bluuebunny/crossref_metadata_2025_split huggingface dataset:
Substance-Related Disorders
Authors: Daley Dennis C. , Douaihy Antoine 
Published: August 2019

Abstract
Substance-induced disorders include intoxication, withdrawal, and other substance- or medication-induced mental disorders such as depression, anxiety, or psychotic symptoms that are associated with use of specific types of substances. When the substances are stopped, the symptoms get better or go away altogether. SUDs include disorders related to use of alcohol, caffeine, cannabis, hallucinogens, inhalants, opioids, sedatives, hypnotics or anxiolytics, stimulants, tobacco, and other (or unknown) substances. Eleven criteria are listed for diagnosis of an SUD. Statistics on SUDs in the United States are given. Advice is offered for family members and significant others who have a loved one with an SUD.
Effects of Substance Use Disorders
Authors: Daley Dennis C. , Douaihy Antoine 
Published: August 2019

Abstract
Effects of an alcohol or drug problem vary from mild to moderate to severe to fatal. As with any mild problem, there is a risk that it can worsen over time and lead to addiction. The effects of an SUD on the user or on the family depend on a combination of factors, including the amount, frequency, and methods of substance use; the presence of a co-occurring medical or psychiatric disorder; the user’s behavior and functioning; exposure to trauma; quality of relationships and social support; positive life experiences; access to treatment and recovery and willingness to stick with it; and motivation for change. Examples of the effects that SUDs can have in various areas of functioning are given.
Relapse After a Period of Recovery
Authors: Daley Dennis C. , Douaihy Antoine 
Published: August 2019

Abstract
Using alcohol or drugs after a period of recovery is called a lapse or a relapse. A lapse refers to the first episode of use, and may or may not lead to a relapse. A relapse refers to continued use of alcohol or drugs after the initial lapse. People with SUDs may lapse or relapse only once, several times, or many times. Although it is possible for anyone to get and stay sober, some people are at greater risk for relapse. It is best to view these people as struggling more than others who do better. Those who relapse are not bad but vulnerable people who have trouble controlling their use.
Treatment and Recovery for the Family
Authors: Daley Dennis C. , Douaihy Antoine 
Published: August 2019

Abstract
For the overall family, recovery involves changing how the family functions. It not only has to adjust to the sobriety of the recovering member (if this person is in recovery) but also has to make changes to function more effectively as a unit. Areas the family may need to address include accepting the SUD, stopping behaviors that reinforce substance use, improving communication, shifting family roles, reestablishing boundaries between generations, and building family togetherness. In some families, problems such as violence or abuse must be addressed. Professional treatment may be needed to address these issues and make changes in how the family functions. The change process can continue after treatment in mutual support programs.
Recovery for Individual Family Members
Authors: Daley Dennis C. , Douaihy Antoine 
Published: August 2019

Abstract
It is common to initially get involved in a family member’s treatment mainly to support him in getting and staying sober. However, as we start learning about SUDs, recovery, and the impact on family members, we may realize that involvement in our own recovery offers us a chance to address our personal issues, make changes, and grow as people. Recovery refers to learning about SUDs and their impact on us, healing from emotional hurts we experienced, and making changes so that we feel better about ourselves and more in control of our lives. This chapter provides an overview of mutual support groups and online resources.
The Hubble Sequence at z ∼ 0 in the IllustrisTNG simulation with deep learning
Authors: Huertas-Company Marc , Rodriguez-Gomez Vicente , Nelson Dylan , Pillepich Annalisa , Bottrell Connor , Bernardi Mariangela , Domínguez-Sánchez Helena , Genel Shy , Pakmor Ruediger , Snyder Gregory F , Vogelsberger Mark 
Published: August 2019

