bluuebunny/crossref_metadata_2025_split huggingface dataset:
Meta-QTL analysis and identification of candidate genes for multiple-traits associated with spot blotch resistance in bread wheat
Authors: Vasistha Neeraj Kumar , Sharma Vaishali , Singh Sahadev , Kaur Ramandeep , Kumar Anuj , Ravat Vikas Kumar , Kumar Rahul , Gupta Pushpendra K. 
Published: June 2024

AbstractIn bread wheat, a literature search gave 228 QTLs for six traits, including resistance against spot blotch and the following five other related traits: (i) stay green; (ii) flag leaf senescence; (iii) green leaf area duration; (iv) green leaf area of the main stem; and (v) black point resistance. These QTLs were used for metaQTL (MQTL) analysis. For this purpose, a consensus map with 72,788 markers was prepared; 69 of the above 228 QTLs, which were suitable for MQTL analysis, were projected on the consensus map. This exercise resulted in the identification of 16 meta-QTLs (MQTLs) located on 11 chromosomes, with the PVE ranging from 5.4% (MQTL7) to 21.8% (MQTL5), and the confidence intervals ranging from 1.5 to 20.7 cM (except five MQTLs with a range of 36.1–57.8 cM). The number of QTLs associated with individual MQTLs ranged from a maximum of 17 in MQTL3 to 8 each in MQTL5 and MQTL8 and 5 each in MQTL7 and MQTL14. The 16 MQTLs, included 12 multi-trait MQTLs; one of the MQTL also overlapped a genomic region carrying the major spot blotch resistance gene Sb1. Of the total 16 MQTLs, 12 MQTLs were also validated through marker-trait associations that were available from earlier genome-wide association studies. The genomic regions associated with MQTLs were also used for the identification of candidate genes (CGs) and led to the identification of 516 CGs encoding 508 proteins; 411 of these proteins are known to be associated with resistance against several biotic stresses. In silico expression analysis of CGs using transcriptome data allowed the identification of 71 differentially expressed CGs, which were examined for further possible studies. The findings of the present study should facilitate fine-mapping and cloning of genes, enabling Marker Assisted Selection.
Analysis of fibrin networks using topological data analysis – a feasibility study
Authors: Berger Martin , Hell Tobias , Tobiasch Anna , Martini Judith , Lindner Andrea , Tauber Helmuth , Bachler Mirjam , Hermann Martin 
Published: June 2024

AbstractBlood clot formation, a crucial process in hemostasis and thrombosis, has garnered substantial attention for its implications in various medical conditions. Microscopic examination of blood clots provides vital insights into their composition and structure, aiding in the understanding of clot pathophysiology and the development of targeted therapeutic strategies. This study explores the use of topological data analysis (TDA) to assess plasma clot characteristics microscopically, focusing on the identification of the elements components, holes and Wasserstein distances. This approach should enable researchers to objectively classify fibrin networks based on their topologic architecture. We tested this mathematical characterization approach on plasma clots formed in static conditions from porcine and human citrated plasma samples, where the effect of dilution and direct thrombin inhibition was explored. Confocal microscopy images showing fluorescence labeled fibrin networks were analyzed. Both treatments resulted in visual differences in plasma clot architecture, which could be quantified using TDA. Significant differences between baseline and diluted samples, as well as blood anticoagulated with argatroban, were detected mathematically. Therefore, TDA could be indicative of clots with compromised stability, providing a valuable tool for thrombosis risk assessment. In conclusion, microscopic examination of plasma clots, coupled with Topological Data Analysis, offers a promising avenue for comprehensive characterization of clot microstructure. This method could contribute to a deeper understanding of clot pathophysiology and thereby refine our ability to assess clot characteristics.
Design and implementation of a high misalignment-tolerance wireless charger for an electric vehicle with control of the constant current/voltage charging
Authors: Ramakrishnan Venkatesan , A Dominic Savio , C Balaji , R Narayanamoorthi , Vishnuram Pradeep , Yang Tiansheng , Bajaj Mohit , Rathore Rajkumar Singh , Zaitsev Ievgen 
Published: June 2024

