bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytosolic co-delivery of miRNA-34a and docetaxel with core-shell nanocarriers via caveolae-mediated pathway for the treatment of metastatic breast cancer
Authors: Zhang Li , Yang Xin , Lv Yaqi , Xin Xiaofei , Qin Chao , Han Xiaopeng , Yang Lei , He Wei , Yin Lifang 
Published: April 2017

AbstractCo-delivery of microRNAs and chemotherapeutic drugs into tumor cells is an attractive strategy for synergetic breast cancer therapy due to their complementary mechanisms. In this work, a core-shell nanocarrier coated by cationic albumin was developed to simultaneously deliver miRNA-34a and docetaxel (DTX) into breast cancer cells for improved therapeutic effect. The co-delivery nanocarriers showed a spherical morphology with an average particle size of 183.9 nm, and they efficiently protected miRNA-34a from degradation by RNase and serum. Importantly, the nanocarriers entered the cytosol via a caveolae-mediated pathway without entrapment in endosomes/lysosomes, thus improving the utilization of the cargo.In vitro,the co-delivery nanocarriers suppressed the expression of anti-apoptosis gene Bcl-2 at both transcription and protein levels, inhibited tumor cell migration and efficiently induced cell apoptosis and cytotoxicity.In vivo, the co-delivery nanocarriers prolonged the blood circulation of DTX, enhanced tumor accumulation of the cargo and significantly inhibited tumor growth and metastasis in 4T1-tumor bearing mice models. Taken together, the present nanocarrier co-loading with DTX and miRNA-34a is a new nanoplatform for the combination of insoluble drugs and gene/protein drugs and provides a promising strategy for the treatment of metastatic breast cancer.
Reading Comprehension Deficits in Adolescents: Addressing Underlying Language Abilities
Authors: Nippold Marilyn A. 
Published: April 2017

Purpose
The purpose of this article is to discuss reading comprehension deficits in adolescents in relation to their word reading skills and lexical and syntactic development. Although reading comprehension strategies (e.g., “Find the main idea”) are often recommended, it is argued that before these can be effective, students' underlying language deficits should be addressed.

Method
Data from a longitudinal study are analyzed to determine the relationship between reading comprehension, word reading, and lexical and syntactic development in adolescents.

Results
The findings indicate that poor reading comprehension in adolescents is predicted by concurrent deficits in word reading ability, lexical development, and syntactic development.

Conclusion
When poor comprehension is accompanied by deficits in word reading ability and/or lexical and syntactic development, intervention should target the underlying areas of deficiency. Studies designed to improve reading comprehension in adolescents are needed.
Reduction of NEP variations for terahertz detectors using Schottky barrier diodes in CMOS
Authors: Kim D.Y. , O Kenneth K. 
Published: April 2017

Variations of low‐frequency noise including flicker and Lorentzian spectra are the dominant source of variation of noise equivalent power (NEP) for terahertz detectors using diode‐connected N‐type MOS (NMOS) transistors. The low‐frequency noise of Schottky diodes fabricated in the same CMOS process as the NMOS detectors are dominated by generation and recombination noise. At 1 MHz modulation frequency, the noise of Schottky barrier diodes (SBDs) and its variation are ∼2× lower than those of diode‐connected NMOS transistors. It should be possible to reduce the variation of NEP by ∼2× using Schottky diode detectors modulated at 1 MHz.
Balanced ring hybrid with arbitrary power division ratio
Authors: Xu Kai , Shi Jin , Lu Jianpeng , Zhang Wei , Chen Jian‐Xin 
Published: April 2017

A balanced ring hybrid with arbitrary power division ratio is proposed. By embedding four half‐wavelength microstrip lines in the traditional single‐ended ring hybrid, the functions of differential‐mode power division, common‐mode suppression, arbitrary power division ratio and port isolation can be achieved at the same time. Higher power division ratio also can be obtained compared with traditional single‐ended design for the achievable maximum characteristic impedance of 120 Ω. A simplified analysis process is proposed by making the balanced port equivalent to a new single‐ended port. To verify the theoretical prediction, one prototype with a power division ratio of 4 : 1 and a size of 0.59 × 0.56λg (λg is the guided wavelength at the centre frequency) is measured and compared with the reported designs. The measured results exhibit the minimum insertion loss of ∼0.2 dB and the operating bandwidth for |SddAA| < −15 dB of 20.9%.
The Impact of Integrated Evaluation of Hemodynamics on Management of Preterm Infants with Late-Onset Compromised Systemic Circulation
Authors: Amer Reem , Kalash Reem , Seshia Mary , Elsayed Yasser 
Published: April 2017

