bluuebunny/crossref_metadata_2025_split huggingface dataset:
The diagnosis and management of vulval intraepithelial neoplasia
Authors: Henderson Ian , Lewis Fiona , Williams Anthony , Yap Jason , Krishna Archana 
Published: December 2023

Key content
High‐risk human papilloma virus (HPV)‐associated vulval high‐grade squamous intraepithelial lesions and HPV‐independent differentiated vulval intraepithelial lesions represent distinct disease processes with different risks of progression to vulval squamous cell carcinoma.
First‐line medical management is appropriate for women with biopsy‐confirmed vulval high‐grade squamous intraepithelial lesions who have been adequately counselled on the risk of occult invasive disease. Topical treatment should be undertaken in the context of a specialist clinic because it is not suitable for all patients.
Surgical management is needed for differentiated vulval intraepithelial neoplasia.
Learning objectives
To understand the clinical, histological, and pathological classification of squamous intraepithelial lesions and diagnostic challenges.
To be able to contribute to the multidisciplinary investigation and diagnosis of squamous intraepithelial lesions.
To understand the basis for patient‐centred counselling on the investigation, diagnosis and treatment of suspected squamous intraepithelial lesions.
Ethical issues
Treatment must be tailored towards the patient's appreciation of risk and benefit, informed by the clinical and pathological features of the disease.
Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets
Authors: Schmidt Nicola , Sielemann Katharina , Breitenbach Sarah , Fuchs Jörg , Pucker Boas , Weisshaar Bernd , Holtgräwe Daniela , Heitkam Tony 
Published: December 2023

SUMMARYSugar beet and its wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNAs are among the fastest evolving parts of the genome, we investigated, if repeatome innovations and losses are linked to chromosomal differentiation and speciation. We traced genome and chromosome‐wide evolution across 13 beet species comprising all sections of the genera Beta and Patellifolia. For this, we combined short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive framework that spans the complete scale from DNA to chromosome to genome. Genome sizes and repeat profiles reflect the separation into three gene pools with contrasting evolutionary patterns. Among all repeats, satellite DNAs harbor most genomic variability, leading to fundamentally different centromere architectures, ranging from chromosomal uniformity in Beta and Patellifolia to the formation of patchwork chromosomes in Corollinae/Nanae. We show that repetitive DNAs are causal for the genome expansions and contractions across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably between beet genomes, leading to the evolution of distinct chromosomal setups in the three gene pools, likely contributing to the barriers in beet breeding. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genomic variability, and chromosomal differentiation and provide a theoretical fundament for understanding barriers in any crop breeding effort.
Nutrient status changes bacterial interactions in a synthetic community
Authors: Qiao Yizhu , Huang Qiwei , Guo Hanyue , Qi Meijie , Zhang He , Xu Qicheng , Shen Qirong , Ling Ning 
Published: December 2023

ABSTRACT
Microbial interactions affect community stability and niche spaces in all ecosystems. However, it is not clear what factors influence these interactions, leading to changes in species fitness and ecological niches. Here, we utilized 16 monocultures and their corresponding pairwise co-cultures to measure niche changes among 16 cultivable bacterial species in a wide range of carbon sources, and we used resource availability as a parameter to alter the interactions of the synthetic bacterial community. Our results suggest that metabolic similarity drives niche deformation between bacterial species. We further found that resource limitation resulted in increased microbial inhibition and more negative interactions. At high resource availability, bacteria exhibited little inhibitory potential and stronger facilitation (in 71% of cases), promoting niche expansion. Overall, our results show that metabolic similarity induces different degrees of resource competition, altering pairwise interactions within the synthetic community and potentially modulating bacterial niches. This framework may lay the basis for understanding complex niche deformation and microbial interactions as modulated by metabolic similarity and resource availability.

