bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlated stabilizing selection shapes the topology of gene regulatory networks
Authors: Petit Apolline J R , Guez Jeremy , Le Rouzic Arnaud 
Published: April 2023

Abstract
The evolution of gene expression is constrained by the topology of gene regulatory networks, as co-expressed genes are likely to have their expressions affected together by mutations. Conversely, co-expression can also be an advantage when genes are under joint selection. Here, we assessed theoretically whether correlated selection (selection for a combination of traits) was able to affect the pattern of correlated gene expressions and the underlying gene regulatory networks. We ran individual-based simulations, applying a stabilizing correlated fitness function to three genetic architectures: a quantitative genetics (multilinear) model featuring epistasis and pleiotropy, a quantitative genetics model where each genes has an independent mutational structure, and a gene regulatory network model, mimicking the mechanisms of gene expression regulation. Simulations showed that correlated mutational effects evolved in the three genetic architectures as a response to correlated selection, but the response in gene networks was specific. The intensity of gene co-expression was mostly explained by the regulatory distance between genes (largest correlations being associated to genes directly interacting with each other), and the sign of co-expression was associated with the nature of the regulation (transcription activation or inhibition). These results concur to the idea that gene network topologies could partly reflect past selection patterns on gene expression.
International Standards for Dementia Workforce Education and Training: A Scoping Review
Authors: Pit Sabrina Winona , Horstmanshof Louise , Moehead Anne , Hayes Oliver , Schache Valerie , Parkinson Lynne 
Published: April 2023

Abstract

Background and Objectives
The increasing number of people with dementia requires transparency and quality dementia education, training, and care. This scoping review aimed to determine the key elements of national or state-wide standards on dementia education and training that could underpin the development of international standards for dementia workforce training and education.

Research Design and Methods
The English-language peer-reviewed and gray literature were searched (2010–20). Key search domains were training, workforce, standards/frameworks, and dementia.

Results
Thirteen standards were identified from the United Kingdom (n = 5), the United States (n = 4), Australia (n = 3), and Ireland (n = 1). Most standards focused on training health care professionals with some including people in customer-centric settings, people living with dementia, and informal carers or the general community. Seventeen training topics were identified in 10 or more of the 13 standards. Cultural safety, rural issues, health care professional self-care, digital literacy, and health promotion topics were less commonly reported. The barriers to standards implementation were lack of organizational support, lack of access to relevant training, low staff literacy, lack of funding, high staff turnover, ineffective past program cycles, and inconsistent service delivery. Enablers included a strong implementation plan, funding, strength of partnerships, and building on previous work.

Discussion and Implications
The U.K. Dementia Skills and Core Training Standard, the Irish Department of Health Dementia Together, and the National Health Services Scotland Standard are the recommended strongest standards for underpinning the development of international standards. It is essential that training standards are tailored to the needs of the consumer, worker, and regions.
Homozygous frameshift variant in POC1B causes male infertility with oligoasthenoteratozoospermia in human and mice
Authors: Hua Juan , Xu Bo , Liu Wenjing , Shi JingTian , Jiang Hui , Zha XiaoJun , Zhang Xiansheng , Wan Yangyang 
Published: April 2023

Abstract
Several different mutations in the proteome of centriole 1 centriolar protein B (POC1B) have been linked to cone dystrophy or cone-rod dystrophy (CORD). However, mutations in POC1B that are associated with both CORD and oligoasthenoteratozoospermia (OAT) have not been reported previously. Here, whole-exome sequencing was performed to identify a homozygous frameshift variant (c.151delG) in POC1B in the two brothers who had been diagnosed with both CORD and OAT from a consanguineous family. Transcript and protein analyses of biological samples from the two patients carrying the variant showed that POC1B protein is lost in sperm cells. The system CRISPR/Cas9 was utilized to create poc1bc.151delG/c.151delG knock-in (KI) mice. Notably, poc1bc.151delG/c.151delG KI male mice presented with OAT phenotype. Additionally, testicular histology and transmission electron microscopy analysis of the testes and sperm indicated that Poc1b mutation results in abnormal formation of acrosomes and flagella. Collectively, according to our experimental data on human volunteers and animal models, biallelic mutations in POC1B can cause OAT and CORD in mice and humans.
Drought stress triggers alterations of adaxial and abaxial stomatal development in basil leaves increasing water-use efficiency
Authors: Driesen Elisa , De Proft Maurice , Saeys Wouter 
Published: April 2023

