bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regularities in the spectrum of chaoticp-modes in rapidly rotating stars
Authors: Evano Benjamin , Lignières François , Georgeot Bertrand 
Published: September 2019

Context.Interpreting the oscillations of massive and intermediate mass stars remains a challenging task. In fast rotators, the oscillation spectrum ofp-modes is a superposition of sub-spectra which corresponds to different types of modes, among which island modes and chaotic modes are expected to be the most visible. This paper is focused on chaotic modes, which have not been thoroughly studied before.Aims.We study the properties of high frequency chaoticp-modes in a polytropic model. Unexpected peaks appear in the frequency autocorrelations of the spectra. Our goal is to find a physical interpretation for these peaks and also to provide an overview of the mode properties.Methods.We used the 2D oscillation code “TOP” to produce the modes and acoustic ray simulations to explore the wave properties in the asymptotic regime. Using the tools developed in the field of quantum chaos (or wave chaos), we derived an expression for the frequency autocorrelation involving the travel time of acoustic rays.Results.Chaotic mode spectra were previously thought to be irregular, that is, described only through their statistical properties. Our analysis shows the existence, in chaotic mode spectra, of a pseudo large separation. This means that chaotic modes are organized in series, such that the modes in each series follow a nearly regular frequency spacing. The pseudo large separation of chaotic modes is very close to the large separation of island modes. Its value is related to the sound speed averaged over the meridional plane of the star. In addition to the pseudo large separation, other correlations appear in the numerically calculated spectra. We explain their origin by the trapping of acoustic rays near the stable islands.
Bönninghausen-Forschung im Spiegel der ZKH und AHZ seit 1985
Authors: Lucae Christian 
Published: September 2019

ZusammenfassungDie „Bönninghausen-Methode“ ist in ihrer jetzigen Ausprägung erst in den letzten Jahrzehnten entstanden. Die Herausgabe einer revidierten Version des „Therapeutischen Taschenbuches“ im Jahre 2000 hat wesentlich zur Renaissance der Methode beigetragen, ebenso die Entwicklung der Polaritätsanalyse mitsamt zugehöriger Software. Außerdem sind einige theoretische Arbeiten erschienen, die die Methode an vielen Punkten aufgearbeitet und präzisiert haben. Viele Beiträge dazu sind in der ZKH und der AHZ nachzulesen. Ausgewählte Arbeiten, die einen wesentlichen Beitrag zur Weiterentwicklung geleistet haben, sollen im vorliegenden Artikel schlaglichtartig vorgestellt werden.
Worst-Case-Szenario: Akutes Koronarsyndrom unter Chemotherapie und moderner Supportivtherapie
Authors: Holzhauer Peter 
Published: September 2019

ZusammenfassungEine 47-jährige Patientin in gutem Allgemeinzustand und ohne bekannte kardiologische Komorbidität wird notfallmäßig mit einem akuten Koronarsyndrom auf einer Intensivstation aufgenommen. Als Grunddiagnose ist ein mit Pankreas-Linksresektion kurativ behandeltes Pankreaskarzinom bekannt. Die Patientin wird postoperativ mit insgesamt 12 Zyklen adjuvanter Chemotherapie nach dem FOLFIRINOX-Protokoll gemäß der PRODIGE-Studie therapiert 1. Zur Vermeidung einer Neutropenie (Risiko > 20%) wurde nach dem ersten und dem zweiten Zyklus jeweils ein Tag nach der Chemotherapie prophylaktisch G-CSF als Lipegfilgrastim appliziert 3. Gleichzeitig lag eine schon länger bekannte Thrombozytose bei Zustand nach Splenektomie vor. Die Patientin war während der Tage des stationären Aufenthaltes mit Enoxaparin antikoaguliert. Die kardiologische Akutdiagnostik ergab ein akutes Koronarsyndrom mit thromboembolischem Verschluss mehrerer Koronararterien, ohne dass eine koronare Herzkrankheit vorlag. Die Patientin wurde kardiologisch interventionell erfolgreich therapiert und konnte zuletzt auch den 12. Zyklus der adjuvanten Chemotherapie komplikationslos abschließen.
Patient and Physician Perceptions of the Impact of Electronic Health Records on the Patient–Physician Relationship
Authors: Eberts Margaret , Capurro Daniel 
Published: September 2019

