bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frequent BRAF mutations suggest a novel oncogenic driver in colonic neuroendocrine carcinoma
Authors: Idrees Kamran , Padmanabhan Chandrasekhar , Liu Eric , Guo Yan , Gonzalez Raul S. , Berlin Jordan , Dahlman Kimberly B. , Beauchamp R. Daniel , Shi Chanjuan 
Published: September 2017

Background and ObjectivesThe World Health Organization (WHO) 2010 has classified GI neuroendocrine neoplasms into neuroendocrine tumor (NET) and high‐grade neuroendocrine carcinoma (NEC). The genetic underpinnings of NEC are poorly understood. The aim of the study was to perform genomic profiling of NEC to better characterize this aggressive disease.MethodsWe identified nine patients with colonic NEC between January 1, 2005 and June 30, 2013. Whole exome sequencing (WES) was performed on tumor DNA from two patients with ≥80% tumor cellularity and matched normal tissue available. Focused BRAF mutational analysis was performed on an additional seven patients via sanger sequencing of BRAF exons 11 and 15.ResultsWe identified BRAF exon 15 mutations (c.A1781G: p.D594G and c.T1799A: p.V600E) by WES in two patients. Upon additional screening of seven colonic NECs for BRAF exon 11 and 15 mutations, we identified BRAF V600E mutations in two of seven specimens (29%). Overall, BRAF exon 15 mutations were present in four of nine colonic NECs.ConclusionColonic NEC is a rare but aggressive tumor with high frequency (44%) of BRAF mutations. Further investigation is warranted to ascertain the incidence of BRAF mutations in a larger population as BRAF inhibition may be a potential avenue of targeted treatment for these patients.
Promotion of early pediatric hearing detection through patient navigation: A randomized controlled clinical trial
Authors: Bush Matthew L. , Taylor Zachary R. , Noblitt Bryce , Shackleford Taylor , Gal Thomas J. , Shinn Jennifer B. , Creel Liza M. , Lester Cathy , Westgate Philip M. , Jacobs Julie A. , Studts Christina R. 
Published: September 2017

Objectives/HypothesisTo assess the efficacy of a patient navigator intervention to decrease nonadherence to obtain audiological testing following failed screening, compared to those receiving the standard of care.MethodsUsing a randomized controlled design, guardian‐infant dyads, in which the infants had abnormal newborn hearing screening, were recruited within the first week after birth. All participants were referred for definitive audiological diagnostic testing. Dyads were randomized into a patient navigator study arm or standard of care arm. The primary outcome was the percentage of patients with follow‐up nonadherence to obtain diagnostic testing. Secondary outcomes were parental knowledge of infant hearing testing recommendations and barriers in obtaining follow‐up testing.ResultsSixty‐one dyads were enrolled in the study (patient navigator arm = 27, standard of care arm = 34). The percentage of participants nonadherent to diagnostic follow‐up during the first 6 months after birth was significantly lower in the patient navigator arm compared with the standard of care arm (7.4% vs. 38.2%) (P = .005). The timing of initial follow‐up was significantly lower in the navigator arm compared with the standard of care arm (67.9 days after birth vs. 105.9 days, P = .010). Patient navigation increased baseline knowledge regarding infant hearing loss diagnosis recommendations compared with the standard of care (P = .004).ConclusionsPatient navigation decreases nonadherence rates following abnormal infant hearing screening and improves knowledge of follow‐up recommendations. This intervention has the potential to improve the timeliness of delivery of infant hearing healthcare; future research is needed to assess the cost and feasibility of larger scale implementation.Level of Evidence1b. Laryngoscope, 127:S1–S13, 2017
Change in Alcohol Intake in Relation to Weight Change in a Cohort of US Men with 24 Years of Follow‐Up
Authors: Downer Mary Kathryn , Bertoia Monica L. , Mukamal Ken J. , Rimm Eric B. , Stampfer Meir J. 
Published: September 2017

