bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss-of-function of an α-SNAP gene confers resistance to soybean cyst nematode
Authors: Usovsky Mariola , Gamage Vinavi A. , Meinhardt Clinton G. , Dietz Nicholas , Triller Marissa , Basnet Pawan , Gillman Jason D. , Bilyeu Kristin D. , Song Qijian , Dhital Bishnu , Nguyen Alice , Mitchum Melissa G. , Scaboo Andrew M. 
Published: November 2023

AbstractPlant-parasitic nematodes are one of the most economically impactful pests in agriculture resulting in billions of dollars in realized annual losses worldwide. Soybean cyst nematode (SCN) is the number one biotic constraint on soybean production making it a priority for the discovery, validation and functional characterization of native plant resistance genes and genetic modes of action that can be deployed to improve soybean yield across the globe. Here, we present the discovery and functional characterization of a soybean resistance gene, GmSNAP02. We use unique bi-parental populations to fine-map the precise genomic location, and a combination of whole genome resequencing and gene fragment PCR amplifications to identify and confirm causal haplotypes. Lastly, we validate our candidate gene using CRISPR-Cas9 genome editing and observe a gain of resistance in edited plants. This demonstrates that the GmSNAP02 gene confers a unique mode of resistance to SCN through loss-of-function mutations that implicate GmSNAP02 as a nematode virulence target. We highlight the immediate impact of utilizing GmSNAP02 as a genome-editing-amenable target to diversify nematode resistance in commercially available cultivars.
Bony-fish-like scales in a Silurian maxillate placoderm
Authors: Cui Xindong , Friedman Matt , Yu Yilun , Zhu You-an , Zhu Min 
Published: November 2023

AbstractMajor groups of jawed vertebrates exhibit contrasting conditions of dermal plates and scales. But the transition between these conditions remains unclear due to rare information on taxa occupying key phylogenetic positions. The 425-million-year-old fishEntelognathuscombines an unusual mosaic of characters typically associated with jawed stem gnathostomes or crown gnathostomes. However, only the anterior part of the exoskeleton was previously known for this very crownward member of the gnathostome stem. Here, we report a near-complete post-thoracic exoskeleton ofEntelognathus. Strikingly, its scales are large and some are rhomboid, bearing distinctive peg-and-socket articulations; this combination was previously only known in osteichthyans and considered a synapomorphy of that group. The presence inEntelognathusof an anal fin spine, previously only found in some stem chondrichthyans, further illustrates that many characters previously thought to be restricted to specific lineages within the gnathostome crown likely arose before the common ancestor of living jawed vertebrates.
Clinical, genetic and structural delineation of RPL13-related spondyloepimetaphyseal dysplasia suggest extra-ribosomal functions of eL13
Authors: Jacob Prince , Lindelöf Hillevi , Rustad Cecilie F. , Sutton Vernon Reid , Moosa Shahida , Udupa Prajna , Hammarsjö Anna , Bhavani Gandham SriLakshmi , Batkovskyte Dominyka , Tveten Kristian , Dalal Ashwin , Horemuzova Eva , Nordgren Ann , Tham Emma , Shah Hitesh , Merckoll Else , Orellana Laura , Nishimura Gen , Girisha Katta M. , Grigelioniene Giedre 
Published: November 2023

AbstractSpondyloepimetaphyseal dysplasia with severe short stature, RPL13-related (SEMD-RPL13), MIM#618728), is a rare autosomal dominant disorder characterized by short stature and skeletal changes such as mild spondylar and epimetaphyseal dysplasia affecting primarily the lower limbs. The genetic cause was first reported in 2019 by Le Caignec et al., and six disease-causing variants in the gene coding for a ribosomal protein, RPL13 (NM_000977.3) have been identified to date. This study presents clinical and radiographic data from 12 affected individuals aged 2–64 years from seven unrelated families, showing highly variable manifestations. The affected individuals showed a range from mild to severe short stature, retaining the same radiographic pattern of spondylar- and epi-metaphyseal dysplasia, but with varying severity of the hip and knee deformities. Two new missense variants, c.548 G>A, p.(Arg183His) and c.569 G>T, p.(Arg190Leu), and a previously known splice variant c.477+1G>A were identified, confirming mutational clustering in a highly specific RNA binding motif. Structural analysis and interpretation of the variants’ impact on the protein suggests that disruption of extra-ribosomal functions of the protein through binding of mRNA may play a role in the skeletal phenotype of SEMD-RPL13. In addition, we present gonadal and somatic mosaicism for the condition.
De novo transcriptome assembly of Dalbergia sissoo Roxb. (Fabaceae) under Botryodiplodia theobromae-induced dieback disease
Authors: Zafar Ummul Buneen , Shahzaib Muhammad , Atif Rana Muhammad , Khan Sultan Habibullah , Niaz Muhammad Zeeshan , Shahzad Khalid , Chughtai Nighat , Awan Faisal Saeed , Azhar Muhammad Tehseen , Rana Iqrar Ahmad 
Published: November 2023

