bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morbigenous brain region and gene detection with a genetically evolved random neural network cluster approach in late mild cognitive impairment
Authors: Bi Xia-an , Liu Yingchao , Xie Yiming , Hu Xi , Jiang Qinghua 
Published: January 2020

Abstract

Motivation
The multimodal data fusion analysis becomes another important field for brain disease detection and increasing researches concentrate on using neural network algorithms to solve a range of problems. However, most current neural network optimizing strategies focus on internal nodes or hidden layer numbers, while ignoring the advantages of external optimization. Additionally, in the multimodal data fusion analysis of brain science, the problems of small sample size and high-dimensional data are often encountered due to the difficulty of data collection and the specialization of brain science data, which may result in the lower generalization performance of neural network.

Results
We propose a genetically evolved random neural network cluster (GERNNC) model. Specifically, the fusion characteristics are first constructed to be taken as the input and the best type of neural network is selected as the base classifier to form the initial random neural network cluster. Second, the cluster is adaptively genetically evolved. Based on the GERNNC model, we further construct a multi-tasking framework for the classification of patients with brain disease and the extraction of significant characteristics. In a study of genetic data and functional magnetic resonance imaging data from the Alzheimer’s Disease Neuroimaging Initiative, the framework exhibits great classification performance and strong morbigenous factor detection ability. This work demonstrates that how to effectively detect pathogenic components of the brain disease on the high-dimensional medical data and small samples.

Availability and implementation
The Matlab code is available at https://github.com/lizi1234560/GERNNC.git.
The identity of two meta-analytic likelihoods and the ignorability of double-zero studies
Authors: Böhning Dankmar , Sangnawakij Patarawan 
Published: January 2020

Summary
In meta-analysis, the conventional two-stage approach computes an effect estimate for each study in the first stage and proceeds with the analysis of effect estimates in the second stage. For counts of events as outcome, the risk ratio is often the effect measure of choice. However, if the meta-analysis includes many studies with no events the conventional method breaks down. As an alternative one-stage approach, a Poisson regression model and a conditional binomial model can be considered where no event studies do not cause problems. The conditional binomial model excludes double-zero studies, whereas this is seemingly not the case for the Poisson regression approach. However, we show here that both models lead to the same likelihood inference and double-zero studies (in contrast to single-zero studies) do not contribute in either case to the likelihood.
Soluble TREM2 is elevated in Parkinson’s disease subgroups with increased CSF tau
Authors: Wilson Edward N , Swarovski Michelle S , Linortner Patricia , Shahid Marian , Zuckerman Abigail J , Wang Qian , Channappa Divya , Minhas Paras S , Mhatre Siddhita D , Plowey Edward D , Quinn Joseph F , Zabetian Cyrus P , Tian Lu , Longo Frank M , Cholerton Brenna , Montine Thomas J , Poston Kathleen L , Andreasson Katrin I 
Published: January 2020

Abstract
Parkinson’s disease is the second most common neurodegenerative disease after Alzheimer’s disease and affects 1% of the population above 60 years old. Although Parkinson’s disease commonly manifests with motor symptoms, a majority of patients with Parkinson’s disease subsequently develop cognitive impairment, which often progresses to dementia, a major cause of morbidity and disability. Parkinson’s disease is characterized by α-synuclein accumulation that frequently associates with amyloid-β and tau fibrils, the hallmarks of Alzheimer’s disease neuropathological changes; this co-occurrence suggests that onset of cognitive decline in Parkinson’s disease may be associated with appearance of pathological amyloid-β and/or tau. Recent studies have highlighted the appearance of the soluble form of the triggering receptor expressed on myeloid cells 2 (sTREM2) receptor in CSF during development of Alzheimer’s disease. Given the known association of microglial activation with advancing Parkinson’s disease, we investigated whether CSF and/or plasma sTREM2 differed between CSF biomarker-defined Parkinson’s disease participant subgroups. In this cross-sectional study, we examined 165 participants consisting of 17 cognitively normal elderly subjects, 45 patients with Parkinson’s disease with no cognitive impairment, 86 with mild cognitive impairment, and 17 with dementia. Stratification of subjects by CSF amyloid-β and tau levels revealed that CSF sTREM2 concentrations were elevated in Parkinson’s disease subgroups with a positive tau CSF biomarker signature, but not in Parkinson’s disease subgroups with a positive CSF amyloid-β biomarker signature. These findings indicate that CSF sTREM2 could serve as a surrogate immune biomarker of neuronal injury in Parkinson’s disease.
More Screening or More Disease? Gonorrhea Testing and Positivity Patterns Among Men in 3 Large Clinical Practices in Massachusetts, 2010–2017
Authors: Willis Sarah J , Elder Heather , Cocoros Noelle , Young Jessica , Marcus Julia L , Eberhardt Karen , Callahan Myfanwy , Herrick Brian , Weiss Michelle , Hafer Ellen , Erani Diana , Josephson Mark , Llata Eloisa , Flagg Elaine W , Hsu Katherine K , Klompas Michael 
Published: January 2020