Objectives To study the impact of integrated evaluation of hemodynamics (IEH), using targeted neonatal echocardiography (TNE), cerebral regional tissue oxygenation (crRTO), and fractional oxygen extraction (FOE), using near-infrared spectroscopy (NIRS) on the management of infants with late-onset compromised systemic circulation (LCSC), and evaluation of the hemodynamic characteristics.
Study Design Retrospective cohort study comparing infants with LCSC who underwent IEH (April 2014 to May 2016) with an earlier EPOCH who did not undergo IEH (January 2012 to March 2014). The primary outcome was the time to recovery.
Results Total 43 infants were included; 18 infants underwent IEH with a median (IQR) 2 (1–3) assessments per infant. The time to recovery was shorter in IEH group with a median (IQR) 28 hours (15–62) compared with non-IEH group 96 hours (30–160). Autoregulation was compromised in 50%, and systemic vascular resistance (SVR) was low in 67%.
Conclusion IEH was associated with shorter time to recovery in infants with LCSC.
Awareness, Prevalence, Treatment, and Control of Hypertension in Western Nepal
Authors: Neupane Dinesh , Shrestha Archana , Mishra Shiva Raj , Bloch Joakim , Christensen Bo , McLachlan Craig S , Karki Arjun , Kallestrup Per 
Published: April 2017

Abstract

BACKGROUND
Hypertension is a significant contributor to cardiovascular and renal diseases. In low-income settings like Nepal, there are few epidemiological studies assessing hypertension burden. Thus, the purpose was to determine prevalence, awareness, treatment, and control of hypertension in Nepal.

METHODS
A cross-sectional survey was conducted in semi-urban area of western Nepal among randomly selected participants, aged between 25 and 65 years. Systolic blood pressure (BP) ≥140 mm Hg and/or diastolic BP of ≥90 mm Hg and/or taking current antihypertensive medicine defined as hypertension.

RESULTS
Study included 2,815 participants, 1,844 were women. The age- and sex-adjusted prevalence of hypertension was 28%. Of the study participants, 17% were daily smokers, 12% harmful alcohol drinkers, 90% consuming low levels of fruit and/or vegetable, and 7% reported low physical activity. Among hypertensive participants, 46% were aware of their preexisting hypertension, 31% were on hypertensive medication, and 15% met BP control targets. Increasing age (odds ratio [OR]: 1.07, 95% confidence interval [CI]: 1.06; 1.08), higher body mass index (OR: 1.09, 95% CI: 1.06; 1.12), men (OR: 1.63, 95% CI: 1.25; 2.14), harmful alcohol intake (Or: 2.46; 95% CI: 1.73; 3.51), family history of hypertension (OR: 1.42; 95% CI: 1.14; 1.76), and diabetes (OR: 2.08, 95% CI: 1.30; 3.33) were independently associated with hypertension.

CONCLUSIONS
The prevalence of hypertension was found high in western Nepal. A number of risk factors were identified as possible drivers of this burden. Thus, there is an urgent need to address modifiable risk factors in semi-urban settings of western Nepal.
GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization
Authors: Boudard Mélanie , Barth Dominique , Bernauer Julie , Denise Alain , Cohen Johanne 
Published: April 2017

Abstract

Motivation
Predicting the 3D structure of RNA molecules is a key feature towards predicting their functions. Methods which work at atomic or nucleotide level are not suitable for large molecules. In these cases, coarse-grained prediction methods aim to predict a shape which could be refined later by using more precise methods on smaller parts of the molecule.

Results
We developed a complete method for sampling 3D RNA structure at a coarse-grained model, taking a secondary structure as input. One of the novelties of our method is that a second step extracts two best possible structures close to the native, from a set of possible structures. Although our method benefits from the first version of GARN, some of the main features on GARN2 are very different. GARN2 is much faster than the previous version and than the well-known methods of the state-of-art. Our experiments show that GARN2 can also provide better structures than the other state-of-the-art methods.

Availability and implementation
GARN2 is written in Java. It is freely distributed and available at http://garn.lri.fr/.

Supplementary information
Supplementary data are available at Bioinformatics online.
FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes
Authors: Parodi Alice C L , Sangalli Laura M , Vantini Simone , Amati Bruno , Secchi Piercesare , Morelli Marco J 
Published: April 2017

Abstract

Summary
Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) generates local accumulations of sequencing reads on the genome (“peaks”), which correspond to specific protein–DNA interactions or chromatin modifications. Peaks are detected by considering their total area above a background signal, usually neglecting their shapes, which instead may convey additional biological information. We present FunChIP, an R/Bioconductor package for clustering peaks according to a functional representation of their shapes: after approximating their profiles with cubic B-splines, FunChIP minimizes their functional distance and classifies the peaks applying a k-mean alignment and clustering algorithm. The whole pipeline is user-friendly and provides visualization functions for a quick inspection of the results. An application to the transcription factor Myc in 3T9 murine fibroblasts shows that clusters of peaks with different shapes are associated with different genomic locations and different transcriptional regulatory activity.