AbstractWireless charging of Electric Vehicles (EVs) has been extensively researched in the realm of electric cars, offering a convenient method. Nonetheless, there has been a scarcity of experiments conducted on low-power electric vehicles. To establish a wireless power transfer system for an electric vehicle, optimal power and transmission efficiency necessitate arranging the coils coaxially. In wireless charging systems, coils often experience angular and lateral misalignments. In this paper, a new alignment strategy is introduced to tackle the misalignment problem between the transmitter and receiver coils in the wireless charging of Electric Vehicles (EVs). The study involves the design and analysis of a coil, considering factors such as mutual inductance and efficiency. Wireless coils with angular misalignment are modelled in Ansys Maxwell simulation software. The proposed practical EV system aims to align the coils using angular motion, effectively reducing misalignment during the parking of two-wheelers. This is achieved by tilting the transmitter coil in the desired direction. Furthermore, micro sensing coils are employed to identify misalignment and facilitate automatic alignment. Additionally, adopting a power control technique becomes essential to achieve both constant current (CC) and constant voltage (CV) modes during battery charging. Integrating CC and CV modes is crucial for efficiently charging lithium-ion batteries, ensuring prolonged lifespan and optimal capacity utilization. The developed system can improve the efficiency of the wireless charging system to 90.3% with a 24 V, 16 Ah Lithium Ion Phosphate (LiFePO4) battery at a 160 mm distance between the coils.
Zedoarondiol inhibits human bronchial smooth muscle cell proliferation through the CAV-1/PDGF signalling pathway
Authors: Lyu Yinglan , Feng Wandi , Song Jingze , Wang Chunguo , Fu Yu , Zhao Baosheng , Meng Yanyan 
Published: June 2024

AbstractAirway remodelling in lung diseases can be treated by inhibiting excessive smooth muscle cell proliferation. Zedoarondiol (Zed) is a natural compound isolated from the Chinese herb Curcuma longa. The caveolin-1 (CAV-1) is widely expressed in lung cells and plays a key role in platelet-derived growth factor (PDGF) signalling and cell proliferation. This study aims to investigate the effect of Zed on human bronchial smooth muscle cell (HBSMC) proliferation and explore its potential molecular mechanisms. We assessed the effect of Zed on the proliferation of PDGF-stimulated HBSMCs and performed proteomic analysis to identify potential molecular targets and pathways. CAV1 siRNA was used to validate our findings in vitro. In PDGF-stimulated HBSMCs, Zed significantly inhibited excessive proliferation of HBSMCs. Proteomic analysis of zedoarondiol-treated HBSMCs revealed significant enrichment of differentially expressed proteins in cell proliferation-related pathways and biological processes. Zed inhibition of HBSMC proliferation was associated with upregulation of CAV1, regulation of the CAV-1/PDGF pathway and inhibition of MAPK and PI3K/AKT signalling pathway activation. Treatment of HBSMCs with CAV1 siRNA partly reversed the inhibitory effect of Zed on HBSMC proliferation. Thus, this study reveals that zedoarondiol potently inhibits HBSMC proliferation by upregulating CAV-1 expression, highlighting its potential value in airway remodelling and related diseases.
Impacts of ACE insertion/deletion variant on cardiometabolic risk factors, premature coronary artery disease, and severity of coronary lesions
Authors: Luo Zhi 
Published: June 2024

