bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tropospheric OH and stratospheric OH and Cl concentrations determined from CH4, CH3Cl, and SF6 measurements
Authors: Li Mengze , Karu Einar , Brenninkmeijer Carl , Fischer Horst , Lelieveld Jos , Williams Jonathan 
Published: August 2018

AbstractThe hydroxyl (OH) radical is the key oxidant in the global atmosphere as it controls the concentrations of toxic gases like carbon monoxide and climate relevant gases like methane. In some regions, oxidation by chlorine (Cl) radical is also important, and in the stratosphere both OH and Cl radicals impact ozone. An empirical method is presented to determine effective OH concentrations in the troposphere and lower stratosphere, based on CH4, CH3Cl, and SF6 data from aircraft measurements (IAGOS-CARIBIC) and a ground-based station (NOAA). Tropospheric OH average values of 10.9 × 105 (σ = 9.6 × 105) molecules cm−3 and stratospheric OH average values of 1.1 × 105 (σ = 0.8 × 105) molecules cm−3 were derived over mean ages derived from SF6. Using CH4 led to higher OH estimates due to the temperature dependence of the CH4 + OH reaction in the troposphere and due to the presence of Cl in the stratosphere. Exploiting the difference in effective OH calculated from CH3Cl and CH4 we determine the main altitude for tropospheric CH4 oxidation to be 4.5 ~ 10.5 km and the average Cl radical concentration in the lower stratosphere to be 1.1 × 104 (σ = 0.6 × 104) molecules cm−3 (with a 35% measurement uncertainty). Furthermore, the data are used to examine the temporal trend in annual average stratospheric OH and Cl radical concentrations between 2010 and 2015. The year 2013 showed highest stratospheric OH and lowest Cl but no clear temporal trend was observed in the data in this period. These data serve as a baseline for future studies of stratospheric circulation changes.
Effect of Renal Impairment on the Pharmacokinetics and Pharmacodynamics of Tofogliflozin (A SELECTIVE SGLT2 Inhibitor) in Patients with Type 2 Diabetes Mellitus
Authors: Ikeda Sachiya , Takano Yasuki , Schwab Dietmar , Portron Agnes , Kasahara-Ito Nahoko , Saito Tomohisa , Iida Satofumi 
Published: August 2018

Abstract
Purpose Tofogliflozin is an orally available selective inhibitor of sodium-glucose co-transporter 2 for treatment of type 2 diabetes mellitus (T2DM). Two studies were conducted to evaluate the effect of renal impairment on pharmacokinetics and pharmacodynamics of tofogliflozin.
Methods The studies were: 1) single dose study in T2DM patients with normal renal function and mild, moderate and severe renal impairment, and 2) multiple dose study for 24 weeks in T2DM patients with normal renal function and moderate renal impairment.
Results Renal function did not have a clinically relevant effect on the PK of tofogliflozin. Urinary glucose excretion up to 24 h after administration of tofogliflozin (UGE24h) decreased with decreasing glomerular filtration rate. Lowering UGE24h resulted in waning glycemic control but not body weight reduction.
Conclusions Single and multiple administrations of tofogliflozin were generally well tolerated in T2DM patients with various renal functions. As far as investigated here, these studies indicate no dose adjustment is required for patients with renal impairment.
Cardiopulmonary Function in Thoracic Wall Deformities: What Do We Really Know?
Authors: Velazco Cristine , Pulivarthi Venkata , Arsanjani Reza , Obermeyer Robert , Jaroszewski Dawn 
Published: August 2018

AbstractPatients with pectus excavatum (PE) frequently present with complaints of exercise intolerance and cardiopulmonary symptoms. There continues to be controversy regarding the physiologic benefits of repair. The aim of this review is to summarize and discuss recent data regarding the cardiopulmonary effects of PE deformity and the evidence for improvement obtained after surgical repair including (1) a greater efficiency of breathing (chest wall mechanics), (2) improvement in pulmonary restrictive deficits, (3) an increase in cardiac chamber size and output, with improved cardiac strain and strain rate, and (4) improvement in exercise capacity.
How does supercoiling regulation on a battery of RNA polymerases impact on bacterial transcription bursting?
Authors: Jing Xiaobo , Loskot Pavel , Yu Jin 
Published: August 2018

