bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Formation of Advanced Scaffolds from Phenols and Anilines
Authors: Canesi Sylvain 
Published: December 2018

This article is an account of our efforts over the last decade to functionalize phenols and anilines at any position and to use these compounds to generate substituted aromatic systems and advanced unsaturated cyclohexanone moieties, enabling the rapid formation of complex structures. Total syntheses of numerous natural products involving such intermediates were achieved.1	Introduction2	ortho-Functionalization of Phenols and Aniline Derivatives Mediated by Iodanes (III) and Synthesis of Panacene2.1	Cross-Coupling with Aniline Derivatives2.2	Dearomative Cycloaddition of Arenes and Heteroarenes2.3	Total Synthesis of Panacene3	meta-Functionalization of Aniline Derivatives and Synthesis of Erysotramidine3.1	meta-Functionalization of Aniline Derivatives3.2	Total Synthesis of Erysotramidine4	para-Functionalization of Phenols and Applications in Total Synthesis4.1	Bimolecular Approach Mediated by Protecting Groups4.2	ipso-Rearrangement4.3	Oxidative Alkyl Shift4.4	Oxidative Prins-Pinacol Rearrangement4.5	Oxidative Prins-Type Reaction4.6	Total Synthesis of (–)-Fortucine4.7	Total Synthesis of Isostrychnine4.8	Total Synthesis of (–)-Strychnopivotine5	Development of a Functional Protecting Group
Diagnosis and Treatment of Infected Shoulder Arthroplasty: Current Concepts Review
Authors: Marcheggiani Muccioli Giulio , Guerra Enrico , Roberti di Sarsina Tommaso , Alesi Domenico , Fratini Stefano , Cammisa Eugenio , Rinaldi Vito , Lullini Giada , Rotini Roberto , Zaffagnini Stefano 
Published: December 2018

AbstractPeriprosthetic shoulder infection (PSI) is an emerging pathology which requires many improvements in diagnosis and treatment to obtain a satisfying success rate. Different approaches have been described. This article summarizes current concepts of diagnostic process and main treatments described in the literature.
Bilateral comparison of luminous flux using lamps as transfer standards (EURAMET.PR-K4.2)
Authors: Dubard J , Obein G , Suryani D 
Published: December 2018

The Laboratoire National de Métrologie et d'Essais, LNE-CNAM (France) and The National Institute of Metrology, RCM LIPI (Indonesia) agreed in December 2013 to conduct a bilateral comparison on luminous flux using a group of lamps as transfer standards.
The aims of the comparison were:
• To link the RCM LIPI realized lumen to the CCPR K4 reference value
• To demonstrate the RCM LIPI capability in calibrating tungsten standards lamps.
The comparison and its protocol were approved by the CCPR and registered with KCDB with the comparison number: EURAMET.PR-K4.2.
KEY WORDS FOR SEARCH
Luminous flux, PR K4, Bilateral Comparison

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCPR, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Analytical and numerical modeling of the process for cluster emergence of objects in a random environment
Authors: Mostovoy Y A , Berdnikov V A 
Published: December 2018

Abstract
The task solution for probing a certain area by a swarm of objects randomly distributed is considered. This requires studying of statistical features for clusters emergence from swarm objects uniformly distributed in order to find such a concentration of the objects in the sensing area in which the number of random clusters will be maximal. Corresponding analytical dependencies have been obtained.
Uromodulin in a Pathway Between Decreased Renal Urate Excretion and Albuminuria
Authors: Krajcoviechova Alena , Marois-Blanchet Francois-Christophe , Troyanov Stephan , Harvey Francois , Dumas Pierre , Tremblay Johanne , Cifkova Renata , Awadalla Philip , Madore Francois , Hamet Pavel 
Published: December 2018