ObjectiveThe aim of this study was to prospectively investigate the potential effects of alcohol by subtype on reported long‐term weight change.MethodsThis study examined changes in alcohol intake (total, wine, light beer, regular beer, and liquor) and simultaneous changes in reported body weight within 4‐year periods from 1986 to 2010 from US men in the Health Professionals Follow‐Up Study. The study adjusted for age, changes in lifestyle and dietary covariates, and cardiovascular risk factors.ResultsThe study included observations of 44,603 four‐year periods from 14,971 men. Total alcohol, total beer, regular beer, and liquor intakes, modeled as the increase in weight per increase in drinks per day, were each directly associated with moderate weight gain over the 4‐year periods, in pounds: total alcohol: 0.23 (0.10 to 0.35); total beer: 0.29 (0.08 to 0.51); regular beer: 0.61 (0.22 to 1.00); and liquor: 0.28 (0.09 to 0.48). Results for wine and light beer were as follows: wine: 0.16 (−0.04 to 0.36) and light beer: −0.38 (−1.07 to 0.08). Results were strongest for men < 55 years old.ConclusionsIncreased alcohol consumption was associated with minor reported weight gain at levels unlikely to be clinically meaningful. Beverage‐specific differences were not substantial enough to make dietary recommendations for weight loss or maintenance by beverage type. The greatest risk of weight gain was among men who increased consumption to levels well above moderation.
The epigenetic modifier PBRM1 restricts the basal activity of the innate immune system by repressing retinoic acid‐inducible gene‐I‐like receptor signalling and is a potential prognostic biomarker for colon cancer
Authors: Shu Xing‐sheng , Zhao Yingying , Sun Yanmei , Zhong Lan , Cheng Yingduan , Zhang Yixiang , Ning Kaile , Tao Qian , Wang Yejun , Ying Ying 
Published: September 2017

AbstractIt has long been known that patients suffering from inflammatory bowel disease (IBD) have an increased risk of developing colorectal cancer (CRC). The innate immune system of host cells provides a first‐line defence against pathogenic infection, whereas an uncontrolled inflammatory response under homeostatic conditions usually leads to pathological consequences, as exemplified by the chronic inflammation of IBD. The key molecules and pathways keeping innate immunity in check are still poorly defined. Here, we report that the chromatin remodeller polybromo‐1 (PBRM1) is a repressor of innate immune signalling mediated by retinoic acid‐inducible gene‐I (RIG‐I)‐like receptors (RLRs). Knockdown of PBRM1 in colon cancer cells increased the expression of two receptor genes (RIG‐I and MDA5) and upregulated interferon (IFN)‐related and inflammation‐related gene signatures. The innate immune signal stimulated by a double‐stranded RNA viral mimic was exaggerated by PBRM1 suppression. PBRM1 cooperated with polycomb protein EZH2 to directly bind the cis‐regulatory elements of RIG‐I and MDA5, thereby suppressing their transcription. Moreover, upregulation of RIG‐I and MDA5 is required for IFN response activation induced by PBRM1 silencing. TRIM25, a protein stimulated by the RLR pathway and IFN production, physically interacted with PBRM1 and induced PBRM1 protein destabilization by promoting its ubiquitination. These findings reveal a PBRM1–RLR regulatory circuit that can keep innate immune activity at a minimal level in resting cells, and also ensure a robust inflammatory response in the case of pathogen invasion. PBRM1 was found to be downregulated in primary tissues from patients with CRC or IBD, and its expression correlated negatively with that of RLR genes and interferon‐stimulated genes in CRC samples. Lower PBRM1 expression was associated with advanced pathological grade and poorer survival of CRC patients, indicating that PBRM1 could serve as a potential prognostic biomarker for CRC. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Strategies and Challenges in Identifying Function for Thousands of sORF‐Encoded Peptides in Meiosis
Authors: Hollerer Ina , Higdon Andrea , Brar Gloria A. 
Published: September 2017

AbstractRecent genomic analyses have revealed pervasive translation from formerly unrecognized short open reading frames (sORFs) during yeast meiosis. Despite their short length, which has caused these regions to be systematically overlooked by traditional gene annotation approaches, meiotic sORFs share many features with classical genes, implying the potential for similar types of cellular functions. We found that sORF expression accounts for approximately 10–20% of the cellular translation capacity in yeast during meiotic differentiation and occurs within well‐defined time windows, suggesting the production of relatively abundant peptides with stage‐specific meiotic roles from these regions. Here, we provide arguments supporting this hypothesis and discuss sORF similarities and differences, as a group, to traditional protein coding regions, as well as challenges in defining their specific functions.
Crystal structure of a novel prolidase from Deinococcus radiodurans identifies new subfamily of bacterial prolidases
Authors: Are Venkata N. , Jamdar Sahayog N. , Ghosh Biplab , Goyal Venuka Durani , Kumar Ashwani , Neema Sanchit , Gadre Rekha , Makde Ravindra D. 
Published: September 2017