AbstractDalbergia sissooRoxb. (Shisham) is a timber-producing species of economic, cultural, and medicinal importance in the Indian subcontinent. In the past few decades, Shisham's dieback disease caused by the fungusBotryodiplodia theobromaehas become an evolving issue in the subcontinent endangering its survival. To gain insights into this issue, a standard transcriptome assembly was deployed to assess the response ofD. sissooat the transcriptomic level under the stress ofB. theobromaeinfection. For RNA isolation, the control and infected leaf tissue samples were taken from 1-year-old greenhouse-grownD. sissooplants after 20 days of stem-base spore inoculation. cDNA synthesis was performed from these freshly isolated RNA samples that were then sent for sequencing. About 18.14 Gb (Giga base) of data was generated using the BGISEQ-500 sequencing platform. In terms of Unigenes, 513,821 were identified after a combined assembly of all samples and then filtering the abundance. The total length of Unigenes, their average length, N50, and GC-content were 310,523,693 bp, 604 bp, 1,101 bp, and 39.95% respectively. The Unigenes were annotated using 7 functional databases i.e., 200,355 (NR: 38.99%), 164,973 (NT: 32.11%), 123,733 (Swissprot: 24.08%), 142,580 (KOG: 27.75%), 139,588 (KEGG: 27.17%), 99,752 (GO: 19.41%), and 137,281 (InterPro: 26.72%). Furthermore, the Transdecoder detected 115,762 CDS. In terms of SSR (Simple Sequence Repeat) markers, 62,863 of them were distributed on 51,508 Unigenes and on the predicted 4673 TF (Transcription Factor) coding Unigenes. A total of 16,018 up- and 19,530 down-regulated Differentially Expressed Genes (DEGs) were also identified. Moreover, the Plant Resistance Genes (PRGs) had a count of 9230. We are hopeful that in the future, these identified Unigenes, SSR markers, DEGs and PRGs will provide the prerequisites for managing Shisham dieback disease, its breeding, and in tree improvement programs.
Evaluation of the performance of GPT-3.5 and GPT-4 on the Polish Medical Final Examination
Authors: Rosoł Maciej , Gąsior Jakub S. , Łaba Jonasz , Korzeniewski Kacper , Młyńczak Marcel 
Published: November 2023

AbstractThe study aimed to evaluate the performance of two Large Language Models (LLMs): ChatGPT (based on GPT-3.5) and GPT-4 with two temperature parameter values, on the Polish Medical Final Examination (MFE). The models were tested on three editions of the MFE from: Spring 2022, Autumn 2022, and Spring 2023 in two language versions—English and Polish. The accuracies of both models were compared and the relationships between the correctness of answers with the answer’s metrics were investigated. The study demonstrated that GPT-4 outperformed GPT-3.5 in all three examinations regardless of the language used. GPT-4 achieved mean accuracies of 79.7% for both Polish and English versions, passing all MFE versions. GPT-3.5 had mean accuracies of 54.8% for Polish and 60.3% for English, passing none and 2 of 3 Polish versions for temperature parameter equal to 0 and 1 respectively while passing all English versions regardless of the temperature parameter value. GPT-4 score was mostly lower than the average score of a medical student. There was a statistically significant correlation between the correctness of the answers and the index of difficulty for both models. The overall accuracy of both models was still suboptimal and worse than the average for medical students. This emphasizes the need for further improvements in LLMs before they can be reliably deployed in medical settings. These findings suggest an increasing potential for the usage of LLMs in terms of medical education.
Evaluation of the surface water quality using global water quality index (WQI) models: perspective of river water pollution
Authors: Khan Md. Habibur Rahman Bejoy , Ahsan Amimul , Imteaz M. , Shafiquzzaman Md. , Al-Ansari Nadhir 
Published: November 2023