AbstractBACKGROUNDThe mechanism explaining the inverse association between renal urate and albumin excretion remains unclear. First, we evaluated the impact of candidate variants in the main urate transporter genes (i.e., SLC2A9, SLC22A12, ABCG2) on the association between fractional excretion of uric acid (FEUA) and urinary albumin/creatinine ratio (uACR). Second, we examined uromodulin and sodium excretion as mediators of the association between FEUA and uACR.METHODSWe performed cross-sectional analysis of 737 French Canadians from the CARTaGENE cohort, a random sample of the Quebec population aged 40–69 years (a total of 20,004 individuals). Individuals with available genotyping and urinary data were obtained from a sub-study including gender-matched pairs with high and low Framingham Risk Score and vascular rigidity index. We further excluded individuals with an estimated glomerular filtration rate &lt;60 ml/min/1.73 m2, glycosuria, and use of confounding medication. A spot urine sample was analyzed. Genotyping was performed using the Illumina Omni2.5–8 BeadChips. Genetic variants were analyzed using an additive model.RESULTSFinal analyses included 593 individuals (45.5% of men; mean age 54.3 ± 8.6). We observed an antagonistic interaction between rs13129697 variant of the SLC2A9 gene and FEUA tertiles on uACR (P = 0.002). Using the mediation analysis, uromodulin explained 32%, fractional excretion of sodium (FENa) 44%, and uromodulin together with FENa explained 70% of the inverse relationship between FEUA and uACR. Bootstrapping process confirmed the role of both mediators.CONCLUSIONSOur data suggest that the association of albuminuria with decreased renal urate excretion may be modified by the transporter SLC2A9, and mediated by uromodulin and sodium handling.
ModL: exploring and restoring regularity when testing for positive selection
Authors: Mingrone Joseph , Susko Edward , Bielawski Joseph P 
Published: December 2018

Abstract

Motivation
Likelihood ratio tests are commonly used to test for positive selection acting on proteins. They are usually applied with thresholds for declaring a protein under positive selection determined from a chi-square or mixture of chi-square distributions. Although it is known that such distributions are not strictly justified due to the statistical irregularity of the problem, the hope has been that the resulting tests are conservative and do not lose much power in comparison with the same test using the unknown, correct threshold. We show that commonly used thresholds need not yield conservative tests, but instead give larger than expected Type I error rates. Statistical regularity can be restored by using a modified likelihood ratio test.

Results
We give theoretical results to prove that, if the number of sites is not too small, the modified likelihood ratio test gives approximately correct Type I error probabilities regardless of the parameter settings of the underlying null hypothesis. Simulations show that modification gives Type I error rates closer to those stated without a loss of power. The simulations also show that parameter estimation for mixture models of codon evolution can be challenging in certain data-generation settings with very different mixing distributions giving nearly identical site pattern distributions unless the number of taxa and tree length are large. Because mixture models are widely used for a variety of problems in molecular evolution, the challenges and general approaches to solving them presented here are applicable in a broader context.

Availability and implementation
https://github.com/jehops/codeml_modl

Supplementary information
Supplementary data are available at Bioinformatics online.
CNValidator: validating somatic copy-number inference
Authors: Smith Lucian P , Yamato Jon A , Kuhner Mary K 
Published: December 2018

Abstract

Motivation
CNValidator assesses the quality of somatic copy-number calls based on coherency of haplotypes across multiple samples from the same individual. It is applicable to any copy-number calling algorithm, which makes calls independently for each sample. This test is useful in assessing the accuracy of copy-number calls, as well as choosing among alternative copy-number algorithms or tuning parameter values.

Results
On a dataset of somatic samples from individuals with Barrett’s Esophagus, CNValidator provided feedback on the correctness of sample ploidy calls and also detected data quality issues.

Availability and implementation
CNValidator is available on GitHub at https://github.com/kuhnerlab/CNValidator.

Supplementary information
Supplementary data are available at Bioinformatics online.
HIV activism in modern Russia: from NGOs to community development
Authors: Nartova Nadya , Krupets Yana , Shilova Anastasiia 
Published: December 2018

Abstract
In the context of the spreading HIV epidemic in Russia and the lack of government's effectiveness in addressing this problem, the role and the importance of HIV activism in protecting the rights and improving the quality of life of HIV positive people have been increasing. This article focuses on the development of the HIV community in St. Petersburg, one of the largest and the most problematic, in terms of the HIV epidemic, cities in Russia. The research was conducted within the qualitative methodology, using ethnographic case-study methods and biographical interviews. The authors use the analysis of field observations and nineteen interviews with men and women involved in HIV activism in St. Petersburg to show how collective actions of NGOs and action groups form the city HIV community through working with different groups and the development of participants' agency.
Hypothermia and cardiac electrophysiology: a systematic review of clinical and experimental data
Authors: Dietrichs Erik Sveberg , Tveita Torkjel , Smith Godfrey 
Published: December 2018

