bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-omics analysis identifies repurposing bortezomib in the treatment of kidney-, nervous system-, and hematological cancers
Authors: Larsson Peter , Olsson Maxim , Sarathchandra Sithumini , Fäldt Beding Anna , Forssell-Aronsson Eva , Kovács Anikó , Karlsson Per , Helou Khalil , Parris Toshima Z. 
Published: August 2024

AbstractRepurposing of FDA-approved drugs is a quick and cost-effective alternative to de novo drug development. Here, we identify genes involved in bortezomib sensitivity, predict cancer types that may benefit from treatment with bortezomib, and evaluate the mechanism-of-action of bortezomib in breast cancer (BT-474 and ZR-75–30), melanoma (A-375), and glioblastoma (A-172) cells in vitro. Cancer cell lines derived from cancers of the blood, kidney, nervous system, and skin were found to be significantly more sensitive to bortezomib than other organ systems. The in vitro studies confirmed that although bortezomib effectively inhibited the β5 catalytic site in all four cell lines, cell cycle arrest was only induced in G2/M phase and apoptosis in A-375 and A-172 after 24h. The genomic and transcriptomic analyses identified 33 genes (e.g. ALDH18A1, ATAD2) associated with bortezomib resistance. Taken together, we identified biomarkers predictive of bortezomib sensitivity and cancer types that might benefit from treatment with bortezomib.
The impact of consuming different types of high-caloric fat diet on the metabolic status, liver, and aortic integrity in rats
Authors: Saleh Nardien Ekram Haliem , Ibrahim Mariam Yahia , Saad Adel Hussein , Abdel-Hakeem Elshymaa A. , Saleh Rabeh Khairy , Habeeb Wagdy N. 
Published: August 2024

AbstractConsumption of high-caloric diets contributes to the alarming number of overweight and obese individuals worldwide, which in turn leads to several diseases and multiple organ dysfunction. Not only has the number of calories taken per day but also the type of fat in the diet has an important impact on health. Accordingly, the purpose of the current study was to examine the impact of different types of high-caloric fat diets on the metabolic status and the integrity of the liver and aorta in albino rats. Adult male albino rats were divided into 6 groups: Control group, long chain-saturated fat group (SFD), long chain-monounsaturated fat (MUFAs) group, long chain-polyunsaturated fat (PUFAs) group, medium-chain fat (MCFAs) group, and short-chain fat (SCFAs) group. Body mass index (BMI), Lee index, and visceral fat amount were reported. Serum levels of insulin, liver transaminases, lipid profile, and different oxidative stress and inflammatory markers were evaluated. Homeostasis Model Assessment of Insulin Resistance (HOMA-IR), and adiponectin/leptin ratio were also calculated. Histopathological examinations of liver and aorta with Masson’s trichrome stain, and immune-staining for Nuclear Factor Erythroid-2-Related Factor-2 (Nrf2) were also done. SFD group showed significantly elevated liver transaminases, inflammatory markers, HOMA-IR, dyslipidemia, reduced adiponectin, and deficient anti-oxidative response compared to other groups together with disturbed hepatic and aortic architecture. Other treated groups showed an improvement. PUFAs group showed the highest level of improvement. Not all high-fat diets are hazardous. Diets rich in PUFAs, MUFAs, MCFAs, or SCFAs may protect against the hazards of high caloric diet.
Assessments of arterial and venous phase radiodensity does not improve carotid near-occlusion diagnostics
Authors: Brunnander Karolina , Henze Alexander , Fox Allan J. , Johansson Elias 
Published: August 2024