AbstractRapid industrialization, urbanization, global warming, and climate change are compromising surface water quality across the globe. Consequently, water conservation is essential for both environmental sustainability and human survival. This study assesses the water quality of the Jamuna River in Bangladesh at five distinct sites during wet and dry seasons. It employs six global water quality indices (WQIs) and contrasts the results with Bangladesh's Environmental Quality Standard (EQS) and the Department of Environment (DoE) criteria. The WQI models used are the Weighted Arithmetic WQI (WAWQI), British Columbia WQI (BCWQI), Canadian Council of Ministers of the Environment WQI (CWQI), Assigned WQI (AWQI), Malaysian WQI (MWQI), and Oregon WQI (OWQI). Fifteen physicochemical parameters were analyzed according to each WQI model's guidelines. The findings reveal that most parameters surpass the standard permissible values. The WQI model results indicate that the average water quality across the five sites falls into the lowest category. A comparison of the WQI models suggests potential correlations between WAWQI and AWQI, as well as between MWQI and OWQI. The straightforward presentation of the WQI models indicates that while the river water requires treatment for household and drinking use, it remains suitable for irrigation. The decline in water quality is likely attributable to human activities, urbanization, municipal waste disposal, and industrial effluents. Authorities must prioritize regular monitoring and assessment of water quality to address the identified challenges. Restoring the water to an acceptable standard will become increasingly difficult without proactive measures.
Robust in-vehicle respiratory rate detection using multimodal signal fusion
Authors: Warnecke Joana M. , Lasenby Joan , Deserno Thomas M. 
Published: November 2023

AbstractContinuous health monitoring in private spaces such as the car is not yet fully exploited to detect diseases in an early stage. Therefore, we develop a redundant health monitoring sensor system and signal fusion approaches to determine the respiratory rate during driving. To recognise the breathing movements, we use a piezoelectric sensor, two accelerometers attached to the seat and the seat belt, and a camera behind the windscreen. We record data from 15 subjects during three driving scenarios (15 min each) city, highway, and countryside. An additional chest belt provides the ground truth. We compare the four convolutional neural network (CNN)-based fusion approaches: early, sensor-based late, signal-based late, and hybrid fusion. We evaluate the performance of fusing for all four signals to determine the portion of driving time and the signal combination. The hybrid algorithm fusing all four signals is most effective in detecting respiratory rates in the city ($$P = 62.42$$

P
=
62.42

), highway ($$P = 62.67$$

P
=
62.67

), and countryside ($$P = 60.94$$

P
=
60.94

). In summary, 60% of the total driving time can be used to measure the respiratory rate. The number of signals used in the multi-signal fusion improves reliability and enables continuous health monitoring in a driving vehicle.
Manufacturing of stretchable substrate with biaxial strain control for highly-efficient stretchable solar cells and displays
Authors: Kwak Ji-Youn , Jeong Ji-Young , Kwon Ye-Pil , Seo Dong-Hyun , Kang Chung-Mo , Kim Dong-Hyeon , Han Jun Sae , Gwak Eun-Ji , Choi Doo-Sun , Kim Ju-Young , Je Tae-Jin , Jeon Eun-chae 
Published: November 2023

AbstractThere has been significant research focused on the development of stretchable materials that can provide a large area with minimal material usage for use in solar cells and displays. However, most materials exhibit perpendicular shrinkage when stretched, which is particularly problematic for polymer-based substrates commonly used in stretchable devices. To address this issue, biaxial strain-controlled substrates have been proposed as a solution to increase device efficiency and conserve material resources. In this study, we present the design and fabrication of a biaxial strain-controlled substrate with a re-entrant honeycomb structure and a negative Poisson’s ratio. Using a precisely machined mold with a shape error of less than 0.15%, we successfully fabricated polydimethylsiloxane substrates with a 500 μm thick re-entrant honeycomb structure, resulting in a 19.1% reduction in perpendicular shrinkage. This improvement translates to a potential increase in device efficiency by 9.44% and an 8.60% reduction in material usage for substrate fabrication. We demonstrate that this design and manufacturing method can be applied to the fabrication of efficient stretchable devices, such as solar cells and displays.
Effect of carbon content on electronic structure of uranium carbides
Authors: Butorin Sergei M. , Bauters Stephen , Amidani Lucia , Beck Aaron , Rossberg André , Weiss Stephan , Vitova Tonya , Kvashnina Kristina O. , Tougait Olivier 
Published: November 2023

AbstractThe electronic structure of UC$$_x$$

x

(x = 0.9, 1.0, 1.1, 2.0) was studied by means of x-ray absorption spectroscopy (XAS) at the C K edge and measurements in the high energy resolution fluorescence detection (HERFD) mode at the U $$M_4$$