Abstract
Moderate therapeutic hypothermia procedures are used in post-cardiac arrest care, while in surgical procedures, lower core temperatures are often utilized to provide cerebral protection. Involuntary reduction of core body temperature takes place in accidental hypothermia and ventricular arrhythmias are recognized as a principal cause for a high mortality rate in these patients. We assessed both clinical and experimental literature through a systematic literature search in the PubMed database, to review the effect of hypothermia on cardiac electrophysiology. From included studies, there is common experimental and clinical evidence that progressive cooling will induce changes in cardiac electrophysiology. The QT interval is prolonged and appears more sensitive to decreases in temperature than the QRS interval. Severe hypothermia is associated with more pronounced changes, some of which are proarrhythmic. This is supported clinically where severe accidental hypothermia is commonly associated with ventricular fibrillation or asystole. J-waves in human electrocardiogram recordings are regularly but not always observed in hypothermia. Its relation to ventricular repolarization and arrhythmias is not obvious. Little clinical data exist on efficacy of anti-arrhythmic drugs in hypothermia, while experimental data show the potential of some agents, such as the class III antiarrhythmic bretylium. It is apparent that QT-prolonging drugs should be avoided.
BLINK: a package for the next level of genome-wide association studies with both individuals and markers in the millions
Authors: Huang Meng , Liu Xiaolei , Zhou Yao , Summers Ryan M , Zhang Zhiwu 
Published: December 2018

Abstract
Big datasets, accumulated from biomedical and agronomic studies, provide the potential to identify genes that control complex human diseases and agriculturally important traits through genome-wide association studies (GWAS). However, big datasets also lead to extreme computational challenges, especially when sophisticated statistical models are employed to simultaneously reduce false positives and false negatives. The newly developed fixed and random model circulating probability unification (FarmCPU) method uses a bin method under the assumption that quantitative trait nucleotides (QTNs) are evenly distributed throughout the genome. The estimated QTNs are used to separate a mixed linear model into a computationally efficient fixed effect model (FEM) and a computationally expensive random effect model (REM), which are then used iteratively. To completely eliminate the computationally expensive REM, we replaced REM with FEM by using Bayesian information criteria. To eliminate the requirement that QTNs be evenly distributed throughout the genome, we replaced the bin method with linkage disequilibrium information. The new method is called Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK). Both real and simulated data analyses demonstrated that BLINK improves statistical power compared to FarmCPU, in addition to remarkably reducing computing time. Now, a dataset with one million individuals and one-half million markers can be analyzed within three hours, instead of one week using FarmCPU.
Path Dependency in Jury Decision Making
Authors: Bindler Anna , Hjalmarsson Randi 
Published: December 2018

Abstract
A large behavioral economics literature is concerned with cognitive biases in individual and group decisions, including sequential decisions. These studies often find a negative path-dependency consistent with mechanisms such as the gambler's fallacy or contrast effects. We provide the first test for such biases in group decision making using observational data. Specifically, we study more than 27,000 verdicts adjudicated sequentially by over 900 juries for high-stake criminal cases at London's Old Bailey Criminal Court in the 18th and 19th centuries. Using jury fixed effects to account for heterogeneity in their baseline propensity to convict, we find that a previous guilty verdict significantly increases the chance of a subsequent guilty verdict by 6.7%–14.1%. This positive autocorrelation is robust to alternative estimation strategies, independent of jury experience and driven by the most recent lag and pairs of similar cases. Such positive path dependency may be explained by sequential assimilation effects, which may reflect a jury's desire to be internally consistent, and short-term “emotional” impacts of the characteristics and/or outcome of one case on another. As in modern-day jury studies, our results highlight that factors independent of the facts and evidence of the current case might affect jury behavior.
Safety and Efficacy of Lofexidine for Medically Managed Opioid Withdrawal: A Randomized Controlled Clinical Trial
Authors: Fishman Marc , Tirado Carlos , Alam Danesh , Gullo Kristen , Clinch Thomas , Gorodetzky Charles W. 
Published: December 2018

