bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Mexican dataset of a repetitive transcranial magnetic stimulation clinical trial on cocaine use disorder patients: SUDMEX TMS
Authors: Angeles-Valdez Diego , Rasgado-Toledo Jalil , Villicaña Viviana , Davalos-Guzman Alan , Almanza Cristina , Fajardo-Valdez Alfonso , Alcala-Lozano Ruth , Garza-Villarreal Eduardo A. 
Published: April 2024

AbstractCocaine use disorder (CUD) is a global health problem with severe consequences, leading to behavioral, cognitive, and neurobiological disturbances. While consensus on treatments is still ongoing, repetitive transcranial magnetic stimulation (rTMS) has emerged as a promising approach for medication-resistant disorders, including substance use disorders. In this context, here we present the SUDMEX-TMS, a Mexican dataset from an rTMS clinical trial involving CUD patients. This longitudinal dataset comprises 54 CUD patients (including 8 females) with data collected at five time points: baseline (T0), two weeks (T1), three months (T2), six months (T3) follow-up, and twelve months (T4) follow-up. The clinical rTMS treatment followed a double-blinded randomized clinical trial design (n = 24 sham/30 active) for 2 weeks, followed by an open-label phase. The dataset includes demographic, clinical, and cognitive measures, as well as magnetic resonance imaging (MRI) data collected at all time points, encompassing structural (T1-weighted), functional (resting-state fMRI), and multishell diffusion-weighted (DWI-HARDI) sequences. This dataset offers the opportunity to investigate the impact of rTMS on CUD participants, considering clinical, cognitive, and multimodal MRI metrics in a longitudinal framework.
Chromosome-scale genome assembly and annotation of Cotoneaster glaucophyllus
Authors: Meng Kaikai , Liao Wenbo , Wei Shaolong , Chen Sufang , Li Mingwan , Ma Yongpeng , Fan Qiang 
Published: April 2024

AbstractCotoneaster glaucophyllus is a semi-evergreen plant that blossoms in late summer, producing dense, attractive, fragrant white flowers with significant ornamental and ecological value. Here, a chromosome-scale genome assembly was obtained by integrating PacBio and Illumina sequencing data with the aid of Hi-C technology. The genome assembly was 563.3 Mb in length, with contig N50 and scaffold N50 values of ~6 Mb and ~31 Mb, respectively. Most (95.59%) of the sequences were anchored onto 17 pseudochromosomes (538.4 Mb). We predicted 35,856 protein-coding genes, 1,401 miRNAs, 655 tRNAs, 425 rRNAs, and 795 snRNAs. The functions of 34,967 genes (97.52%) were predicted. The availability of this chromosome-level genome will provide valuable resources for molecular studies of this species, facilitating future research on speciation, functional genomics, and comparative genomics within the Rosaceae family.
Endophytic fungi of Panax sokpayensis produce bioactive ginsenoside Compound K in flask fermentation
Authors: Rai Subecha , Singh Laishram Shantikumar , Shaanker Ramanan Uma , Jeyaram Kumaraswamy , Parija Tithi , Sahoo Dinabandhu 
Published: April 2024

AbstractEndophytes of Panax have the potential to produce their host plant secondary metabolites, ginsenosides. Panax sokpayensis, an endemic traditional medicinal plant of the Sikkim Himalayas was explored for the isolation of endophytic fungi. In the present study, we have isolated 35 endophytic fungal cultures from the rhizome of P. sokpayensis and screened for ginsenosides production by HPLC by comparing the peak retention time with that of standard ginsenosides. The HPLC analysis revealed that out of 35 isolates, the mycelial extracts of four fungal endophytes (PSRF52, PSRF53, PSRF49 and PSRF58) exhibited peaks with a similar retention time of the standard ginsenoside, Compound K (CK). LC–ESI–MS/MS analysis led to the confirmation of ginsenoside CK production by the four fungal endophytes which showed a compound with m/z 639.6278, similar to that of standard ginsenoside CK with yield in potato dextrose broth flask fermentation ranging from 0.0019 to 0.0386 mg/g of mycelial mass in dry weight basis. The four prospective fungal endophyte isolates were identified as Thermothielavioides terrestris PSRF52, Aspergillus sp. PSRF49, Rutstroemiaceae sp. strain PSRF53, and Phaeosphaeriaceae sp. strain PSRF58 based on ITS sequencing. The present finding highlights the need for further study on growth optimization and other culture parameters to exploit the endophytes as an alternative source for ginsenoside CK production.
Modeling health and well-being measures using ZIP code spatial neighborhood patterns
Authors: Jain Abhi , LaValley Michael , Dukes Kimberly , Lane Kevin , Winter Michael , Spangler Keith R. , Cesare Nina , Wang Biqi , Rickles Michael , Mohammed Shariq 
Published: April 2024