Abstract
The physiological control of stomatal opening by which plants adjust for water availability has been extensively researched. However, the impact of water availability on stomatal development has not received as much attention, especially for amphistomatic plants. Therefore, the acclimation of stomatal development in basil (Ocimum basilicum L.) leaves was investigated. Our results show that leaves developed under water-deficit conditions possess higher stomatal densities and decreased stomatal length for both the adaxial and abaxial leaf sides. Although the stomatal developmental reaction to water deficit was similar for the two leaf surfaces, it was proven that adaxial stomata are more sensitive to water stress than abaxial stomata, with more closed adaxial stomata under water-deficit conditions. Furthermore, plants with leaves containing smaller stomata at higher densities possessed a higher water use efficiency. Our findings highlight the importance of stomatal development as a tool for long-term acclimation to limit water loss, with minimal reduction in biomass production. This highlights the central role that stomata play in both the short (opening) and long-term (development) reaction of plants to water availability, making them key tools for efficient resource use and anticipation of future environmental changes.
Association of gallstone disease with risk of colorectal cancer: a systematic review and meta-analysis of observational studies
Authors: Polychronidis Georgios , Siddiqi Haziq , Ali Ahmed Fasih , Papatheodorou Stefania , Giovannucci Edward L , Song Mingyang 
Published: April 2023

Abstract

Background
Numerous studies have assessed the association of gallstones or cholecystectomy (CE) with risk of colorectal cancer (CRC). However, the findings are mixed.

Objective
To systematically review and meta-analyse the association between the presence of gallstone disease (GD), or CE and the incidence of CRC. Secondary endpoints were the risk based on type of exposure, study design, tumour subsites and sex.

Methods
PubMed and EMBASE were searched from September 2020 to May 2021. The protocol was registered on the Open Science Foundation Platform. We identified and classified studies according to their design into prospective cohort, population-based case-control, hospital-based case-control and necropsy studies reporting CRC incidence among individuals with diagnosed GD or after CE (or both). Among 2157 retrieved studies, 65 (3%) met the inclusion criteria. We followed the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) reporting guidelines. Data were extracted by two independent reviewers. We evaluated the quality of the study according to the Newcastle-Ottawa Scale and only studies with a score of 6 and above were included in the final analyses. We pooled log-transformed odds ratios/risk ratios from the available adjusted models to estimate a summary relative risk (RR) and 95% confidence interval (CI) in a random-effects model. The primary outcome was overall CRC incidence. We also conducted secondary analyses according to sex and CRC subsites (proximal colon, distal colon and rectum). The outcome was measured by RRs with 95% CIs.

Results
The overall association of GD and/or CE with CRC was RR = 1.15 (1.08; 1.24), primarily driven by hospital-based case-control studies [RR = 1.61 (1.29; 2.01)], whereas a more modest association was found in population-based case-control and cohort studies [RR = 1.10 (1.02; 1.19)]. Most hospital-based case-control and necropsy studies reported estimates that were adjusted for age and sex only, leaving room for residual confounding; therefore we restricted to population-based case-control and cohort studies for our subsequent analyses. Similar associations were found for women [RR = 1.21 (1.05; 1.4) and men (RR = 1.24 (1.06; 1.44)]. When assessed by CRC subsites, GD and CE were primarily associated with higher risk of proximal colon cancer [RR = 1.16 (1.07; 1.26)] but not distal colon cancer [RR = 0.99 (0.96; 1.03)] or rectal cancer [RR = 0.94 (0.89; 1.00)].

