding of the mechanisms of genetic diseases. The performance of high-throughput computational methods to this end is evaluated mostly based on the Pearson correlation coefficient between predicted and observed data, assuming that the upper bound would be 1 (perfect correlation). However, the performance of these predictors can be limited by the distribution and noise of the experimental data. Here we estimate, for the first time, a theoretical upper-bound to the ΔΔG prediction performances imposed by the intrinsic structure of currently available ΔΔG data.

Results
Given a set of measured ΔΔG protein variations, the theoretically “best predictor” is estimated based on its similarity to another set of experimentally determined ΔΔG values. We investigate the correlation between pairs of measured ΔΔG variations, where one is used as a predictor for the other. We analytically derive an upper bound to the Pearson correlation as a function of the noise and distribution of the ΔΔG data. We also evaluate the available datasets to highlight the effect of the noise in conjunction with ΔΔG distribution. We conclude that the upper bound is a function of both uncertainty and spread of the ΔΔG values, and that with current data the best performance should be between 0.7 and 0.8, depending on the dataset used; higher Pearson correlations might be indicative of overtraining. It also follows that comparisons of predictors using different datasets are inherently misleading.

Supplementary information
Supplementary data are available at Bioinformatics online.
Mental health and parenting stress in mothers of children with diabetes treated in a patient-centred medical home
Authors: Cohen L Adelyn , Limbers Christine A 
Published: October 2018

AbstractBackgroundMothers of children with diabetes are at-risk for experiencing parenting stress and diminished mental/emotional health. To the best of our knowledge, no studies to date have examined whether there are differences in these outcomes between mothers whose diabetic child is managed in a patient-centred medical home or not.ObjectiveThe objective of the present study was to assess whether there were differences in mental health and parenting stress among mothers whose diabetic child was managed in a patient-centred medical home or not.MethodsTwo hundred fifty-three mothers of children with diabetes (mean age = 12.50 years; SD = 3.90) from the 2011–2012 National Survey of Children’s Health were included in this study. Hierarchical multiple regression was conducted to determine the amount of variance that having a patient-centred medical home contributed to maternal emotional/mental health and parenting stress.ResultsAfter controlling for child sex, age, race/ethnicity and family poverty level, patient-centred medical home status was associated with better mental health for mothers and less parenting stress. Effective care coordination was the only subcomponent of the patient-centred medical home that significantly contributed to the variance in mother’s mental/emotional health and parenting stress.ConclusionsReceiving care in a patient-centred medical home, particularly the care coordination component, may mitigate some of the negative maternal effects of managing a child’s diabetes.
Pointwise-in-time error estimates for an optimal control problem with subdiffusion constraint
Authors: Jin Bangti , Li Buyang , Zhou Zhi 
Published: October 2018

Abstract
In this work we present numerical analysis for a distributed optimal control problem, with box constraint on the control, governed by a subdiffusion equation that involves a fractional derivative of order $\alpha \in (0,1)$ in time. The fully discrete scheme is obtained by applying the conforming linear Galerkin finite element method in space, L1 scheme/backward Euler convolution quadrature in time, and the control variable by a variational-type discretization. With a space mesh size $h$ and time stepsize $\tau $ we establish the following order of convergence for the numerical solutions of the optimal control problem: $O(\tau ^{\min ({1}/{2}+\alpha -\epsilon ,1)}+h^2)$ in the discrete $L^2(0,T;L^2(\varOmega ))$ norm and $O(\tau ^{\alpha -\epsilon }+\ell _h^2h^2)$ in the discrete $L^{\infty }(0,T;L^2(\varOmega ))$ norm, with any small $\epsilon&gt;0$ and $\ell _h=\ln (2+1/h)$. The analysis relies essentially on the maximal $L^p$-regularity and its discrete analogue for the subdiffusion problem. Numerical experiments are provided to support the theoretical results.
An observation-based perspective of winter haze days in four major polluted regions of China
Authors: Mao Lu , Liu Run , Liao Wenhui , Wang Xuemei , Shao Min , Liu Shaw Chen , Zhang Yuanhang 
Published: October 2018