AbstractIndividual-level assessment of health and well-being permits analysis of community well-being and health risk evaluations across several dimensions of health. It also enables comparison and rankings of reported health and well-being for large geographical areas such as states, metropolitan areas, and counties. However, there is large variation in reported well-being within such large spatial units underscoring the importance of analyzing well-being at more granular levels, such as ZIP codes. In this paper, we address this problem by modeling well-being data to generate ZIP code tabulation area (ZCTA)-level rankings through spatially informed statistical modeling. We build regression models for individual-level overall well-being index and scores from five subscales (Physical, Financial, Social, Community, Purpose) using individual-level demographic characteristics as predictors while including a ZCTA-level spatial effect. The ZCTA neighborhood information is incorporated by using a graph Laplacian matrix; this enables estimation of the effect of a ZCTA on well-being using individual-level data from that ZCTA as well as by borrowing information from neighboring ZCTAs. We deploy our model on well-being data for the U.S. states of Massachusetts and Georgia. We find that our model can capture the effects of demographic features while also offering spatial effect estimates for all ZCTAs, including ones with no observations, under certain conditions. These spatial effect estimates provide community health and well-being rankings of ZCTAs, and our method can be deployed more generally to model other outcomes that are spatially dependent as well as data from other states or groups of states.
Task demand mediates the interaction of spatial and temporal attention
Authors: Palmieri Helena , Carrasco Marisa 
Published: April 2024

AbstractPsychophysical studies typically test attentional mechanisms in isolation, but in everyday life they interact to optimize human behavior. We investigated whether spatial and temporal attention interact in two orientation discrimination experiments that vary in task demand. We manipulated temporal and spatial attention separately and conjointly with well-established methods for testing each spatial or temporal attention. We assessed sensitivity (d′) and reaction time for every combination of spatial and timing cues, each of which was valid, neutral, or invalid. Spatial attention modulated sensitivity (d′) and speed (reaction time) across temporal attention conditions. Temporal attention modulated sensitivity and speed under high- but not low- task demands. Furthermore, spatial and temporal attention interacted for the high-demand task. This study reveals that task demand matters; in a simple task spatial attention suffices to improve performance, whereas in a more demanding task both spatial and temporal attention interact to boost performance, albeit in a subadditive fashion.
Impacts of commodity prices and governance on the expansion of tropical agricultural frontiers
Authors: Miranda Javier , Britz Wolfgang , Börner Jan 
Published: April 2024

AbstractDeforestation in the tropics remains a significant global challenge linked to carbon emissions and biodiversity loss. Agriculture, forestry, wildfires, and urbanization have been repeatedly identified as main drivers of tropical deforestation. Understanding the underlying mechanisms behind these direct causes is crucial to navigate the multiple tradeoffs between competing forest uses, such as food and biomass production (SDG 2), climate action (SDG 13), and life on land (SDG 15). This paper develops and implements a global-scale empirical approach to quantify two key factors affecting land use decisions at tropical forest frontiers: agricultural commodity prices and national governance. It relies on data covering the period 2004–2015 from multiple public sources, aggregated to countries and agro-ecological zones. Our analysis confirms the persistent influence of commodity prices on agricultural land expansion, especially in forest-abundant regions. Economic and environmental governance quality co-determines processes of expansion and contraction of agricultural land in the tropics, yet at much smaller magnitudes than other drivers. We derive land supply elasticities for direct use in standard economic impact assessment models and demonstrate that our results make a difference in a Computable General Equilibrium framework.
Mining genomic regions associated with agronomic and biochemical traits in quinoa through GWAS
Authors: Rahman Hifzur , Vikram Prashant , Hu Yulan , Asthana Sugandha , Tanaji Abhinav , Suryanarayanan Padmaktshni , Quadros Chris , Mehta Lovely , Shahid Mohammed , Gkanogiannis Anestis , Thushar Sumitha , Balazadeh Salma , Mueller-Roeber Bernd , Becerra Lopez-Lavalle Luis Augusto , Wei Tong , Singh Rakesh Kumar 
Published: April 2024

