bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning for BMS analysis and optimisation
Authors: Mesa-Jiménez J J , Stokes L , Yang Q , Livina V N 
Published: September 2020

Abstract
In large buildings, linking heating, cooling or ventilation systems between themselves and to physical spaces is a very time-consuming task that requires highly skilled engineering knowledge, as all these systems are interconnected and they have a certain influence to each other (ventilation systems are often connected to heating and cooling), which often makes task of locating the sources of error or anomalies very time consuming and difficult as they are performed manually. A different approach would be to work out relationships and equipment linkage from time series data provided by the sensors, thus inferring equipment links from which anomalies can be traced back to the source more easily. This paper proposes a data-based solution to obtain equipment relationships based on cross-correlations to relate Air Handling Units (AHUs) to their respective areas of operation. We also propose a methodology, in particular for AHUs, to identify whether or not to trust correlations based on the difference between supply and return temperature. A case study is presented based a large building with 16 AHU systems.
Reducing Bias Due to Exposure Measurement Error Using Disease Risk Scores
Authors: Richardson David B , Keil Alexander P , Cole Stephen R , Edwards Jessie K 
Published: September 2020

Abstract
Suppose that an investigator wants to estimate an association between a continuous exposure variable and an outcome, adjusting for a set of confounders. If the exposure variable suffers classical measurement error, in which the measured exposures are distributed with independent error around the true exposure, then an estimate of the covariate-adjusted exposure-outcome association may be biased. We propose an approach to estimate a marginal exposure-outcome association in the setting of classical exposure measurement error using a disease score–based approach to standardization to the exposed sample. First, we show that the proposed marginal estimate of the exposure-outcome association will suffer less bias due to classical measurement error than the covariate-conditional estimate of association when the covariates are predictors of exposure. Second, we show that if an exposure validation study is available with which to assess exposure measurement error, then the proposed marginal estimate of the exposure-outcome association can be corrected for measurement error more efficiently than the covariate-conditional estimate of association. We illustrate both of these points using simulations and an empirical example using data from the Orinda Longitudinal Study of Myopia (California, 1989–2001).
Baseline Drinking Patterns in Non-Treatment Seeking Problem Drinkers
Authors: Baskerville Wave-Ananda , Nieto Steven J , Ho Diana , Towns Brandon , Grodin Erica N , Li Caesar , Burnette Elizabeth , Donato Suzanna , Ray Lara A 
Published: September 2020

AbstractAimsNatural processes of change have been documented in treatment-seekers who begin to reduce their drinking in anticipation of treatment. The study examined whether non-treatment-seeking problem drinkers would engage in drinking reduction in anticipation of participating in a research study.MethodsNon-treatment-seeking problem drinkers (n = 935) were culled from five behavioral pharmacology studies. Participants reported on their alcohol use during the past 30 days using the Timeline Followback. Cluster analysis identified distinct groups/clusters based on drinking patterns over the 30-day pre-visit period. The identified clusters were compared on demographic and clinical measures.ResultsThree distinct clusters were identified (a) heavy-decreasing drinking group (n = 255, 27.27%); (b) a moderate-stable drinking group (n = 353, 37.75%) and (c) low-stable drinking group (n = 327, 34.97%). The three clusters differed significantly on a host of measures including pre-visit drinking (age at first drink, drinking days, drinks per week, drinks per drinking day), alcohol use severity, alcohol craving, readiness for change, depression and anxiety levels. These differences were alcohol dose-dependent such that the heavier drinking group reported the highest levels on all constructs, followed by the moderate group, and the low drinking group last.ConclusionsBaseline drinking patterns of non-treatment-seekers were generally stable and pre-visit reductions were only observed among the heavy drinking group. This generally stable pattern stands in contrast to previous reports for treatment-seeking samples. Nevertheless, the heavier drinking group, which is most similar to treatment-seekers, displayed pre-study drinking reduction. Overall, naturalistic processes of change may pose less of a threat to randomization and testing in this population.
Artificial Neural Networks (ANNs) and Partial Least Squares (PLS) Regression in the Quantitative Analysis of Respirable Crystalline Silica by Fourier-Transform Infrared Spectroscopy (FTIR)
Authors: Salehi Mina , Zare Asma , Taheri Ali 
Published: September 2020

