bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interrelated role of Klotho and calcium-sensing receptor in parathyroid hormone synthesis and parathyroid hyperplasia
Authors: Fan Yi , Liu Weiqing , Bi Ruiye , Densmore Michael J. , Sato Tadatoshi , Mannstadt Michael , Yuan Quan , Zhou Xuedong , Olauson Hannes , Larsson Tobias E. , Toka Hakan R. , Pollak Martin R. , Brown Edward M. , Lanske Beate 
Published: April 2018

Significance
Secondary hyperparathyroidism (SHPT) is a severe consequence of chronic kidney disease. A better understanding of the mechanisms controlling the progression of SHPT and the regulation of parathyroid hormone (PTH) production is clinically relevant. Utilizing parathyroid gland (PTG)-specific knockout mouse models, we demonstrated calcium-sensing receptor (CaSR) and Klotho together regulate PTH synthesis and PTG growth, and that Klotho contributes to PTH suppression in the absence of CaSR. Klotho exerts an independent function in mediating PTH secretion under chronic hypocalcemia and in suppressing PTG cell proliferation. Moreover, the results revealed a previously unidentified interaction between PTG-expressed CaSR and Klotho. These findings highlight the essential and interrelated roles for CaSR and Klotho to prevent parathyroid hyperplasia, suggesting potential treatment strategies to control PTH synthesis and hyperparathyroidism.
Cell contraction induces long-ranged stress stiffening in the extracellular matrix
Authors: Han Yu Long , Ronceray Pierre , Xu Guoqiang , Malandrino Andrea , Kamm Roger D. , Lenz Martin , Broedersz Chase P. , Guo Ming 
Published: April 2018

Significance
The behavior of cells is strongly affected by the mechanics of their surroundings. In tissues, cells interact with the extracellular matrix, a 3D network of biopolymers with a highly nonlinear elastic response. We introduce a method exploiting this matrix nonlinearity to infer mechanical stresses in 3D. Using this method, we demonstrate that cell contractility induces large stresses, which generate a massive stiffness gradient over an extended region in 3D matrices of collagen, fibrin, and Matrigel. Our work highlights the importance of nonlinear matrix mechanics at the microscopic scale and suggests a concrete mechanism through which cells can control their microenvironment and mechanically communicate with each other.
Axial to transverse energy mixing dynamics in octupole-based magnetostatic antihydrogen traps
Authors: Zhong A , Fajans J , Zukor A F 
Published: April 2018

Abstract
The nature of the trajectories of antihydrogen atoms confined in an octupole minimum-B trap is of great importance for upcoming spectroscopy, cooling, and gravity experiments. Of particular interest is the mixing time between the axial and transverse energies for the antiatoms. Here, using computer simulations, we establish that almost all trajectories are chaotic, and then quantify the characteristic mixing time between the axial and transverse energies. We find that there are two classes of trajectories: for trajectories whose axial energy is higher than about 20% of the total energy, the axial energy substantially mixes within about 10 s, whereas for trajectories whose axial energy is lower than about 10% of the total energy, the axial energy remains nearly constant for 1000 s or longer.
Counting zeros in quaternion algebras using Jacobi forms
Authors: Boylan Hati̇ce , Skoruppa Nils-Peter , Zhou Haigang 
Published: April 2018

We use the theory of Jacobi forms to study the number of elements in a maximal order of a definite quaternion algebra over the field of rational numbers whose characteristic polynomial equals a given polynomial. A certain weighted average of such numbers equals (up to some trivial factors) the Hurwitz class number

H
(
4
n
−

r
2

)

H(4n-r^2)

. As a consequence we obtain new proofs for Eichler’s trace formula and for formulas for the class and type number of definite quaternion algebras. As a secondary result we derive explicit formulas for Jacobi Eisenstein series of weight

2
2

on

Γ
0

(
N
)

\Gamma _0(N)

and for the action of Hecke operators on Jacobi theta series associated to maximal orders of definite quaternion algebras.
SnapperDB: a database solution for routine sequencing analysis of bacterial isolates
Authors: Dallman Timothy , Ashton Philip , Schafer Ulf , Jironkin Aleksey , Painset Anais , Shaaban Sharif , Hartman Hassan , Myers Richard , Underwood Anthony , Jenkins Claire , Grant Kathie 
Published: April 2018