AbstractQuinoa (Chenopodium quinoa Willd.), an Andean crop, is a facultative halophyte food crop recognized globally for its high nutritional value and plasticity to adapt to harsh conditions. We conducted a genome-wide association study on a diverse set of quinoa germplasm accessions. These accessions were evaluated for the following agronomic and biochemical traits: days to 50% flowering (DTF), plant height (PH), panicle length (PL), stem diameter (SD), seed yield (SY), grain diameter (GD), and thousand-grain weight (TGW). These accessions underwent genotyping-by-sequencing using the DNBSeq-G400R platform. Among all evaluated traits, TGW represented maximum broad-sense heritability. Our study revealed average SNP density of ≈ 3.11 SNPs/10 kb for the whole genome, with the lowest and highest on chromosomes Cq1B and Cq9A, respectively. Principal component analysis clustered the quinoa population in three main clusters, one clearly representing lowland Chilean accessions, whereas the other two groups corresponded to germplasm from the highlands of Peru and Bolivia. In our germplasm set, we estimated linkage disequilibrium decay to be ≈ 118.5 kb. Marker-trait analyses revealed major and consistent effect associations for DTF on chromosomes 3A, 4B, 5B, 6A, 7A, 7B and 8B, with phenotypic variance explained (PVE) as high as 19.15%. Nine associations across eight chromosomes were also found for saponin content with 20% PVE by qSPN5A.1. More QTLs were identified for PL and TGW on multiple chromosomal locations. We identified putative candidate genes in the genomic regions associated with DTF and saponin content. The consistent and major-effect genomic associations can be used in fast-tracking quinoa breeding for wider adaptation across marginal environments.
Dexrazoxane inhibits the growth of esophageal squamous cell carcinoma by attenuating SDCBP/MDA-9/syntenin-mediated EGFR-PI3K-Akt pathway activation
Authors: Du Ruijuan , Xiao Nan , Han Li , Guo KeLei , Li Kai , Chen Zhiguo , Zhang Hui , Zhou Zijun , Huang Yunlong , Zhao Xulin , Bian Hua 
Published: April 2024

AbstractSyndecan-binding protein (SDCBP) was reported to stimulate the advancement of esophageal squamous cell carcinoma (ESCC) and could potentially be a target for ESCC treatment. There is a growing corpus of research on the anti-tumor effects of iron chelators; however, very few studies have addressed the involvement of dexrazoxane in cancer. In this study, structure-based virtual screening was employed to select drugs targeting SDCBP from the Food and Drug Administration (FDA)-approved drug databases. The sepharose 4B beads pull-down assay revealed that dexrazoxane targeted SDCBP by interacting with its PDZ1 domain. Additionally, dexrazoxane inhibited ESCC cell proliferation and anchorage-independent colony formation via SDCBP. ESCC cell apoptosis and G2 phase arrest were induced as measured by the flow cytometry assay. Subsequent research revealed that dexrazoxane attenuated the binding ability between SDCBP and EGFR in an immunoprecipitation assay. Furthermore, dexrazoxane impaired EGFR membrane localization and inactivated the EGFR/PI3K/Akt pathway. In vivo, xenograft mouse experiments indicated that dexrazoxane suppressed ESCC tumor growth. These data indicate that dexrazoxane might be established as a potential anti-cancer agent in ESCC by targeting SDCBP.
Bayesian geochemical correlation and tomography
Authors: Bloem Hugo , Curtis Andrew 
Published: April 2024