Conclusions
Gallstones are associated with a modestly increased risk of colon cancer, primarily in the proximal colon.
The Effect of Pollen Diet Composition and Quantity on Diapause Survival and Performance in an Annual Pollinator (Bombus Impatiens)
Authors: Treanore E D , Ramos-Medero A V , Garcia J , Amsalem E 
Published: April 2023

Synopsis
Most pollination services are provided by annual bees that go through a winter diapause, during which they are exposed to extreme temperatures, pathogens, and starvation. The ability of bees to successfully face these stressors during diapause and subsequently initiate a nest depends on their overall nutritional state and an adequate preparatory diet.
Here, we used queens of the common eastern bumble bee, Bombus impatiens, to examine how pollen diets varying in their protein to lipid ratio and total nutrient amounts affected queen performance during and after diapause. We compared diapause survival and reproductive performance post-diapause across different diets and found that queen survival was highest when pollen had a nutritional ratio of approximately 5:1 (protein to lipid). This diet is significantly enriched in proteins compared to the pollen fed to bumble bees in the lab (1:1) or commonly available in agricultural landscapes. Altering the quantity of macronutrients within this ratio did not improve survival or performance. Our results emphasize the importance of adequate nutrition for diapause performance in bees with annual life cycles and the importance of providing annual bees with floral provisioning based on their individual nutritional targets.
Population pharmacokinetics and target attainment analyses to identify a rational empirical dosing strategy for cefepime in critically ill patients
Authors: An Guohua , Creech C Buddy , Wu Nan , Nation Roger L , Gu Kenan , Nalbant Demet , Jimenez-Truque Natalia , Fissell William , Patel Pratish C , Fishbane Nicholas , Watanabe Amy , Rolsma Stephanie , Kirkpatrick Carl M J , Landersdorfer Cornelia B , Winokur Patricia 
Published: April 2023

Abstract

Objectives
We aimed to identify rational empirical dosing strategies for cefepime treatment in critically ill patients by utilizing population pharmacokinetics and target attainment analysis.

Patients and methods
A prospective and opportunistic pharmacokinetic (PK) study was conducted in 130 critically ill patients in two ICU sites. The plasma concentrations of cefepime were determined using a validated LC-MS/MS method. All cefepime PK data were analysed simultaneously using the non-linear mixed-effects modelling approach. Monte Carlo simulations were performed to evaluate the PTA of cefepime at different MIC values following different dose regimens in subjects with different renal functions.

Results
The PK of cefepime in critically ill patients was best characterized by a two-compartment model with zero-order input and first-order elimination. Creatinine clearance and body weight were identified to be significant covariates. Our simulation results showed that prolonged 3 h infusion does not provide significant improvement on target attainment compared with the traditional intermittent 0.5 h infusion. In contrast, for a given daily dose continuous infusion provided much higher breakpoint coverage than either 0.5 h or 3 h intermittent infusions. To balance the target attainment and potential neurotoxicity, cefepime 3 g/day continuous infusion appears to be a better dosing regimen than 6 g/day continuous infusion.

Conclusions
Continuous infusion may represent a promising strategy for cefepime treatment in critically ill patients. With the availability of institution- and/or unit-specific cefepime susceptibility patterns as well as individual patients’ renal function, our PTA results may represent useful references for physicians to make dosing decisions.
Selective extinction at the end-Cretaceous and appearance of the modern Decapoda
Authors: Schweitzer Carrie E , Feldmann Rodney M 
Published: April 2023

AbstractExtinction and origination of genera and families of marine Decapoda at the end of the Cretaceous established the modern fauna. Podotrematous crabs suffered high extinction levels, whereas heterotrematous crabs experienced both extinction and radiation. Anomuran decapods exhibited high extinction levels at the generic but not family level. In general, family extinctions predominantly occurred among podotrematous and heterotrematous crabs, which also exhibit overall shorter family ranges. Possible refugia promoted survival of genera and families into the Paleocene, whereas habitation of the Western Interior Seaway ensured high levels of extinction. Areas proximal to the Chicxulub impact site experienced moderate levels of extinction. Habitat specialists preferentially survived the end-Cretaceous extinction in some clades. Heterotrematous crabs recovered rapidly in the Paleocene, especially in the siliciclastic environments of the Americas. Because decapod crustaceans are highly variable in morphology, habitat, and ecology, no one pattern of extinction and recovery can explain the end-Cretaceous decapod extinction event. Rather, a mosaic of responses in various decapod groups led to their differential survival.
Consumer-Driven Memorialization
Authors: Anderson Stephanie , Hamilton Kathy 
Published: April 2023