ABSTRACT
We analyse the optical morphologies of galaxies in the IllustrisTNG simulation at z ∼ 0 with a convolutional neural network trained on visual morphologies in the Sloan Digital Sky Survey. We generate mock SDSS images of a mass complete sample of $\sim 12\, 000$ galaxies in the simulation using the radiative transfer code SKIRT and include PSF and noise to match the SDSS r-band properties. The images are then processed through the exact same neural network used to estimate SDSS morphologies to classify simulated galaxies in four morphological classes (E, S0/a, Sab, Scd). The CNN model classifies simulated galaxies in one of the four main classes with the same uncertainty as for observed galaxies. The mass–size relations of the simulated galaxies divided by morphological type also reproduce well the slope and the normalization of observed relations which confirms a reasonable diversity of optical morphologies in the TNG suite. However we find a weak correlation between optical morphology and Sersic index in the TNG suite as opposed to SDSS which might require further investigation. The stellar mass functions (SMFs) decomposed into different morphologies still show some discrepancies with observations especially at the high-mass end. We find an overabundance of late-type galaxies ($\sim 50{{\ \rm per\ cent}}$ versus $\sim 20{{\ \rm per\ cent}}$) at the high-mass end [log(M*/M⊙) > 11] of the SMF as compared to observations according to the CNN classifications and a lack of S0 galaxies ($\sim 20{{\ \rm per\ cent}}$ versus $\sim 40{{\ \rm per\ cent}}$) at intermediate masses. This work highlights the importance of detailed comparisons between observations and simulations in comparable conditions.
What determines the sizes of bars in spiral galaxies?
Authors: Erwin Peter 
Published: August 2019

ABSTRACT
I use volume- and mass-limited subsamples and recently published data from the Spitzer Survey of Stellar Structure in Galaxies (S4G) to investigate how the size of bars depends on galaxy properties. The known correlation between bar semimajor axis a and galaxy stellar mass (or luminosity) is actually bimodal: for $\log \, (M_{\star }/\mathrm{M}_{\odot })\lesssim 10.1$, bar size is almost independent of stellar mass ($a \propto M_{\star }^{0.1}$), while it is a strong function for higher masses ($a \propto M_{\star }^{0.6}$). Bar size is a slightly stronger function of galaxy half-light radius Re and (especially) exponential disc scale length h (a ∝ h0.8). Correlations between stellar mass and galaxy size can explain the bar-size–M⋆ correlation – but only for galaxies with $\log \, (M_{\star }/\mathrm{M}_{\odot })\lesssim 10.1$; at higher masses, there is an extra dependence of bar size on M⋆ itself. Despite theoretical arguments that the presence of gas can affect bar growth, there is no evidence for any residual dependence of bar size on (present-day) gas mass fraction. The traditional dependence of bar size on Hubble type (longer bars in early-type discs) can be explained as a side effect of stellar mass–Hubble-type correlations. Finally, I show that galaxy size (Re or h) can be modelled as a function of stellar mass and both bar presence and bar size: barred galaxies tend to be more extended than unbarred galaxies of the same mass, with larger bars correlated with larger sizes.
The AGN fuelling/feedback cycle in nearby radio galaxies – II. Kinematics of the molecular gas
Authors: Ruffa Ilaria , Davis Timothy A , Prandoni Isabella , Laing Robert A , Paladino Rosita , Parma Paola , de Ruiter Hans , Casasola Viviana , Bureau Martin , Warren Joshua 
Published: August 2019

ABSTRACT
This is the second paper of a series exploring the multicomponent (stars, warm and cold gas, and radio jets) properties of a sample of 11 nearby low-excitation radio galaxies, with the aim of better understanding the active galactic nuclei (AGN) fuelling/feedback cycle in these objects. Here, we present a study of the molecular gas kinematics of six sample galaxies detected in 12CO(2-1) with the Atacama Large Millimeter/submillimeter Array (ALMA). In all cases, our modelling suggests that the bulk of the gas in the observed (sub-)kpc CO discs is in ordered rotation. Nevertheless, low-level distortions are ubiquitous, indicating that the molecular gas is not fully relaxed into the host galaxy potential. The majority of the discs, however, are only marginally resolved, preventing us from drawing strong conclusions. NGC 3557 and NGC 3100 are special cases. The features observed in the CO velocity curve of NGC 3557 allow us to estimate a supermassive black hole (SMBH) mass of (7.10 ± 0.02) × 108 M⊙, in agreement with expectations from the MSMBH–σ* relation. The rotation pattern of NGC 3100 shows distortions that appear to be consistent with the presence of both a position angle and an inclination warp. Non-negligible radial motions are also found in the plane of the CO disc, likely consistent with streaming motions associated with the spiral pattern found in the inner regions of the disc. The dominant radial motions are likely to be inflows, supporting a scenario in which the cold gas is contributing to the fuelling of the AGN.
Error formulae for the energy-dependent cross-spectrum
Authors: Ingram Adam 
Published: August 2019