IMPORTANCE
Understanding the intricate dynamics of microbial interactions is crucial for unraveling the stability and ecological roles of diverse ecosystems. However, the factors driving these interactions, leading to shifts in species fitness and ecological niches, remain inadequately explored. We demonstrate that metabolic similarity serves as a key driver of niche deformation between bacterial species. Resource availability emerges as a pivotal parameter, affecting interactions within the community. Our findings reveal heightened microbial inhibition and more negative interactions under resource-limited conditions. The prevalent facilitation is observed under conditions of high resource availability, underscoring the potential for niche expansion in such contexts. These findings emphasize that metabolic similarity induces varying degrees of resource competition, thereby altering pairwise interactions within the synthetic community and potentially modulating bacterial niches. Our workflow has broad implications for understanding the roles of metabolic similarity and resource availability in microbial interactions and for designing synthetic microbial communities.
New Gland Type Discovered in Cestodes: Neurosecretory Neurons Release a Secret into the Fish Host
Authors: Biserova N. M. , Kutyrev I. A. , Malakhov V. V. 
Published: December 2023

AbstractFree endings of peripheral neurosecretory neurons (NNs) were found in the tegument of plerocercoids of five species of parasitic cestodes of fish in an ultrastructural study. The free terminals secreted vesicles on the tegument surface and into the host body. Secretion was experimentally shown to increase in response to the host fish blood serum. In the cestode body, NNs form paracrine-type contacts near the cell membranes of the frontal glands, the tegument, and muscles, functioning as endocrine glands. Simultaneously, NNs function as exocrine glands and secrete the so-called manipulative factors, which influence the physiology of the host.
Association of alpha globin gene copy number with exhaled nitric oxide in a cross-sectional study of healthy Black adults
Authors: Ruhl A Parker , Jackson Jarrett M , Carhuas Carlos J , Niño de Rivera Jessica G , Fay Michael P , Weinberg J Brice , Que Loretta G , Ackerman Hans C 
Published: December 2023

IntroductionThe genetic determinants of fractional exhalation of nitric oxide (FeNO), a marker of lung inflammation, are understudied in Black individuals. Alpha globin (HBA) restricts nitric oxide signalling in arterial endothelial cells via interactions with nitric oxide synthase; however, its role in regulating the release of NO from respiratory epithelium is less well understood. We hypothesised that anHBAgene deletion, common among Black individuals, would be associated with higher FeNO.MethodsHealthy Black adults were enrolled at four study sites in North Carolina from 2005 to 2008. FeNO was measured in triplicate using a nitric oxide analyzer. The −3.7 kbHBAgene deletion was genotyped using droplet digital PCR on genomic DNA. The association of FeNO withHBAcopy number was evaluated using multivariable linear regression employing a linear effect ofHBAcopy number and adjusting for age, sex and serum immunoglobulin-E levels. Post-hoc analysis employing a recessive mode of inheritance was performed.Results895 individuals were in enrolled in the study and 720 consented for future genetic research; 643 had complete data and were included in this analysis. Median (25th, 75th) FeNO was 20 (13, 31) ppb.HBAgenotypes were: 30 (4.7%) -a/-a, 197 (30.6%) -a/aa, 405 (63%) aa/aa and 8 (1.2%) aa/aaa. Subjects were 35% male with median age 20 (19, 22) years. Multivariable linear regression analysis revealed no association between FeNO andHBAcopy number (β=−0.005 (95% CI −0.042 to 0.033), p=0.81). In the post-hoc sensitivity analysis, homozygosity for the HBA gene deletion was associated with higher FeNO (β=0.107 (95% CI 0.003 to 0.212); p=0.045).ConclusionWe found no association betweenHBAcopy number and FeNO using a prespecified additive genetic model. However, a post hoc recessive genetic model found FeNO to be higher among subjects homozygous for theHBAdeletion.
Performance of non-binary athletes in mass-participation running events
Authors: Armstrong John , Sullivan Alice , Perry George M 
Published: December 2023