AbstractTo accurately reconstruct palaeoenvironmental change through time it is important to determine which rock samples were deposited contemporaneously at different sites or transects, as erroneous correlation may lead to incorrectly inferred processes and rates. To correlate samples, current practice interpolates geological age between datable units along each transect, then temporal signatures observed in geochemical logs are matched between transects. Unfortunately spatiotemporally variable and unknown rates of sedimentary deposition create highly nonlinear space-time transforms, significantly altering apparent geochemical signatures. The resulting correlational hypotheses are also untestable against independent transects, because correlations have no spatially-predictive power. Here we use geological process information stored within neural networks to correlate spatially offset logs nonlinearly and geologically. The same method creates tomographic images of geological age and geochemical signature across intervening rock volumes. Posterior tomographic images closely resemble the true depositional age throughout the inter-transect volume, even for scenarios with long hiatuses in preserved geochemical signals. Bayesian probability distributions describe data-consistent variations in the results, showing that centred summary statistics such as mean and variance do not adequately describe correlational uncertainties. Tomographic images demonstrate spatially predictive power away from geochemical transects, creating novel hypotheses attributable to each geochemical correlation which are testable against independent data.
Malignant features of minipig melanomas prior to spontaneous regression
Authors: Débare Héloïse , Blanc Fany , Piton Guillaume , Leplat Jean-Jacques , Vincent-Naulleau Silvia , Rivière Julie , Vilotte Marthe , Marthey Sylvain , Lecardonnel Jérôme , Coville Jean-Luc , Estellé Jordi , Rau Andrea , Bourneuf Emmanuelle , Egidy Giorgia 
Published: April 2024

AbstractIn MeLiM minipigs, melanomas develop around birth, can metastasize, and have histopathologic characteristics similar to humans. Interestingly, MeLiM melanomas eventually regress. This favorable outcome raises the question of their malignancy, which we investigated. We clinically followed tens of tumors from onset to first signs of regression. Transcriptome analysis revealed an enrichment of all cancer hallmarks in melanomas, although no activating or suppressing somatic mutation were found in common driver genes. Analysis of tumor cell genomes revealed high mutation rates without UV signature. Canonical proliferative, survival and angiogenic pathways were detected in MeLiM tumor cells all along progression stages. Functionally, we show that MeLiM melanoma cells are capable to grow in immunocompromised mice, with serial passages and for a longer time than in MeLiM pigs. Pigs set in place an immune response during progression with dense infiltration by myeloid cells while melanoma cells are deficient in B2M expression. To conclude, our data on MeLiM melanomas reveal several malignancy characteristics. The combination of these features with the successful spontaneous regression of these tumors make it an outstanding model to study an efficient anti-tumor immune response.
Failure mechanism and bearing force of CFRP strengthened square hollow section under compressive load
Authors: Huang Can , Wei Yan-hui , Ma Ke-jian , Liu Zhuo-qun , Tian Peng-gang , Zhao Bing-zhen 
Published: April 2024

AbstractCarbon fibre-reinforced polymer (CFRP) plates can efficiently repair or enhance the mechanical properties of the square hollow section. However, the loading end of such a CFRP-strengthened member is prone to local bearing failure under compressive load. Given this limitation, an innovative CFRP-plate-strengthened square hollow section composite member (CFRP-SHSCM) was raised, and the thick-walled section was welded on both ends of the thin-walled steel column. The mechanical properties of CFRP-SHSCMs were investigated through parameter finite element (FE) analysis, focusing on the influence of the amount of CFRP layers (nc), the slenderness ratio (λ), the initial geometric imperfections (v0), the CFRP layouts (2S and 4S) and the length of the exposed steel column (Le). The load–displacement curves, the bearing force, and typical failure modes were also acquired. Results indicated that with increasing nc and v0, and decreasing λ, the conventional CFRP-SHSCMs were prone to local bearing failure with poor ductility, leading to the insufficient use of the CFRP plate, in contrast, the improved CFRP-SHSCMs primarily underwent overall buckling failure and exhibited better bearing force and ductility. Finally, the modified Perry-Robertson formula was put forward to predict the ultimate load of the CFRP-SHSCMs. The coefficients of variation between the FE simulation and the theoretical results were 0.00436 and 0.0292, respectively.
Insights into the cumulative effect of Colletotrichum gloeosporioides and Fusarium acutatum causing anthracnose-twister disease complex of onion
Authors: Dutta Ram , Jayalakshmi K. , Kumar Satish , Radhakrishna A. , Manjunathagowda Dalasanuru Chandregowda , Sharath M. N. , Gurav Vishal S. , Mahajan Vijay 
Published: April 2024

