bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ensemble of kernel ridge regression-based small molecule–miRNA association prediction in human disease
Authors: Wang Chun-Chun , Zhu Chi-Chi , Chen Xing 
Published: September 2021

Abstract
MicroRNAs (miRNAs) play crucial roles in human disease and can be targeted by small molecule (SM) drugs according to numerous studies, which shows that identifying SM–miRNA associations in human disease is important for drug development and disease treatment. We proposed the method of Ensemble of Kernel Ridge Regression-based Small Molecule–MiRNA Association prediction (EKRRSMMA) to uncover potential SM–miRNA associations by combing feature dimensionality reduction and ensemble learning. First, we constructed different feature subsets for both SMs and miRNAs. Then, we trained homogeneous base learners based on distinct feature subsets and took the average of scores obtained from these base learners as SM–miRNA association score. In EKRRSMMA, feature dimensionality reduction technology was employed in the process of construction of feature subsets to reduce the influence of noisy data. Besides, the base learner, namely KRR_avg, was the combination of two classifiers constructed under SM space and miRNA space, which could make full use of the information of SM and miRNA. To assess the prediction performance of EKRRSMMA, we conducted Leave-One-Out Cross-Validation (LOOCV), SM-fixed local LOOCV, miRNA-fixed local LOOCV and 5-fold CV based on two datasets. For Dataset 1 (Dataset 2), EKRRSMMA got the Area Under receiver operating characteristic Curves (AUCs) of 0.9793 (0.8871), 0.8071 (0.7705), 0.9732 (0.8586) and 0.9767 ± 0.0014 (0.8560 ± 0.0027). Besides, we conducted four case studies. As a result, 32 (5-Fluorouracil), 19 (17β-Estradiol), 26 (5-Aza-2′-deoxycytidine) and 11 (cyclophosphamide) out of top 50 predicted potentially associated miRNAs were confirmed by database or experimental literature. Above evaluation results demonstrated that EKRRSMMA is reliable for predicting SM–miRNA associations.
LRez: a C++ API and toolkit for analyzing and managing Linked-Reads data
Authors: Morisse Pierre , Lemaitre Claire , Legeai Fabrice 
Published: September 2021

Abstract

Motivation
Linked-Reads technologies combine both the high quality and low cost of short-reads sequencing and long-range information, through the use of barcodes tagging reads which originate from a common long DNA molecule. This technology has been employed in a broad range of applications including genome assembly, phasing and scaffolding, as well as structural variant calling. However, to date, no tool or API dedicated to the manipulation of Linked-Reads data exist.

Results
We introduce LRez, a C++ API and toolkit that allows easy management of Linked-Reads data. LRez includes various functionalities, for computing numbers of common barcodes between genomic regions, extracting barcodes from BAM files, as well as indexing and querying BAM, FASTQ and gzipped FASTQ files to quickly fetch all reads or alignments containing a given barcode. LRez is compatible with a wide range of Linked-Reads sequencing technologies, and can thus be used in any tool or pipeline requiring barcode processing or indexing, in order to improve their performances.

Availability and implementation
LRez is implemented in C++, supported on Unix-based platforms and available under AGPL-3.0 License at https://github.com/morispi/LRez, and as a bioconda module.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Valid sequential inference on probability forecast performance
Authors: Henzi Alexander , Ziegel Johanna F 
Published: September 2021

SummaryProbability forecasts for binary events play a central role in many applications. Their quality is commonly assessed with proper scoring rules, which assign forecasts numerical scores such that a correct forecast achieves a minimal expected score. In this paper, we construct e-values for testing the statistical significance of score differences of competing forecasts in sequential settings. E-values have been proposed as an alternative to $p$-values for hypothesis testing, and they can easily be transformed into conservative $p$-values by taking the multiplicative inverse. The e-values proposed in this article are valid in finite samples without any assumptions on the data-generating processes. They also allow optional stopping, so a forecast user may decide to interrupt evaluation, taking into account the available data at any time, and still draw statistically valid inference, which is generally not true for classical $p$-value-based tests. In a case study on post-processing of precipitation forecasts, state-of-the-art forecast dominance tests and e-values lead to the same conclusions.
Fruit development, structure and histology inNelumbo(Nelumbonaceae: Proteales)
Authors: Romanov Mikhail S , Bobrov Alexey V F C H , Romanova Ekaterina S , Zdravchev Nikita S , Sorokin Alexey N 
Published: September 2021