Abstract
Objectives Limited studies have been performed in South America to assess patient and physician perceptions of electronic health record (EHR) usage. We aim to study the perceptions of patients and physicians regarding the impact of EHRs on the patient–physician relationship.
Methods We use a survey instrument to assess the physician computer experience and opinions regarding EHR impact on various aspects of patient care. An additional survey is used to assess patient opinions related to their medical visit. Surveys are administered in two outpatient clinics in a private, academic health care network.
Results While a majority of physicians believed that EHRs have an overall positive impact on the quality of health care, many physicians had negative perceptions of the impact of EHRs on the patient–physician relationship. A majority of patients felt comfortable with their physician's use of the EHR and felt that their physician was able to maintain good personal contact while using the computer.
Conclusion Although physicians believe EHRs have a generally positive impact on the overall quality of care, the EHR's impact on the patient–physician relationship is still of concern. Patients do not perceive a negative interference from the EHR on the patient–physician relationship.
Classification and Management of Donor-Site Wound Complications in the Profunda Artery Perforator Flap for Breast Reconstruction
Authors: Cho Min-Jeong , Teotia Sumeet S. , Haddock Nicholas T. 
Published: September 2019

Abstract
Background Profunda artery perforator (PAP) flap breast reconstruction has emerged as a popular choice for patients who are not optimal candidates for autologous breast reconstruction using abdominal-based techniques such as the deep inferior epigastric perforator flap. Despite increased utilization of PAP flaps, there are no previous studies on the donor-site morbidity. In this study, we present risk factors, classification of thigh wounds, and our management of donor-site wounds.
Methods Retrospective review of 69 patients who underwent PAP flap from 2013 to 2016 was performed. Demographic, patient characteristic, and flap data were collected. Postoperative photographs of donor sites were reviewed, and the wounds were classified into three types: type I—normal wound, type II—minor scab, and type III—dehiscence.
Results Of the 69 patients (130 flaps), there were 13 patients (17 flaps) with wound dehiscence (13%), 8 patients with cellulitis (8.5%), 2 patients with seroma (3%), and 1 patient with hematoma (1.5%). The patients with wound dehiscence had statistically higher body mass index (BMI) (29.2 vs. 26.5) with p-value < 0.05 than the patients without wound complications. These patients had higher flap weight (514 vs. 439.7 g), were older (50.8 vs. 48.6 years old), and had a higher chance of being a diabetic (6 vs. 2%), but statistical significance was not achieved. The patients with dehiscence were managed with local wound care (63%), wound vacuum (26%), and operative intervention (11%).
Conclusion Our study shows that BMI plays a significant role in the development of postoperative thigh wounds, and all wounds occurred at the medial thigh. However, the majority of the study population did not require any intervention, and revision of scar using the posterior thigh advancement flaps can be used to improve the gluteal aesthetics. We believe findings from our study can help plastic surgeons to counsel and assist patients who will undergo breast reconstruction with a PAP flap.
Wine Regulations
Authors: Meloni Giulia , Anderson Kym , Deconinck Koen , Swinnen Johan 
Published: September 2019

AbstractThis paper provides an overview and analysis of wine regulations in an international and historical comparative perspective. Wine is an excellent sector to study government interventions because for centuries wine markets have been subject to many government regulations that differ greatly within and between countries. Wine consumption taxes, for example, range from zero in some countries to more than 100% in others. The European Union has extensive quantity and quality regulations for wine, while other major producers such as Australia and the United States are much less regulated. After a general overview of current regulations and historical evolutions, we analyze three key wine regulations in more detail: consumption taxes, planting rights, and geographical indications. Most wine regulations reveal a tension between the public interest and vested private interests.
The Value of Terroir: A Historical Analysis of the Bordeaux and Champagne Geographical Indications
Authors: Haeck Catherine , Meloni Giulia , Swinnen Johan 
Published: September 2019