Abstract

Summary
Real-time surveillance of infectious disease using whole genome sequencing data poses challenges in both result generation and communication. SnapperDB represents a set of tools to store bacterial variant data and facilitate reproducible and scalable analysis of bacterial populations. We also introduce the ‘SNP address’ nomenclature to describe the relationship between isolates in a population to the single nucleotide resolution. We announce the release of SnapperDB v1.0 a program for scalable routine SNP analysis and storage of microbial populations.

Availability and implementation
SnapperDB is implemented as a python application under the open source BSD license. All code and user guides are available at https://github.com/phe-bioinformatics/snapperdb. Reference genomes and SnapperDB configs are available at https://github.com/phe-bioinformatics/snapperdb_references.
A sequence family database built on ECOD structural domains
Authors: Liao Yuxing , Schaeffer R Dustin , Pei Jimin , Grishin Nick V 
Published: April 2018

Abstract

Motivation
The ECOD database classifies protein domains based on their evolutionary relationships, considering both remote and close homology. The family group in ECOD provides classification of domains that are closely related to each other based on sequence similarity. Due to different perspectives on domain definition, direct application of existing sequence domain databases, such as Pfam, to ECOD struggles with several shortcomings.

Results
We created multiple sequence alignments and profiles from ECOD domains with the help of structural information in alignment building and boundary delineation. We validated the alignment quality by scoring structure superposition to demonstrate that they are comparable to curated seed alignments in Pfam. Comparison to Pfam and CDD reveals that 27 and 16% of ECOD families are new, but they are also dominated by small families, likely because of the sampling bias from the PDB database. There are 35 and 48% of families whose boundaries are modified comparing to counterparts in Pfam and CDD, respectively.

Availability and implementation
The new families are now integrated in the ECOD website. The aggregate HMMER profile library and alignment are available for download on ECOD website (http://prodata.swmed.edu/ecod).

Supplementary information
Supplementary data are available at Bioinformatics online.
Ribopeaks: a web tool for bacterial classification through m/z data from ribosomal proteins
Authors: Tomachewski Douglas , Galvão Carolina Weigert , de Campos Júnior Arion , Guimarães Alaine Margarete , Ferreira da Rocha José Carlos , Etto Rafael Mazer 
Published: April 2018

Abstract

Summary
MALDI-TOF MS is a rapid, sensitive and economic tool for bacterial identification. Highly abundant bacterial proteins are detected by this technique, including ribosomal proteins (r-protein), and the generated mass spectra are compared with a MALDI-TOF MS spectra database. Currently, it allows mainly the classification of clinical bacteria due to the limited number of environmental bacteria included in the spectra database. We present a wide-ranging bacterium classifier tool, called Ribopeaks, which was created based on r-protein data from the Genbank. The Ribopeaks database has more than 28 500 bacterial taxonomic records. It compares the incoming m/z data from MALDI-TOF MS analysis with models stored in the Ribopeaks database created by machine learning and then taxonomically classifies the bacteria.

Availability and implementation
The software is available at http://www.ribopeaks.com.

Supplementary information
Supplementary data are available at Bioinformatics online.
IRscope: an online program to visualize the junction sites of chloroplast genomes
Authors: Amiryousefi Ali , Hyvönen Jaakko , Poczai Peter 
Published: April 2018

Abstract

Motivation
Genome plotting is performed using a wide range of visualizations tools each with emphasis on a different informative dimension of the genome. These tools can provide a deeper insight into the genomic structure of the organism.

Results
Here, we announce a new visualization tool that is specifically designed for chloroplast genomes. It allows the users to depict the genetic architecture of up to ten chloroplast genomes in the vicinity of the sites connecting the inverted repeats to the short and long single copy regions. The software and its dependent libraries are fully coded in R and the reflected plot is scaled up to realistic size of nucleotide base pairs in the vicinity of the junction sites. We introduce a website for easier use of the program and R source code of the software to be used in case of preferences to be changed and integrated into personal pipelines. The input of the program is an annotation GenBank (.gb) file, the accession or GI number of the sequence or a DOGMA output file. The software was tested using over a 100 embryophyte chloroplast genomes and in all cases a reliable output was obtained.