Abstract
Transcription plays an essential role in gene expression. The transcription bursting in bacteria has been suggested to be regulated by positive supercoiling accumulation in front of a transcribing RNA polymerase (RNAP) together with gyrase binding on DNA to release the supercoiling. In this work, we study the supercoiling regulation in the case of a battery of RNAPs working together on DNA by constructing a multi-state quantitative model, which allows gradual and stepwise supercoiling accumulation and release in the RNAP transcription. We solved for transcription characteristics under the multi-state bursting model for a single RNAP transcription, and then simulated for a battery of RNAPs on DNA with T7 and Escherichia coli RNAP types of traffic, respectively, probing both the average and fluctuation impacts of the supercoiling regulation. Our studies show that due to the supercoiling accumulation and release, the number of RNAP molecules loaded onto the DNA vary significantly along time in the traffic condition. Though multiple RNAPs in transcription promote the mRNA production, they also enhance the supercoiling accumulation to suppress the production. In particular, the fluctuations of the mRNA transcripts become highly pronounced for a battery of RNAPs transcribing together under the supercoiling regulation, especially for a long process of transcription elongation. In such an elongation process, though a single RNAP can work at a high duty ratio, multiple RNAPs are hardly able to do so. Our multi-state model thus provides a systematical characterization of the quantitative features of the bacterial transcription bursting; it also supports improved physical examinations on top of this general modeling framework.
CharGer: clinical Characterization of Germline variants
Authors: Scott Adam D , Huang Kuan-Lin , Weerasinghe Amila , Mashl R Jay , Gao Qingsong , Martins Rodrigues Fernanda , Wyczalkowski Matthew A , Ding Li 
Published: August 2018

Abstract

Summary
CharGer (Characterization of Germline variants) is a software tool for interpreting and predicting clinical pathogenicity of germline variants. CharGer gathers evidence from databases and annotations, provided by local tools and files or via ReST APIs, and classifies variants according to ACMG guidelines for assessing variant pathogenicity. User-designed pathogenicity criteria can be incorporated into CharGer’s flexible framework, thereby allowing users to create a customized classification protocol.

Availability and implementation
Source code is freely available at https://github.com/ding-lab/CharGer and is distributed under the GNU GPL-v3.0 license. Software is also distributed through the Python Package Index (PyPI) repository. CharGer is implemented in Python 2.7 and is supported on Unix-based operating systems.

Supplementary information
Supplementary data are available at Bioinformatics online.
Impacts of small-scale fisheries on mangrove fish assemblages
Authors: Reis-Filho José Amorim , Harvey Euan S , Giarrizzo Tommaso 
Published: August 2018

AbstractThe data requirements and resources needed to develop effective indicators of fishing impacts on target stocks may often be great, especially for mangrove fisheries where, for example, tidal cycles sequentially flood and drain the habitat as a result of natural processes. Here, we used underwater video systems to evaluate the impact of small-scale fisheries on mangrove fish assemblages at four levels of fishing pressure (low, medium, high, and no pressure). The lowest values of species richness and abundance were recorded in the areas fished most intensively. Conversely, the highest species richness and the occurrence of larger-bodied fish were recorded in areas of reduced fishing activity, which was surprisingly similar to the “no fishing” areas. The slopes of the community size spectra steepened in response to exploitation, while the relative abundance of medium-sized fish (16–25 cm) declined. Fishing for local or regional markets, rather than subsistence, also led to a decrease in the abundance of larger fish (&gt;41 cm). The marked response of population parameters to fishing pressure reflected the impact of unregulated small-scale fisheries on areas of mangroves. Fishery management practices that ignore contemporary changes in these environments are likely to overestimate long-term yields, leading to overfishing. Thus, size-based approaches to evaluating fishing pressure were suitable for detecting negative responses from the mangrove fish assemblages. A next step will be to integrate size- and species-based ecological approaches that provide mechanisms to address pronounced decreases in specific species as a more profitable indicator of fishing impacts on mangrove fish assemblages. This approach will allow the development of effective conservation and management strategies.
Harmful algal blooms and climate change: exploring future distribution changes
Authors: Townhill Bryony L , Tinker Jonathan , Jones Miranda , Pitois Sophie , Creach Veronique , Simpson Stephen D , Dye Stephen , Bear Elizabeth , Pinnegar John K 
Published: August 2018