Abstract

Background
Gonorrhea diagnosis rates in the United States increased by 75% during 2009–2017, predominantly in men. It is unclear whether the increase among men is being driven by more screening, an increase in the prevalence of disease, or both. We sought to evaluate changes in gonorrhea testing patterns and positivity among men in Massachusetts.

Methods
The analysis included men (aged ≥15 years) who received care during 2010–2017 in 3 clinical practice groups. We calculated annual percentages of men with ≥1 gonorrhea test and men with ≥1 positive result, among men tested. Log-binomial regression models were used to examine trends in these outcomes. We adjusted for clinical and demographic characteristics that may influence the predilection to test and probability of gonorrhea disease.

Results
On average, 306 348 men had clinical encounters each year. There was a significant increase in men with ≥1 gonorrhea test from 2010 (3.1%) to 2017 (6.4%; adjusted annual risk ratio, 1.12; 95% confidence interval, 1.12–1.13). There was a significant, albeit lesser, increase in the percentage of tested men with ≥1 positive result (1.0% in 2010 to 1.5% in 2017; adjusted annual risk ratio, 1.07; 95% confidence interval, 1.04–1.09).

Conclusions
We estimated significant increases in the annual percentages of men with ≥1 gonorrhea test and men with ≥1 positive gonorrhea test result between 2010 and 2017. These results suggest that observed increases in gonorrhea rates could be explained by both increases in screening and the prevalence of gonorrhea.
Direct Measurement of Iodine Production by Sonic Extracts of Polymorphonuclear Leukocytes
Authors: DeChatelet Lawrence R , McCall Charles E , Cooper M Robert 
Published: January 2020

Abstract
We describe an enzymatic reaction between iodide ion, H2O2, and neutrophil sonicates, in which free iodine is formed. Some characteristics of the reaction are: (a) it is catalyzed by sonic extracts of human neutrophils, by purified horseradish peroxidase, or purified human myeloperoxidase, but not by sonic extracts of rabbit alveolar macrophages or beef liver catalase; (b) iodine is the product, as shown by its absorption spectrum and the absorption spectrum of the starch adduct; (c) the reaction is proportional to the amount of neutrophil sonicate added, and has a pH optimum near 4.0. Reaction is not linear with respect to time, owing to denaturation of the enzyme. Kinetic data indicate that the enzyme may be allosteric with respect to iodide and is inhibited by high concentrations of H2O2. These represent possible sources of control of the reaction.
Impact of functional studies on exome sequence variant interpretation in early-onset cardiac conduction system diseases
Authors: Hayashi Kenshi , Teramoto Ryota , Nomura Akihiro , Asano Yoshihiro , Beerens Manu , Kurata Yasutaka , Kobayashi Isao , Fujino Noboru , Furusho Hiroshi , Sakata Kenji , Onoue Kenji , Chiang David Y , Kiviniemi Tuomas O , Buys Eva , Sips Patrick , Burch Micah L , Zhao Yanbin , Kelly Amy E , Namura Masanobu , Kita Yoshihito , Tsuchiya Taketsugu , Kaku Bunji , Oe Kotaro , Takeda Yuko , Konno Tetsuo , Inoue Masaru , Fujita Takashi , Kato Takeshi , Funada Akira , Tada Hayato , Hodatsu Akihiko , Nakanishi Chiaki , Sakamoto Yuichiro , Tsuda Toyonobu , Nagata Yoji , Tanaka Yoshihiro , Okada Hirofumi , Usuda Keisuke , Cui Shihe , Saito Yoshihiko , MacRae Calum A , Takashima Seiji , Yamagishi Masakazu , Kawashiri Masa-aki , Takamura Masayuki 
Published: January 2020

Abstract

Aims
The genetic cause of cardiac conduction system disease (CCSD) has not been fully elucidated. Whole-exome sequencing (WES) can detect various genetic variants; however, the identification of pathogenic variants remains a challenge. We aimed to identify pathogenic or likely pathogenic variants in CCSD patients by using WES and 2015 American College of Medical Genetics and Genomics (ACMG) standards and guidelines as well as evaluating the usefulness of functional studies for determining them.

