bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting potential microbe–disease associations based on multi-source features and deep learning
Authors: Wang Liugen , Wang Yan , Xuan Chenxu , Zhang Bai , Wu Hanwen , Gao Jie 
Published: July 2023

AbstractStudies have confirmed that the occurrence of many complex diseases in the human body is closely related to the microbial community, and microbes can affect tumorigenesis and metastasis by regulating the tumor microenvironment. However, there are still large gaps in the clinical observation of the microbiota in disease. Although biological experiments are accurate in identifying disease-associated microbes, they are also time-consuming and expensive. The computational models for effective identification of diseases related microbes can shorten this process, and reduce capital and time costs. Based on this, in the paper, a model named DSAE_RF is presented to predict latent microbe–disease associations by combining multi-source features and deep learning. DSAE_RF calculates four similarities between microbes and diseases, which are then used as feature vectors for the disease-microbe pairs. Later, reliable negative samples are screened by k-means clustering, and a deep sparse autoencoder neural network is further used to extract effective features of the disease-microbe pairs. In this foundation, a random forest classifier is presented to predict the associations between microbes and diseases. To assess the performance of the model in this paper, 10-fold cross-validation is implemented on the same dataset. As a result, the AUC and AUPR of the model are 0.9448 and 0.9431, respectively. Furthermore, we also conduct a variety of experiments, including comparison of negative sample selection methods, comparison with different models and classifiers, Kolmogorov–Smirnov test and t-test, ablation experiments, robustness analysis, and case studies on Covid-19 and colorectal cancer. The results fully demonstrate the reliability and availability of our model.
Insights into the morphology and evolution of orbicules in the Spermacoce clade (Spermacoceae-Rubiaceae) and implications for systematics
Authors: Nuñez-Florentin Mariela , Verstraete Brecht , Salas Roberto M , Dessein Steven 
Published: July 2023

Abstract
The orbicules are tiny structures of sporopollenin that occur on the interior wall of anthers in several groups of plants, and they are associated with pollen grains and tapetal cells. Although their function remains still unresolved, they have been widely used in systematics. Rubiaceae is one of the most studied families in this aspect. However, scarce information is available about the orbicules in the tribe Spermacoceae, especially in the Spermacoce clade. The main objectives of this work were to investigate the occurrence, general morphology, evolution, and systematic utility of the orbicular characters in the Spermacoce clade. We investigated the presence/absence, size, abundance, shape, and ornamentation of orbicules in 104 specimens from 84 species in the Spermacoce clade using scanning electron microscopy (SEM). On the basis of these features, the ancestral state reconstruction analyses were performed on a custom-made phylogeny by stochastic character mapping. The orbicules are present in 38 (44%) of 84 analysed species, corresponding to 13 genera (56%) of the Spermacoce clade. Seven genera have orbicules in all analysed species, eight genera lack orbicules in all analysed species, and six genera show both presence and absence of orbicules. The absence of orbicules was estimated to be the ancestral state for the Spermacoce clade and the presence of orbicules evolved several times independently within Clade B. The absence of orbicules in the common ancestor of the Spermacoce clade can be seen as one of the independent losses that occurred during the evolutionary history of the Rubiaceae.
Stress specifically deteriorates working memory in peripheral neuropathic pain and fibromyalgia
Authors: Jacobsen Henrik Børsting , Brun Aurora , Stubhaug Audun , Reme Silje Endresen 
Published: July 2023