AbstractNelumbonaceae, along with Proteaceae and Platanaceae, comprise a sister clade to the family Sabiaceae in the order Proteales, although these families were previously not considered to be related. In this work, we investigated fruitlet development in Nelumbo with a special focus on the principal events of fruitlet ontogenesis and its pericarp histogenesis, aiming to determine whether fruit structure and histology can provide characters supporting current systematic positions and affinities of these families and reveal potential synapomorphies for the order. We demonstrated for the first time that each carpel comprises a biseriate outer and inner epidermis and thick mesophyll with numerous air canals, which differentiate after pollination into a pericarp with a biseriate palisade exocarp and undifferentiated endocarp. The mesocarp differentiated into a protective hard peripheral zone and a soft inner zone. We propose the following additional autapomorphies for Nelumbonaceae: (1) the development of a specific zone of palisade cells of the subdermal layer of the exocarp with U-shaped cell walls thickening to form a light line around the locule, and potentially preventing apoplastic water transport; (2) the presence of a soft inner parenchymatous zone of the pericarp comprising numerous air cavities, channels and layers of spongy parenchyma, which can function as a seed cushion; (3) simultaneous growth of pollinated and unpollinated fruiting carpels up until the middle developmental stages; and (4) intensive development of the embryo and the seed at the late developmental stage in both Nelumbo spp., which has not been reported in any other member of Proteales. The presence of numerous vascular bundles in the fruitlets of Nelumbonaceae, Platanaceae and some Proteaceae is a synapomorphy for these three families forming a well-supported clade in Proteales.
Antibiotic Overuse and Stewardship at Hospital Discharge: The Reducing Overuse of Antibiotics at Discharge Home Framework
Authors: Vaughn Valerie M , Hersh Adam L , Spivak Emily S 
Published: September 2021

Abstract
Though opportunities exist to improve antibiotic prescribing across the care spectrum, discharge from acute hospitalization is an increasingly recognized source of antibiotic overuse. Antimicrobials are prescribed to more than 1 in 8 patients at hospital discharge; approximately half of which could be improved. Key targets for antibiotic stewardship at discharge include unnecessary antibiotics, excess duration, avoidable fluoroquinolones, and improving (or avoiding) intravenous antibiotic therapy. Barriers to discharge antibiotic stewardship include the perceived “high stakes” of care transitions during which patients move from intense to infrequent observation, difficulties in antibiotic measurement to guide improvement at discharge, and poor communication across silos, particularly with skilled nursing facilities. In this review, we discuss what is currently known about antibiotic overuse at hospital discharge, key barriers, and targets for improving antibiotic prescribing at discharge and we introduce an evidence-based framework, the Reducing Overuse of Antibiotics at Discharge Home Framework, for conducting discharge antibiotic stewardship.
Plasma microRNA Interindividual Variability in Healthy Individuals, Pregnant Women, and an Individual with a Stably Altered Neuroendocrine Phenotype
Authors: Max Klaas E.A. , Wang Victoria R. , Chang Michael S. , Liau Jonathan , Weiss Zachary R. , Morgan Stephanie , Li Jenny , Bogardus Kimberly A. , Morozov Pavel , Suryawanshi Hemant , Akat Kemal M. , Ben-Dov Iddo Z. , Hurley Arlene M. , Dowd Kathleen , Williams Zev , Tuschl Thomas 
Published: September 2021