AbstractPrevious studies on the value ofterroir, or more generally geographical indications (GI), used hedonic techniques. We use historical data and exploit temporal and geographical variations in the introduction of wine GIs in early twentieth century France to study the impact on the price of specific wines in the years and decades following their introduction. We find large effects of GIs on prices of some Champagne wines, but no significant impact on Bordeaux or other Champagne wines.
Exploring evolutionary theories of plant defence investment using field populations of the deadly carrot
Authors: Martinez-Swatson Karen , Kjøller Rasmus , Cozzi Federico , Simonsen Henrik Toft , Rønsted Nina , Barnes Christopher 
Published: September 2019

Abstract

Background and Aims
There are a number of disparate models predicting variation in plant chemical defences between species, and within a single species over space and time. These can give conflicting predictions. Here we review a number of these theories, before assessing their power to predict the spatial–temporal variation of thapsigargins between and within populations of the deadly carrot (Thapsia garganica). By utilizing multiple models simultaneously (optimum defence theory, growth rate hypothesis, growth–differentiation balance hypothesis, intra–specific framework and resource exchange model of plant defence), we will highlight gaps in their predictions and evaluate the performance of each.

Methods
Thapsigargins are potent anti-herbivore compounds that occur in limited richness across the different plant tissues of T. garganica, and therefore represent an ideal system for exploring these models. Thapsia garganica plants were collected from six locations on the island of Ibiza, Spain, and the thapsigargins quantified within reproductive, vegetative and below-ground tissues. The effects of sampling time, location, mammalian herbivory, soil nutrition and changing root-associated fungal communities on the concentrations of thapsigargins within these in situ observations were analysed, and the results were compared with our model predictions.

Key Results
The models performed well in predicting the general defence strategy of T. garganica and the above-ground distribution of thapsigargins, but failed to predict the considerable proportion of defences found below ground. Models predicting variation over environmental gradients gave conflicting and less specific predictions, with intraspecific variation remaining less understood.

Conclusion
Here we found that multiple models predicting the general defence strategy of plant species could likely be integrated into a single model, while also finding a clear need to better incorporate below-ground defences into models of plant chemical defences. We found that constitutive and induced thapsigargins differed in their regulation, and suggest that models predicting intraspecific defences should consider them separately. Finally, we suggest that in situ studies be supplemented with experiments in controlled environments to identify specific environmental parameters that regulate variation in defences within species.
XII—What’s Wrong with the Consequence Argument: A Compatibilist Libertarian Response
Authors: List Christian 
Published: September 2019

Abstract
The most prominent argument for the incompatibility of free will and determinism is Peter van Inwagen’s consequence argument. I offer a new diagnosis of what is wrong with this argument. Proponents and critics typically accept the way the argument is framed, and only disagree on whether the premisses and rules of inference are true. I suggest that the argument involves a category mistake: it conflates two different levels of description, namely, the physical level at which we describe the world from the perspective of fundamental physics and the agential level at which we describe agents and their actions. My diagnosis is based on an account of free will as a higher-level phenomenon. I call this account ‘compatibilist libertarianism’, for reasons that will become clear. Although the paper addresses a primarily metaphysical question, it uses tools similar to those employed in philosophy-of-science work on determinism and indeterminism, higher-level phenomena, and dynamical systems.
Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages
Authors: Davín Adrián A , Tricou Théo , Tannier Eric , de Vienne Damien M , Szöllősi Gergely J 
Published: September 2019

Abstract

Summary
Here we present Zombi, a tool to simulate the evolution of species, genomes and sequences in silico, that considers for the first time the evolution of genomes in extinct lineages. It also incorporates various features that have not to date been combined in a single simulator, such as the possibility of generating species trees with a pre-defined variation of speciation and extinction rates through time, simulating explicitly intergenic sequences of variable length and outputting gene tree—species tree reconciliations.