AbstractThe hypothesis of this study was that evaluation of radiodensity assessment beyond a carotid stenosis in arterial and/or venous phase can be used to separate near-occlusion and conventional ≥ 50% stenosis. We prospectively included participants with ≥ 50% carotid stenosis with inclusion preference for cases with extracranial internal carotid artery (ICA) asymmetry. All participants were examined with a research biphasic computed tomography angiography (CTA) protocol (arterial and venous phase). Reference diagnosis was set by interpretation on CTA and radiodensity difference between ipsilateral and contralateral ICA (c-corrected) or vertebral (v-corrected) was compared. We included 93 participants, 62 with near-occlusion and 31 with conventional ≥ 50% stenosis. Just beyond the stenosis, median c-corrected radiodensity was − 20 Hounsfield units (HU) among near-occlusions and − 1 HU among conventional ≥ 50% stenoses (p < 0.001) in the arterial phase. For the venous phase, these findings were + 17 HU and + 3 HU (p = 0.007). Similar group differences were seen for v-correction. No parameter had good diagnostic performance, area under the curve ≤ 0.82. With specificity set at ≥ 95%, detected near-occlusions were foremost those with large side-to-side differences in distal ICA-diameter. Carotid near-occlusions can have reduced radiodensity beyond the stenosis in arterial phases and increased radiodensity in venous phases compared to a reference artery—which was not clearly seen for conventional stenoses. However, these radiodensity findings are best seen in near-occlusion cases that are not diagnostically challenging, while they work poorly as additional diagnostic aids.
Rare heterozygous variants in paediatric steroid resistant nephrotic syndrome – a population-based analysis of their significance
Authors: Platt C. J. , Bierzynska A. , Ding W. , Saleem S. A. , Koziell A. , Saleem M. A. 
Published: August 2024

AbstractGenetic testing in nephrotic syndrome may identify heterozygous predicted-pathogenic variants (HPPVs) in autosomal recessive (AR) genes that are known to cause disease in the homozygous or compound heterozygous state. In such cases, it can be difficult to define the variant’s true significance and questions remain about whether a second pathogenic variant has been missed during analysis or whether the variant is an incidental finding. There are now known to be over 70 genes associated with nephrotic syndrome, the majority inherited as an AR trait. Knowledge of whether such HPPVs occur with equal frequency in patients compared to the general population would assist interpretation of their significance. Exome sequencing was performed on 187 Steroid-Resistant Nephrotic Syndrome (SRNS) paediatric patients recruited to a UK rare disease registry plus originating from clinics at Evelina, London. 59 AR podocytopathy linked genes were analysed in each patient and a list of HPPVs created. We compared the frequency of detected HPPVs with a ‘control’ population from the gnomAD database containing exome data from approximately 50,000 individuals. A bespoke filtering process was used for both patients and controls to predict ‘likely pathogenicity’ of variants. In total 130 Caucasian SRNS patients were screened across 59 AR genes and 201 rare heterozygous variants were identified. 17/201 (8.5%) were assigned as ‘likely pathogenic’ (HPPV) using our bespoke filtering method. Comparing each gene in turn, for SRNS patients with a confirmed genetic diagnosis, in 57 of the 59 genes we found no statistically significant difference in the frequency of these HPPVs between patients and controls (In genes ARHGDIA and TP53RK, we identified a significantly higher number of HPPVs in the control population compared with the patients when filtering was performed with ‘high stringency’ settings only). In the SRNS patients without a genetics diagnosis confirmed, there was no statistically significant difference identified in any gene between patient and control. In children with SRNS, we propose that identification of HPPV in AR podocytopathy linked genes is not necessarily representative of pathogenicity, given that the frequency is similar to that seen in controls for the majority. Whilst this may not exclude the presence of genetic kidney disease, this type of heterozygous variant is unlikely to be causal and each result must be interpreted in its clinical context.
Eccentric exercise-induced delayed onset trunk muscle soreness alters high-density surface EMG-torque relationships and lumbar kinematics
Authors: Arvanitidis Michail , Jiménez-Grande David , Haouidji-Javaux Nadège , Falla Deborah , Martinez-Valdes Eduardo 
Published: August 2024