Abstract
Respirable crystalline silica (RCS) overexposure can lead to the development of silicosis which is a chronic, irreversible, potentially fatal respiratory disease. The most significant prerequisite for any silica exposure control plan is an accurate occupational exposure assessment. The results of crystalline silica analysis are often affected by other mineral interferences and are influenced by an analyst’s knowledge of mineralogy to accurately interpret infrared spectra and correct matrix interferences. Partial least squares (PLS) and artificial neural networks (ANNs) are two multivariate calibration methods to overcome the problem of spectral interferences without the need for an analyst intervention. The performance of these two methods in quantitative analysis of quartz in the presence of mineral interferences was evaluated and compared in this study. Fifty mixtures with different crystalline silica content ratios were prepared by mixing quartz with four common mineral interferences including kaolinite, albite, muscovite, and amorphous silica. Fourier-transform infrared spectra of the mixtures were split into training and test datasets. The optimal architecture of the ANN model was achieved using a two-level full factorial design experiment and data were modeled using ANN and PLS regression analysis. Root mean squared error of prediction values of 1.69 and 6.12 µg quartz for ANN and PLS models, respectively, revealed the fact that the both models performed very well in quantitative analysis of quartz in the presence of mineral interferences, with a better relative performance of the ANN model which can be related to the inherent nonlinear predictive ability of ANNs. Given the excellent predictive ability of the ANN model which can deal with a completely overlapped peak without any need of user’s intervention, it is recommended that the ANN model be optimized in future studies and utilized for reliable and rapid on-field assessment of RCS exposure.
Influence of niche breadth and position on the historical biogeography of seafaring scincid lizards
Authors: Richmond Jonathan Q , Ota Hidetoshi , Grismer L Lee , Fisher Robert N 
Published: September 2020

AbstractNiche breadth and position can influence diversification among closely related species or populations, yet limited empirical data exist concerning the predictability of the outcomes. We explored the effects of these factors on the evolution of the Emoia atrocostata species group, an insular radiation of lizards in the western Pacific Ocean and Indo-Australasia composed of both endemic and widespread species that differ in niche occupancy. We used molecular data and phylogeographical diffusion models to estimate the timing and patterns of range expansion, and ancestral reconstruction methods to infer shifts in ecology. We show evidence of multidirectional spread from a centre of origin in western Micronesia, and that the phyletic diversity of the group is derived from a putative habitat specialist that survives in the littoral zone. This species is composed of paraphyletic lineages that represent stages or possible endpoints in the continuum toward speciation. Several descendant species have transitioned to either strand or interior forest habitat, but only on remote islands with depauperate terrestrial faunas. Our results suggest that the atrocostata group might be in the early phases of a Wilsonian taxon cycle and that the capacity to tolerate salt stress has promoted dispersal and colonization of remote oceanic islands. Divergence itself, however, is largely driven by geographical isolation rather than shifts in ecology.
Unity in diversity: phylogenetics and taxonomy of Rhabdoweisiaceae (Dicranales, Bryophyta)
Authors: Fedosov Vladimir E , Fedorova Alina V , Larraín Juan , Santos Marina B , Stech Michael , Kučera Jan , Brinda John C , Tubanova Dolgor Ya , Von Konrat Matt , Ignatova Elena A , Ignatov Michael S 
Published: September 2020

AbstractMolecular phylogenetic reconstructions of Rhabdoweisiaceae based on plastid (trnS-rps4 and trnL-F) and mitochondrial (nad5) DNA sequences and a comprehensive taxon sampling were performed, including 15 out of 16 genera currently attributed to the family, taxa recently found belonging to Rhabdoweisiaceae and expanded outgroups from related families of Dicranidae. The suggested revised delimitation of the family comprises Camptodontium (previously referred to Dicranaceae), three subaquatic species currently classified in Blindia (Seligeriaceae), and Glyphomitrium (previously referred to Ptychomitriaceae, Erpodiaceae or its own family) and Eucamptodon perichaetialis (the type species of the genus, previously referred to Dicnemonaceae). The emended delimitation of Rhabdoweisiaceae thus adds to the already high morphological heterogeneity resulting from the divergent evolution of specialized traits in different lineages of epiphytes and saxicolous hygrophytes. Taxonomic inferences from the phylogenetic analyses include segregation of three new genera, Pseudoblindia (for species currently recognized as Kiaeria falcata, Blindia robusta, B. lewinskyae and B. inundata), Ripariella (for Kiaeria riparia) and Brideliella (for Oncophorus wahlenbergii, O. demetrii and Symblepharis lindigii). Hollia is reinstated for the dicnemonoid Australasian species previously classified in Eucamptodon. Additionally, we propose to merge (1) Oreoweisia, Pocsiella and Pseudohyophila with Cynodontium, and (2) Kiaeria s.s. with Arctoa. Furthermore, we propose to limit Oncophorus to O. virens and O. integerrimus and expand the circumscription of Symblepharis to accommodate O. crispifolius, O. dendrophilus, O. elongatus and O. raui. The generic status and inclusion in Rhabdoweisiaceae are confirmed for Cnestrum and the recently described Notocynodontium, and the exclusion of Amphidium, Dichodontium, Holodontium and Hymenoloma from the family is supported.
Subthalamic stimulation impairs stopping of ongoing movements
Authors: Lofredi Roxanne , Auernig Georg Cem , Irmen Friederike , Nieweler Johanna , Neumann Wolf-Julian , Horn Andreas , Schneider Gerd-Helge , Kühn Andrea A 
Published: September 2020