Availability and implementation
The package is implemented in R and is available under Artistic Licence 2.0 from the Bioconductor website (http://bioconductor.org/packages/FunChIP).

Supplementary information
Supplementary data are available at Bioinformatics online.
A reference human genome dataset of the BGISEQ-500 sequencer
Authors: Huang Jie , Liang Xinming , Xuan Yuankai , Geng Chunyu , Li Yuxiang , Lu Haorong , Qu Shoufang , Mei Xianglin , Chen Hongbo , Yu Ting , Sun Nan , Rao Junhua , Wang Jiahao , Zhang Wenwei , Chen Ying , Liao Sha , Jiang Hui , Liu Xin , Yang Zhaopeng , Mu Feng , Gao Shangxian 
Published: April 2017

Abstract
Background: BGISEQ-500 is a new desktop sequencer developed by BGI. Using DNA nanoball and combinational probe anchor synthesis developed from Complete Genomics™ sequencing technologies, it generates short reads at a large scale. Findings: Here, we present the first human whole-genome sequencing dataset of BGISEQ-500. The dataset was generated by sequencing the widely used cell line HG001 (NA12878) in two sequencing runs of paired-end 50 bp (PE50) and two sequencing runs of paired-end 100 bp (PE100). We also include examples of the raw images from the sequencer for reference. Finally, we identified variations using this dataset, estimated the accuracy of the variations, and compared to that of the variations identified from similar amounts of publicly available HiSeq2500 data. Conclusions: We found similar single nucleotide polymorphism (SNP) detection accuracy for the BGISEQ-500 PE100 data (false positive rate [FPR] = 0.00020%, sensitivity = 96.20%) compared to the PE150 HiSeq2500 data (FPR = 0.00017%, sensitivity = 96.60%) better SNP detection accuracy than the PE50 data (FPR = 0.0006%, sensitivity = 94.15%). But for insertions and deletions (indels), we found lower accuracy for BGISEQ-500 data (FPR = 0.00069% and 0.00067% for PE100 and PE50 respectively, sensitivity = 88.52% and 70.93%) than the HiSeq2500 data (FPR = 0.00032%, sensitivity = 96.28%). Our dataset can serve as the reference dataset, providing basic information not just for future development, but also for all research and applications based on the new sequencing platform.
Comparing Outcomes and Cost of 3 Surgical Treatments for Sagittal Synostosis: A Retrospective Study Including Procedure-Related Cost Analysis
Authors: Garber Sarah T. , Karsy Michael , Kestle John R.W. , Siddiqi Faizi , Spanos Stephen P. , Riva-Cambrin Jay 
Published: April 2017

Abstract

BACKGROUND
Neurosurgical techniques for repair of sagittal synostosis include total cranial vault (TCV) reconstruction, open sagittal strip (OSS) craniectomy, and endoscopic strip (ES) craniectomy.

OBJECTIVE
To evaluate outcomes and cost associated with these 3 techniques.

METHODS
Via retrospective chart review with waiver of informed consent, the last consecutive 100 patients with sagittal synostosis who underwent each of the 3 surgical correction techniques before June 30, 2013, were identified. Clinical, operative, and process of care variables and their associated specific charges were analyzed along with overall charge.

RESULTS
The study included 300 total patients. ES patients had fewer transfusion requirements (13% vs 83%, P < .001) than TCV patients, fewer days in intensive care (0.3 vs 1.3, P < .001), and a shorter overall hospital stay (1.8 vs 4.2 d, P < .001), and they required fewer revisions (1% vs 6%, P = .05). The mean charge for the endoscopic procedure was $21 203, whereas the mean charge for the TCV reconstruction was $45 078 (P < .001). ES patients had more preoperative computed tomography scans (66% vs 44%, P = .003) than OSS patients, shorter operative times (68 vs 111 min, P < .001), and required fewer revision procedures (1% vs 8%, P < .001). The mean charge for the endoscopic procedure was $21 203 vs $20 535 for the OSS procedure (P = .62).