Abstract
I present analytic error formulae for the energy-dependent cross-spectrum and rms spectrum, which are Fourier statistics widely used to probe the rapid X-ray variability observed from accreting compact objects. The new formulae cover the modulus, phase, real and imaginary parts of the cross-spectrum, and are valid for any value of intrinsic coherence between variability in different energy bands. I show that existing error formulae (including that for the phase lag), which are valid for a single cross-spectrum or power spectrum, lead to over-fitting when applied to the energy-dependent cross-spectrum - which consists of cross-spectra between individual energy channels and a common reference band. I also introduce an optimal, unbiased way to define the reference band and an accurate way to calculate the intrinsic coherence between energy bands. I find that the traditional use of the old formulae has likely had a rather benign impact on the literature, but recommend the use of the new formulae in future wherever appropriate, since they are more accurate and are no harder to implement than existing error estimates. A code to implement the new error formulae on observational data is available online.
Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species
Authors: Mugal Carina F , Kutschera Verena E , Botero-Castro Fidel , Wolf Jochen B W , Kaj Ingemar 
Published: August 2019

AbstractThe ratio of nonsynonymous over synonymous sequence divergence, dN/dS, is a widely used estimate of the nonsynonymous over synonymous fixation rate ratio ω, which measures the extent to which natural selection modulates protein sequence evolution. Its computation is based on a phylogenetic approach and computes sequence divergence of protein-coding DNA between species, traditionally using a single representative DNA sequence per species. This approach ignores the presence of polymorphisms and relies on the indirect assumption that new mutations fix instantaneously, an assumption which is generally violated and reasonable only for distantly related species. The violation of the underlying assumption leads to a time-dependence of sequence divergence, and biased estimates of ω in particular for closely related species, where the contribution of ancestral and lineage-specific polymorphisms to sequence divergence is substantial. We here use a time-dependent Poisson random field model to derive an analytical expression of dN/dS as a function of divergence time and sample size. We then extend our framework to the estimation of the proportion of adaptive protein evolution α. This mathematical treatment enables us to show that the joint usage of polymorphism and divergence data can assist the inference of selection for closely related species. Moreover, our analytical results provide the basis for a protocol for the estimation of ω and α for closely related species. We illustrate the performance of this protocol by studying a population data set of four corvid species, which involves the estimation of ω and α at different time-scales and for several choices of sample sizes.
On Rimsky-Korsakov’s False (Hexatonic) Progressions Outside the Limits of a Tonality
Authors: Ewell Philip 
Published: August 2019

AbstractIt is well known that Nikolai Rimsky-Korsakov used various types of octatonicism in his music, and that he likely passed on this eight-note device to his students, including, most famously, Igor Stravinsky. However, little work has been done with respect to Rimsky-Korsakov’s use of hexatonicism, despite its frequent appearance in his music. Octatonic and hexatonic structures arise naturally in Rimsky’s concept of “false progressions” along the cycle of minor and major thirds, respectively, a concept that he included at the end of his influential harmony textbook from 1885. In this article I examine his use of hexatonicism and demonstrate how it was a significant part of both his pedagogy and his compositions. In music examples selected from his operas, I identify three types of hexatonic structures and suggest specific dramatic and expressive functions for why he may have used them. I then discuss Rimsky’s own beliefs, expressed in his writings, about the hexatonic collection, which he called “wild” and “luring.” Ultimately, I aim to enrich the discourse on Rimsky-Korsakov the teacher, writer, and composer, beyond the typical Western narrative of Rimsky-Korsakov as, primarily, the teacher of Igor Stravinsky.
Novel bioinformatics quality control metric for next-generation sequencing experiments in the clinical context
Authors: Ivanov Maxim , Ivanov Mikhail , Kasianov Artem , Rozhavskaya Ekaterina , Musienko Sergey , Baranova Ancha , Mileyko Vladislav 
Published: August 2019