Abstract
The subthalamic nucleus is part of a global stopping network that also includes the presupplementary motor area and inferior frontal gyrus of the right hemisphere. In Parkinson’s disease, subthalamic deep brain stimulation improves movement initiation and velocity, but its effect on stopping of ongoing movement is unknown. Here, we examine the relation between movement stopping and connectivity of stimulation volumes to the stopping network. Stop and go times were collected in 17 patients with Parkinson’s disease on and off subthalamic stimulation during visually cued initiation and termination of continuous, rotational movements. Deep brain stimulation contacts were localized; the stimulation volume computed and connectivity profiles estimated using an openly available, normative structural connectome. Subthalamic stimulation significantly increased stop times, which correlated with the connectivity of the stimulation volume to presupplementary motor area and inferior frontal gyrus of the right hemisphere. The robustness of this finding was validated using three separate analysis streams: voxel-wise whole-brain connectivity, region of interest connectivity and a tract-centred method. Our study sheds light on the role of the fronto-subthalamic inhibitory triangle in stopping of ongoing movements and may inspire circuit based adaptive stimulation strategies for control of stopping impairment, possibly reflected in stimulation-induced dyskinesia.
Df(h15q13)/+ Mouse Model Reveals Loss of Astrocytes and Synaptic-Related Changes of the Excitatory and Inhibitory Circuits in the Medial Prefrontal Cortex
Authors: Al-Absi Abdel-Rahman , Qvist Per , Glerup Simon , Sanchez Connie , Nyengaard Jens R 
Published: September 2020

Abstract
The 15q13.3 deletion is associated with multiple neurodevelopmental disorders including epilepsy, schizophrenia, and autism. The Df(h15q13)/+ mouse model was recently generated that recapitulates several phenotypic features of the human 15q13.3 deletion syndrome (DS). However, the biological substrates underlying these phenotypes in Df(h15q13)/+ mice have not yet been fully characterized. RNA sequencing followed by real-time quantitative PCR, western blotting, liquid chromatography-mass spectrometry, and stereological analysis were employed to dissect the molecular, structural, and neurochemical phenotypes of the medial prefrontal cortex (mPFC) circuits in Df(h15q13)/+ mouse model. Transcriptomic profiling revealed enrichment for astrocyte-specific genes among differentially expressed genes, translated by a decrease in the number of glial fibrillary acidic protein positive cells in mPFC of Df(h15q13)/+ mice compared with wild-type mice. mPFC in Df(h15q13)/+ mice also showed a deficit of the inhibitory presynaptic marker GAD65, in addition to a reduction in dendritic arborization and spine density of pyramidal neurons from layers II/III. mPFC levels of GABA and glutamate neurotransmitters were not different between genotypes. Our results suggest that the 15q13.3 deletion modulates nonneuronal circuits in mPFC and confers molecular and morphometric alterations in the inhibitory and excitatory neurocircuits, respectively. These alterations potentially contribute to the phenotypes accompanied with the 15q13.3DS.
Mass Screening of Asymptomatic Persons for Severe Acute Respiratory Syndrome Coronavirus 2 Using Saliva
Authors: Yokota Isao , Shane Peter Y , Okada Kazufumi , Unoki Yoko , Yang Yichi , Inao Tasuku , Sakamaki Kentaro , Iwasaki Sumio , Hayasaka Kasumi , Sugita Junichi , Nishida Mutsumi , Fujisawa Shinichi , Teshima Takanori 
Published: September 2020

Abstract

Background
Coronavirus disease 2019 (COVID-19) has rapidly evolved to become a global pandemic, largely owing to the transmission of its causative virus through asymptomatic carriers. Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in asymptomatic people is an urgent priority for the prevention and containment of disease outbreaks in communities. However, few data are available in asymptomatic persons regarding the accuracy of polymerase chain reaction testing. In addition, although self-collected saliva samples have significant logistical advantages in mass screening, their utility as an alternative specimen in asymptomatic persons is yet to be determined.