CONCLUSION
The ES craniectomy for sagittal synostosis appeared to have less morbidity and a potential cost savings compared with the TCV reconstruction. The charges were similar to those incurred with OSS craniectomy, but patients had a shorter length of stay and fewer revisions.
Highly Successful Hepatitis C Virus (HCV) Treatment Outcomes in Human Immunodeficiency Virus/HCV-Coinfected Patients at a Large, Urban, Ryan White Clinic
Authors: Patel Manish , Rab Saira , Kalapila Aley G. , Kyle Alison , Okosun Ike Solomon , Miller Lesley 
Published: April 2017

Abstract

Background
The introduction of direct-acting antivirals (DAAs) created a major paradigm shift in the treatment of chronic hepatitis C. Currently, there is little “real-world” data regarding hepatitis C virus (HCV) treatment outcomes in the human immunodeficiency virus (HIV)/HCV-coinfected population.

Methods
This retrospective cohort study examined HCV treatment outcomes of HIV/HCV-coinfected patients at a large, urban, Ryan White-funded clinic caring for an underserved population. All HIV patients initiating HCV treatment from January 1, 2013 to November 30, 2015 were included in the analysis. The primary end point was sustained virologic response 12 weeks after the end of therapy (SVR12).

Results
A total of 172 patients initiated HCV treatment within the study period: 79% were male, 83% were black, 95% were HCV genotype 1, 79% were HCV treatment naive, and 16% had cirrhosis. At baseline, median CD4 was 494 cells/μL (interquartile range, 316–722) and 92% had HIV ribonucleic acid less than 40 copies/mL. The most common DAA initiated was ledipasvir/sofosbuvir (LDV/SOF) (85%), with 92% receiving 12 weeks of treatment. Overall, SVR12 was 93% by intention-to-treat analysis and 98% by per-protocol analysis. The majority of patients on LDV/SOF did not report any adverse effect. One patient in the ribavirin plus SOF group discontinued treatment due to adverse effect.

Conclusions
In a cohort of mainly black, male, HIV/HCV-coinfected patients at a large, urban, Ryan White clinic, HCV treatment with DAAs resulted in high SVR12 rates and was well tolerated despite real-world challenges including medication access barriers and drug interaction concerns.
Rotavirus Vaccine Schedules and Vaccine Response Among Infants in Low- and Middle-Income Countries: A Systematic Review
Authors: Gruber Joann F. , Gruber Lucinda M. , Weber Rachel Palmieri , Becker-Dreps Sylvia , Jonsson Funk Michele 
Published: April 2017

Abstract

Background
Rotavirus vaccine schedules may impact vaccine response among children in low- and middle-income countries (LMICs). Our objective was to review the literature evaluating the effects of monovalent (RV1) or pentavalent rotavirus vaccines schedules on vaccine response.

Methods
We searched PubMed, Web of Science, Embase, and ClinicalTrials.gov for eligible trials conducted in LMICs comparing ≥2 vaccine schedules and reporting immunologic response or efficacy. We calculated seroconversion proportion differences and geometric mean concentration (GMC) ratios with 95% confidence intervals.

Results
We abstracted data from 8 eligible trials of RV1. The point estimates for seroconversion proportions difference ranged from −0.25 to −0.09 for the 6/10-week schedule compared with 10/14. The range for the 6/10/14- compared with 10/14-week schedule was −0.02 to 0.10. Patterns were similar for GMC ratios and efficacy estimates.

Conclusions
The commonly used 6/10-week RV1 schedule in LMICs may not be optimal. Further research on the effect of rotavirus schedules using clinical endpoints is essential.
Immunological Predictors of Nonresponse to Directly Acting Antiviral Therapy in Patients With Chronic Hepatitis C and Decompensated Cirrhosis
Authors: Childs Kate , Merritt Elliot , Considine Aisling , Sanchez-Fueyo Alberto , Agarwal Kosh , Martinez-Llordella Marc , Carey Ivana 
Published: April 2017