AbstractBackgroundExtracellular RNAs (exRNAs) in biofluids are amenable to quantitative analysis and proposed as noninvasive biomarkers for monitoring organ function. Cell-lineage-specific microRNAs (miRNAs) are present in plasma as soluble ribonucleoproteins or enclosed in exRNA carriers and transported through the vasculature. However, more extensive studies of healthy individuals are needed to gain insights into the variability of plasma miRNA abundance and composition.MethodsThe exRNA composition of platelet-depleted plasma collected twice from 236 healthy individuals was characterized by small RNA sequencing. Plasma of pregnant women featuring dramatically increased placental miRNAs and samples from subject P12 with noticeably increased epithelial- and neuroendocrine-origin miRNAs were included for comparison. The miRNA content of 10 000g and 100 000g pellet fractions of plasma generated by ultracentrifugation was also determined. Data analysis methods included Pearson correlation, differential gene expression, and unsupervised clustering.ResultsThe abundance changes for more variable miRNAs in plasma of normal individuals correlated between coexpressed cell-lineage-specific miRNAs of the liver, neuroendocrine organs, epithelial cells, and muscle. ExRNA of pellet fractions contained &lt;2% of total plasma miRNA with modest enrichment of lineage-specific and variable miRNAs compared to supernatant. The abundance fold changes of miRNAs observed in pregnancy and P12 compared to normal exceeded interquartile variability of healthy individuals. The neuroendocrine miRNA signature of P12 persisted for more than 4 years and was absent in other individuals.ConclusionsThis study defines the framework and effect size for screening of extensive plasma collections for miRNA phenotypes and biomarker discovery.
Association Between Proposed Definitions of Clinical Remission/Response and Well-Being in Patients With Crohn’s Disease
Authors: Sandborn William J , Lewis James D , Panes Julian , Loftus Edward V , D’Haens Geert , Yu Zhuqing , Huang Bidan , Lacerda Ana P , Pangan Aileen L , Feagan Brian G 
Published: September 2021

Abstract

Background and Aims
Patient-reported outcomes are recommended endpoints in Crohn’s disease [CD] trials. The association between patient-reported general well-being relative to symptoms of diarrhoea and abdominal pain [AP] in patients with moderate to severe CD was explored.

Methods
Patients from three randomized, placebo-controlled, double-blind adalimumab or upadacitinib studies with average daily very soft/liquid stool frequency [SF] ≥4 and/or AP score ≥2 at baseline were included. Using electronic diaries, patients reported general well-being [seven-point Likert scale; 1 = worst; 7 = best] in item 10 of the Inflammatory Bowel Disease Questionnaire [IBDQ]. Changes in well-being and clinical outcomes of SF and AP from baseline to week 12 or 16, and the relationship between well-being and clinical outcomes were evaluated using cumulative distribution function and probability density function curves.

Results
In total, 858 patients with CD were included [adalimumab, n = 695; upadacitinib, n = 163]. Patients who achieved clinical remission [SF ≤2.8, AP score ≤1.0, neither worse than baseline] were more likely than those not in clinical remission to report IBDQ item 10 response in the 6–7 group category but not IBDQ categories ≤5. Higher IBDQ score for item 10 [6–7] was associated with lower SF and AP score. Greater point increases in IBDQ item 10 were associated with a greater percentage decrease in clinical parameters; a ≥25–30% decrease in SF or AP was associated with a ≥1-point improvement in IBDQ.

Conclusions
An association between improvements in patient-reported general well-being and clinical remission/response was observed using outcomes of SF and AP, supporting the clinical remission/response endpoint definitions used in clinical studies of CD.
Clinical Trial Registrations [ClinicalTrials.gov]: NCT00077779 [CHARM]; NCT00348283 [EXTEND]; NCT02365649 [CELEST].
Within-plant Distributions and Density of Amblyseius swirskii (Acari: Phytoseiidae) as Influenced by Interactions Between Plastic Mulch and Vegetable Crop Species
Authors: Razzak Mohammad A , Seal Dakshina R , Schaffer Bruce , Liburd Oscar E , Colee James 
Published: September 2021

Abstract
Plastic mulch of different colors and ultraviolet (UV) reflectivity individually or combined with released arthropod predators is an important component of an integrated pest management strategy. In 2015 and 2016, we evaluated the density and within-plant distribution of a released predatory mite, Amblyseius swirskii Athius-Henriot (Acari: Phytoseiidae) in snap bean (Phaseolus vulgaris L.), cucumber (Cucumis sativus L.), yellow squash (Cucurbita pepo L.), eggplant (Solanum melongena L.), Jalapeno pepper (Capsicum annuum L.), and tomato (Solanum lycopersicum L.) grown on different plastic mulches. The mulch treatments evaluated were: metalized top and black bottom, metalized top and white bottom, black-on-black, black-on-white, white-on-black, and bare soil with no mulch. Crop species had a significant effect on the density of A. swirskii. Eggplant and cucumber had higher numbers of A. swirskii than the other crops tested in 2015. In 2016, the density of A. swirskii was higher on eggplant than on cucumber. There was a variation in the distribution of A. swirskii in different strata of the plant canopies with the highest number in the bottom stratum of each crop, which was positively correlated with the population of Thrips palmi Karny (Thysanoptera: Thripidae). Mulch type had no effect on the density or distribution of A. swirskii in any strata of any of the crops tested. The results of this study indicate that releasing A. swirskii is compatible with the use of UV-reflective mulch. This information about host preference and within-plant distribution of A. swirskii should be of value in pest management programs for the crops studied.
Demand Shocks and Firm Investment: Micro-Evidence from Fiscal Retrenchment in Italy
Authors: Coviello Decio , Marino Immacolata , Nannicini Tommaso , Persico Nicola 
Published: September 2021