AbstractXaa‐Pro peptidases (XPP) are dinuclear peptidases of MEROPS M24B family that hydrolyze Xaa‐Pro iminopeptide bond with a trans‐proline at the second position of the peptide substrate. XPPs specific towards dipeptides are called prolidases while those that prefer longer oligopeptides are called aminopeptidases P. Though XPPs are strictly conserved in bacterial and archaeal species, the structural and sequence features that distinguish between prolidases and aminopeptidases P are not always clear. Here, we report 1.4 Å resolution crystal structure of a novel XPP from Deinococcus radiodurans (XPPdr). XPPdr forms a novel dimeric structure via unique dimer stabilization loops of N‐terminal domains such that their C‐terminal domains are placed far apart from each other. This novel dimerization is also the consequence of a different orientation of N‐terminal domain in XPPdr monomer than those in other known prolidases. The enzymatic assays show that it is a prolidase with broad substrate specificity. Our structural, mutational, and molecular dynamics simulation analyses show that the conserved Arg46 of N‐terminal domain is important for the dipeptide selectivity. Our BLAST search found XPPdr orthologs with conserved sequence motifs which correspond to unique structural features of XPPdr, thus identify a new subfamily of bacterial prolidases.
Tuning Excitonic Properties of Monolayer MoS2 with Microsphere Cavity by High‐Throughput Chemical Vapor Deposition Method
Authors: Mi Yang , Zhang Zhepeng , Zhao Liyun , Zhang Shuai , Chen Jie , Ji Qingqing , Shi Jianping , Zhou Xiebo , Wang Rui , Shi Jia , Du Wenna , Wu Zhiyong , Qiu Xiaohui , Zhang Qing , Zhang Yanfeng , Liu Xinfeng 
Published: September 2017

AbstractTuning the optical properties of 2D direct bandgap semiconductors is crucial for applications in photonic light source, optical communication, and sensing. In this work, the excitonic properties of molybdenum disulphide (MoS2) are successfully tuned by directly depositing it onto silica microsphere resonators using chemical vapor deposition method. Multiple whispering gallery mode (WGM) peaks in the emission wavelength range of ≈650–750 nm are observed under continuous wave excitation at room temperature. Time‐resolved photoluminescence (TRPL) and femtosecond transient absorption (TA) spectroscopy are conducted to study light‐matter interaction dynamics of the MoS2 microcavities. TRPL study suggests radiative recombination rate of carrier‐phonon scattering and interband transition processes in MoS2 is enhanced by a factor of ≈1.65 due to Purcell effect in microcavities. TA spectroscopy study shows modulation of the interband transition process mainly occurs at PB‐A band with an estimated F ≈ 1.60. Furthermore, refractive index sensing utilizing WGM peaks of MoS2 is established with sensitivity up to ≈150 nm per refractive index unit. The present work provides a large‐scale and straightforward method for coupling atomically thin 2D gain media with cavities for high‐performance optoelectronic devices and sensors.
Prevention of preterm birth with pessary in singletons (PoPPS): randomized controlled trial
Authors: Dugoff L. , Berghella V. , Sehdev H. , Mackeen A. D. , Goetzl L. , Ludmir J. 
Published: September 2017