Methods and results
We performed WES of 23 probands diagnosed with early-onset (&lt;65 years) CCSD and analysed 117 genes linked to arrhythmogenic diseases or cardiomyopathies. We focused on rare variants (minor allele frequency &lt; 0.1%) that were absent from population databases. Five probands had protein truncating variants in EMD and LMNA which were classified as ‘pathogenic’ by 2015 ACMG standards and guidelines. To evaluate the functional changes brought about by these variants, we generated a knock-out zebrafish with CRISPR-mediated insertions or deletions of the EMD or LMNA homologs in zebrafish. The mean heart rate and conduction velocities in the CRISPR/Cas9-injected embryos and F2 generation embryos with homozygous deletions were significantly decreased. Twenty-one variants of uncertain significance were identified in 11 probands. Cellular electrophysiological study and in vivo zebrafish cardiac assay showed that two variants in KCNH2 and SCN5A, four variants in SCN10A, and one variant in MYH6 damaged each gene, which resulted in the change of the clinical significance of them from ‘Uncertain significance’ to ‘Likely pathogenic’ in six probands.

Conclusion
Of 23 CCSD probands, we successfully identified pathogenic or likely pathogenic variants in 11 probands (48%). Functional analyses of a cellular electrophysiological study and in vivo zebrafish cardiac assay might be useful for determining the pathogenicity of rare variants in patients with CCSD. SCN10A may be one of the major genes responsible for CCSD.
Projecting Stand Survival and Basal Area Based on a Self-Thinning Model for Chinese Fir Plantations
Authors: Zhang Xiongqing , Cao Quang V , Wang Hanchen , Duan Aiguo , Zhang Jianguo 
Published: January 2020

Abstract
The self-thinning rule has played a critical role in controlling stand stocking and modeling stand development in forest stands. Chinese fir (Cunninghamia lanceolata) is a native and fast-growing tree species used for timber production and is widely grown in southern China. Effective management of this important tree species requires accurate and reasonable predictions of stand growth and survival. Remeasured data from 48 plots distributed in Fujian, Jiangxi, Guangxi, and Sichuan provinces were used to develop models to predict stand survival and basal area based on the self-thinning trajectories. These trajectories were constructed using a self-thinning slope of –1.605, as suggested by Reineke (1933) (Method 1), and the slopes estimated either from two groups of sites (Method 2) or from climate variables (Method 3). Results indicated that the stand growth and survival models using Method 3 performed best, followed by Method 2 and Method 1. In addition, stand growth and survival curves predicted from Method 3 were more similar in shape to those from the observed values, as compared with Method 1. Overall, the models based on the self-thinning lines using climate-sensitive slopes provided reasonable predictions of the stand development dynamics. Therefore, these results facilitate modeling of the relation between stand growth/survival and self-thinning under climate change.
The Genome of the Great Gerbil Reveals Species-Specific Duplication of an MHCII Gene
Authors: Nilsson Pernille , Solbakken Monica H , Schmid Boris V , Orr Russell J S , Lv Ruichen , Cui Yujun , Song Yajun , Zhang Yujiang , Baalsrud Helle T , Tørresen Ole K , Stenseth Nils Chr , Yang Ruifu , Jakobsen Kjetill S , Easterday William Ryan , Jentoft Sissel 
Published: January 2020