Availability and implementation
Source code and manual are freely available in https://github.com/AADavin/ZOMBI/.

Supplementary information
Supplementary data are available at Bioinformatics online.
A fast and memory efficient MLCS algorithm by character merging for DNA sequences alignment
Authors: Liu Sen , Wang Yuping , Tong Wuning , Wei Shiwei 
Published: September 2019

Abstract

Motivation
Multiple longest common subsequence (MLCS) problem is searching all longest common subsequences of multiple character sequences. It appears in many fields such as data mining, DNA alignment, bioinformatics, text editing and so on. With the increasing in sequence length and number of sequences, the existing dynamic programming algorithms and the dominant point-based algorithms become ineffective and inefficient, especially for large-scale MLCS problems.

Results
In this paper, by considering the characteristics of DNA sequences with many consecutively repeated characters, we first design a character merging scheme which merges the consecutively repeated characters in the sequences. As a result, it shortens the length of sequences considered and saves the space of storing all sequences. To further reduce the space and time costs, we construct a weighted directed acyclic graph which is much smaller than widely used directed acyclic graph for MLCS problems. Based on these techniques, we propose a fast and memory efficient algorithm for MLCS problems. Finally, the experiments are conducted and the proposed algorithm is compared with several state-of-the art algorithms. The experimental results show that the proposed algorithm performs better than the compared state-of-the art algorithms in both time and space costs.

Availability and implementation
https://www.ncbi.nlm.nih.gov/nuccore and https://github.com/liusen1006/MLCS.
Metric learning on expression data for gene function prediction
Authors: Makrodimitris Stavros , Reinders Marcel J T , van Ham Roeland C H J 
Published: September 2019

Abstract

Motivation
Co-expression of two genes across different conditions is indicative of their involvement in the same biological process. However, when using RNA-Seq datasets with many experimental conditions from diverse sources, only a subset of the experimental conditions is expected to be relevant for finding genes related to a particular Gene Ontology (GO) term. Therefore, we hypothesize that when the purpose is to find similarly functioning genes, the co-expression of genes should not be determined on all samples but only on those samples informative for the GO term of interest.

Results
To address this, we developed Metric Learning for Co-expression (MLC), a fast algorithm that assigns a GO-term-specific weight to each expression sample. The goal is to obtain a weighted co-expression measure that is more suitable than the unweighted Pearson correlation for applying Guilt-By-Association-based function predictions. More specifically, if two genes are annotated with a given GO term, MLC tries to maximize their weighted co-expression and, in addition, if one of them is not annotated with that term, the weighted co-expression is minimized. Our experiments on publicly available Arabidopsis thaliana RNA-Seq data demonstrate that MLC outperforms standard Pearson correlation in term-centric performance. Moreover, our method is particularly good at more specific terms, which are the most interesting. Finally, by observing the sample weights for a particular GO term, one can identify which experiments are important for learning that term and potentially identify novel conditions that are relevant, as demonstrated by experiments in both A. thaliana and Pseudomonas Aeruginosa.

Availability and implementation
MLC is available as a Python package at www.github.com/stamakro/MLC.

Supplementary information
Supplementary data are available at Bioinformatics online.
Three Years of Progress Toward Achieving Hepatitis C Elimination in the Country of Georgia, April 2015–March 2018
Authors: Tsertsvadze Tengiz , Gamkrelidze Amiran , Chkhartishvili Nikoloz , Abutidze Akaki , Sharvadze Lali , Kerashvili Vakhtang , Butsashvili Maia , Metreveli David , Gvinjilia Lia , Shadaker Shaun , Nasrullah Muazzam , Adamia Ekaterine , Zeuzem Stefan , Afdhal Nezam , Arora Sanjeev , Thornton Karla , Skaggs Beth , Kuchuloria Tinatin , Lagvilava Maia , Sergeenko David , Averhoff Francisco 
Published: September 2019

Abstract

Background
In April 2015, in collaboration with the US Centers for Disease Control and Prevention and Gilead Sciences, the country of Georgia embarked on the world’s first hepatitis C elimination program. We aimed to assess progress toward elimination targets 3 years after the start of the elimination program.