AbstractBackgroundSustained virological response rates (SVRs) to directly acting antiviral (DAA) therapy for hepatitis C virus (HCV) are lower in decompensated cirrhosis. Markers of innate immunity predict nonresponse to interferon-based HCV treatment; however, whether they are associated with the response to DAAs in patients with decompensation is not known.MethodsInformation on demographics, adherence, viral kinetics, and resistance were gathered prospectively from a cohort with decompensated cirrhosis treated with 12 weeks of DAAs. C-X-C motif chemokine-10 (CXCL-10) level and T-cell and natural killer (NK) cell phenotype were analyzed pretreatment and at 4 and 12 weeks of treatment.ResultsOf 32 patients, 24 of 32 (75%) achieved SVR (responders). Eight of 32 (25%) experienced relapse after the end of treatment (nonresponders). There were no differences in demographics or adherence between groups. Nonresponders had higher CXCL-10; 320 pg/mL (179461) vs 109 pg/mL (88170) in responders (P &lt; .001) and differential CXCL-10 dynamics. Nonresponders had lower NK cell frequency, higher expression of activation receptor NKp30, and lower frequency of the NK subset CD56−CD16+.ConclusionsNonresponders to DAAs displayed a different NK phenotype and CXCL-10 profile to responders. Nonresponders did not have poorer adherence or baseline virological resistance, and this shows that immunological parameters are associated with treatment response to interferon-free treatment for HCV in individuals with decompensated cirrhosis.
The Presence of Human Immunodeficiency Virus-Associated Neurocognitive Disorders Is Associated With a Lower Adherence to Combined Antiretroviral Treatment
Authors: Kamal Susan , Locatelli Isabella , Wandeler Gilles , Sehhat Asemaneh , Bugnon Olivier , Metral Melanie , Du Pasquier Renaud , Gutbrod Klemens , Cavassini Matthias , Schneider Marie P. ,   and the Swiss HIV Cohort Study
Published: April 2017

AbstractBackgroundHuman immunodeficiency virus (HIV)-associated neurocognitive disorders (HAND) are defined according to their diagnostic degrees as follows: asymptomatic neurocognitive impairment, mild neurocognitive disorder, and HIV-associated dementia. Because high adherence to combined antiretroviral therapy (cART) is required to maintain viral suppression among HIV-infected patients, it is important to investigate the impact of HAND on medication adherence. Our study hypothesis was that patients with HAND had a lower medication adherence than patients who did not have HAND.MethodsThis was an observational, exploratory, 2-center pilot study of patients who had a state-of-the-art neurocognitive assessment performed between January 2011 and June 2015 while also being followed at their respective adherence clinics. Adherence was measured with electronic monitors. Patients’ sociodemographic characteristics, HIV viral load, and CD4 counts were retrieved from the Swiss HIV Cohort Study database. At each time t, adherence was computed as the proportion of patients taking medication as prescribed at that time.ResultsWe included 59 patients, with a median (Q1, Q3) age of 53 years (47–58) and 39 (66%) were male participants. Twenty-two patients (35%) had no neurocognitive deficits, 16 (27%) patients had HAND, and 21 (35%) patients had non-HAND (mostly depression). Implementation over 3 years showed a significant decline (50%) in medication adherence among patients diagnosed with HAND in comparison with patients who had a normal neuropsychological status or a non-HIV-related cognitive deficit (implementation stayed 90% during follow-up).ConclusionsOur findings support the hypothesis that HAND is associated with reduced cART adherence.
Low-Quality Housing Is Associated With Increased Risk of Malaria Infection: A National Population-Based Study From the Low Transmission Setting of Swaziland
Authors: Dlamini Nomcebo , Hsiang Michelle S. , Ntshalintshali Nyasatu , Pindolia Deepa , Allen Regan , Nhlabathi Nomcebo , Novotny Joseph , Kang Dufour Mi-Suk , Midekisa Alemayehu , Gosling Roly , LeMenach Arnaud , Cohen Justin , Dorsey Grant , Greenhouse Bryan , Kunene Simon 
Published: April 2017

Abstract

Background
Low-quality housing may confer risk of malaria infection, but evidence in low transmission settings is limited.

Methods
To examine the relationship between individual level housing quality and locally acquired infection in children and adults, a population-based cross-sectional analysis was performed using existing surveillance data from the low transmission setting of Swaziland. From 2012 to 2015, cases were identified through standard diagnostics in health facilities and by loop-mediated isothermal amplification in active surveillance, with uninfected subjects being household members and neighbors. Housing was visually assessed in a home visit and then classified as low, high, or medium quality, based on housing components being traditional, modern, or both, respectively.

Results
Overall, 11426 individuals were included in the study: 10960 uninfected and 466 infected (301 symptomatic and 165 asymptomatic). Six percent resided in low-quality houses, 26% in medium-quality houses, and 68% in high-quality houses. In adjusted models, low- and medium-quality construction was associated with increased risk of malaria compared with high-quality construction (adjusted odds ratio [AOR], 2.11 and 95% confidence interval [CI], 1.26–3.53 for low vs high; AOR, 1.56 and 95% CI, 1.15–2.11 for medium vs high). The relationship was independent of vector control, which also conferred a protective effect (AOR, 0.67; 95% CI, .50–.90) for sleeping under an insecticide-treated bed net or a sprayed structure compared with neither.

Conclusions
Our study adds to the limited literature on housing quality and malaria risk from low transmission settings. Housing improvements may offer an attractive and sustainable additional strategy to support countries in malaria elimination.