Availability and implementation
Source codes and the online suit available at https://irscope.shinyapps.io/irapp/ or https://github.com/Limpfrog/irscope.
Gross Negligence (Medical) Manslaughter and the Puzzling Implications of Negligent Ignorance: Rose v R [2017] EWCA Crim 1168
Authors: Mullock Alexandra 
Published: April 2018

ABSTRACT
This commentary explores the Court of Appeal’s decision in the case of Rose1 in order to assess the risk of liability for gross negligence manslaughter currently faced by the medical profession in the event that negligence causes the death of a patient. Subtly modifying the test established in Adomako,2Rose confirms that in order to be potentially liable, there must be a serious risk of death that was, rather than ought to have been, obvious/foreseeable to the defendant. Consequently, in more complex cases where the serious risk of death is not immediately obvious, negligently failing to assess risk seems to prevent potential liability on the basis that the putative defendant was in a position of negligent ignorance.
Antifungal susceptibilities, in vitro production of virulence factors and activities of ceragenins against Candida spp. isolated from vulvovaginal candidiasis
Authors: Hacioglu Mayram , Guzel Cagla Bozkurt , Savage Paul B , Tan A Seher Birteksoz 
Published: April 2018

Abstract
Vulvovaginal candidiasis (VVC) is the second most common cause of vaginitis after bacterial vaginosis, affecting millions of women worldwide every year. Candida albicans is the most frequent agent of VVC followed by other species of Candida such as C. glabrata and C. parapsilosis. Out of a total of 100 clinical isolates of Candida spp. obtained from patients diagnosed with VVC, 84 were identified as C. albicans, while the remaining isolates were identified as non–-albicans Candida strains. Phospholipases and proteinases were produced by a majority of the C. albicans strains and esterases and hemolysins a minority of these strains. Among the non–C. albicans strains, only a few of the strains produced these proteins. Nearly all of the isolates formed biofilms. Our results showed that the butoconazole, clotrimazole, and fluconazole were active against C. albicans and less so against the non–albicans Candida strains. The MIC90 of amphotericin B and nystatins were 2 and 4 μg/ml, respectively, against either C. albicans or non–albicans Candida spp. Representative ceragenins (CSA-13, CSA-131, and CSA-138), developed as mimics of endogenous antimicrobial peptides, were active against fluconazole-resistant strains, both alone and in combination with fluconazole. These results suggest the potential use of ceragenins in treating VVC, including infections caused by fluconazole-resistant isolates.
Circular polarization of gravitational waves from non-rotating supernova cores: a new probe into the pre-explosion hydrodynamics
Authors: Hayama Kazuhiro , Kuroda Takami , Kotake Kei , Takiwaki Tomoya 
Published: April 2018

Abstract
We present an analysis of the circular polarization of gravitational waves (GWs) using results from three-dimensional (3D), general relativistic (GR) core-collapse simulations of a non-rotating 15 M⊙ star. For the signal detection, we perform a coherent network analysis taking into account the four interferometers of LIGO Hanford, LIGO Livingston, VIRGO, and KAGRA. We focus on the Stokes V parameter, which directly characterizes the asymmetry of the GW circular polarization. We find that the amplitude of the GW polarization becomes bigger for our 3D-GR model that exhibits strong activity of the standing accretion shock instability (SASI). Our results suggest that the SASI-induced accretion flows to the proto-neutron star (PNS) lead to a characteristic, low-frequency modulation (100–200 Hz) in both the waveform and the GW circular polarization. By estimating the signal-to-noise ratio of the GW polarization, we demonstrate that the detection horizon of the circular polarization extends by more than a factor of several times farther comparing to that of the GW amplitude. Our results suggest that the GW circular polarization, if detected, could provide a new probe into the pre-explosion hydrodynamics such as the SASI activity and the g-mode oscillation of the PNS.
Aneurysm Size is the Strongest Risk Factor for Intracranial Aneurysm Growth in the Eastern Finnish Population
Authors: Björkman Joel , Frösen Juhana , Tähtinen Olli , Huttunen Terhi , Huttunen Jukka , Kurki Mitja I , von und zu Fraunberg Mikael , Koivisto Timo , Manninen Hannu , Jääskeläinen Juha E , Lindgren Antti E 
Published: April 2018