AbstractThe great gerbil (Rhombomys opimus) is a social rodent living in permanent, complex burrow systems distributed throughout Central Asia, where it serves as the main host of several important vector-borne infectious pathogens including the well-known plague bacterium (Yersinia pestis). Here, we present a continuous annotated genome assembly of the great gerbil, covering over 96% of the estimated 2.47-Gb genome. Taking advantage of the recent genome assemblies of the sand rat (Psammomys obesus) and the Mongolian gerbil (Meriones unguiculatus), comparative immunogenomic analyses reveal shared gene losses within TLR gene families (i.e., TLR8, TLR10, and the entire TLR11-subfamily) for Gerbillinae, accompanied with signs of diversifying selection of TLR7 and TLR9. Most notably, we find a great gerbil-specific duplication of the MHCII DRB locus. In silico analyses suggest that the duplicated gene provides high peptide binding affinity for Yersiniae epitopes as well as Leishmania and Leptospira epitopes, putatively leading to increased capability to withstand infections by these pathogens. Our study demonstrates the power of whole-genome sequencing combined with comparative genomic analyses to gain deeper insight into the immunogenomic landscape of the great gerbil and its close relatives.
Annual sea level variations in the Red Sea observed using GNSS
Authors: Alothman A O , Bos M , Fernandes R , Radwan Ali M , Rashwan M 
Published: January 2020

SUMMARY
Annual sea level variations in the Red Sea have amplitudes of 15–20 cm as observed using various techniques such as tide gauges, satellite altimetry and recently Gravity Recovery and Climate Experiment (GRACE) satellite data. In this study, we demonstrate that Global Navigation Satellite System (GNSS) observations can also be used to measure the effect of these sea level variations. The extra water mass presses on the seafloor, which causes horizontal and vertical deformations. Using time-series from 10 coastal GNSS stations, we observe annual horizontal and vertical loading displacements with amplitudes of 2–5 mm. When correcting for atmospheric, hydrological and surface water loading and a residual geocentre motion, significant annual signals of approximately 0.5 and 2 mm are still observed for the horizontal and vertical components, respectively. In the northern Red Sea, the observed annual signals and predicted annual sea level loading show good agreement. This confirms that the signal is mostly a result of the variations in water mass and thermal expansion. Furthermore, we conclude that the uncertainties in the hydrological model over Ethiopia and Eritrea influence the loading over the southern Red Sea, which was underestimated in previous studies using GRACE data.
Sequential modelling of the 2016 Central Italy earthquake cluster using multisource satellite observations and quantitative assessment of Coulomb stress change
Authors: Xu Qian , Chen Qiang , Zhao Jingjing , Liu Xianwen , Yang Yinghui , Zhang Yijun , Liu Guoxiang 
Published: January 2020

SUMMARYA sequence of earthquake events consisting of three large shocks occurred in Central Italy from August to October in 2016 with the duration of almost 2 months. The preliminary study on the seismic mechanism suggests that the sequence of events is the result from the activity of the SW dipping Mt Bove–Mt Vettore–Mt Gorzano normal fault system. For investigation and understanding of the coseismic faulting of the seismogenic fault alignment, we collect a set of comprehensive satellite observations including the Sentinel-1A, ALOS-2/PALSAR-2 and GPS data to map the coseismic surface deformation and estimate the source models in this study. The derived faulting model for the first Amatrice event is characterized by two distinct slip asperities suggesting that it is a predominantly normal dip-slip motion with slight strike-slip component. The second event, Visso earthquake is almost a purely normal rupture. The third Norcia event is dominated by the normal dip-slip rupture of the seismogenic fault, and has propagated up to the ground with significant slip. The three faulting models are then utilized to quantify the Coulomb failure stress (CFS) change over the seismic zone. First, the CFS change on the subsequent two seismogenic faults of the earthquake sequence is estimated, and the derived positive CFS change induced by the preceding earthquakes suggests that the early events have positive effects on triggering the subsequent seismicity. We then explore the response relation of the aftershocks including 961 events with magnitudes larger than M 3.0 to the CFS change over the seismic zone. It suggests that the rupture pattern of the aftershocks is similar to the major shocks with predominantly normal dip-slip. To assess the risk of the future seismic hazard, we analyse quantitatively the spatial distribution of aftershock occurrence and CFS transfer at the seismogenic depth, indicating that the ruptures of the three major shocks do partly release the accumulated strain on the associated fault alignment as well as the dense aftershock, but the CFS increase zone with few aftershocks in the southwest of the eastern Quaternary fault alignment of Central Italy poses the potential of further rupture. In particular, the distribution of aftershock migration also suggests that the north extension of the Mt Bove fault is the potential zone with rupture risk.
Collective Management of Copyright in Greece After the Implementation of Directive 2014/26/EU
Authors: Stavridou Sylvia 
Published: January 2020