Abstract
This study aimed to explore the influence of chronic stress, measured through hair cortisol, on executive functions in individuals with chronic pain. We expected that there would be significant differences in chronic stress and executive functioning between pain patients and healthy controls, as well as between primary and secondary pain classifications. We also hypothesized that hair cortisol concentration was predictive of worse performance on tests of executive functions, controlling for objective and subjective covariates. For this study, 122 participants provided a hair sample (n = 40 with fibromyalgia; n = 24 with peripheral neuropathic pain; n = 58 matched healthy controls). Eighty-four of these participants also completed highly detailed testing of executive functions (n = 40 with fibromyalgia; n = 24 with peripheral neuropathic pain; n = 20 healthy controls). To assess differences in stress levels and executive functions, t-tests were used to compare patients with controls as well as fibromyalgia with peripheral neuropathic pain. Then, univariate regressions were used to explore associations between stress and executive functioning in both chronic pain classifications. Any significant univariate associations were carried over to hierarchical multivariate regression models. We found that patients with chronic pain had significantly higher cortisol levels than healthy controls, but all groups showed similar executive functioning. Hierarchical multiple regression analyses disclosed that in a model controlling for age, sex and pain medication usage, hair cortisol levels explained 8% of the variance in spatial working memory strategy in individuals with chronic pain. The overall model explained 24% of the variance in spatial working memory. In a second model using imputed data, including both objective and subjectively reported covariates, hair cortisol levels explained 9% of the variance, and the full model 31% of the variance in spatial working memory performance. Higher levels of cortisol indicated worse performance. In this study, an applied measure of chronic stress, namely hair cortisol, explained a substantial part of the variance on a spatial working memory task. The current results have important implications for understanding and treating cognitive impairments in chronic pain.
Standardized 4-point scoring scale of [18F]-FDG PET/CT imaging helps in the diagnosis of renal and hepatic cyst infections in patients with autosomal dominant polycystic kidney disease: a validation cohort
Authors: Demuynck Selina , Lovinfosse Pierre , Seidel Laurence , Jentjens Sander , Mekahli Djalila , Jouret François , Bammens Bert , Goffin Karolien 
Published: July 2023

ABSTRACT

Background
Autosomal dominant polycystic kidney disease (ADPKD) is prone to multiple complications, including cyst infection (CyI). 2-Deoxy-2-[18F]fluoro-d-glucose positron emission tomography/computed tomography ([18F]-FDG PET/CT) imaging has proved useful in the diagnosis of renal and hepatic CyI. A 4-point scale comparing the uptake of [18F]-FDG in the suspected infected cyst versus the hepatic physiological background has been recently proposed. We performed an independent validation of this semi-quantitative scoring system.

Methods
All ADPKD patients hospitalized between January 2009 and November 2019 who underwent an [18F]-FDG PET/CT for suspected CyI were retrospectively identified using computer-based databases. Medical files were reviewed. CyI was conventionally defined by the combination of fever (≥38°C), abdominal pain, increased plasma C-reactive protein levels (≥70 mg/L), absence of any other cause of inflammation and favourable outcome after ≥21 days of antibiotics. [18F]-FDG uptake of the suspected CyI was evaluated using a 4-point scale comparing the uptake of [18F]-FDG around the infected cysts with the uptake in the hepatic parenchyma. Statistics were performed using SAS version 9.4.

Results
Fifty-one [18F]-FDG PET/CT scans in 51 patients were included, of which 11 were cases of CyI. The agreement between the 4-point scale and the gold-standard criteria of CyI was significant [odds ratio of 6.03 for CyI in case of a score ≥3 (P = .014)]. The corresponding sensitivity, specificity, and positive and negative predictive values of [18F]-FDG PET/CT using the 4-point scale were 64% [Clopper–Pearson 95% confidence interval (CI) 30%–89%], 78% (95% CI 62%–89%), 44% (95% CI 20%–70%) and 89% (95% CI 73%–97%), respectively.

Conclusions
Our independent validation cohort confirms the use of a semi-quantitative 4-point scoring system of [18F]-FDG PET/CT imaging in the diagnosis of CyI in patients with ADPKD. Considering its performance metrics with high specificity and negative predictive value, the scoring system is particularly useful to distinguish other causes of clinical inflammation than CyI and as such avoid unnecessarily long antibiotic treatment.
Investigation of the non-size-determined T4N0-2M0 non-small-cell lung cancer: what is the proper T category for the tumour with additional nodules in different lobes of ipsilateral lung?
Authors: Cai Jing-Sheng , Li Yun , Yang Fan , Wang Xun 
Published: July 2023

Abstract

OBJECTIVES
This study aimed to explore the prognostic disparity among T4N0-2M0 non-small-cell lung cancer (NSCLC) patients with different T4 descriptors.