AbstractColletotrichum is an important plant pathogenic fungi that causes anthracnose/-twister disease in onion. This disease was prevalent in the monsoon season from August to November months and the symptoms were observed in most of the fields. This study aimed to investigate the pathogenicity and cumulative effect, if any of Colletotrichum gloeosporioides and Fusarium acutatum. The pot experiment was laid out to identify the cause responsible for inciting anthracnose-twister disease, whether the Colletotrichum or Fusarium or both, or the interaction of pathogens and GA3. The results of the pathogenicity test confirmed that C. gloeosporioides and F. acutatum are both pathogenic. C. gloeosporioides caused twisting symptoms independently, while F.acutatum independently caused only neck elongation. The independent application of GA3 did not produce any symptoms, however, increased the plant height. The combined treatment of C. gloeosporioides and F. acutatum caused twisting, which enhanced upon interaction with GA3 application giving synergistic effect. The acervuli were found in lesions infected with C. gloeosporioides after 8 days of inoculation on the neck and leaf blades. Symptoms were not observed in untreated control plants. Koch's postulates were confirmed by reisolating the same pathogens from the infected plants.
Nomogram for predicting in-hospital mortality in trauma patients undergoing resuscitative endovascular balloon occlusion of the aorta: a retrospective multicenter study
Authors: Yu Byungchul , Cho Jayun , Kang Byung Hee , Kim Kyounghwan , Kim Dong Hun , Chang Sung Wook , Jung Pil Young , Heo Yoonjung , Kang Wu Seong 
Published: April 2024

AbstractRecently, resuscitative endovascular balloon occlusion of the aorta (REBOA) had been introduced as an innovative procedure for severe hemorrhage in the abdomen or pelvis. We aimed to investigate risk factors associated with mortality after REBOA and construct a model for predicting mortality. This multicenter retrospective study collected data from 251 patients admitted at five regional trauma centers across South Korea from 2015 to 2022. The indications for REBOA included patients experiencing hypovolemic shock due to hemorrhage in the abdomen, pelvis, or lower extremities, and those who were non-responders (systolic blood pressure (SBP) < 90 mmHg) to initial fluid treatment. The primary and secondary outcomes were mortality due to exsanguination and overall mortality, respectively. After feature selection using the least absolute shrinkage and selection operator (LASSO) logistic regression model to minimize overfitting, a multivariate logistic regression (MLR) model and nomogram were constructed. In the MLR model using risk factors selected in the LASSO, five risk factors, including initial heart rate (adjusted odds ratio [aOR], 0.99; 95% confidence interval [CI], 0.98–1.00; p = 0.030), initial Glasgow coma scale (aOR, 0.86; 95% CI 0.80–0.93; p < 0.001), RBC transfusion within 4 h (unit, aOR, 1.12; 95% CI 1.07–1.17; p < 0.001), balloon occlusion type (reference: partial occlusion; total occlusion, aOR, 2.53; 95% CI 1.27–5.02; p = 0.008; partial + total occlusion, aOR, 2.04; 95% CI 0.71–5.86; p = 0.187), and post-REBOA systolic blood pressure (SBP) (aOR, 0.98; 95% CI 0.97–0.99; p < 0.001) were significantly associated with mortality due to exsanguination. The prediction model showed an area under curve, sensitivity, and specificity of 0.855, 73.2%, and 83.6%, respectively. Decision curve analysis showed that the predictive model had increased net benefits across a wide range of threshold probabilities. This study developed a novel intuitive nomogram for predicting mortality in patients undergoing REBOA. Our proposed model exhibited excellent performance and revealed that total occlusion was associated with poor outcomes, with post-REBOA SBP potentially being an effective surrogate measure.