AbstractHarmful algae can cause death in fish, shellfish, marine mammals, and humans, via their toxins or from effects associated with their sheer quantity. There are many species, which cause a variety of problems around north-west Europe, and the frequency and distribution of algal blooms have altered in the recent past. Species distribution modelling was used to understand how harmful algal species may respond in the future to climate change, by considering environmental preferences and how these may shift. Most distribution studies to date use low resolution global model outputs. In this study, high resolution, downscaled shelf seas climate projections for the north-west European shelf were nested within lower resolution global projections, to understand how the distribution of harmful algae may change by the mid to end of century. Projections suggest that the habitat of most species (defined by temperature, salinity, depth, and stratification) will shift north this century, with suitability increasing in the central and northern North Sea. An increase in occurrence here might lead to more frequent detrimental blooms if wind, irradiance and nutrient levels are also suitable. Prioritizing monitoring of species in these susceptible areas could help in establishing early-warning systems for aquaculture and health protection schemes.
Foliation by Area-constrained Willmore Spheres Near a Nondegenerate Critical Point of the Scalar Curvature
Authors: Ikoma Norihisa , Malchiodi Andrea , Mondino Andrea 
Published: August 2018

AbstractLet $(M,g)$ be a three-dimensional Riemannian manifold. The goal of the paper is to show that if $P_{0}\in M$ is a nondegenerate critical point of the scalar curvature, then a neighborhood of $P_{0}$ is foliated by area-constrained Willmore spheres. Such a foliation is unique among foliations by area-constrained Willmore spheres having Willmore energy less than $32\pi $; moreover, it is regular in the sense that a suitable rescaling smoothly converges to a round sphere in the Euclidean three-dimensional space. We also establish generic multiplicity of foliations and the 1st multiplicity result for area-constrained Willmore spheres with prescribed (small) area in a closed Riemannian manifold. The topic has strict links with the Hawking mass.
Homology Smale–Barden Manifolds with K-contact but not Sasakian Structures
Authors: Muñoz Vicente , Rojo Juan Angel , Tralle Aleksy 
Published: August 2018

Abstract
Kollár has found subtle obstructions to the existence of Sasakian structures on five-dimensional manifolds. In the present article we develop methods of using these obstructions to distinguish K-contact manifolds from Sasakian ones. In particular, we find the first example of a closed $5$-manifold $M$ with $H_1(M,\mathbb{Z})=0,$ which is K-contact but which carries no semi-regular Sasakian structures.
Outcomes of Pediatric Central Nervous System Tuberculosis in California, 1993–2011
Authors: Duque-Silva Alexandra , Hampole Varsha , Cheng Yi-Ning , Flood Jennifer , Barry Pennan M 
Published: August 2018

Abstract

Background
Our goal was to describe the characteristics and posttreatment outcomes of pediatric patients with central nervous system (CNS) tuberculosis (TB) and to identify factors associated with poor outcome.

Methods
We included children aged 0 to 18 years with CNS TB reported to the California TB registry between 1993 and 2011. Demographics, clinical characteristics, severity of disease at presentation (Modified Medical Research Council stage I, II, or III [III is most severe]), treatment, and outcomes during the year after treatment completion were abstracted systematically from the medical and public health records. Patient outcomes were categorized as good or poor on the basis of disability in hearing, vision, language, ambulation, and development and other neurologic deficits.

Results
Among 151 pediatric CNS TB cases reported between 1993 and 2011 in California for which records were available, 92 (61%) cases included sufficient information to determine outcome. Overall, 55 (60%) children had a poor outcome. After we adjusted for age (0 to 4 years), children with stage III severity (vs I or II; prevalence rate ratio [PRR], 1.4 [95% confidence interval (CI), 1.1–1.9]), a protein concentration of >100 mg/dL on initial lumbar puncture (PRR, 1.2 [95% CI, 1.03–1.4]), or infarct on neuroimaging (PRR, 1.2 [95% CI, 1.04–1.3]) were at increased risk for a poor outcome. In multivariate analysis, an age of 0 to 4 years (vs >4 years; PRR, 1.4 [95% CI, 1.2–1.7]) and a stage II or III Modified Medical Research Council score (vs stage I; PRR, 1.2 [95% CI, 1.03–1.5]) remained significantly associated with poor outcome.