Abstract
An observation-based approach is used to examine key characteristics of winter haze days in four major polluted regions in China. Major findings in this study are: first, there was no significant trend in the number of winter haze days in most provinces and districts in eastern China from 1973 to 2012, contrary to the 2.5-fold increase in the emissions of particulate matter and its precursors (PM emissions) in the same period of time. Second, meteorological and climate conditions rather than PM emissions are in control of the interannual variabilities and trends of winter haze days. These interannual variabilities (ranging from 24 to 125%) pose a substantial masking effect that must be overcome by any control of PM emissions before its impact becomes statistically detectable. Finally, we find that global warming may have contributed significantly to the trend of winter haze days in eastern China.
Effectiveness of Village Health Worker–Delivered Smoking Cessation Counseling in Vietnam
Authors: Jiang Nan , Siman Nina , Cleland Charles M , Van Devanter Nancy , Nguyen Trang , Nguyen Nam , Shelley Donna 
Published: October 2018

Abstract

Introduction
Smoking prevalence is high in Vietnam, yet tobacco dependence treatment (TDT) is not widely available.

Methods
We conducted a quasiexperimental study that compared the effectiveness of health care provider advice and assistance (ARM 1) versus ARM 1 plus village health worker (VHW) counseling (ARM 2) on abstinence at 6-month follow-up. This study was embedded in a larger two-arm cluster randomized controlled trial conducted in 26 community health centers (CHCs) in Vietnam. Subjects (N = 1318) were adult patients who visited any participating CHC during the parent randomized controlled trial intervention period and were self-identified as current tobacco users (cigarettes and/or water pipe).

Results
At 6-month follow-up, abstinences rates in ARM 2 were significantly higher than those in ARM 1 (25.7% vs. 10.5%; p &lt; .001). In multivariate analyses, smokers in ARM 2 were almost three times more likely to quit compared with those in ARM 1 (adjusted odds ratio [AOR] = 2.96, 95% confidence interval [CI] = 1.78% to 4.92%). Compared to cigarette-only smokers, water pipe–only smokers (AOR = 0.4, 95% CI = 0.26% to 0.62%) and dual users (AOR = 0.62, 95% CI = 0.45% to 0.86%) were less likely to achieve abstinence; however, the addition of VHW counseling (ARM 2) was associated with higher quit rates compared with ARM 1 alone for all smoker types.

Conclusion
A team approach in TDT programs that offer a referral system for health care providers to refer smokers to VHW-led cessation counseling is a promising and potentially scalable model for increasing access to evidence-based TDT and increasing quit rates in low middle-income countries (LMICs). TDT programs may need to adapt interventions to improve outcomes for water pipe users.

Implications
The study fills literature gaps on effective models for TDT in LMICs. The addition of VHW-led cessation counseling, available through a referral from primary care providers in CHCs in Vietnam, to health care provider’s brief cessation advice, increased 6-month biochemically validated abstinence rates compared to provider advice alone. The study also demonstrated the potential effectiveness of VHW counseling on reducing water pipe use. For LMICs, TDT programs in primary care settings with a referral system to VHW-led cessation counseling might be a promising and potentially scalable model for increasing access to evidence-based treatment.
Sums of Kloosterman sums in the prime geodesic theorem
Authors: Balkanova Olga , Frolenkov Dmitry 
Published: October 2018

Abstract
We develop a new method for studying sums of Kloosterman sums related to the spectral exponential sum. As a corollary, we obtain a new proof of the estimate of Soundararajan and Young for the error term in the prime geodesic theorem.
NICU Discharge Feeding Bundle Improves Accuracy of Postdischarge Feeding Preparation and Potentially Prevents Readmission
Authors: Vollrath Kimberly , Rosenberg Adam , Gabrielski Lisbeth , Deacon Jane , Marshall Susan , Rihn Andrew , Grover Theresa 
Published: October 2018

Background:
Hospitalized infants often need fortified human milk and formulas for growth in the neonatal intensive care unit and postdischarge. Parents must learn how to properly mix infant feedings.
At the initial Children's Hospital Colorado follow-up visit, baseline data revealed a 50% rate of mixing inaccuracy of discharge feeding recipes and identified the readmission of 2 infants with life-threatening hypernatremia. A gap in discharge teaching was identified. A quality improvement project was implemented at 2 affiliated neonatal intensive care units.

Purpose/Aim:
The aim of this study was to improve parental comfort and efficacy in infant feeding preparation during hospitalization, reduce mixing inaccuracy postdischarge, and prevent readmission. The primary aim was to improve the accuracy rate at follow-up to 75% within 12 months and the sustain mixing accuracy rate at follow-up to above 95% for an additional 24 months.