Methods
We conducted a mass screening study to compare the utility of nucleic acid amplification, such as reverse-transcription polymerase chain reaction testing, using nasopharyngeal swab (NPS) and saliva samples from each individual in 2 cohorts of asymptomatic persons: the contact-tracing cohort and the airport quarantine cohort.

Results
In this mass screening study including 1924 individuals, the sensitivities of nucleic acid amplification testing with NPS and saliva specimens were 86% (90% credible interval, 77%–93%) and 92% (83%–97%), respectively, with specificities &gt;99.9%. The true concordance probability between the NPS and saliva tests was estimated at 0.998 (90% credible interval, .996–.999) given the recent airport prevalence of 0.3%. In individuals testing positive, viral load was highly correlated between NPS and saliva specimens.

Conclusion
Both NPS and saliva specimens had high sensitivity and specificity. Self-collected saliva specimens are valuable for detecting SARS-CoV-2 in mass screening of asymptomatic persons.
Clinical Epidemiology of Hospitalized Patients With Coronavirus Disease 2019 (COVID-19) in Japan: Report of the COVID-19 Registry Japan
Authors: Matsunaga Nobuaki , Hayakawa Kayoko , Terada Mari , Ohtsu Hiroshi , Asai Yusuke , Tsuzuki Shinya , Suzuki Setsuko , Toyoda Ako , Suzuki Kumiko , Endo Mio , Fujii Naoki , Suzuki Michiyo , Saito Sho , Uemura Yukari , Shibata Taro , Kondo Masashi , Izumi Kazuo , Terada-Hirashima Junko , Mikami Ayako , Sugiura Wataru , Ohmagari Norio 
Published: September 2020

Abstract

Background
There is limited understanding of the characteristics of patients with coronavirus disease 2019 (COVID-19) requiring hospitalization in Japan.

Methods
This study included 2638 cases enrolled from 227 healthcare facilities that participated in the COVID-19 Registry Japan (COVIREGI-JP). The inclusion criteria for enrollment of a case in COVIREGI-JP are both (1) a positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) test and (2) inpatient treatment at a healthcare facility.

Results
The median age of hospitalized patients with COVID-19 was 56 years (interquartile range [IQR], 40–71 years). More than half of cases were male (58.9%, 1542/2619). Nearly 60% of the cases had close contact to confirmed or suspected cases of COVID-19. The median duration of symptoms before admission was 7 days (IQR, 4–10 days). The most common comorbidities were hypertension (15%, 396/2638) and diabetes without complications (14.2%, 374/2638). The number of nonsevere cases (68.2%, n = 1798) was twice the number of severe cases (31.8%, n = 840) at admission. The respiratory support during hospitalization includes those who received no oxygen support (61.6%, 1623/2636) followed by those who received supplemental oxygen (29.9%, 788/2636) and invasive mechanical ventilation/extracorporeal membrane oxygenation (8.5%, 225/2636). Overall, 66.9% (1762/2634) of patients were discharged home, while 7.5% (197/2634) died.

Conclusions
We identified the clinical epidemiological features of COVID-19 in hospitalized patients in Japan. When compared with existing inpatient studies in other countries, these results demonstrated fewer comorbidities and a trend towards lower mortality.
Shiga Toxin–Producing Escherichia coli Transmission via Fecal Microbiota Transplant
Authors: Zellmer Caroline , Sater Mohamad R A , Huntley Miriam H , Osman Majdi , Olesen Scott W , Ramakrishna Bharat 
Published: September 2020

Abstract
Fecal microbiota transplantation (FMT) is recommended therapy for multiply recurrent Clostridioides difficile infection. We report adverse events in 7 patients who received FMT from a stool donor who was colonized with Shiga toxin–producing Escherichia coli (STEC). No patients died of FMT-transmitted STEC. Improved screening can likely avoid future transmission.
Trimethoprim-sulfamethoxazole Versus Azithromycin for the Treatment of Undifferentiated Febrile Illness in Nepal: A Double-blind, Randomized, Placebo-controlled Trial
Authors: Giri Abhishek , Karkey Abhilasha , Dangol Sabina , Arjyal Amit , Pokharel Sunil , Rijal Samita , Gajurel Damodar , Sharma Rabi , Lamsal Kamal , Shrestha Pradip , Prajapati Gayatri , Pathak Saruna , Shrestha Sita Ram , K.C Raj Kumar , Pandey Sujata , Thapa Abishkar , Shrestha Nistha , Thapa Raj Kumar , Poudyal Buddhi , Phuong Dung Nguyen Thi , Baker Stephen , Kestelyn Evelyne , Geskus Ronald , Thwaites Guy , Basnyat Buddha 
Published: September 2020

Abstract

Background
Azithromycin and trimethoprim-sulfamethoxazole (SXT) are widely used to treat undifferentiated febrile illness (UFI). We hypothesized that azithromycin is superior to SXT for UFI treatment, but the drugs are noninferior to each other for culture-confirmed enteric fever treatment.