ABSTRACTObjectiveTo determine if pessary use prevents preterm birth (PTB) in women with singleton pregnancy, with short cervical length (CL) measured on transvaginal sonography (TVS) and without prior spontaneous PTB (sPTB).MethodsThis was an open‐label multicenter randomized trial of asymptomatic women presenting at 18 + 0 to 23 + 6 weeks' gestation with a singleton pregnancy, CL ≤ 25 mm on TVS and no prior sPTB. sPTB included those with spontaneous onset of labor and those with rupture of membranes prior to labor. Subjects were randomized to receive either a Bioteque cup pessary or no pessary. Pessaries were inserted by trained maternal–fetal medicine staff. Vaginal progesterone was recommended to women with CL ≤ 20 mm. The primary outcome was PTB < 37 weeks. A sample size of 121 women in each group (n = 242) was needed to detect a reduction in the primary outcome from 30% in the no‐pessary group to 15% in the pessary group. The trial was stopped early before complete enrollment.ResultsBetween 17 March 2014 and 29 July 2016, 17 383 women underwent CL measurement on TVS. Of these, 422 (2.4%) had CL ≤ 25 mm and 391 (92.7%) met the full eligibility criteria, of which 122 (31.2%) agreed to randomization. Sixty‐one (50%) women were randomized to the pessary group and 61 (50%) to the no‐pessary group. Baseline characteristics were similar between the groups. There were no significant differences between the pessary and no‐pessary groups in the rate of PTB < 37 weeks (43% vs 40%; relative risk 1.09; 95% CI, 0.71–1.68) or in secondary outcomes, such as rate of PTB < 34 weeks, rate of PTB < 28 weeks, gestational age at delivery, birth weight and rate of composite adverse neonatal outcome.ConclusionsCervical pessary use was not associated with prevention of PTB in women with a singleton pregnancy, short CL on TVS and no prior sPTB in this small, underpowered randomized controlled trial. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
Characterizing vertical migration of Microcystis aeruginosa and conditions for algal bloom development based on a light‐driven migration model
Authors: Yao Bo , Liu Qingquan , Gao Yong , Cao Zhixian 
Published: September 2017

AbstractLight‐driven vertical migration is critical in dense aggregation of Microcystis aeruginosa during algal blooms under reduced turbulence conditions in natural water bodies. This study examined the vertical migration characteristics of Microcystis aeruginosa in calm water based on a colony migration model with consideration of cell density change, and demonstrated the effects of mucilage fraction, colony size, irradiance intensity, and water turbidity. The results suggest that colonies with larger radii and under higher irradiance usually had a larger daily averaged retention time at the water surface (DRT). In addition to colony size, mucilage was found to be important in changing the vertical migration behavior of Microcystis colonies, in which increasing mucilage volume fraction can increase the migrating velocity of the colony as well as the length of time it remains at the water surface. Increase of light extinction also favors the aggregation of colonies at the surface. An approximate critical value of 2400 µmol photons m2 s−1 for maximum irradiance was found for persistent algal bloom development under the given simulation conditions. Extremely small colonies exposed to irradiance below the critical value were not likely to migrate to the water surface to form algal blooms. According to the DRT values, three regions with different ranges of irradiance and colony size were proposed as the critical conditions for algal bloom development. Rough comparisons to field observations suggested that these results were reasonable and meaningful, and have the potential to be applied in real cases following further validation by more detailed investigations.
Synthesis and Performance Evaluation of CO2/N2 Switchable Tertiary Amine Gemini Surfactant
Authors: Zhou Ming , Wang Gang , Xu Yaoyang , Zhang Ze , Li Sisi , Hu Buhua , Zhao Yunlong 
Published: September 2017

AbstractA type of switchable tertiary amine Gemini surfactant, N,N′‐di(N,N‐dimethyl propylamine)‐N,N′‐didodecyl ethylenediamine, was synthesized by two substitution reactions with 3‐chloro‐1‐(N,N‐dimethyl) propylamine, bromododecane and ethylene diamine as main raw materials. The structure of the product was characterized by FTIR and 1H‐NMR. We also investigated the surface tension when CO2 was bubbled in different concentrations of surfactant solution and the influence of different CO2 volumes on surface tension under a constant surfactant concentration. Finally the surface tension curve and the related parameters were acquired by surface tension measurements. The experimental results showed that the structure of the synthesized compounds were in conformity with the expected structure of the surfactant, and displayed a better surface activity after bubbling CO2. The critical micelle concentration (CMC) surface tension at CMC (γcmc) pC20 (negative logarithm of the surfactant's molar concentration C20, required to reduce the surface tension by 20 mN/m) surface excess (Γmax) at air/solution interface and the minimum area per surfactant molecule at the air/solution interface (Amin) were determined. Results indicate that the target product had good surface activity after bubbling CO2.
PGBR extract ameliorates TNF‐α induced insulin resistance in hepatocytes
Authors: Chen Fu‐Chih , Shen Kuo‐Ping , Chen Jin‐Bor , Lin Hui‐Li , Hao Chi‐Long , Yen Hsueh‐Wei , Shaw Shyh‐Yu 
Published: September 2017