Methods
We constructed a hepatitis C virus (HCV) care cascade for adults in Georgia, based on the estimated 150 000 persons aged ≥18 years with active HCV infection. All patients who were screened or entered the treatment program during April 2015–March 2018 were included in the analysis. Data on the number of persons screened for HCV were extracted from the national HCV screening database. For the treatment component, we utilized data from the Georgia National HCV treatment program database. Available treatment options included sofosbuvir and ledipasvir/sofosbuvir–based regimens.

Results
Since April 2015, a cumulative 974 817 adults were screened for HCV antibodies; 86 624 persons tested positive, of whom 61 925 underwent HCV confirmatory testing. Among the estimated 150 000 adults living with chronic hepatitis C in Georgia, 52 856 (35.1%) were diagnosed, 45 334 (30.2%) initiated treatment with direct-acting antivirals, and 29 090 (19.4%) achieved a sustained virologic response (SVR). Overall, 37 256 persons were eligible for SVR assessment; of these, only 29 620 (79.5%) returned for evaluation. The SVR rate was 98.2% (29 090/29 620) in the per-protocol analysis and 78.1% (29 090/37 256) in the intent-to-treat analysis.

Conclusions
Georgia has made substantial progress in the path toward eliminating hepatitis C. Scaling up of testing and diagnosis, along with effective linkage to treatment services, is needed to achieve the goal of elimination.
Alendronate Improves Bone Mineral Density in Children and Adolescents Perinatally Infected With Human Immunodeficiency Virus With Low Bone Mineral Density for Age
Authors: Jacobson Denise L , Lindsey Jane C , Gordon Catherine , Hazra Rohan , Spiegel Hans , Ferreira Flavia , Amaral Fabiana R , Pagano-Therrien Jesica , Gaur Aditya , George Kathy , Benson Jane , Siberry George K 
Published: September 2019

Abstract

Background
Children and adolescents with perinatal human immunodeficiency virus (HIV) infection and with low bone mineral density (BMD) may be at higher risk of osteoporosis and fractures in later life than their uninfected peers. Bisphosphonate therapy has been shown to reduce fractures in adults with osteoporosis, but has not been formally studied in youths living with HIV.

Methods
Fifty-two children and adolescents (aged 11–24 years) perinatally infected with HIV with low lumbar spine (LS) BMD (Z score &lt; −1.5) were randomized to receive once-weekly alendronate or placebo in a double-blind cross-over study designed to assess the safety and efficacy of 48 and 96 weeks of alendronate in the United States and Brazil. All participants received daily calcium carbonate and vitamin D supplementation and were asked to engage in regular weight-bearing exercise. Safety and efficacy are summarized for the initial 48 weeks of the trial.

Results
Grade 3 or higher abnormal laboratory values, signs, or symptoms developed in 5 of 32 (16%) participants on alendronate and 2 of 18 (11%) on placebo (P &gt; .99). No cases of jaw osteonecrosis, atrial fibrillation, or nonhealing fractures were reported. Mean increases (95% confidence interval) in LS BMD over 48 weeks were significantly larger on alendronate (20% [14%–25%]) than placebo (7% [5%–9%]) (P &lt; .001). Similar improvements were seen for whole body BMD.

Conclusions
In this small study in children and adolescents perinatally infected with HIV with low LS BMD, 48 weeks of alendronate was well-tolerated, showed no safety concerns, and significantly improved LS and whole body BMD compared to participants on vitamin D/calcium supplementation and exercise alone.

Clinical Trials Registration
NCT00921557.