Methods
We conducted a double-blind, randomized, placebo-controlled trial of azithromycin (20 mg/kg/day) or SXT (trimethoprim 10 mg/kg/day plus sulfamethoxazole 50 mg/kg/day) orally for 7 days for UFI treatment in Nepal. We enrolled patients &gt;2 years and &lt;65 years of age presenting to 2 Kathmandu hospitals with temperature ≥38.0°C for ≥4 days without localizing signs. The primary endpoint was fever clearance time (FCT); secondary endpoints were treatment failure and adverse events.

Results
From June 2016 to May 2019, we randomized 326 participants (163 in each arm); 87 (26.7%) had blood culture–confirmed enteric fever. In all participants, the median FCT was 2.7 days (95% confidence interval [CI], 2.6–3.3 days) in the SXT arm and 2.1 days (95% CI, 1.6–3.2 days) in the azithromycin arm (hazard ratio [HR], 1.25 [95% CI, .99–1.58]; P = .059). The HR of treatment failures by 28 days between azithromycin and SXT was 0.62 (95% CI, .37–1.05; P = .073). Planned subgroup analysis showed that azithromycin resulted in faster FCT in those with sterile blood cultures and fewer relapses in culture-confirmed enteric fever. Nausea, vomiting, constipation, and headache were more common in the SXT arm.

Conclusions
Despite similar FCT and treatment failure in the 2 arms, significantly fewer complications and relapses make azithromycin a better choice for empirical treatment of UFI in Nepal.

Clinical Trials Registration
NCT02773407.
Phenotypic clustering of dilated cardiomyopathy patients highlights important pathophysiological differences
Authors: Verdonschot Job A J , Merlo Marco , Dominguez Fernando , Wang Ping , Henkens Michiel T H M , Adriaens Michiel E , Hazebroek Mark R , Masè Marco , Escobar Luis E , Cobas-Paz Rafael , Derks Kasper W J , van den Wijngaard Arthur , Krapels Ingrid P C , Brunner Han G , Sinagra Gianfranco , Garcia-Pavia Pablo , Heymans Stephane R B 
Published: September 2020

Abstract

Aims
The dilated cardiomyopathy (DCM) phenotype is the result of combined genetic and acquired triggers. Until now, clinical decision-making in DCM has mainly been based on ejection fraction (EF) and NYHA classification, not considering the DCM heterogenicity. The present study aimed to identify patient subgroups by phenotypic clustering integrating aetiologies, comorbidities, and cardiac function along cardiac transcript levels, to unveil pathophysiological differences between DCM subgroups.

Methods and results
We included 795 consecutive DCM patients from the Maastricht Cardiomyopathy Registry who underwent in-depth phenotyping, comprising extensive clinical data on aetiology and comorbodities, imaging and endomyocardial biopsies. Four mutually exclusive and clinically distinct phenogroups (PG) were identified based upon unsupervised hierarchical clustering of principal components: [PG1] mild systolic dysfunction, [PG2] auto-immune, [PG3] genetic and arrhythmias, and [PG4] severe systolic dysfunction. RNA-sequencing of cardiac samples (n = 91) revealed a distinct underlying molecular profile per PG: pro-inflammatory (PG2, auto-immune), pro-fibrotic (PG3; arrhythmia), and metabolic (PG4, low EF) gene expression. Furthermore, event-free survival differed among the four phenogroups, also when corrected for well-known clinical predictors. Decision tree modelling identified four clinical parameters (auto-immune disease, EF, atrial fibrillation, and kidney function) by which every DCM patient from two independent DCM cohorts could be placed in one of the four phenogroups with corresponding outcome (n = 789; Spain, n = 352 and Italy, n = 437), showing a feasible applicability of the phenogrouping.

Conclusion
The present study identified four different DCM phenogroups associated with significant differences in clinical presentation, underlying molecular profiles and outcome, paving the way for a more personalized treatment approach.