AbstractPre‐germinated brown rice (PGBR) could ameliorate metabolic syndrome, however, not much research estimates the effect of PGBR extract on insulin resistance. The aim of this study is to examine the effects of PGBR extract in TNF‐α induced insulin resistance. HepG2 cells, hepatocytes, were cultured in DMEM medium and added with 5 μM insulin or with insulin and 30 ng/ml TNF‐α or with insulin, TNF‐α and PGBR extract (50, 100, 300 μg/ml). The glucose levels of the medium were decreased by insulin, demonstrating insulin promoted glucose uptake into cell. However, TNF‐α inhibited glucose uptake into cells treated with insulin. Moreover, insulin increased the protein expressions of AMP‐activated protein kinase (AMPK), insulin receptor substrate‐1 (IRS‐1), phosphatidylinositol‐3‐kinase‐α (PI3K‐α), serine/threonine kinase PI3K‐linked protein kinase B (Akt/PKB), glucose transporter‐2 (GLUT‐2), glucokinase (GCK), peroxisome proliferator activated receptor‐α (PPAR‐α) and PPAR‐γ. TNF‐α activated p65 and MAPKs (JNK1/2 and ERK1/2) which worsened the expressions of AMPK, IRS‐1, PI3K‐α, Akt/PKB, GLUT‐2, GCK, glycogen synthase kinase‐3 (GSK‐3), PPAR‐α and PPAR‐γ. Once this relationship was established, we added PGBR extract to cell with insulin and TNF‐α. We found glucose levels of medium were lowered and that the protein expressions of AMPK, IRS‐1, PI3K‐α, Akt/PKB, GLUT‐2, GCK, GSK‐3, PPAR‐α, PPAR‐γ and p65, JNK1/2 were also recovered. In conclusion, this study found that TNF‐α inhibited insulin stimulated glucose uptake and aggravated related proteins expressions, suggesting that it might cause insulin resistance. PGBR extract was found to ameliorate this TNF‐α induced insulin resistance, suggesting that it might be used in the future to help control insulin resistance.
Law-Making as a Strategy for Change: Indonesia’s New Village Law
Authors: VEL Jacqueline , ZAKARIA Yando , BEDNER Adriaan 
Published: September 2017

AbstractIn 2014, the Indonesian president signed a new Village Law (no. 6/2014). This statute started a new phase in the ongoing history of village governance policy, moving the village from a position as an administrative unit in a top-down system towards one of an autonomous community. The present article analyses how distinct “policy communities” in Indonesia started a process that helped shape the 2014 Village Law in order to promote their long-term political agendas, how their involvement was facilitated by the particular features of Indonesia’s law-making process, and how they managed to get a Bill passed that went against considerable vested interest from government bureaucracies. However, they have been less successful in securing implementation of the new law, as this process is still dominated by the government bureaucracies that were “defeated” in the law-making process.
Ashley Smith and Incarcerated Young Women: Marginalized at Any Age
Authors: Cesaroni Carla , Peterson-Badali Michele 
Published: September 2017

Abstract
Nineteen-year-old Ashley Smith died by her own hand in 2007 in a women’s correctional facility in Ontario, Canada. The subject of the coroner’s inquest into her death was her carceral experience and the failure of the system (leading to her death) during her time in adult federal corrections. The general focus of the inquest was on the state of federal women’s corrections in Canada and the mental health issues experienced by many incarcerated women. We produced a report and provided expert testimony at the inquest regarding the need for a developmentally informed correctional framework. In this article, which is based on our inquest report and testimony, we argue that a developmental perspective is a vital lens for understanding the incarceration experience of young women.
Sentencing Ashley Smith: How Prison Conditions Relate to the Aims of Punishment
Authors: Kerr Lisa 
Published: September 2017

Abstract
Ashley Smith’s experience in the adult prison system flowed from certain of its systemic features. This article considers whether and how it is possible to reconcile the basic commitments of sentencing law, including the legal aims of punishment, with that systemic portrait. The youth court that ordered Smith’s transfer to adult custody relied upon an idealized conception of adult imprisonment, just as ordinary adult sentencing courts do. Judges purport to stipulate the severity of punishment, but tend not to consider how prison conditions will shape the severity of the sanction. Even where a particular defendant is likely to face unique difficulties in custody, courts tend to take notice in limited and rare ways. Smith’s experience in adult custody challenges us to more clearly identify, and to consider extending, doctrinal sentencing rules that represent a judicial concern with the effects and prospects of imprisonment in particular cases.