Abstract

BACKGROUND
Saccular intracranial aneurysm (sIA) growth during follow-up is associated with high risk for subsequent rupture. Finnish patients have been suggested to have higher risk for subarachnoid hemorrhage, but follow-up studies of sIA growth in the Finnish population are scarce.

OBJECTIVE
To identify the strongest risk factors for sIA growth in Eastern Finnish population by studying 205 patients with 350 unruptured sIAs with angiographic follow-up imaging.

METHODS
In this population-based cohort study, we included unruptured sIA patients from the Kuopio University Hospital Intracranial Aneurysm Patient and Family database with at least 6 mo of angiographic follow-up after the diagnosis of sIAs. Angiograms were re-evaluated to detect aneurysms with growth of at least 1.0 mm. Cox regression analysis with patient- and aneurysm-related risk factors was used to calculate hazard ratios with 95% confidence intervals for growth. In addition, we tested the diagnostic value of previously introduced PHASES score for the prediction of sIA growth in Eastern Finnish population.

RESULTS
Of the 350 unruptured aneurysms, 36 (10.3%) showed growth during median follow-up of 1.7 yr and total follow-up of 790 yr. In the multivariate Cox regression analysis, sIA size and location in the middle cerebral artery were significant risk factors for sIA growth. In receiver operator characteristic curves, both PHASES score and sIA size had relatively low areas under the curve.

CONCLUSION
Our study indicates that aneurysm size is the strongest risk factor for aneurysm growth in Eastern Finnish population. Further studies are required to identify new risk factors for aneurysm growth.
Cardiovascular Effects of Hookah Smoking: Potential Implications for Cardiovascular Risk
Authors: Rezk-Hanna Mary , Benowitz Neal L 
Published: April 2018

AbstractIntroductionSmoking is a major cause of cardiovascular morbidity and mortality worldwide. Hookah (ie, waterpipe) smoking is a centuries-old revived yet understudied global epidemic of tobacco use. Because of the traditional set-up of a hookah-pipe, in addition to inhaling tobacco-combustion products, smokers are also exposed to large amounts of charcoal combustion products from the burning charcoal briquettes used to heat the hookah flavored tobacco. Despite being heavily advertised and actively glamorized in the mass media as a healthier tobacco alternative, the toxicological constituents of hookah smoke—including nicotine, carbon monoxide, particulates, oxidants, heavy metals, phenols and flavorants—indicate the potential to cause adverse cardiovascular events.MethodsHerein, we review evidence on hookah smoke toxicological constituents, cardiovascular effects and potential mechanisms by which hookah smoke aerosol could cause cardiovascular disease.ResultsThe evidence reviewed here indicates that contrary to the widespread popular belief that hookah is a healthier tobacco alternative, the constituents of hookah smoke aerosol contains similar chemicals compared to cigarette smoke, many of which are known to be harmful to cardiovascular health and mediated by similar pathophysiologic processes. Because the burning charcoal briquettes are a unique source of toxicant emissions specific to hookah smoking, some constituents differ in their quantities from cigarettes with some of their cardiovascular effects unknown.ConclusionsTo date, much more is known about the constituents and their toxicology than about the effects of hookah smoking on human cardiovascular health. Further research on long-term consequences of hookah use is needed.ImplicationsThis review provides an overview on the potential impact of hookah smoking on cardiovascular health. Readers will gain an insight into evidence on its toxicological constituents, human health effects, and pathophysiological mechanisms by which hookah smoking might cause cardiovascular disease. The review also highlights current research gaps regarding the cardiovascular consequences of hookah smoking, specifically the long-term consequences in the United States and Europe among flavored-hookah tobacco users.
Effects of Branched-Chain Amino Acid Supplementation on Spontaneous Seizures and Neuronal Viability in a Model of Mesial Temporal Lobe Epilepsy
Authors: Gruenbaum Shaun E. , Dhaher Roni , Rapuano Amedeo , Zaveri Hitten P. , Tang Amber , de Lanerolle Nihal , Eid Tore 
Published: April 2018