Abstract
The Collective Management Law (L. 4481/17) transposed Directive 2014/26/EU into national law, and also set a voluminous legal framework on collective management with intensive state intervention. This placed Greece’s collective management organisations (CMOs) in a less favourable operating condition compared with those in other Member States. The implementation procedure in Greece plunged the music market into crisis, and showed that many national CMOs were unprepared to adapt to the new burdensome administrative measures and overloaded the existing competent authority with a variety of monitoring and supervisory tasks. The challenge for legislative initiatives and supervisory mechanisms remains to strike a balance between the quest for transparency and accountability and the viability of smaller and weaker CMOs. This article aims to give a short survey of the new legal framework on collective management in relation to the current day-to-day situation and the case law.
Participatory constitution-making: Introduction
Authors: Choudhry Sujit , Tushnet Mark 
Published: January 2020

Abstract
At least since the late eighteenth century, constitutions have been understood as emanations of the will of “the People,” as the ultimate expression of an inherent popular sovereignty. In the form of theories of constituent power, accounts of constitutional foundations blended notional or conceptual “descriptions” of the People, which anchored the political legitimacy of constitutional orders in the idea of hypothetical consent, with empirical claims that the nation’s actual people were represented in constitution-making processes through elected delegates and thereby were the authors of and gave consent to its fundamental law. As part of the third wave of democratization, there was an important shift in what popular participation consisted of—from indirect participation by elected representatives to direct, popular participation in the constitution-making process. As a matter of constitutional process, this led to the growing practice, and expectation, that major constitutional changes should be ratified through referenda.
Circulating Forms of B-Type Natriuretic Peptide in Very Preterm Infants
Authors: Harris Sarah L , Troughton Richard , Lewis Lynley , Austin Nicola , Pemberton Chris 
Published: January 2020

Abstract

Background
B-type natriuretic peptide (BNP) is a cardiac hormone released with an N-terminal fragment (NTproBNP) under conditions of ventricular pressure or volume overload. BNP has been proposed for use as a biomarker of cardiac dysfunction in premature infants in the setting of hemodynamically significant patent ductus arteriosus (HsPDA) and bronchopulmonary dysplasia (BPD). In adult settings the presence of proBNP and glycosylated isoforms may affect assay interpretation. However, there are limited data on how immature preterm physiology may affect BNP or NTproBNP levels and no published data on post-translational BNP processing in premature infants.

Methods
Pooled serial plasma samples from preterm infants born at less than 30 weeks gestation were analyzed for BNP congeners using Luminex® assay and high performance liquid chromatography. Samples were grouped according to clinical status: Group 1, no HsPDA and no BPD, Group 2 HsPDA and no/mild BPD, Group 3 HsPDA and moderate/severe BPD.

Results
Plasma from 15 infants was analyzed, and across all three groups NTproBNP predominated with minimal amounts of other isoforms; no glycosylation was detected.

Conclusions
NTproBNP appears to be the predominant isoform across each of our clinical groups in our pooled sample analysis with no evidence of significant glycosylation. This suggests NTproBNP is likely to be a robust marker in this clinical setting.
Leveraging the health information technology infrastructure to advance federal research priorities
Authors: Zayas-Cabán Teresa , Abernethy Amy P , Brennan Patricia Flatley , Devaney Stephanie , Kerlavage Anthony R , Ramoni Rachel , White P Jon 
Published: January 2020

Abstract
Ensuring that federally funded health research keeps pace with the explosion of health data depends on better information technology (IT), access to high-quality electronic health data, and supportive policies. Because it prominently funds and conducts health research, the U.S. federal government needs health IT to rapidly evolve and has the ability to drive that evolution. The Office of the National Coordinator for Health Information Technology developed the National Health IT Priorities for Research: A Policy and Development Agenda (the Agenda) that identifies health IT priorities for research in consultation with relevant federal agencies. This article describes support for the Agenda from the Food and Drug Administration, the National Institutes of Health, and the Veterans Health Administration. Advancing the Agenda will benefit these agencies and support their missions as well as the entire ecosystem leveraging the health IT infrastructure or using data from health IT systems for research.