AbstractAngiotensin-converting enzyme (ACE) is closely related to cardiometabolic risk factors and atherosclerosis. This study aims to investigate whether the insertion/deletion (I/D) variant of ACE gene impacts cardiometabolic risk factors, premature coronary artery disease (PCAD), and severity of coronary lesions. PubMed, Cochrane Library, Central, CINAHL, and ClinicalTrials.gov were searched until December 22, 2023. 94,270 individuals were included for the analysis. Carriers of DD genotype had higher levels of triglycerides (TG), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), systolic blood pressure (SBP), diastolic blood pressure (DBP), body mass index (BMI), and waist circumference (WC) than carriers of II or ID genotypes. In addition, carriers of DD genotype were at high risk of PCAD and multiple vessel lesions. The impacts of ACE I/D variant on lipid levels were significant in American individuals but stronger in male individuals. In contrast, the impacts of ACE I/D variant on PCAD and severity of coronary lesions were primarily significant in Caucasian individuals. This study indicates that the ACE I/D variant has a slight but significant impact on cardiometabolic risk factors, PCAD, and severity of coronary lesions. Angiotensin-converting enzyme inhibitors (ACEI) may benefit high-risk populations with ACE DD genotype to prevent PCAD and multiple vessel lesions.PROSPERO registration number: CRD42023426732
QM-DLA: an efficient qubit mapping method based on dynamic look-ahead strategy
Authors: Liu Hui , Zhang Bingjie , Zhu Yu , Yang Hanxiao , Zhao Bo 
Published: June 2024

AbstractQuantum computing has already demonstrated great computational potential across multiple domains and has received more and more attention. However, due to the connectivity limitations of Noisy Intermediate-Scale Quantum (NISQ) devices, most of the quantum algorithms cannot be directly executed without the help of inserting SWAP gates. Nevertheless, more SWAP gates lead to a longer execution time and, inevitably, lower fidelity of the algorithm. To this end, this paper proposes an optimized qubit mapping algorithm based on a dynamic look-ahead strategy to minimize the number of SWAP gates inserted. Firstly, a heuristic algorithm is proposed based on maximizing physical qubit connectivity to generate the optimal initial qubit mapping, which reduces the need for logical qubit shifts during subsequent SWAP gate insertion. Secondly, in the form of directed acyclic graphs, we identify quantum gates that violate the constraints of physical coupling and insert SWAP gates to remap qubits, thereby overcoming the limitations of qubit interactions. Finally, the optimal SWAP gate insertion strategy is built by comparing the cost of different SWAP gate insertion strategies through a multi-window look-ahead strategy to reduce the number of SWAP gates inserted. The experimental results show that the strategy in this paper decreases the number of SWAP gate insertions and significantly reduces the depth of quantum circuits when performing qubit mapping compared with state-of-the-art methods.
Comprehensive studies reveal physiological and genetic diversity in traditional rice cultivars for UV-B sensitivity
Authors: Senapati Preetam Kumar , Kariali Ekamber , Kisan Kuntala , Sahu Binod Bihari , Naik Arya Kumar Dibyananda , Panda Debabrata , Tripathy Santanu Kumar , Mohapatra Sanjukta , Mohapatra Pravat Kumar 
Published: June 2024

AbstractAcclimation to crop niches for thousands of years has made indigenous rice cultivars better suited for stress-prone environments. Still, their response to UV-B resiliency is unknown. 38 rice landraces were grown in cemented pots in a randomised block design with three replicates under open field conditions in Sambalpur University in the wet season of 2022. Half of the plants in each of the cultivars were administered UV-B radiation at the panicle emergence stage in an adjustable UV-B chamber permitting sunlight, and the effects of the stress on various morpho-physiological features, such as spikelet sterility, flag leaf photosynthetic and flavonoid pigment contents, and lipid peroxidation activities, were estimated for calibration of stress resistance. The experiment identified Swarnaprabha and Lalkain as the most sensitive and resilient to stress respectively, and the differential response between them was further revealed in the expression of genes related to UV-B sensitivity. Subject to the stress, Swarnaprabha exhibited symptoms of injuries, like leaf burns, and a higher loss of various photosynthetic parameters, such as pigment contents, SPAD and Fv/Fm, ETR and qP values, while NPQ increased only in Lalkain. Exposure to UV-B increased the total phenolic and flavonoid contents in Lalkain while depressing them in Swarnaprabha. Such an effect amounted to a higher release of fluorescent energy in the latter. The levels of expression of gene families controlling flavonoid activation and UV-B signal transduction, such as OsWRKY, OsUGT, OsRLCK, OsBZIP, OsGLP, and CPD photolyase were similar in both the cultivars in the control condition. However, exposure to UV-B stress overexpressed them in resilient cultivars only. The magnitude of expression of the genes and the impact of the stress on photosynthetic parameters, phenolic compounds and pubescent hair structure at the panicle emergence stage could be valid indicators among indigenous rice for UV-B tolerance.
Caspase-4 promotes metastasis and interferon-γ-induced pyroptosis in lung adenocarcinoma
Authors: Chiba Yosuke , Doi Tomomitsu , Obayashi Kunie , Sumida Kazuhiro , Nagasaka Shohei , Wang Ke-Yong , Yamasaki Kei , Masago Katsuhiro , Matsushita Hirokazu , Kuroda Hiroaki , Yatera Kazuhiro , Endo Motoyoshi 
Published: June 2024