Background:
The essential branched-chain amino acids (BCAAs) leucine, isoleucine, and valine have recently emerged as a potential novel treatment for medically refractory epilepsy. Blood-derived BCAAs can readily enter the brain, where they contribute to glutamate biosynthesis and may either suppress or trigger acute seizures. However, the effects of BCAAs on chronic (ie, spontaneous recurrent) seizures and epilepsy-associated neuron loss are incompletely understood.

Materials and Methods:
Sixteen rats with mesial temporal lobe epilepsy were randomized into 2 groups that could drink, ad libitum, either a 4% solution of BCAAs in water (n=8) or pure water (n=8). The frequency and relative percent of convulsive and nonconvulsive spontaneous seizures were monitored for a period of 21 days, and the brains were then harvested for immunohistochemical analysis.

Results:
Although the frequency of convulsive and nonconvulsive spontaneous recurrent seizures over a 3-week drinking/monitoring period were not different between the groups, there were differences in the relative percent of convulsive seizures in the first and third week of treatment. Moreover, the BCAA-treated rats had over 25% fewer neurons in the dentate hilus of the hippocampus compared with water-treated controls.

Conclusions:
Acute BCAA supplementation reduces seizure propagation, whereas chronic oral supplementation with BCAAs worsens seizure propagation and causes neuron loss in rodents with mesial temporal lobe epilepsy. These findings raise the question of whether such supplementation has a similar effect in humans.
Comparative Usefulness of Sepsis-3, Burn Sepsis, and Conventional Sepsis Criteria in Patients With Major Burns
Authors: Yoon Jaechul , Kym Dohern , Hur Jun , Kim Youngmin , Yang Hyeong-Tae , Yim Haejun , Cho Yong Suk , Chun Wook 
Published: April 2018

Objectives:
We evaluated the ability of new sepsis (S3) criteria (compared with previous definitions of sepsis [S1] and burn sepsis criteria) to accurately determine the mortality in severe burns patients with sepsis.

Design:
This was retrospective cohort study.

Setting:
The Burn ICU of Burn Center, Hangang Sacred Heart Hospital, Hallym University, Seoul, Korea.

Patients:
A total of 1,185 adult patients (mean age, 49.1 yr) were admitted between January 2009 and December 2015.

Interventions:
The 1,185 patients enrolled in the present study and were then re-evaluated based on S1, burn sepsis, and S3 criteria, following which 565 patients, 812 patients, and 809 patients were diagnosed with sepsis based on S1, burn sepsis, S3 criteria, respectively.

Measurements and Main Results:
For diagnostic performance, sensitivity, specificity, predictive value, and likelihood ratio were calculated. The area under the curve of the receiver operating characteristic curve was calculated to determine the accuracy of mortality prediction. The optimal cutoff value of Sequential Organ Failure Assessment score was calculated by the decision tree method. Total body surface area burned was 33.4%. Patients were identified with sepsis using S1 (812), S3 (809), and burn sepsis (565) criteria. Overall mortality was 20.3%, highest (82.2%) and lowest (26.5%) occurred with new septic shock (SH3) and S3, respectively. The sensitivity and specificity for burn sepsis (84.6% and 61.8%) and SH3 (63.1% and 96.5%) were reported. Area under the curve values for Sequential Organ Failure Assessment scores were the highest in all sepsis categories. With Sequential Organ Failure Assessment score greater than or equal to 6 (with infection), the accuracy was 0.86 (95% CI, 0.82–0.89).

Conclusions:
The S3 criteria failed to show superior prognostic accuracy for mortality in severely burned patients. Sequential Organ Failure Assessment score greater than or equal to 6 may be a better criterion for the diagnosis of sepsis in burns patients.