ObjectivesTo test the hypothesis that, controlling for age, natal-sex differences in running performance are lower among non-binary athletes than in the rest of the population. To test the hypothesis that natal-male non-binary athletes outperform natal-female non-binary athletes.MethodsA secondary analysis of 166 race times achieved by non-binary athletes within a data set of 85 173 race times derived from races with a non-binary category in the New York Road Runners database. The natal sex of non-binary athletes was modelled probabilistically using US Social Security Administration data when it could not be derived from previous races. Race times were used as the outcome variable in linear models with explanatory variables derived from natal sex, gender identity, age and the event being raced. Statistical significance was estimated using Monte Carlo methods as the model was not Gaussian.ResultsThere was no evidence that controlling for age, natal-sex differences in running performance are lower among non-binary athletes. Natal-male non-binary athletes outperform natal-female non-binary athletes at a confidence level of p=0.1%.ConclusionsBoth natal sex and gender identity may be useful explanatory variables for the performance of athletes in mass-participation races. It is, therefore, valuable to include both variables in data collection.
Risk factor analyses of contrast leakage and contrast-induced encephalopathy following coil embolization for unruptured intracranial aneurysm
Authors: Kim Kyung Hwan , Yang Kiyoon , Jeong Eun-Oh , Lee Han-Joo , Jeong Heewon , Choi Seung-Won , Kim Seon-Hwan , Koh Hyeon-Song , Kwon Hyon-Jo 
Published: December 2023

BackgroundContrast-induced encephalopathy (CIE) following endovascular interventions is a rare but serious complication. This study aimed to investigate the risk factors of contrast leakage (CL) and CIE in patients who underwent coil embolization of unruptured intracranial aneurysms (UIAs).MethodsPatients with UIAs who underwent coil embolization at a single tertiary institute between January 2019 and January 2022 were enrolled retrospectively. CL was defined as cortical or subcortical contrast enhancement with effacement of the cortical sulci. CIE was defined as the new onset of neurological deficits associated with CL. Following the procedure, all patients underwent CT scans, and MRI scans were performed on those with symptoms. Patient and procedural risk factors were investigated.ResultsIn total, 459 patients were analyzed. The median procedure time and contrast dose were 69 min and 96 mL, respectively. CL was evident in 35 patients. In the multivariate analysis, hypertension, large aneurysm, longer procedure time, and greater contrast dose were associated with CL. CIE was diagnosed in 19 patients, and the risk factors included large aneurysm, longer procedure time, and greater contrast dose. The procedure time was predictive of both CL (P<0.001) and CIE (P=0.01). The optimal cut-off value for procedure time was 81.5 min. All CIE patients recovered completely within 8–96 hours.ConclusionsA large aneurysm and prolonged procedure time may increase the patient’s risk of CL and CIE due to increased contrast exposure. Patients who underwent a procedure that exceeded 1.5 hours necessitate post-procedure evaluation and monitoring.
Cluster properties of heavy nuclei predicted with the Barcelona-Catania-Paris-Madrid energy density functional
Authors: Giuliani Samuel A. , Robledo Luis M. 
Published: December 2023

AbstractWe study the cluster emission properties of $$^{224}$$

224

Ra and $$^{238}$$

238

Pu employing the Barcelona-Catania-Paris-Madrid (BCPM) energy density functional (EDF). Starting from two-dimensional potential energy surfaces, coexisting fission paths are identified. A fission valley located at large octupole deformations, corresponding to a highly-asymmetric mass distribution, is found in both nuclei. As the corresponding fragments are dominated by the presence of $$^{208}$$

208

Pb, we can relate this fission path to the emergence of cluster emission. Using the octupole moment as collective degree of freedom, we compute the cluster decay half-lives and study the impact of collective inertias, pairing strength and collective zero-point energy. The agreement with experimental data resembles the results obtained for spontaneous fission half-lives, indicating the capability of BCPM to consistently describe a large variety of fission phenomena, including cluster emission.
B-physics from lattice gauge theory
Authors: Tsang J. Tobias , Della Morte Michele 
Published: December 2023

AbstractWe discuss the main issues in dealing with heavy quarks on the lattice and shortly present the different approaches used. We discuss a selection of computations covering first the b-quark mass and the $$B_{(s)}$$