Abstract
As the use of next-generation sequencing (NGS) for the Mendelian diseases diagnosis is expanding, the performance of this method has to be improved in order to achieve higher quality. Typically, performance measures are considered to be designed in the context of each application and, therefore, account for a spectrum of clinically relevant variants. We present EphaGen, a new computational methodology for bioinformatics quality control (QC). Given a single NGS dataset in BAM format and a pre-compiled VCF-file of targeted clinically relevant variants it associates this dataset with a single arbiter parameter. Intrinsically, EphaGen estimates the probability to miss any variant from the defined spectrum within a particular NGS dataset. Such performance measure virtually resembles the diagnostic sensitivity of given NGS dataset. Here we present case studies of the use of EphaGen in context of BRCA1/2 and CFTR sequencing in a series of 14 runs across 43 blood samples and 504 publically available NGS datasets. EphaGen is superior to conventional bioinformatics metrics such as coverage depth and coverage uniformity. We recommend using this software as a QC step in NGS studies in the clinical context. Availability: https://github.com/m4merg/EphaGen or https://hub.docker.com/r/m4merg/ephagen.
Comparison of the removal of uraemic toxins with medium cut-off and high-flux dialysers: a randomized clinical trial
Authors: Belmouaz Mohamed , Bauwens Marc , Hauet Thierry , Bossard Valentin , Jamet Pierre , Joly Florent , Chikhi Elise , Joffrion Sandrine , Gand Elise , Bridoux Frank 
Published: August 2019

AbstractBackgroundAccumulation of middle-weight uraemic toxins in haemodialysis (HD) patients results in increased morbidity and mortality. Whether medium cut-off HD (MCO-HD) improves removal of middle-weight uraemic toxins remains to be demonstrated.MethodsThis cross-over prospective study included 40 patients randomly assigned to receive either 3 months of MCO-HD followed by 3 months of high-flux HD (HF-HD), or vice versa. The primary endpoint was myoglobin reduction ratio (RR) after 3 months of MCO-HD. Secondary endpoints were the effect of MCO-HD on other middle-weight toxins and protein-bound toxins, and on parameters of nutrition, inflammation, anaemia and oxidative stress.ResultsCompared with HF-HD, MCO-HD provided higher mean RR of myoglobin (36 ± 8 versus 57 ± 13%, P < 0.0001), beta2-microglobulin (68 ± 6 versus 73 ± 15%, P = 0.04), prolactin (32 ± 13 versus 59 ± 11%, P < 0.0001), fibroblast growth factor 23 (20 ± 21 versus 41 ± 22%, P = 0.0002), homocysteine (43 ± 7 versus 46 ± 9%, P = 0.03) and higher median RR of kappa [54 (48–58) versus 70 (63–74)%, P < 0.0001] and lambda free light chain (FLC) [15 (9–22) versus 44 (38–49)%, P < 0.0001]. Mean ± SD pre-dialysis levels of beta2-microglobulin (28.4 ± 5.6 versus 26.9 ± 5.1 mg/L, P = 0.01) and oxidized low-density lipoprote (6.9 ± 4.4 versus 5.5 ± 2.5 pg/mL, P = 0.04), and median (interquartile range) kappa FLC [145 (104–203) versus 129 (109–190) mg/L, P < 0.03] and lambda FLC [106 (77–132) versus 89 (62–125) mg/L, P = 0.002] were significantly lower. Mean albumin levels decreased significantly (38.2 ± 4.1 versus 36.9 ± 4.3 g/L, P = 0.004), without an effect on nutritional status as suggested by unchanged normalized protein catabolic rate and transthyretin level.ConclusionsCompared with HF-HD, MCO-HD provides higher myoglobin and other middle molecules RR and is associated with moderate hypoalbuminemia. The potential benefits of this strategy on long-term clinical outcomes deserve further evaluation.
Effects of Very Low Nicotine Content Cigarettes on Smoking Behavior and Biomarkers of Exposure in Menthol and Non-menthol Smokers
Authors: Denlinger-Apte Rachel L , Kotlyar Michael , Koopmeiners Joseph S , Tidey Jennifer W , Luo Xianghua , Benowitz Neal L , Jensen Joni A , Ikuemonisan Joshua O , Pacek Lauren R , Smith Tracy T , Vandrey Ryan , Donny Eric C , Hatsukami Dorothy K 
Published: August 2019

Abstract

Introduction
Because 30% of cigarettes sold in the United States are characterized as menthol cigarettes, it is important to understand how menthol preference may affect the impact of a nicotine reduction policy.