Abstract
Consumer research has focused on market-mediated efforts to memorialize the past, but this overshadows the issues that arise when consumers, as nonprofessionals, make the past consumable. Consumer-driven memorialization is defined as consumer engagement with traces of the past in memoryscapes of low market-mediation that creates a complex interplay of remembering and forgetting. Based on an ethnographic study of urban exploration, we theorize that consumer-driven memorialization comprises two practices of tracing and trace-making. Tracing involves consumer attempts to recover traces of the past, while trace-making involves consumer attempts to create traces for the future. Consumers enact multiple roles during consumer-driven memorialization: explorers experience the past, archaeologists materialize the past, artists aestheticize the past, and historians narrate the past. The theorization of consumer-driven memorialization offers three contributions. First, the dimensions of consumer-driven memorialization broaden understanding of what constitutes a consumable past in contexts of low market-mediation. Second, we explain how the ideological and material challenges that emerge in consumer-driven memorialization generate a complex interplay between remembering and forgetting. Third, we shed light on how consumer-driven memorialization is inscribed in space.
Jamestown Canyon virus (Bunyavirales: Peribunyaviridae) vector ecology in a focus of human transmission in New Hampshire, USA
Authors: Poggi Joseph D , Conery Colin , Mathewson Abigail , Bolton Denise , Lovell Rebecca , Harrington Laura C , Notarangelo Marco 
Published: April 2023

Abstract
Jamestown Canyon virus disease (JCVD) is a potentially neuroinvasive condition caused by the arbovirus Jamestown Canyon virus (JCV). Human cases of JCVD have increased in New Hampshire (NH) over the past decade, but vector surveillance is limited by funding and person power. We conducted mosquito surveillance with a focus on human JCVD cases south central NH during 2021. Routine surveillance with CDC miniature traps baited with CO2 (lights removed) was supplemented by a paired trapping design to test the collection efficiency of octenol, and New Jersey light traps. We performed virus testing, blood meal analysis, and compared morphological identification with DNA barcoding. Over 50,000 mosquitoes were collected representing 28 species. Twelve JCV-positive pools were derived from 6 species of more than 1,600 pools tested. Of those, Aedes excrucians/stimulans (MLE 4.95, Diptera: Culicidae, Walker, 1856, 1848), and Aedes sticticus (MLE 2.02, Meigen, 1838) had the highest JCV infection rates, and Aedes canadensis (MLE 0.13, Theobold, 1901) and Coquillettidia perturbans (0.10, Diptera: Culicidae, Walker, 1856) had the lowest infection rates. One hundred and fifty-one blood meals were matched to a vertebrate host. All putative vectors fed on the amplifying host of JCV, white-tailed deer (36–100% of bloodmeals). Putative vectors that fed on human hosts included Aedes excrucians (8%), Anopheles punctipennis (25%, Diptera: Culicidae, Say, 1823), and Coquillettidia perturbans (51%). CDC traps baited with CO2 were effective for collecting putative vectors. DNA barcoding enhanced morphological identifications of damaged specimens. We present the first ecological overview of JCV vectors in NH.
Gray-Level Co-occurrence Matrix Analysis of Nuclear Textural Patterns in Laryngeal Squamous Cell Carcinoma: Focus on Artificial Intelligence Methods
Authors: Valjarevic Svetlana , Jovanovic Milan B , Miladinovic Nenad , Cumic Jelena , Dugalic Stefan , Corridon Peter R , Pantic Igor 
Published: April 2023

Abstract
Gray-level co-occurrence matrix (GLCM) and discrete wavelet transform (DWT) analyses are two contemporary computational methods that can identify discrete changes in cell and tissue textural features. Previous research has indicated that these methods may be applicable in the pathology for identification and classification of various types of cancers. In this study, we present findings that squamous epithelial cells in laryngeal carcinoma, which appear morphologically intact during conventional pathohistological evaluation, have distinct nuclear GLCM and DWT features. The average values of nuclear GLCM indicators of these cells, such as angular second moment, inverse difference moment, and textural contrast, substantially differ when compared to those in noncancerous tissue. In this work, we also propose machine learning models based on random forests and support vector machine that can be successfully trained to separate the cells using GLCM and DWT quantifiers as input data. We show that, based on a limited cell sample, these models have relatively good classification accuracy and discriminatory power, which makes them suitable candidates for future development of AI-based sensors potentially applicable in laryngeal carcinoma diagnostic protocols.
Defining the relationship between phylogeny, clinical manifestation, and phenotype for Trichophyton mentagrophytes/interdigitale complex; a literature review and taxonomic recommendations
Authors: Švarcová Michaela , Větrovský Tomáš , Kolařík Miroslav , Hubka Vit 
Published: April 2023