Abstract
We study the effect of a persistent demand shock on corporate factor utilisation. Our identification strategy leverages a legislative change designed to permanently reduce spending in certain targeted municipalities. This change generates an arguably exogenous drop in the revenue of procurement firms, which differs depending on each firm’s reliance for its revenue on procurement in the targeted municipalities. We find that firms responded to the demand shock by cutting capital rather than labour. We propose a theoretical mechanism based on the irreversibility of capital investment.
Reducing the impact of the coronavirus on disadvantaged migrants and ethnic minorities
Authors: Kumar Bernadette N , Hargreaves Sally , Agyemang Charles , James Rosemary A , Blanchet Karl , Gruer Laurence 
Published: September 2021

Abstract
Studies from several countries have shown that the COVID-19 pandemic has disproportionally affected migrants. Many have numerous risk factors making them vulnerable to infection and poor clinical outcome. Policies to mitigate this effect need to take into account public health principles of inclusion, universal health coverage and the right to health. In addition, the migrant health agenda has been compromised by the suspension of asylum processes and resettlement, border closures, increased deportations and lockdown of camps and excessively restrictive public health measures. International organizations including the World Health Organization and the World Bank have recommended measures to actively counter racism, xenophobia and discrimination by systemically including migrants in the COVID-19 pandemic response. Such recommendations include issuing additional support, targeted communication and reducing barriers to accessing health services and information. Some countries have had specific policies and outreach to migrant groups, including facilitating vaccination. Measures and policies targeting migrants should be evaluated, and good models disseminated widely.
Genetic influence on components of wood density variation in white spruce
Authors: Soro André , Lenz Patrick , Hassegawa Mariana , Roussel Jean-Romain , Bousquet Jean , Achim Alexis 
Published: September 2021

AbstractConifer breeding programmes are increasingly selecting for wood quality in addition to growth so to ensure a sufficient flow of high-quality fibre from future forest plantations. As wood density is one of the most frequently used indicators of wood quality, there is a growing interest to consider this trait in selection, and thus enhance the properties of end-use products from planted trees. However, wood density varies at different scales within trees, with pith-to-bark patterns and year-to-year fluctuations representing two important sources of variation. From both physiological and end-use points of view, it is desirable to produce stems with limited pith-to-bark and year-to-year wood density variation. In the present study, we assessed patterns of pith-to-bark and year-to-year variation in 2196 wood density patterns and evaluated the genetic control of traits characterizing this variation. The experimental data came from a 15-year-old white spruce genetic trial representing 93 full-sib families replicated in two contrasting environments in Quebec, Canada. To separate pith-to-bark from year-to-year variation, non-linear models were developed to describe pith-to-bark patterns of variation in the mean ring density (MRD) of individual trees as well as for latewood density (LWD) and latewood proportion. We observed that pith-to-bark variation was more under genetic control than year-to-year variation, for which only LWD and proportion of latewood width to overall ring width reached moderate genetic control. Little genotype-by-environment interaction was observed although wood density patterns differed significantly between sites. The present approach could help identify trees or families that tend to have limited pith-to-bark and year-to-year variation in wood density as part of tree genetic improvement programmes to provide future trees with more uniform and desirable wood attributes.
Sn attenuation tomography of southeastern Tibet: new constraints on lithospheric mantle deformation
Authors: Tiwari Ashwani Kant , Singh Chandrani , Sandvol Eric , Mukhopadhyay Sagarika , Singh Arun , Gupta Arun Kumar 
Published: September 2021