Conclusions
Pediatric patients with CNS TB in California are left with high rates of disabling clinical sequelae after treatment. The identification of modifiable factors is critical for improving outcomes.
Permissive Metaepistemology
Authors: Thorstad David 
Published: August 2018

AbstractRecent objections to epistemic permissivism have a metaepistemic flavor. Impermissivists argue that their view best accounts for connections between rationality, planning and deference. Impermissivism is also taken to best explain the value of rational belief and normative assessment. These objections pose a series of metaepistemic explanatory challenges for permissivism. In this paper, I illustrate how permissivists might meet their explanatory burdens by developing two permissivist metaepistemic views which fare well against the explanatory challenges.
Rapid Stretch Injury to Peripheral Nerves: Biomechanical Results
Authors: Mahan Mark A , Yeoh Stewart , Monson Ken , Light Alan 
Published: August 2018

Abstract

BACKGROUND
Although most adult brachial plexus injuries result from high-speed mechanisms, no laboratory model has been created to mimic rapid-stretch nerve injuries. Understanding the biomechanical response of nerves to rapid stretch is essential to understanding clinical injury patterns and developing models that mimic the clinical scenario.

OBJECTIVE
To assess the influence of rate, loading direction, and excursion of stretch injuries on the biomechanical properties of peripheral nerves.

METHODS
The sciatic nerves of 138 Sprague-Dawley rats were dissected and subjected to rapid- and slow-stretch methods. Maximal nerve strain, persistent deformation, regional strain variation, and location of nerve failure were recorded.

RESULTS
Nerve rupture was primarily determined by weight-drop momentum >1 N/sec (odds ratio = 27.8, P < .0001), suggesting a threshold condition. Loading direction strongly determined maximal strain at rupture (P = .028); pull along the nerve axis resulted in nerve rupture at lower strain than orthogonal loading. Regional variations in nerve compliance and rupture location correlated with anatomic zones. Nerve branch anatomy was the largest contributing factor on maximum strain and rupture location. Rapidly stretched nerves are characterized by a zone of elastic recovery, followed by inelastic response at increasing strain, and finally rupture.

CONCLUSION
The large variation in previous results for nerve strain at rupture can be attributed to different testing conditions and is largely due to loading direction or segment of nerve tested, which has significant clinical implications. Nerve stretch injuries do not reflect a continuous variability to applied force but instead fall into biomechanical patterns of elastic, inelastic, and rupture injuries.
James and Hume
Authors: Inukai Yumiko 
Published: August 2018

Abstract
James contends that the rejection of conjunctive relations in experience leads Hume to the empirically groundless notion of discrete elements of experience, which James takes as the critical point that differentiates his empiricism from Hume’s. In this chapter, I argue that James is not right about this: Hume not only allows but employs experienced conjunctive relations in his explanations for the generation of our naturally held beliefs about the self and the world. There are indeed striking similarities between their accounts: they both use the relations of resemblance, temporal continuity, constancy, coherence, and regularity, and the self. Also, objects are constructed out of basic elements in their systems—pure experience and perceptions, respectively. Although collapsing the inner and outer worlds of the subject and object into one world (of pure experience for James and of perceptions for Hume) may seem unintuitive, this is exactly what allows them to preserve our ordinary sense of our experiences of objects.
Psychology and Philosophy in the Work of William James
Authors: Leary David E. 
Published: August 2018

Abstract
This chapter reviews the relations between psychology and philosophy in the work of William James. Though initially committed to limiting the role of philosophy in his psychological work, James eventually realized that an admixture of philosophy and psychology would not spoil “two good things,” as he had feared, and that it was in any case unavoidable. In fact, many of the basic pillars of his psychology depend upon philosophical distinctions, and many of the premises of his philosophy are drawn from psychological analyses. And while James focused more on psychology in his early years and more on philosophy toward the end of his life, his philosophical interests preceded his study of psychology, and his psychological interests extended throughout his career. An excursus treating James’s views on logic and the nonlogical, toward the end of the chapter, underscores the primacy of experience over analysis in James’s thought, both in psychology and philosophy.
High sustained virologic response rate using generic directly acting antivirals in the treatment of chronic hepatitis C virus Egyptian patients: single-center experience
Authors: El-Nahaas Saeed M. , Fouad Rabab , Elsharkawy Aisha , Khairy Marwa , Elhossary Walied , Anwar Ismail , Abdellatif Zeinab , Maher Rabab M. , Bekheet Nader , Esmat Gamal 
Published: August 2018

Background
Hepatitis C virus (HCV) is a major health problem in Egypt, with a high prevalence of genotype 4.