AbstractWe aimed to assess high-density surface electromyography (HDsEMG)-torque relationships in the presence of delayed onset trunk muscle soreness (DOMS) and the effect of these relationships on torque steadiness (TS) and lumbar movement during concentric/eccentric submaximal trunk extension contractions. Twenty healthy individuals attended three laboratory sessions (24 h apart). HDsEMG signals were recorded unilaterally from the thoracolumbar erector spinae with two 64-electrode grids. HDsEMG-torque signal relationships were explored via coherence (0–5 Hz) and cross-correlation analyses. Principal component analysis was used for HDsEMG-data dimensionality reduction and improvement of HDsEMG-torque-based estimations. DOMS did not reduce either concentric or eccentric trunk extensor muscle strength. However, in the presence of DOMS, improved TS, alongside an altered HDsEMG-torque relationship and kinematic changes were observed, in a contraction-dependent manner. For eccentric trunk extension, improved TS was observed, with greater lumbar flexion movement and a reduction in δ-band HDsEMG-torque coherence and cross-correlation. For concentric trunk extensions, TS improvements were observed alongside reduced thoracolumbar sagittal movement. DOMS does not seem to impair the ability to control trunk muscle force, however, perceived soreness induced changes in lumbar movement and muscle recruitment strategies, which could alter motor performance if the exposure to pain is maintained in the long term.
Non-invasive detection of hazardous materials with a thermal-to-epithermal neutron station: a feasibility study towards practical application
Authors: Silarski Michał , Dziedzic-Kocurek Katarzyna , Drużbicki Kacper , Reterski Radosław , Grabowski Patryk , Krzystyniak Matthew 
Published: August 2024

AbstractThe growing scale of the devastation that even a single terrorist attack can cause requires more effective methods for the detection of hazardous materials. In particular, there are no solutions for effectively monitoring threats at sea, both for the off-shore infrastructure and ports. Currently, state-of-the-art detection methods determine the density distribution and the shapes of tested subjects but only allow for a limited degree of substance identification. This work aims to present a feasibility study of the possible usage of several methods available on the thermal-to-epithermal neutron station, VESUVIO, at the ISIS neutron and muon spallation source, UK, for the detection of hazardous materials. To this end, we present the results of a series of experiments performed concurrently employing neutron transmission and Compton scattering using melamine, a commonly used explosive surrogate, in order to determine its signal characteristics and limits of detection and quantitation. The experiments are supported by first-principles modelling, providing detailed scrutiny of the material structure and the nuclear dynamics behind the neutron scattering observables.
Comprehensive study on structural, electronic, optical, elastic, and transport properties of natural mercury sulphohalides via DFT computation
Authors: Hariharan M. , Eithiraj R. D. 
Published: August 2024

AbstractThe Mercury Sulphohalides have attracted significant attention in the fields of solar cells and thermoelectric applications. This study delves into the fundamental characteristics, including structural, elasticity, electronic behavior, phonon stability, optical properties, and transport features of AgHgSZ (Z = Br, I) through computational simulations based on Density Functional Theory (DFT) using WIEN2k software. Meticulous calculations of the phonon band structure ensure dynamic stability. The semiconductor nature with indirect band gaps (1.833 eV and 1.832 eV) for Mercury Sulphohalides (Br, I), as revealed by their band structures, suggests diverse photovoltaic and transport applications. Mechanical assessments show stable ductility for AgHgSBr and brittleness for AgHgSI, along with anisotropy and resistance to scratching. Optical properties exhibit anisotropy and significant UV absorption. Analysis of effective masses, exciton binding energy, and exciton Bohr radius suggests low exciton binding energy and classification under Mott-Wannier excitons. Positive thermopower results indicate holes as the predominant charge carriers in AgHgSBr and AgHgSI materials. Moreover, essential thermoelectric factors are examined, revealing the compounds’ potential for thermoelectric applications. Notably, the figure of merit (ZT) at 300 K for AgHgSBr and AgHgSI are calculated to be 0.41 and 0.13, respectively. While these values are low at 300 K, they indicate promising potential for thermoelectric applications at higher temperatures. In summary, this investigation provides valuable understanding into the photovoltaic and thermoelectric properties of AgHgSZ (Z = Br, I) materials, potentially paving the way for further exploration in this domain.
ASD-similar social behaviour scores affect stimulus generalization in family dogs
Authors: Ujfalussy Dorottya J. , Gergely Anna , Petró Eszter , Topál József 
Published: August 2024