METHODS
T3-4N0-2M0 NSCLC patients were included. Patients were assigned to 7 subgroups: T3, T4 tumours with size larger than 70 mm (T4-size), T4 tumours with aorta/vena cava/heart invasion (T4-blood vessels), T4 tumours with vertebra invasion (T4-vertebra), T4 tumours with carina/trachea invasion (T4-carina/trachea), T4 tumours with additional tumour nodules in different lobes of ipsilateral lung (T4-add) and T4 tumours had at least 2 T4 descriptors (T4-multiple). Univariable and multivariable Cox analyses were used to explore the effect of T4 category on overall survival. Kaplan–Meier method with log-rank test was used to compare survival differences among subgroups. Propensity score matching was used to minimize the bias caused by imbalanced covariates between groups.

RESULTS
A total of 41 303 eligible T3-4N0-2M0 NSCLC cases were included (17 057 T3 cases and 24 246 T4 cases). There were 10 682 cases, 573 cases, 557 cases, 64 cases, 2888 cases and 9482 cases in the T4-size, T4-blood vessels, T4-vertebra, T4-carina/trachea, T4-add and T4-multiple subgroups, respectively. Multivariable Cox analyses revealed that T4-add patients had the best prognosis in the entire cohort and in several subgroups. In the matched cohort of T4-add and T4-size and T4-add and T3, the survival of T4-add patients was superior to that of T4-size patients (P &lt; 0.001) but was comparable to that of T3 patients (P = 0.115).

CONCLUSIONS
Among NSCLC patients with different T4 descriptors, T4-add patients had the best prognosis. T4-add patients and T3 patients had similar survivals. Herein, we proposed that T4-add patients should be downstaged from T4 to T3 category. Our results served as a novel supplement to the proposals for the T category revision.
Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence
Authors: Healy Timothy M , Burton Ronald S 
Published: July 2023

Abstract
All mitochondrial-encoded proteins and RNAs function through interactions with nuclear-encoded proteins, which are critical for mitochondrial performance and eukaryotic fitness. Coevolution maintains inter-genomic (i.e., mitonuclear) compatibility within a taxon, but hybridization can disrupt coevolved interactions, resulting in hybrid breakdown. Thus, mitonuclear incompatibilities may be important mechanisms underlying reproductive isolation and, potentially, speciation. Here we utilize Pool-seq to assess the effects of mitochondrial genotype on nuclear allele frequencies in fast- and slow-developing reciprocal inter-population F2 hybrids between relatively low-divergence populations of the intertidal copepod Tigriopus californicus. We show that mitonuclear interactions lead to elevated frequencies of coevolved (i.e., maternal) nuclear alleles on two chromosomes in crosses between populations with 1.5% or 9.6% fixed differences in mitochondrial DNA nucleotide sequence. However, we also find evidence of excess mismatched (i.e., noncoevolved) alleles on three or four chromosomes per cross, respectively, and of allele frequency differences consistent with effects involving only nuclear loci (i.e., unaffected by mitochondrial genotype). Thus, our results for low-divergence crosses suggest an underlying role for mitonuclear interactions in variation in hybrid developmental rate, but despite substantial effects of mitonuclear coevolution on individual chromosomes, no clear bias favoring coevolved interactions overall.
Genome-wide screen identifies host loci that modulate Mycobacterium tuberculosis fitness in immunodivergent mice
Authors: Meade Rachel K , Long Jarukit E , Jinich Adrian , Rhee Kyu Y , Ashbrook David G , Williams Robert W , Sassetti Christopher M , Smith Clare M 
Published: July 2023