AbstractCaspase-4 (CASP4) is a member of the inflammatory caspase subfamily and promotes inflammation. Here, we report that CASP4 in lung adenocarcinoma cells contributes to both tumor progression via angiogenesis and tumor hyperkinesis and tumor cell killing in response to high interferon (IFN)-γ levels. We observe that elevated CASP4 expression in the primary tumor is associated with cancer progression in patients with lung adenocarcinoma. Further, CASP4 knockout attenuates tumor angiogenesis and metastasis in subcutaneous tumor mouse models. CASP4 enhances the expression of genes associated with angiogenesis and cell migration in lung adenocarcinoma cell lines through nuclear factor kappa-light chain-enhancer of activated B cell signaling without stimulation by lipopolysaccharide or tumor necrosis factor. CASP4 is induced by endoplasmic reticulum stress or IFN-γ via signal transducer and activator of transcription 1. Most notably, lung adenocarcinoma cells with high CASP4 expression are more prone to IFN-γ-induced pyroptosis than those with low CASP4 expression. Our findings indicate that the CASP4 level in primary lung adenocarcinoma can predict metastasis and responsiveness to high-dose IFN-γ therapy due to cancer cell pyroptosis.
Scalable design of orthogonal DNA barcode libraries
Authors: Gowri Gokul , Sheng Kuanwei , Yin Peng 
Published: June 2024

AbstractOrthogonal DNA barcode library design is an essential task in bioengineering. Here we present seqwalk, an efficient method for designing barcode libraries that satisfy a sequence symmetry minimization (SSM) heuristic for orthogonality, with theoretical guarantees of maximal or near-maximal library size under certain design constraints. Seqwalk encodes SSM constraints in a de Bruijn graph representation of sequence space, enabling the application of recent advances in discrete mathematics1 to the problem of orthogonal sequence design. We demonstrate the scalability of seqwalk by designing a library of >106 SSM-satisfying barcode sequences in less than 20 s on a standard laptop.
A Comparison of Hearing Thresholds, and the Resulting Prescribed Gain and Hearing Aid Outputs, Using Gold Standard Audiometry and the TympaHealth Hearing Assessment Tool
Authors: Saunders Gabrielle H. , Walker Adam , Heal Calvin , Ramdoo Krishan 
Published: June 2024

Objective:
Phone- and tablet-based hearing testing systems are now widely available. Here, we evaluated one such system from TympaHealth by comparing air conduction thresholds and resultant hearing aid targets and output, measured with the TympaHealth system with those measured using standard audiometry.

Design:
The hearing thresholds of 35 adults were measured using standard audiometry and the TympaHealth system. Each set of thresholds was used to generate NAL-NL2 targets and program a hearing aid. The data from each system were compared.

Results:
Bland–Altman analyses showed overall mean differences between thresholds measured with each system to be small, with 85% of TympaHealth thresholds being within ±5 dB of the standard audiometric thresholds, although TympaHealth thresholds were higher (poorer) than the standard audiometric thresholds. The hearing aid targets and gains generated from the standard audiometric thresholds were lower (less amplification) than those generated from the TympaHealth thresholds but again, mean differences at each frequency were small and likely imperceptible.