SUMMARY
We have formulated a 2-D Sn attenuation tomographic model to investigate the uppermost mantle shear wave Q and its tectonic implications beneath southeastern Tibet near Namche Barwa. To achieve our objective, we first compute interstation Q values using the two station method (TSM) analysis on 618 station pairs obtained from 26 regional earthquakes (Mw ≥5.5) with epicentral distances ranging from 5° to 15° recorded at 47 seismic stations belonging to the Namche Barwa network (XE network, 2003−2004). Furthermore, the QSn tomographic model is generated by utilizing these interstation Q values. QSn values are varying from 101 to 490 in the region. The tomography image reveals high attenuation (≤200 Q values) in the central region. Regions of low attenuation (&gt;200 Q values) are observed in the southern part and in some small regions beneath the northern side of the study area. Consecutive high-low-high QSn values have been observed in the south part of the Lhasa block. The obtained QSn values, along with the prior isotropic Pn velocity model of the study area, indicate that the scattering effect is causing significant Sn wave energy dissipation due to structural heterogeneity present in the uppermost mantle beneath the region. This may be the result of the break-up of the subducting Indian Plate beneath the area.
On the low-frequency elastic response of Pierre Shale during temperature cycles
Authors: Rørheim Stian , Bauer Andreas , Holt Rune M 
Published: September 2021

SUMMARYTemperature affects elastic rock properties but is less-studied and thus less-understood than pressure and stress. Thermal effects on dispersion are experimentally observed herein from seismic to ultrasonic frequencies: Young’s moduli and Poisson’s ratios plus P- and S-wave velocities are determined by forced oscillation (FO) from 1 to 144 Hz and by pulse transmission at 500 kHz. Despite being the dominant sedimentary rock type, shales receive less experimental attention than sandstones and carbonates. To our knowledge, no other FO studies on shale at above ambient temperatures exist. Temperature fluctuations are enforced by two temperature cycles from 20 via 40 to 60 °C and vice versa. Measured rock properties are initially irreversible but become reversible with increasing number of heating and cooling segments. Rock property sensitivity to temperature is likewise reduced. It is revealed that dispersion shifts towards higher frequencies with increasing temperature (reversible if decreased), Young’s moduli and P-wave velocity maxima occur at 40 °C for frequencies below 56 Hz, and S-wave velocities remain unchanged with temperature (if the first heating segment is neglected) at seismic frequencies. In comparison, ultrasonic P- and S-wave velocities are found to decrease with increasing temperatures. Behavioural differences between seismic and ultrasonic properties are attributed to decreasing fluid viscosity with temperature. We hypothesize that our ultrasonic recordings coincide with the transition-phase separating the low- and high-frequency regimes while our seismic recordings are within the low-frequency regime.
Pathways linking parental health literacy with health behaviours directed at the child: a scoping review
Authors: Pawellek Maja , Kopf Felicitas Maria , Egger Nina , Dresch Carolin , Matterne Uwe , Brandstetter Susanne 
Published: September 2021

SummaryHealth literacy (HL) is thought to be crucial for the management of the manifold demands relating to child health which parents are faced with. Albeit many studies have investigated parental HL and health behaviours (HBs) directed at the child, knowledge about the pathways which link parental HL with HB is scarce. The aim of this scoping review was to identify and comprehensively describe the variety of pathways linking parental HL with HBs directed at the child which were empirically analysed in previous studies. Following established scoping review methods database searches were conducted in MEDLINE, EMBASE, PsycINFO and WebofScience on 5 March 2020. Eligibility criteria included primary, empirical studies assessing parental HL and HB directed at the child in the general parent population. Titles and abstracts were screened independently by six reviewers for potentially relevant publications and data were extracted using standardized data extraction forms. The search identified 6916 articles for title and abstract screening. After full-text review, 50 studies were included in this review. Most studies (N = 24) assumed a direct association between HL and HBs and only few studies (N = 4) used more complex models investigating different pathways or mediation and/or moderation models. Overall, the evidence on the underlying pathways linking parental HL and HBs directed at the child is mixed and fairly limited. Therefore, hypothesis-driven research and integration of results into theoretical frameworks is needed for advancing both the research on HL and public health practice.