Objectives:To investigate the safety and efficacy of lofexidine for treating opioid withdrawal syndrome (OWS) and facilitating completion of opioid withdrawal.Methods:A multicenter, double-blind, placebo-controlled study was conducted at 18 US centers from June 2013 to December 2014. Participants (n = 603) aged ≥18 years, dependent on short-acting opioids, and seeking withdrawal treatment, randomized 3:3:2 to receive lofexidine 2.88 mg/d (n = 222), lofexidine 2.16 mg/d (n = 230), or placebo (n = 151) for 7 days. Primary outcome was the Short Opiate Withdrawal Scale of Gossop (SOWS-Gossop) scores rating withdrawal symptoms over days 1 to 7.Results:Participants were of mean age, 35 years; 71% male. Pairwise differences in overall SOWS-Gossop log-transformed least squares means were statistically significant for lofexidine 2.16 mg (difference, −0.21; 95% CI, −0.37 to −0.04;P = 0.02) and 2.88 mg (−0.26; 95% CI, −0.44 to −0.09;P = 0.003) compared with placebo. Fewer than half of participants in both groups completed the study. Completion rates for lofexidine 2.16 mg (41.5%; odds ratio [OR], 1.85;P = 0.007) and 2.88 mg (39.6%; OR, 1.71;P = 0.02) were significantly better compared with placebo (27.8%). Overall adverse event (AE) rates were similar across groups. Common AEs for lofexidine included orthostatic hypotension, hypotension, and bradycardia, but resulted in few study discontinuations.Conclusions:Lofexidine 2.16 mg and 2.88 mg significantly reduced symptoms of OWS versus placebo, and increased absolute rates of completing the 7-day study by 14% and 12%, respectively (a relative increase of 85% and 71%). Data suggest that lofexidine is a generally safe and effective nonopioid treatment for opioid withdrawal. Lofexidine could serve as a withdrawal treatment option when a nonopioid agent is preferred or required, when agonist-assisted withdrawal is unavailable, when agonist discontinuation caused OWS, and during induction into maintenance treatment with opioid agonists or antagonists.Trial Registration:ClinicalTrials.gov identifier: NCT01863186.
Gene-function studies in systemic lupus erythematosus
Authors: Rosetti Florencia , de la Cruz Abigail , Crispín José C. 
Published: December 2018

Purpose of review
The aim of this review is to discuss recent developments in our understanding of how systemic lupus erythematosus (SLE)-associated genes contribute to autoimmunity.

Recent findings
Gene-function studies have revealed mechanisms through which SLE-associated alleles of IFIH1, TNFAIP3, IRF5, and PRDM1 likely contribute to the development of autoimmunity. Novel research has identified Mac-1 (encoded by ITGAM), CaMK4, and iRhom2 as plausible therapeutic targets in lupus nephritis.

Summary
The work discussed in this review has broad implications for our understanding of the pathogenesis of SLE and for the development of novel therapeutic strategies.
The microbiome in systemic autoimmune disease: mechanistic insights from recent studies
Authors: Dehner Carina , Fine Rebecca , Kriegel Martin A. 
Published: December 2018

Purpose of review
The resident bacterial communities and the host immune system have coevolved for millennia. However, recent changes in modern societies have disrupted this coevolutionary homeostasis and contributed to a rise in immune-mediated conditions. The purpose of this review is to provide an overview of recently elucidated mechanisms of how certain taxa within the bacterial microbiome propagate autoimmunity.

Recent findings
Interactions between the bacterial microbiome with innate and adaptive immune cells propagate autoreactivity, chronic inflammation, and tissue damage in susceptible hosts. These interactions contribute to autoimmune diseases such as rheumatoid arthritis or systemic lupus erythematosus, which are the focus of this review. Recent findings suggest that autoimmune manifestations in genetically susceptible individuals can arise through cross-reactivity with commensal orthologs of autoantigens or commensal-mediated posttranslational modification of autoantigens. Physiologic responses to gut, oral, or skin commensal bacteria can thus be misdirected toward such autoantigens in susceptible hosts. In addition, recent studies highlight that a breach of the gut barrier and translocation of commensal bacteria to non-gut organs can trigger several autoimmune pathways that can be prevented by commensal vaccination or dietary interventions.