Aim
This study aimed to evaluate the safety and efficacy of generic sofosbuvir (SOF) plus generic daclatasvir (DAC) with or without ribavirin in the treatment of Egyptian chronic HCV patients compared with the use of brand drugs.

Materials and methods
An observational study that included 234 Egyptian chronic HCV patients was carried out. Patients were classified into two groups: group A (101 patients) received brand SOF 400 mg plus brand DAC 60 mg and group B (134 patients) received generic SOF 400 mg plus generic DAC 60 mg with or without ribavirin for 12 weeks. The end point was a sustained virological response at 12 weeks after treatment.

Results
Thirty-eight (37.2%) patients in group A were treatment experienced compared with 12 (9.02%) patients in group B; there were 39 (38%) cirrhotic patients in group A and 22 (16.5%) cirrhotic patients in group B. In group A, 50% of patients received ribavirin, while in group B, 42.1% of patients received ribavirin. All patients were followed up; all of them attended their week 12 post-treatment visit with negative HCV RNA, with achievement of sustained virological response at 12 in 100% of patients receiving generic drugs (group B) and 99% of patients receiving brand drugs (group A). Generic SOF and DAC were well tolerated, with mild adverse events including fatigue and headache.

Conclusion
Use of generic SOF and DAC with or without ribavirin is an extremely effective and a well-tolerated treatment for Egyptian chronic HCV patients.
Sofosbuvir based regimens in the treatment of chronic hepatitis C genotype 1 infection in African–American patients: a community-based retrospective cohort study
Authors: Gayam Vijay , Tiongson Benjamin , Khalid Mazin , Mandal Amrendra K. , Mukhtar Osama , Gill Arshpal , Garlapati Pavani , Shrestha Binav , Khalid Mowyad , Chakraborty Sandipan , Guss Debra , Sherigar Jagannath , Mansour Mohammed , Mohanty Smruti 
Published: August 2018

Background
Direct-acting antiviral (DAA) drugs have been highly effective in the treatment of chronic hepatitis C (HCV) infection. Limited data exist comparing the safety, tolerability, and efficacy of DAAs in African–American (AA) patients with chronic hepatitis C genotype 1 (HCV GT-1) in the community practice setting. We aim to evaluate treatment response of DAAs in these patients.

Patients and methods
All the HCV GT-1 patients treated with DAAs between January 2014 and January 2018 in a community clinic setting were retrospectively analyzed. Pretreatment baseline patient characteristics, treatment efficacy with a sustained virologic response at 12 weeks post-treatment (SVR12), and adverse reactions were assessed.

Results
Two-hundred seventy-eight patients of AA descent were included in the study. One-hundred sixty-two patients were treated with ledipasvir/sofosbuvir (SOF)±ribavirin, 38 were treated with simeprevir/SOF±ribavirin, and 38 patients were treated with SOF/velpatasvir. Overall, SVR at 12 weeks was achieved in 94.6% in patients who received one of the three DAA regimens (93.8% in ledipasvir/SOF group, 92.1% in simeprevir/SOF group, and 97.4% in SOF/velpatasvir group). Previous treatment experience, HCV RNA levels and HIV status had no statistical significance on overall SVR achievement (P=0.905, 0.680, and 0.425, respectively). Compensated cirrhosis in each of the treatment groups did not influence overall SVR of 12. The most common adverse effect was fatigue (27%). None of the patients discontinued the treatment because of adverse events.

Conclusion
In the real-world setting, DAAs are safe, effective, and well tolerated in African–American patients with chronic HCV GT-1 infection with a high overall SVR rate of 94.6%. Treatment rates did not differ on the basis of previous treatment and compensated cirrhosis status.