Methods/Interventions:
A literature review was conducted; potential barriers were identified and strategies developed to recognize the relationships between the aim and the changes to be tested. Implementation of standardized teaching focused on the teach-back technique. Education included mixing demonstration and written instructions. Parents were expected to correctly mix the recipe 3 times before discharge.

Results:
Mixing accuracy at the initial clinic follow-up visit improved to 97%. No readmissions were reported from inaccurately prepared feedings.

Implications for Practice:
Collaborative quality improvement project with standardized teaching provided improved feeding safety and parental comfort with accuracy of discharge instructions. Primary care providers need to be aware of the importance of accurate formula or fortified human milk preparation and verify accuracy of the specific discharge recipes at the initial visit.
An Evaluation of the IOLMaster 700
Authors: Bullimore Mark A. , Slade Stephen , Yoo Paul , Otani Todd 
Published: October 2018

Objectives:
To evaluate the repeatability and reproducibility of the Carl Zeiss Meditec IOLMaster 700, which uses swept-source optical coherence tomography technology, along with its agreement with the IOLMaster 500 and Lenstar LS 900.

Methods:
In a clinical practice, complete measurements were taken on one eye of 100 subjects: 51 with cataracts and 49 with clear lenses. Three sets of measurements were taken by 3 operators with three different IOLMaster 700 units, and one operator took 3 measurements with the IOLMaster 500 and the Lenstar. A random-effects model of analysis of variance was used to estimate the repeatability and reproducibility. The 95% limits of agreement (95% LoA) were calculated for all comparisons.

Results:
Comparing the IOLMaster 700 and IOLMaster 500 in cataract patients, 95% LoA were −0.01 to +0.06 mm for axial length, −0.44 to +0.27 D for corneal power, and −0.18 to +0.17 mm for anterior chamber depth. Comparing the IOLMaster 700 and Lenstar for corneal thickness and lens thickness yielded 95% LoA of −4 to +13 μm and −0.26 to +0.41 mm, respectively. The repeatability and reproducibility limits for the IOLMaster 700 were ±0.014 and ±0.023 mm for axial length; ±0.26 and ±0.27 D for corneal power; ±7 and ±11 μm for corneal thickness; ±0.02 and ±0.02 mm for anterior chamber depth; and ±0.02 and ±0.05 mm for lens thickness, respectively.

Conclusions:
There was good agreement between the IOLMaster 700 and comparator instruments and superior or equivalent precision. Some differences were noted, but not considered clinically meaningful.
Stenciling-Based “Prick and Print” Technique for Harvesting Shaped Corneal Grafts for Management of Peripheral Corneal Perforations
Authors: Parmar Gautam Singh , Ghodke Bhushan , Bose Sunandini , Meena Ashok Kumar 
Published: October 2018

Purpose:
To evaluate a new surgical technique (“prick and print”) for harvesting shaped donor corneal grafts in cases with perforated peripheral ulcerative keratitis (PUK).

Methods:
We conducted a retrospective case series at a tertiary center. Medical records of 13 patients with perforated PUK, who underwent tectonic eccentric keratoplasty using the stenciling-based prick and print technique during the past 1 year, were reviewed. All patients (15 eyes of 13 patients) received grafts of varying sizes and shapes (14 crescentic and 1 biconvex). Factors evaluated were tectonic integrity, graft apposition, and complications, if any. Surgical success was defined as maintenance of corneal integrity and healing of PUK.

Results:
Mean age of patients was 40.6 ± 19.4 years. Mean follow-up was 10 months. We achieved surgical success in 80% (12/15 eyes) of cases. Two eyes had graft infection, and regrafting (large circular graft) was performed for both. One eye developed new-site PUK, which was managed medically, and the graft remained viable tectonically. After surgery, 9 eyes achieved a best-corrected visual acuity of logarithm of the minimum angle of resolution +0.3 or better. No cases had graft rejection or peripheral anterior synechiae by final follow-up.