B

(
s
)

meson decay constants as the consolidated results (neglecting isospin breaking corrections). In the second part, we consider recent calculations of form factors for tree-level semileptonic decays with emphasis on the tensions between the results produced by different collaborations. We propose benchmark quantities and tests suited to investigate the origin of such tensions. Finally, we review computations of the bag parameters parameterising neutral meson mixing and provide an overview on a few recent developments in the field.
Evaluating reservoir properties and seal capacities of volcaniclastic rocks for hydrocarbon containment and their application to CO
2
storage
Authors: Passey Simon R. , McLean Charlotte E. 
Published: December 2023

Abstract

Volcaniclastic rocks are commonly overlooked as reservoirs or seals in hydrocarbon plays because their compositions are variably unstable and reactive during burial diagenesis. This study investigated the petrography and petrophysical characteristics of 60 volcaniclastic and four siliciclastic samples from three Paleogene volcanic provinces – East Greenland, Faroe Islands and Ethiopia. The volcaniclastic samples have highly variable helium porosities (average 25.2%), but negligible total optical porosities (average 1.9%), implying reduced reservoir potential. The samples have, however, highly variable air permeabilities (average 11 mD), suggesting that they could make tight reservoirs. The permeabilities are related to either early calcite cements or the devitrification of volcanic glass. Mercury injection capillary pressure data were collected for a subset of 33 samples that at leakage/breakthrough saturations could, under near-surface conditions, hold oil column heights of between 4 and 1181 m (average 240 m). The best seals consistently have zeolite contents of >20 vol% owing to their small pore throat radii. Conversely, the worst seals are dominated by smectite and a conspicuous absence of zeolite minerals. The zeolite-rich volcaniclastic rocks could, therefore, make good shallow seals. These features also apply to CO
2
storage, but questions remain about the reactivity of the volcanic material and secondary minerals with injected CO
2
, but also the adsorbent properties of zeolites, particularly clinoptilolite, in the presence of CO
2
.
Protecting Life-Saving Medical Devices from Cyberattack
Authors: Vakulov Alex 
Published: December 2023

The
Communications
website, https://cacm.acm.org, features more than a dozen bloggers in the BLOG@CACM community. In each issue of
Communications
, we'll publish selected posts or excerpts.

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Follow us on Twitter at http://twitter.com/blogCACM
https://cacm.acm.org/blogs/blog-cacm
Alex Vakulov ponders how to protect the Internet of Medical Things.
RGB-based colorimetric method for the analysis of water alkalinity using Cordyline fruticosa extracts as visual indicator
Authors: Parungao Christian Alex C. , Reyes Darwin F. 
Published: December 2023

Leaf extracts of <em>Cordyline fruticosa</em> was used as a natural visual indicator for a digital image-based analytical procedure for the measurement of water alkalinity. A smartphone and ImageJ were used to capture and process the images, respectively. This work sought to develop and evaluate a greener strategy of using of <em>Cordyline fruticosa</em> leaf extract as natural indicator, in a digital image-based colorometric set-up using smartphone. Under optimized conditions, the linear working range was from 40 to 160 ppm of CaCO<sub>3</sub>, with a calibration sensitivity of 5 x 10<sup>-3</sup> ppm and a coefficient of correlation (r<sup>2</sup>) = 0.998. The limit of detection and quantification were 39 ppm and 117 ppm, respectively. A 10,000 ppm CaCO<sub>3</sub> solution was tested using the proposed method and the results statistically agree with the results obtained from titrimetric methods. The study presented a simple analytical procedure that can be develop and apply for the assessment of pollution that could pose serious human and environmental health hazards.
Identification of Clinical Drivers of Left Atrial Enlargement Through Genomics of Left Atrial Size
Authors: Agrawal Vineet , Manouchehri Ali , Vaitinadin Nataraja S. , Shi Mingjian , Bagheri Minoo , Gupta Deepak K. , Kullo Iftikhar J. , Luo Yuan , McNally Elizabeth M. , Puckelwartz Megan J. , Ferguson Jane F. , Wells Quinn S. , Mosley Jonathan D. 
Published: December 2023

BACKGROUND:
Greater left atrial size is associated with a higher incidence of cardiovascular disease and mortality, but the full spectrum of diagnoses associated with left atrial enlargement in sex-stratified clinical populations is not well known. Our study sought to identify genetic risk mechanisms affecting left atrial diameter (LAD) in a clinical cohort.