Abstract
This study looked for correlations between molecular identification, clinical manifestation, and morphology for Trichophyton interdigitale and Trichophyton mentagrophytes. For this purpose, a total of 110 isolates were obtained from Czech patients with various clinical manifestations of dermatophytosis. Phenotypic characters were analyzed, and the strains were characterized using multilocus sequence typing. Among the 12 measured/scored phenotypic features, statistically significant differences were found only in growth rates at 37 °C and in the production of spiral hyphae, but none of these features is diagnostic. Correlations were found between T. interdigitale and higher age of patients and between clinical manifestations such as tinea pedis or onychomychosis. The MLST approach showed that internal transcribed spacer (ITS) genotyping of T. mentagrophytes isolates has limited practical benefits because of extensive gene flow between sublineages. Based on our results and previous studies, there are few taxonomic arguments for preserving both species names. The species show a lack of monophyly and unique morphology. On the other hand, some genotypes are associated with predominant clinical manifestations and sources of infections, which keep those names alive. This practice is questionable because the use of both names confuses identification, leading to difficulty in comparing epidemiological studies. The current identification method using ITS genotyping is ambiguous for some isolates and is not user-friendly. Additionally, identification tools such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry fail to distinguish these species. To avoid further confusion and to simplify identification in practice, we recommend using the name T. mentagrophytes for the entire complex. When clear differentiation of populations corresponding to T. interdigitale and Trichophyton indotineae is possible based on molecular data, we recommend optionally using a variety rank: T. mentagrophytes var. interdigitale and T. mentagrophytes var. indotineae.
Carbon monoxide emission lines reveal an inverted atmosphere in the ultra hot Jupiter WASP-33 b consistent with an eastward hot spot
Authors: van Sluijs Lennart , Birkby Jayne L , Lothringer Joshua , Lee Elspeth K H , Crossfield Ian J M , Parmentier Vivien , Brogi Matteo , Kulesa Craig , McCarthy Don , Charbonneau David 
Published: April 2023

ABSTRACT
We report the first detection of CO emission at high spectral resolution in the day-side infrared thermal spectrum of an exoplanet. These emission lines, found in the atmosphere of the transiting ultra hot Jupiter (UHJ) WASP-33 b, provide unambiguous evidence of its thermal inversion. Using spectra from the MMT Exoplanet Atmosphere Survey (MEASURE, R ∼ 15 000), covering pre- and post-eclipse phases, we cross-correlate with 1D PHOENIX spectral templates to detect CO at S/N = 7.9 ($v_{\rm {sys}}=0.15^{+0.64}_{-0.65}$ km s−1, $K_{\rm {p}}=229.5^{+1.1}_{-1.0}$ km s−1). Moreover, using cross-correlation-to-log-likelihood mapping, we find that the scaling parameter which controls the spectral line contrast changes with phase. We thus use the general circulation model SPARC/MITgcm post-processed by the 3D gCMCRT radiative transfer code to interpret this variation, finding it consistent with an eastward-shifted hot spot. Pre-eclipse, when the hot spot faces Earth, the thermal profiles are shallower leading to smaller line contrast despite greater overall flux. Post-eclipse, the western part of the day-side faces Earth and has much steeper thermal profiles, leading to larger line contrast despite less overall flux. This demonstrates that within the log-likelihood framework, even relatively moderate resolution spectra can be used to understand the 3D nature of close-in exoplanets, and that resolution can be traded for photon-collecting power when the induced Doppler-shift is sufficiently large. We highlight CO as a good probe of UHJ thermal structure and dynamics that does not suffer from stellar activity, unlike species that are also present in the host star e.g. iron lines.