Conclusions:
The stenciling-based prick and print technique for making shaped donor corneal grafts may offer a simple, easy-to-learn surgical technique that can be used to make any shape or pattern of donor corneal grafts without involving the optical center, even in extensive peripheral corneal lesions.
Streptococcal Infections and Exacerbations in PANDAS
Authors: Nielsen Marie Ødum , Köhler-Forsberg Ole , Hjorthøj Carsten , Benros ME , Nordentoft Merete , Orlovska-Waast Sonja 
Published: October 2018

Background:
The pediatric autoimmune neuropsychiatric disorders associated with streptococcal infection (PANDAS) hypothesis suggests an association between group A beta-hemolytic streptococcus (GABHS) infections and subsequent onset or exacerbation of neuropsychiatric symptoms, such as obsessive-compulsive disorder or tic disorders.

Methods:
We performed a systematic review and meta-analysis including longitudinal, prospective studies on exacerbations of neuropsychiatric symptoms associated with GABHS infections in children with PANDAS. We searched PubMed and EMBASE through August 14, 2017. Two independent reviewers extracted data and we used random-effects analysis to calculate rate ratios (RR).

Results:
Three studies were included with a total of 82 PANDAS cases and 127 control children with obsessive-compulsive disorder or chronic tic disorder. PANDAS cases had a nonsignificantly increased RR of 2.33 [95% confidence interval [CI]: 0.63–8.70, P = 0.21, I
2 = 28.3%] for exacerbations of neuropsychiatric symptoms in temporal proximity to a GABHS infection and no increased risk of GABHS infections (RR = 0.99, 95% CI: 0.56–1.73, P = 0.97, I
2 = 45%) compared with the control children. However, PANDAS cases had an increased risk of neuropsychiatric exacerbations in general with a RR of 1.54 (95% CI: 1.12–2.11, P = 0.008, I
2 = 0%) compared with the control children. The studies had methodologic heterogeneity, high risk of selection bias and differed concerning case definition and infection measures.

Conclusions:
Our findings did not show significant evidence concerning higher rates of temporally associated GABHS infections and exacerbations of neuropsychiatric symptoms in children with PANDAS. The included studies were small and limited by low GABHS rates and exacerbations. Future studies with large population sizes and routine evaluations are needed to thoroughly examine the PANDAS hypothesis.
PROspective Evaluation of Chronic Pancreatitis for EpidEmiologic and Translational StuDies
Authors: Yadav Dhiraj , Park Walter G. , Fogel Evan L. , Li Liang , Chari Suresh T. , Feng Ziding , Fisher William E. , Forsmark Christopher E. , Jeon Christie Y. , Habtezion Aida , Hart Phil A. , Hughes Steven J. , Othman Mohamed O. , Rinaudo Jo Ann S. , Pandol Stephen J. , Tirkes Temel , Serrano Jose , Srivastava Sudhir , Van Den Eeden Stephen K. , Whitcomb David C. , Topazian Mark , Conwell Darwin L. 
Published: October 2018

Abstract
Prospective Evaluation of Chronic Pancreatitis for Epidemiologic and Translational Studies (PROCEED) is the first prospective, observational cohort study of chronic pancreatitis (CP) in the United States. The primary goals of PROCEED are to define disease progression, test the predictive capability of candidate biomarkers, and develop a platform to conduct translational and mechanistic studies in CP. Using objective and consensus-driven criteria, PROCEED will enroll adults at different stages of CP—controls, suspected CP, and definite CP. In addition to collecting detailed information using structured case report forms and protocol-mandated evaluations at baseline and during follow-up, PROCEED will establish a linked biorepository of blood, urine, saliva, stool, pancreatic fluid, and pancreatic tissue. Enrollment for PROCEED began in June 2017. As of July 1, 2018, nine clinical centers of the Consortium for the Study of Chronic Pancreatitis, Diabetes, and Pancreatic Cancer are enrolling, and 350 subjects have completed baseline evaluation. In conclusion, PROCEED will provide the most accurate and reliable estimates to date on progression of CP. The established cohort and biorepository will facilitate numerous analyses, leading to new strategies for diagnosis, methods to monitor disease progression, and treatment of CP.
Solid Pseudopapillary Neoplasm of the Pancreas in a Young Pediatric Patient
Authors: Bender Alexandra M. , Thompson Elizabeth D. , Hackam David J. , Cameron John L. , Rhee Daniel S. 
Published: October 2018