METHODS:

Using Vanderbilt deidentified electronic health record, we studied 6163 females and 5993 males of European ancestry who had at least 1 LAD measure and available genotyping. A sex-stratified polygenic score was constructed for LAD variation and tested for association against 1680
International Classification of Diseases
code–based phenotypes. Two-sample univariable and multivariable Mendelian randomization approaches were used to assess etiologic relationships between candidate associations and LAD.

RESULTS:

A phenome-wide association study identified 25
International Classification of Diseases
code–based diagnoses in females and 11 in males associated with a polygenic score of LAD (false discovery rate q<0.01), 5 of which were further evaluated by Mendelian randomization (waist circumference [WC], atrial fibrillation, heart failure, systolic blood pressure, and coronary artery disease). Sex-stratified differences in the genetic associations between risk factors and a polygenic score for LAD were observed (WC for females; heart failure, systolic blood pressure, atrial fibrillation, and WC for males). By multivariable Mendelian randomization, higher WC remained significantly associated with larger LAD in females, whereas coronary artery disease, WC, and atrial fibrillation remained significantly associated with larger LAD in males.

CONCLUSIONS:
In a clinical population, we identified, by genomic approaches, potential etiologic risk factors for larger LAD. Further studies are needed to confirm the extent to which these risk factors may be modified to prevent or reverse adverse left atrial remodeling and the extent to which sex modifies these risk factors.
Nematodes as bioindicators of soil health in different land uses in the São Francisco River Valley, Brazil
Authors: Caixeta Larissa de B. , Silva Juliane V.C. de L. da , Castañeda Nancy E.N. , Castro José M. da C. e , Cares Juvenil E. 
Published: December 2023

Summary
Brazilian Caatinga is one of the most diverse, seasonally dry, tropical forests of the world and is threatened by strong land use pressure and poor protection. One way of understanding changes in the soil conditions caused by anthropogenic activities is using the nematode assemblages as potential bioindicators. This study analysed changes in nematode communities in three different types of land use (natural forest-CA, natural area with accumulation of salts-SS, and agricultural growing areas, such as cover crops-CC for cattle and fruit trees-IC) in the Caatinga, in the sub-median region of the São Francisco River Valley (SFRV), Pernambuco, northeastern Brazil. We recorded a total of 63 262 nematode individuals, representing 42 genera, belonging to 23 families. Nematode abundance, diversity and maturity indices were highest in the CC and lowest in the SS. Among the nematode trophic groups, bacterivores, omnivores + predators and plant parasites were significantly affected by type of land use. Different soil properties were related to the differences in taxonomic composition among the natural and agricultural areas, accounting for 26.6% of the total variation. In general, our results indicate that soil salinisation and desertification in the natural areas, as well as soils subjected to cover crops and fruit tree production, significantly influenced the composition of nematode communities in the São Francisco River Valley.
Limitations of XAI Methods for Process-Level Understanding in the Atmospheric Sciences
Authors: Silva Sam J. , Keller Christoph A. 
Published: December 2023

Abstract
Explainable artificial intelligence (XAI) methods are becoming popular tools for scientific discovery in the Earth and atmospheric sciences. While these techniques have the potential to revolutionize the scientific process, there are known limitations in their applicability that are frequently ignored. These limitations include that XAI methods explain the behavior of the AI model and not the behavior of the training dataset, and that caution should be used when these methods are applied to datasets with correlated and dependent features. Here, we explore the potential cost associated with ignoring these limitations with a simple case study from the atmospheric chemistry literature – learning the reaction rate of a bimolecular reaction. We demonstrate that dependent and highly correlated input features can lead to spurious process-level explanations. We posit that the current generation of XAI techniques should largely only be used for understanding system-level behavior and recommend caution when using XAI methods for process-level scientific discovery in the Earth and atmospheric sciences.