Abstract
Genetic differences among mammalian hosts and among strains of Mycobacterium tuberculosis (Mtb) are well-established determinants of tuberculosis (TB) patient outcomes. The advent of recombinant inbred mouse panels and next-generation transposon mutagenesis and sequencing approaches has enabled dissection of complex host–pathogen interactions. To identify host and pathogen genetic determinants of Mtb pathogenesis, we infected members of the highly diverse BXD family of strains with a comprehensive library of Mtb transposon mutants (TnSeq). Members of the BXD family segregate for Mtb-resistant C57BL/6J (B6 or B) and Mtb-susceptible DBA/2J (D2 or D) haplotypes. The survival of each bacterial mutant was quantified within each BXD host, and we identified those bacterial genes that were differentially required for Mtb fitness across BXD genotypes. Mutants that varied in survival among the host family of strains were leveraged as reporters of “endophenotypes,” each bacterial fitness profile directly probing specific components of the infection microenvironment. We conducted quantitative trait loci (QTL) mapping of these bacterial fitness endophenotypes and identified 140 host–pathogen QTL (hpQTL). We located a QTL hotspot on chromosome 6 (75.97–88.58 Mb) associated with the genetic requirement of multiple Mtb genes: Rv0127 (mak), Rv0359 (rip2), Rv0955 (perM), and Rv3849 (espR). Together, this screen reinforces the utility of bacterial mutant libraries as precise reporters of the host immunological microenvironment during infection and highlights specific host–pathogen genetic interactions for further investigation. To enable downstream follow-up for both bacterial and mammalian genetic research communities, all bacterial fitness profiles have been deposited into GeneNetwork.org and added into the comprehensive collection of TnSeq libraries in MtbTnDB.
A Life of Leisure? Investigating the Differential Impact of Retirement on Leisure Activity
Authors: Tunney Orlaith , Henkens Kène , van Solinge Hanna 
Published: July 2023

Abstract

Objectives
Remaining active in older adulthood is widely endorsed by governments and policy-makers as a way of promoting public health and curbing welfare spending. Despite links between greater leisure activity in older adulthood and better health, cognitive function, and subjective well-being, there is a dearth of research investigating the impact of retirement on leisure activity engagement. Therefore, the primary goal of this study is to address this knowledge gap and investigate the impact of retirement on leisure activity engagement.

Methods
Using panel data from 2 waves of a large-scale longitudinal survey of Dutch older workers (N = 4,927), we investigated the impact of retirement on hours spent engaging in physical, social, and self-development activities. We further investigated the differential impact of retirement on leisure activity in retirement based on various sociodemographic characteristics.

Results
Although leisure activity increased across all 3 activity domains, conditional change ordinal least square regression models revealed that retirement resulted in significantly greater increases in activity relative to nonretirees. Additional analyses including interaction terms revealed that the impact of retirement on self-development and social activity differed significantly based on gender and education.

Discussion
Our study demonstrates that while time in leisure activity largely increases in response to retirement the nature and magnitude of the impact of retirement on leisure activity is not uniform. From a policy perspective, findings that certain groups, namely men and lower-­educated individuals, may be at greater risk of lower activity levels may help guide interventions promoting active aging and retirement.
A Riemann–Hilbert Approach to the Perturbation Theory for Orthogonal Polynomials: Applications to Numerical Linear Algebra and Random Matrix Theory
Authors: Ding Xiucai , Trogdon Thomas 
Published: July 2023

Abstract
We establish a new perturbation theory for orthogonal polynomials using a Riemann–Hilbert approach and consider applications in numerical linear algebra and random matrix theory. This new approach shows that the orthogonal polynomials with respect to two measures can be effectively compared using the difference of their Stieltjes transforms on a suitably chosen contour. Moreover, when two measures are close and satisfy some regularity conditions, we use the theta functions of a hyperelliptic Riemann surface to derive explicit and accurate expansion formulae for the perturbed orthogonal polynomials. In contrast to other approaches, a key strength of the methodology is that estimates can remain valid as the degree of the polynomial grows. The results are applied to analyze several numerical algorithms from linear algebra, including the Lanczos tridiagonalization procedure, the Cholesky factorization, and the conjugate gradient algorithm. As a case study, we investigate these algorithms applied to a general spiked sample covariance matrix model by considering the eigenvector empirical spectral distribution and its limits. For the first time, we give precise estimates on the output of the algorithms, applied to this wide class of random matrices, as the number of iterations diverges. In this setting, beyond the first order expansion, we also derive a new mesoscopic central limit theorem for the associated orthogonal polynomials and other quantities relevant to numerical algorithms.
Genotype by environment interaction and heteroscedasticity influence the expression of parasite resistance in Katahdin sheep
Authors: Arisman Brian C , Burke Joan M , Morgan James L M , Lewis Ronald M 
Published: July 2023