Abstract
Solid pseudopapillary neoplasms (SPNs) are the most common pediatric pancreatic tumor; however, most data in children are extrapolated from adults. This study describes a young presentation of SPN in a 5-year-old girl and presents a comprehensive systematic review of the literature regarding SPNs in children. A systematic review was performed using PubMed and Embase for all articles in English using predetermined search terms, including “solid pseudopapillary neoplasm” and “pediatric” and historical terms for SPN. A total of 523 pediatric patients were identified in 135 articles. Eighty-three percent of patients were female, and median age was 13.6 years. Abdominal pain was the most frequent presenting symptom (78%), and median tumor size was 8.2 cm. The pancreatic head was involved in 46% of cases. Computed tomographic scan was the most common imaging modality (87%), and 61% were diagnosed by fine needle aspiration. Surgical resection was reported in 507 patients, with a complication rate of 21.1% reported in 393 patients. Only 3.8% received adjuvant therapy, and 6.7% had recurrent disease. Solid pseudopapillary neoplasms of the pancreas are rare tumors in childhood. Male sex and pancreatic head involvement are seen more often in children than in adults. Surgery remains the mainstay of treatment with excellent results.
Use of Chlorhexidine to Prevent Ventilator-Associated Pneumonia in a Long-term Care Setting
Authors: McCue Margaret K. , Palmer Glen A. 
Published: October 2018

Background:
The purpose of this study was to explore the use of the oral decontamination solution chlorhexidine (CHX) to reduce ventilator-associated pneumonia (VAP) in a long-term ventilator care setting over time. Most of the research in this area has been conducted in acute and intensive care settings.

Methods:
This study was a retrospective medical record review conducted in a long-term care facility with a dedicated ventilator unit. Veterans records (N = 12) were accessed for this study. The study covered 50 months, with a 43-month time period during which CHX was administered.

Results:
While the sample size was small, many of the veterans on ventilators used CHX for years without an incident of VAP.

Conclusions:
These findings support using CHX to significantly reduce the number of days of intravenous antibiotics used to treat VAP with little side effects.
A Case Report of Pediatric Clear Cell Carcinoma of the Urinary Bladder Associated With Polyomavirus
Authors: Saleem Atif , Brown Ryanne A. , Higgins John P. T. , Troxell Megan L. , Kunder Christian A. , Pinsky Benjamin A. , Zambrano Eduardo , Kao Chia-Sui 
Published: October 2018

Abstract
Clear cell carcinoma of the bladder is a rare, aggressive malignancy with fewer than 60 reported cases to date, and it has never been described in a pediatric patient. We describe a urinary bladder tumor in an 8-year-old girl, which demonstrated similar features to clear cell carcinoma of the female genital tract with additional strong expression of SV40 large T antigen by immunohistochemistry. The patient had a history of severe infantile Crohn’s disease refractory to medical therapy, necessitating eventual stem cell transplant, complicated by graft-versus-host disease. Subsequent magnetic resonance enterography showed an incidental mass arising from the bladder dome, for which a partial cystectomy was performed. Histologically, the tumor demonstrated high-grade cytologic features with hobnail morphology, organized in various architectures, including solid, papillary, and tubulocystic, with strong and diffuse expression of PAX8, CK7, p53, and SV40 by immunohistochemistry. Additional stains were performed, and SALL4, GATA3, and napsin A were focally positive, whereas ER, WT1, and p63 were all negative. The overall features were consistent with clear cell carcinoma. The patient is currently alive with no evidence of disease at 1-year follow-up, status post–partial cystectomy without adjunct therapy. Clear cell carcinoma of the bladder is a rare malignancy that may occur in pediatric patients and may be associated with polyomavirus.
18F-NaF PET/CT in Prostatic Calculi
Authors: Raynor William Y. , Al-Zaghal Abdullah , Werner Thomas J. , Høilund-Carlsen Poul F. , Alavi Abass 
Published: October 2018

Abstract
Primary prostatic calculi commonly present asymptomatically in men over the age of 50 years. Individual calculi form when the secretory tube is blocked by inflammation, prostatic secretions, or corpora amylacea. Although small prostatic calculi have been described as a component of normal aging, increased prevalence of calculi has been associated with benign prostatic hyperplasia and prostatitis. We are presenting prostatic calcification in a 69-year-old man as incidentally detected on 18F-NaF PET/CT. Although previous publications have reported 18F-NaF uptake portraying calcification in soft tissue, these findings demonstrate a new domain in which to assess calcium metabolism using 18F-NaF PET/CT.