M
4

and $$L_3$$

L
3

edges. The full-relativistic density functional theory calculations taking into account the $$5f-5f$$

5
f
-
5
f

Coulomb interaction U and spin-orbit coupling (DFT+U+SOC) were also performed for UC and UC$$_2$$

2

. While the U $$L_3$$

L
3

HERFD-XAS spectra of the studied samples reveal little difference, the U $$M_4$$

M
4

HERFD-XAS spectra show certain sensitivity to the varying carbon content in uranium carbides. The observed gradual changes in the U $$M_4$$

M
4

HERFD spectra suggest an increase in the C 2p-U 5f charge transfer, which is supported by the orbital population analysis in the DFT+U+SOC calculations, indicating an increase in the U 5f occupancy in UC$$_2$$

2

as compared to that in UC. On the other hand, the density of states at the Fermi level were found to be significantly lower in UC$$_2$$

2

, thus affecting the thermodynamic properties. Both the x-ray spectroscopic data (in particular, the C K XAS measurements) and results of the DFT+U+SOC calculations indicate the importance of taking into account U and SOC for the description of the electronic structure of actinide carbides.
High viral suppression and detection of dolutegravir-resistance associated mutations in treatment-experienced Tanzanian adults living with HIV-1 in Dar es Salaam
Authors: Bwire George M. , Aiko Beatrice Godwin , Mosha Idda H. , Kilapilo Mary S. , Mangara Alli , Kazonda Patrick , Swai Janeth P. , Swalehe Omary , Jordan Michael R. , Vercauteren Jurgen , Sando David , Temba David , Shao Amani , Mauka Wilhellmuss , Decouttere Catherine , Vandaele Nico , Sangeda Raphael Z. , Killewo Japhet , Vandamme Anne-Mieke 
Published: November 2023

AbstractTo curb HIV infection rate in Tanzania, antiretroviral therapy (ART) has been scaled up since 2006, and in 2019, the country shifted to regimen including dolutegravir as a default first line. We assessed the success of ART and the contribution of HIV drug resistance (HIVDR) to unsuppressed viral loads. Between February and May 2023 a cross-sectional survey with random sampling was conducted in the six clinics in an urban cohort in Dar es Salaam. Patients with unsuppresed viral loads (local criteria viral load (VL) ≥ 1000 copies/mL) were tested for HIVDR mutations using the WHO adapted protocol for plasma samples. Mutations were interpreted using the Stanford HIVDR database. In total 600 individuals participated in this survey, the majority were female (76.83%), mean age ($$\pm$$
±
standard deviation) was 44.0 ($$\pm$$
±
11.6) years. The median duration on ART (interquartile range) was 6.5 (3.9–10.2) years. Approximately 99% were receiving tenofovir + lamivudine + dolutegravir as a fixed dose combination. VL testing was successful in 99.67% (598/600) of survey patients and only 33 had VL ≥ 1000 copies/mL, resulting in a viral suppression level of 94.48% (565/598, 95% CI 92.34–96.17%). For 23 samples, protease and reverse transcriptase (RT) genotyping were successful, with 13 sequences containing RT inhibitor surveillance drug resistance mutations (SDRMs) (56.5%). No SDRM against protease inhibitors were detected. Thirty samples were successfully genotyped for integrase with 3 sequences (10.08%) containing integrase strand transfer inhibitor (INSTI) SDRMs. In samples successfully genotyped in the three genetic regions, 68.18% (16/22) had a genotypic susceptibility score (GSS) ≥ 2.5 for the concurrent regimen, implying factors beyond drug resistance caused the unsuppressed viral load. For five patients, GSS indicated that HIVDR may have caused the unsuppressed viral load. All three patients with INSTI resistance mutations were highly resistant to dolutegravir and accumulated nucleoside and non-nucleoside RT inhibitor HIVDR mutations. Although in this cohort the last 95 UNAIDS target was almost achieved, HIVDR mutations, including INSTIs resistance mutations were detected in HIV-positive individuals taking ART for at least one year. We recommend the design and implementation of high-impact interventions to prevent the increase of HIVDR, failure of dolutegravir and address the non-resistance factors in the study area.
Customized virtual reality naturalistic scenarios promoting engagement and relaxation in patients with cognitive impairment: a proof-of-concept mixed-methods study
Authors: Pardini Susanna , Gabrielli Silvia , Gios Lorenzo , Dianti Marco , Mayora-Ibarra Oscar , Appel Lora , Olivetto Silvia , Torres Alina , Rigatti Patty , Trentini Emanuela , Leonardelli Lucia , Bernardi Michela , Lucianer Marzia , Forti Stefano , Novara Caterina 
Published: November 2023