Conclusion:
These findings support the possibility that valid hearing testing can take place outside of a clinical booth using portable systems like that from TympaHealth, opening up the possibility of testing hearing and fitting hearing aids through pharmacies, opticians, and in care homes.
Asteroseismic measurement of core and envelope rotation rates for 2006 red giant branch stars
Authors: Li Gang , Deheuvels Sébastien , Ballot Jérôme 
Published: June 2024

Context. Tens of thousands of red giant stars in the Kepler data exhibit solar-like oscillations. The mixed-mode characteristics of their oscillations enable us to study the internal physics from the core to the surface, such as differential rotation. However, envelope rotation rates have only been measured for about a dozen red giant branch (RGB) stars so far. This limited the theoretical interpretation of angular momentum transport in post-main sequence phases.
Aims. We report the measurements of g-mode properties and differential rotation in the largest sample of Kepler RGB stars.
Methods. We applied a new approach to calculate the asymptotic frequencies of mixed modes, which accounts for so-called near-degeneracy effects (NDEs) and leads to improved measurements of envelope rotation rates. By fitting these asymptotic expressions to the observations, we obtained measurements of the properties of g modes (period spacing, ΔΠ1, coupling factor, q, g-mode offset term, εg, small separation, δν01) and the internal rotation (mean core, Ωcore, and envelope, Ωenv, rotation rates).
Results. Among 2495 stars with clear mixed-mode patterns, we found that 800 show doublets and 1206 show triplets, while the remaining stars do not show any rotational splittings. We measured core rotation rates for 2006 red giants, doubling the size of pre-existing catalogues. This led us to discover an over-density of stars that are narrowly distributed around a well-defined ridge in the plane, showing core rotation rate versus evolution along the RGB. These stars could experience a different angular momentum transport compared to other red giants. With this work, we also increased the sample of stars with measured envelope rotation rates by two orders of magnitude. We found a decreasing trend between envelope rotation rates and evolution, implying that the envelopes slow down with expansion, as expected. We found 243 stars whose envelope rotation rates are significantly larger than zero. For these stars, the core-to-envelope rotation ratios are around Ωcore/Ωenv ∼ 20 and show a large spread with evolution. Several stars show extremely mild differential rotations, with core-to-surface ratios between 1 and 2. These stars also have very slow core rotation rates, suggesting that they go through a peculiar rotational evolution. We also discovered more stars located below the ΔΠ1–Δν degeneracy sequence, which presents an opportunity to study the history of plausible stellar mergers.
A low cosmic-ray ionisation rate in the pre-stellar core Ophiuchus/H-MM1
Authors: Harju J. , Vastel C. , Sipilä O. , Redaelli E. , Caselli P. , Pineda J. E. , Belloche A. , Wyrowski F. 
Published: June 2024

Aims. We test the use of three common molecular ions, ortho-H2D+ (oH2D+), N2H+, and DCO+, as probes of the internal structure and kinematics of a dense, starless molecular cloud core.
Methods. The pre-stellar core H-MM1 in Ophiuchus was mapped in the oH2D+(110 − N2H+(4 − 3), and DCO+ (5 − 4) lines with the Large APEX sub-Millimeter Array (LAsMA) multi-beam receiver of the Atacama Pathfinder EXperiment (APEX) telescope. We also ran a series of chemistry models to predict the abundance distributions of the observed molecules, and to estimate the effect of the cosmic-ray ionisation rate on their abundances.
Results. The three line maps show different distributions. The oH2D+ map is extended and outlines the general structure of the core, N2H+ mainly shows the density maxima, and the DCO+ emission peaks are shifted towards one edge of the core where a region of enhanced desorption had previously been found. According to the chemical simulation, the fractional oH2D+ abundance remains relatively high in the centre of the core, and its column density correlates strongly with the cosmic-ray ionisation rate, ζH2. Simulated line maps constrain the cosmic-ray ionisation rate to be low, between 5 × 10−18 s−1 and 1 × 10−17 s−1 in the H-MM1 core. This estimate agrees with the gas temperature measured in the core.
Conclusions. The present observations show that very dense, cold gas in molecular clouds can be traced by mapping the ground-state line of oH2D+ and high-J transitions of DCO+ and N2H+, despite the severe depletion of the latter two molecules. Modelling line emission of oH2D+ provides a straightforward method of determining the cosmic-ray ionisation rate in dense clouds, where the primary ion, H3+, is not observable.