Methods
In a recent trial, non-treatment-seeking smokers were randomly assigned to receive very low nicotine cigarettes (VLNC; 0.4 mg nicotine/g tobacco) or normal nicotine cigarettes (NNC; 15.5 mg/g) for 20 weeks. On the basis of preference, participants received menthol or non-menthol cigarettes. We conducted multivariable regression analyses to examine whether menthol preference moderated the effects of nicotine content on cigarettes per day (CPD), breath carbon monoxide (CO), urinary total nicotine equivalents (TNE), urinary 2-cyanoethylmercapturic acid (CEMA), and abstinence.

Results
At baseline, menthol smokers (n = 346) reported smoking fewer CPD (14.9 vs. 19.2) and had lower TNE (52.8 vs. 71.6 nmol/mg) and CO (17.7 vs. 20.5 ppm) levels than non-menthol smokers (n = 406; ps &lt; .05). At week 20, significant interactions indicated that menthol smokers had smaller treatment effects than non-menthol smokers for CPD (–6.4 vs. –9.3), TNE (ratio of geometric means, 0.22 vs. 0.10) and CEMA (ratio, 0.56 vs. 0.37; ps &lt; .05), and trended toward a smaller treatment effect for CO (–4.5 vs. –7.3 ppm; p = .06). Odds ratios for abstinence at week 20 were 1.88 (95% confidence interval [CI] = 0.8 to 4.4) for menthol and 9.11 (95% CI = 3.3 to 25.2) for non-menthol VLNC smokers (p = .02) relative to the NNC condition.

Conclusions
Although menthol smokers experienced reductions in smoking, toxicant exposure, and increases in quitting when using VLNC cigarettes, the magnitude of change was smaller than that observed for non-menthol smokers.

Implications
Results of this analysis suggest that smokers of menthol cigarettes may respond to a nicotine reduction policy with smaller reductions in smoking rates and toxicant exposure than would smokers of non-menthol cigarettes.
Intradural Extramedullary Surgical Lysis of an Arachnoid Web of the Spine: 2-Dimensional Operative Video
Authors: Hussain Ibrahim , Nisson Peyton L , Kim Samuel , Baaj Ali A 
Published: August 2019

Abstract
Arachnoid web of the spine (AWS) is a rare and subtle lesion that can have severe neurological consequences. Patients typically present with progressive myelopathic symptoms and have no more than a slight indentation of spinal cord on imaging, commonly referred to as the “scalpel sign.” A unique feature associated with this lesion is the extent of (and sometimes the rapidity of) the recovery that occurs following treatment. In this operative video, we highlight the treatment of a 32-yr-old male with a history of lumbar spondylosis, who, over a 2 wk period, developed progressive spasticity and weakness of the entire left lower extremity and left foot numbness. Magnetic resonance imaging revealed a T4-T5 “scalpel sign” and spinal cord compression on computed topography myelogram, which was subsequently taken to the operating theater. The major steps in this video include the following: A) a summary of the patient's presentation and preoperative imaging, B) the technical steps in the surgical lysis of the AWS, and C) his postoperative course. The patient tolerated the procedure well, demonstrating a rapid improvement in symptoms postoperative day 1. At the time of most recent follow-up (4 mo), the patient remains neurologically intact with a full return to his neurologic baseline. Surgical lysis of AWS demonstrated to be a curative procedure with rapid neurological recovery, showing no signs of recurrence or regression. Consent was given by the patient for the use of deidentified images and the intraoperative video for educational purposes at the time consent was obtained for the surgical procedure, in accordance with our institution's policy.