AbstractBeing immersed in a natural context has a beneficial and pervasive impact on well-being. Virtual Reality (VR) is a technology that can help expose people to naturalistic scenarios virtually, overcoming obstacles that prevent them from visiting real natural environments. VR could also increase engagement and relaxation in older adults with and without cognitive impairment. The main aim of this study is to investigate the feasibility of a customized naturalistic VR scenario by assessing motion-sickness effects, engagement, pleasantness, and emotions felt. Twenty-three individuals with a diagnosis of cognitive impairment living in a long-term care home participated in our study. At the end of the entire VR experimental procedure with older adults, five health staff operators took part in a dedicated assessment phase focused on evaluating the VR procedure's usability from their individual perspectives. The tools administered were based on self-reported and observational tools used to obtain information from users and health care staff professionals. Feasibility and acceptance proved to be satisfactory, considering that the VR experience was well-tolerated and no adverse side effects were reported. One of the major advantages emerged was the opportunity to deploy customized environments that users are not able to experience in a real context.Trial Registration: National Institute of Health (NIH) U.S. National Library of Medicine, ClinicalTrials.gov NCT05863065 (17/05/2023).
The expression changes of PD-L1 and immune response mediators are related to the severity of primary bone tumors
Authors: Eghtedari Amir Reza , Vaezi Mohammad Amin , Safari Elaheh , Salimi Vahid , Safizadeh Banafsheh , Babaheidarian Pegah , Abiri Amene , Mahdinia Elmira , Alireza Mirzaei  , Mokhles Parisa , Tavakoli-Yaraki Masoumeh 
Published: November 2023

AbstractThe expression pattern, diagnostic value, and association of PD-L1, IFN-γ and TGF-β with bone tumor type, severity, and relapse are determined in this study. 300 human samples from patients with osteosarcoma, Ewing sarcoma, and GCT were enrolled. The PD-L1 gene and protein expression were assessed by qRT-PCR and immunohistochemistry, respectively. ELISA and flow cytometry was used to detect cytokines and CD4/CD8 T cell percentages, respectively. A considerable increase in PD-L1 level was detected in bone tumor tissues at both gene and protein levels that was considerable in osteosarcoma and Ewing sarcoma. A positive correlation was detected regarding the PD-L1 and tumor metastasis and recurrence in osteosarcoma and Ewing sarcoma. The increased IFN-γ level was detected in patients with metastatic, and recurrent osteosarcoma tumors that were in accordance with the level of TGF-β in these samples. The simultaneous elevation of IFN-γ and TGF-β was detected in Ewing sarcoma and GCT, also the CD4 + /CD8 + ratio was decreased significantly in patients with osteosarcoma compared to GCT tumors. The elevated levels of PD-L1, TGF- β, and IFN-γ were associated with bone tumor severity that can provide insights into the possible role of this axis in promoting immune system escape, suppression, and tumor invasion.
Cellular senescence triggers intracellular acidification and lysosomal pH alkalinized via ATP6AP2 attenuation in breast cancer cells
Authors: Li Wei , Kawaguchi Kosuke , Tanaka Sunao , He Chenfeng , Maeshima Yurina , Suzuki Eiji , Toi Masakazu 
Published: November 2023

AbstractSeveral chemotherapeutic drugs induce senescence in cancer cells; however, the mechanisms underlying intracellular pH dysregulation in senescent cells remain unclear. Adenosine triphosphatase H+ transporting accessory protein 2 (ATP6AP2) plays a critical role in maintaining pH homeostasis in cellular compartments. Herein, we report the regulatory role of ATP6AP2 in senescent breast cancer cells treated with doxorubicin (Doxo) and abemaciclib (Abe). A decline in ATP6AP2 triggers aberrant pH levels that impair lysosomal function and cause immune profile changes in senescent breast cancer cells. Doxo and Abe elicited a stable senescent phenotype and altered the expression of senescence-related genes. Additionally, senescent cells show altered inflammatory and immune transcriptional profiles due to reprogramming of the senescence-associated secretory phenotype. These findings elucidate ATP6AP2-mediated cellular pH regulation and suggest a potential link in immune profile alteration during therapy-induced senescence in breast cancer cells, providing insights into the mechanisms involved in the senescence response to anticancer therapy.