Summary
Complex host–microbiota interactions contribute to systemic autoimmunity outside the gut. On a molecular level, posttranslational modification of, and cross-reactivity with, autoantigens represent mechanisms of how the microbiota mediates autoimmunity. On a cellular level, translocation of live gut bacteria across a dysfunctional gut barrier allows for direct interactions with immune and tissue cells, instigating autoimmunity systemically.
Sacubitril/Valsartan in Daily Clinical Practice: Data From a Prospective Registry
Authors: Vicent Lourdes , Esteban-Fernández Alberto , Gómez-Bueno Manuel , De-Juan Javier , Díez-Villanueva Pablo , Iniesta Ángel Manuel , Ayesta Ana , González-Saldívar Hugo , Rojas-González Antonio , Bover-Freire Ramón , Iglesias Diego , García-Aguado Marcos , Perea-Egido Jesús A. , Martínez-Sellés Manuel 
Published: December 2018

Abstract:
Sacubitril/valsartan (SV) is a new therapy in heart failure with reduced ejection fraction. Our aim was to determine the efficacy and safety of this drug daily clinical practice. We performed a multicenter registry in 10 hospitals. All patients who started SV from October 2016 to March 2017 on an outpatient basis were included. A total of 427 patients started treatment with SV. Mean follow-up was 7.0 ± 0.1 months. Forty-nine patients (11.5%) discontinued SV, and 12 (2.8%) died. SV discontinuation was associated with higher cardiovascular (hazard ratio 13.22, 95% confidence interval, 6.71–15.73, P < 0.001) and all-cause mortality (hazard ratio 13.51, 95% confidence interval 3.22–56.13, P < 0.001). Symptomatic hypotension occurred in 71 patients (16.6%). Baseline N-terminal pro–B-type natriuretic peptide levels, functional class, and left ventricular ejection fraction improved at the end of follow-up in patients who continued with SV (all P values ≤0.001). This improvement was not significant in patients with SV discontinuation. SV has a good tolerability in patients from daily clinical practice. SV withdrawal in patients with heart failure and reduced ejection fraction was independently associated with increased all-cause mortality. Patients who continued with SV presented an improvement in functional class left ventricular ejection fraction and N-terminal pro–B-type natriuretic peptide levels.
Atorvastatin Improves Doxorubicin-Induced Cardiac Dysfunction by Modulating Hsp70, Akt, and MAPK Signaling Pathways
Authors: Gao Ge , Jiang Shiliang , Ge Lili , Zhang Shanshan , Zhai Chungang , Chen Wenqiang , Sui Shujian 
Published: December 2018

Abstract:
Atorvastatin is a lipid-regulating drug that is commonly used in clinical practice and can stabilize plaques. Increasing evidence shows that statins have anti–heart failure (HF) effects, but their specific mechanism is not clear. The purpose of this study was to investigate the cardioprotective effects of atorvastatin on HF in rats and its mechanism. Continuous intraperitoneal injection of 2.5 mg/kg/w doxorubicin for 6 weeks, with a cumulative dose of 15 mg/kg, was used to induce a rat model of HF. Then, the rats were treated with low-dose atorvastatin, high-dose atorvastatin, or saline for 4 weeks. In the DOX-treated groups, echocardiography showed decreases in left ventricular ejection fraction and fractional shortening and increases in left ventricular end-diastolic diameter and left ventricular posterior wall thickness compared with those in the control group, and increased levels of brain natriuretic peptide and Hsp70 were also found in the doxorubicin-treated groups. Compared with saline intervention, atorvastatin ameliorated left ventricular ejection fraction, fractional shortening, left ventricular end-diastolic diameter, and left ventricular posterior wall thickness (a significant difference was observed only in the high-dose group) and reduced serum brain natriuretic peptide. Hematoxylin and eosin staining showed that atorvastatin ameliorated myocardial injury. The improvement in cardiac function induced by atorvastatin was accompanied by increased Hsp70 expression, decreased p-ERK and p-JNK expression, and a reduction in myocardial fibrosis shown by Masson staining. In addition, atorvastatin had a protective effect on the myocardial apoptosis signaling pathway, with increased p-Akt expression and downregulated cleaved caspase-3 expression, and the reduction in myocardial apoptosis was confirmed by a TUNEL assay. Therefore, our experiments demonstrated that atorvastatin may protect cardiac function by modulating Hsp70, p-Akt, p-ERK, and p-JNK signaling to reduce myocardial fibrosis and myocardial apoptosis.