Abstract
Increasingly, sheep producers are choosing breeds that express resistance to gastrointestinal parasites due to reduced efficacy of anthelminthic drugs. One such breed is Katahdin. Katahdins are raised in various climates and management systems in the United States, which can be combined into eco-management clusters to describe production environments more holistically. The objectives of this study were to determine if genotype by environment interaction (G × E) and heteroscedasticity existed across these eco-management clusters for traits indicative of parasite resistance. Body weights (BW), FAMACHA scores (FAM), and fecal egg counts (FEC) were collected at around 90 d in 3,527 Katahdin lambs delineated into nine eco-management clusters. A tri-variate animal model including birth-rearing type, sex, and dam age (as a quadratic covariate) as fixed effects, and eco-management cluster, direct additive, uncorrelated maternal environmental (for BW), and residual as random effects, was fitted with ASReml. Heritability estimates for BW, FEC, and FAM were 0.36 ± 0.07, 0.31 ± 0.07, and 0.26 ± 0.05, respectively. The genetic (additive) correlation between BW with FEC was −0.26 ± 0.08 and with FAM was −0.16 ± 0.08, and thereby favorable. Heritabilities were also estimated univariately within eco-management clusters and ranged from 0.30 ± 0.05 to 0.37 ± 0.05 for BW, 0.18 ± 0.12 to 0.50 ± 0.13 for FEC, and 0.07 ± 0.06 to 0.40 ± 0.19 for FAM. Significant genetic and phenotypic heteroscedasticity among eco-management clusters was detected in FEC and FAM. A sire by eco-management cluster interaction term was added to the initial model fitted to evaluate G × E. This interaction defined substantial variation (P &lt; 0.01) in all traits and explained 12% (FEC) to 20% (BW) of the phenotypic variation. Accounting for G × E and heteroscedasticity in the design and implementation of breeding programs may introduce operational challenges. Still, doing so would improve the efficacy of selection programs to improve parasite resistance.
∆8-THC-COOH cross-reactivity with cannabinoid immunoassay kits and interference in chromatographic testing methods
Authors: Mullen Lawrance D , Hart E. Dale , Vikingsson Svante , Winecker Ruth E , Hayes Eugene , Flegel Ron 
Published: July 2023

Abstract
Because of structural similarities, the presence of 11-Nor-9-carboxy-∆8-tetrahydrocannabinol (∆8-THC-COOH) in a urine specimen might interfere with testing for 11-Nor-9-carboxy-∆9-tetrahydrocannabinol (∆9-THC-COOH). A set of samples containing ∆8-THC-COOH with concentrations ranging from 10 to 120 ng/mL were tested at cut-offs of 20, 50 and 100 ng/mL using cannabinoid immunoassay reagents from three different manufacturers. Cross-reactivities ranged from 87% to 112% for ∆8-THC-COOH at the cut-off of 50 ng/mL for the three different platforms. Additionally, samples containing both ∆8-THC-COOH and ∆9-THC-COOH were fortified by the National Laboratory Certification Program (NLCP). U.S. Department of Health and Human Services (HHS)–Certified Laboratories tested the samples to determine the interference of ∆8-THC-COOH on confirmatory tests commonly used in workplace drug testing laboratories for the confirmation and quantification of ∆9-THC-COOH. When evaluating confirmation and quantification of ∆9-THC-COOH in the presence of ∆8-THC-COOH, unreportable results for ∆9-THC-COOH were observed because of chromatographic interference or mass ratio failures. However, there were no false-positive ∆9-THC-COOH reports from any HHS-certified laboratory.
On The Problem of Defending Basic Equality: Natural Law and The Substance View
Authors: Friberg-Fernros Henrik 
Published: July 2023

Abstract
While most theorists agree with the claim that human beings have high and equal moral standing, there are strong disagreements about how to justify this claim. These disagreements arise because there are different ways of managing the difficulty of finding a basis for this claim, which is sufficiently substantial to do this justifying work, but not vary in degree in order to not give rise to inequality of moral considerability. The aim of this paper is to review previous attempts to address this difficulty and to demonstrate why they fail and then to defend another way of dealing with this challenge by applying two views: the substance view on the human person and the natural-law account of morality. My claim is that this approach has comparative advantages because it provides a binary and a normatively significant basis of justification for equality without being implausibly inclusive.