AbstractGeneralization, the tendency to respond in the same way to different but similar stimuli, is one of the main cognitive abilities that make category formation possible and thus is a prerequisite for efficiency in learning. Individuals with autism spectrum disorder (ASD) experience pervasive difficulty with producing generalized responses across materials, people, places, and contexts. Increasing evidence suggests that “ASD-like” social impairments appear endogenously and spontaneously in family dogs providing a high-validity model for understanding the phenotypic expression of human ASD. The present study aims to further investigate the dog model of ASD by the approach of searching for analogues in dogs showing “ASD-like” social impairments of cognitive phenomena in humans specific to ASD, specifically impairments of generalization abilities. We have tested 18 family dogs with formerly established “ASD-like” behaviour scores (F1, F2, F3) in a generalization task involving three conditions (size, colour and texture). We found a significant association between F1 scores and test performance as well as improvement during testing sessions. Our study provides further support for the notion that dogs with lower social competence—similarly to humans with ASD—exhibit attentional and perceptual abnormalities, such as being sensitive to minor changes to a non-adaptive extent.
Null‐depth coordinated synthesis design approach to azimuthal null frequency scanning antennas
Authors: Mao Xiao‐Hui , Lu Wen‐Jun , Ji Fei‐Yan , Zhu Lei 
Published: August 2024

AbstractA novel synthesis design approach to multimode resonant, azimuthal null frequency scanning antennas (ANFSAs) coordinated by null‐depth is presented. The antenna is composed of a principal radiator and an auxiliary one fed by different ports. A synthesis chart gauged by different null‐depths is developed to determine the respective exciting amplitude and phase conditions for the principal and auxiliary radiators. As is theoretically demonstrated and numerically verified, the ANFSA can exhibit an adjustable null‐depth varying from −12∼−30 dB. A three‐port unequal‐split power divider with the simplest configuration is properly designed, utilised and integrated to meet the oriented power and phase conditions. A prototype with in‐band null‐depth of −30 dB is designed, fabricated and validated in such a way that its available bandwidth can reach up to 32.7%, and the null can continuously scan from φ = 160°–275° in azimuth plane.
Cultural roots of the myopia boom in Confucian Asia and their implications
Authors: Yii Fabian 
Published: August 2024

AbstractCurrent evidence implicates educational pressures and reduced outdoor time as major causes of myopia. This paper examines the ongoing battle against the myopia epidemic in East Asia, including its cultural offshoots such as Singapore, where over 80% of young adults are myopic. East Asian societies share deeply rooted Confucian values that attach great importance to education and familial obligations, with heavy parental investment in education and the perception that academic excellence reflects filial piety. Coupled with a strong emphasis on standardised test results, East Asian children face intense educational pressures from a young age. Existing education-based myopia prevention strategies focus either on top-down school reforms to promote more outdoor time for students during school hours or on bottom-up awareness initiatives encouraging lifestyle changes. However, the entrenched Confucian worldview suggests that more extensive top-down reforms aimed at reducing competition in education, combined with widespread bottom-up awareness initiatives targeting the public—particularly parents, given their active involvement in children’s education outside of school—may be required to truly turn the tide on myopia.
Neuromorphic learning and recognition in WO3−x thin film-based forming-free flexible electronic synapses
Authors: Mohapatra R Archana B , Mhaskar Chinmayee Mandar , Sahu Mousam Charan , Sahoo Satyaprakash , Roy Chaudhuri Ayan 
Published: August 2024

Abstract
In pursuing advanced neuromorphic applications, this study introduces the successful engineering of a flexible electronic synapse based on WO3−x
, structured as W/WO3−x
/Pt/Muscovite-Mica. This artificial synapse is designed to emulate crucial learning behaviors fundamental to in-memory computing. We systematically explore synaptic plasticity dynamics by implementing pulse measurements capturing potentiation and depression traits akin to biological synapses under flat and different bending conditions, thereby highlighting its potential suitability for flexible electronic applications. The findings demonstrate that the memristor accurately replicates essential properties of biological synapses, including short-term plasticity (STP), long-term plasticity (LTP), and the intriguing transition from STP to LTP. Furthermore, other variables are investigated, such as paired-pulse facilitation, spike rate-dependent plasticity, spike time-dependent plasticity, pulse duration-dependent plasticity, and pulse amplitude-dependent plasticity. Utilizing data from flat and differently bent synapses, neural network simulations for pattern recognition tasks using the Modified National Institute of Standards and Technology dataset reveal a high recognition accuracy of ∼95% with a fast learning speed that requires only 15 epochs to reach saturation.
Alan Author strikes again: more on confirming conjunctions of disconfirmed hypotheses
Authors: Koscholke Jakob 
Published: August 2024

Abstract
The so-called Alan Author Effect is a surprising phenomenon in Bayesian Confirmation Theory. It occurs when a piece of evidence e confirms the conjunction of two hypotheses h1∧h2 but at the same time disconfirms each hypothesis h1 and h2 individually. In this paper, I present a new and prima facie stronger version of this effect where additionally, the evidence e confirms the conjunction of the negated hypotheses ¬h1∧¬h2. I say ‘prima facie’ because it can be shown that this seemingly stronger effect and the original effect are actually coextensional. I use this insight to formulate a new sufficient (and also necessary) condition for the two equivalent effects. I also examine how likely the two effects are to occur with the help of Monte Carlo simulation methods.
Anatomical and physiological responses of roots and rhizomes in Oryza longistaminata to soil water gradients
Authors: Song Zhiwei , Lin Chen , Pedersen Ole , Jiménez Juan 
Published: August 2024

Abstract

Background and Aims
Roots and rhizomes are crucial for the adaptation of clonal plants to soil water gradients. Oryza longistaminata, a rhizomatous wild rice, is of particular interest for perennial rice breeding owing to its resilience in abiotic stress conditions. Although root responses to soil flooding are well studied, rhizome responses to water gradients remain underexplored. We hypothesize that physiological integration of Oryza longistaminata mitigates heterogeneous water-deficit stress through interconnected rhizomes, and both roots and rhizomes respond to contrasting water conditions.

Methods
We investigated the physiological integration between mother plants and ramets, measuring key photosynthetic parameters (photosynthetic and transpiration rates and stomatal conductance) using an infrared gas analyser. Moreover, root and rhizome responses to three water regimes (flooding, well watered and water deficit) were examined by measuring radial water loss and apparent permeance to O2, along with histochemical and anatomical characterization.

Key Results
Our experiment highlights the role of physiological integration via interconnected rhizomes in mitigating water-deficit stress. Severing rhizome connections from mother plants or ramets exposed to water-deficit conditions led to significant decreases in key photosynthetic parameters, underscoring the importance of rhizome connections in bidirectional stress mitigation. Additionally, O. longistaminata rhizomes exhibited constitutive suberized and lignified apoplastic barriers, and such barriers were induced in roots in water stress. Anatomically, both rhizomes and roots respond in a similar manner to water gradients, showing smaller diameters in water-deficit conditions and larger diameters in flooding conditions.

Conclusion
Our findings indicate that physiological integration through interconnected rhizomes helps to alleviate water-deficit stress when either the mother plant or the ramet is experiencing water deficit, while the counterpart is in control conditions. Moreover, O. longistaminata can adapt to various soil water regimes by regulating anatomical and physiological traits of roots and rhizomes.
Improved allele-specific single-cell copy number estimation in low-coverage DNA-sequencing
Authors: Weiner Samson , Li Bingjun , Nabavi Sheida 
Published: August 2024

Abstract

Motivation
Advances in whole-genome single-cell DNA sequencing (scDNA-seq) have led to the development of numerous methods for detecting copy number aberrations (CNAs), a key driver of genetic heterogeneity in cancer. While most of these methods are limited to the inference of total copy number, some recent approaches now infer allele-specific CNAs using innovative techniques for estimating allele-frequencies in low coverage scDNA-seq data. However, these existing allele-specific methods are limited in their segmentation strategies, a crucial step in the CNA detection pipeline.

Results
We present SEACON (Single-cell Estimation of Allele-specific COpy Numbers), an allele-specific copy number profiler for scDNA-seq data. SEACON uses a Gaussian Mixture Model to identify latent copy number states and breakpoints between contiguous segments across cells, filters the segments for high-quality breakpoints using an ensemble technique, and adopts several strategies for tolerating noisy read-depth and allele frequency measurements. Using a wide array of both real and simulated datasets, we show that SEACON derives accurate copy numbers and surpasses existing approaches under numerous experimental conditions, and identify its strengths and weaknesses.

Availability and implementation
SEACON is implemented in Python and is freely available open-source from https://github.com/NabaviLab/SEACON and https://doi.org/10.5281/zenodo.12727008.