bluuebunny/crossref_metadata_2025_split huggingface dataset:
Omics approaches to understand the MADS-box gene family in common bean (Phaseolus vulgaris L.) against drought stress
Authors: Okay Aybüke , Kırlıoğlu Tarık , Durdu Yasin Şamil , Akdeniz Sanem Şafak , Büyük İlker , Aras E.Sümer 
Published: January 2024

AbstractMADS-box genes are known to play important roles in diverse aspects of growth/devolopment and stress response in several plant species. However, no study has yet examined about MADS-box genes in P. vulgaris. In this study, a total of 79 PvMADS genes were identified and classified as type I and type II according to the phylogenetic analysis. While both type I and type II PvMADS classes were found to contain the MADS domain, the K domain was found to be present only in type II PvMADS proteins, in agreement with the literature. All chromosomes of the common bean were discovered to contain PvMADS genes and 17 paralogous gene pairs were identified. Only two of them were tandemly duplicated gene pairs (PvMADS-19/PvMADS-23 and PvMADS-20/PvMADS-24), and the remaining 15 paralogous gene pairs were segmentally duplicated genes. These duplications were found to play an important role in the expansion of type II PvMADS genes. Moreover, the RNAseq and RT-qPCR analyses showed the importance of PvMADS genes in response to drought stress in P. vulgaris.
Child temperament as a longitudinal predictor of mother–adolescent interaction quality: are effects independent of child and maternal mental health?
Authors: Fleck Leonie , Fuchs Anna , Williams Katharina , Moehler Eva , Resch Franz , Koenig Julian , Kaess Michael 
Published: January 2024

AbstractAdaptive parent–child interaction plays a major role in healthy child development. Caregiver mental health problems can negatively impact parent–child interaction. In turn, interactional quality is often studied as a predictor of child outcome. However, child characteristics supposedly shape parent–child interactions as well. Given associations between child and caregiver mental health and child temperament, this study aimed at differentiating their effects on dyadic interaction quality in adolescence. Child temperament and character at age 5 were investigated as longitudinal predictors of observed mother–adolescent interactional quality at age 14 in a community sample (N = 76). It was examined whether these effects were independent of maternal and child mental health and earlier dysfunctional interaction. Lower novelty seeking, higher reward dependence, and higher cooperativeness separately predicted higher dyadic interactional quality at age 14. Controlling regressions for dysfunctional interaction at age 5, which was a significant negative predictor of later interactional quality, cancelled out the effects of novelty seeking and cooperativeness. Past or concurrent maternal or child psychopathology did not explain variance in mother–adolescent interaction. Applying backward selection, a model including reward dependence and dysfunctional interaction at age 5 and concurrent maternal stress showed the best fit for explaining dyadic interaction quality. Results suggest that enduring rather than transient child features predict interactional quality in a community sample. Effects of temperament are not better explained by those of psychopathology, but a combination of child, maternal, and dyadic features predicted dyadic behaviour best. Selective prevention should target parenting in the context of challenging child characteristics specifically.
Pd-H as an irreplaceable model system for the study of hydrogen electrosorption in aqueous and non-aqueous electrolytes
Authors: Hubkowska K. , Pająk M. , Monikowska D. , Czerwiński A. 
Published: January 2024

AbstractEven though Pd-H system has been known since the nineteenth century, it is still of interest to scientists. Pd thin film electrode (called as a Limited Volume Electrode – LVE) is able to electrosorb hydrogen form aqueous (acid, base) and non-aqueous electrolytes (e.g. ionic liquids). Therefore Pd-H is an irreplaceable model system for the study of hydrogen electrosorption in different media. The paper presents: (1) short overview of the study of hydrogen sorption in Pd, (2) the detailed description of the electrochemical measurement methods and (3) the equations for the determination of hydrogen electrosorption charges needed to hydrogen electrosorption isotherms creation. The presented approach can be applied for laboratory work. The results show that Pd-LVE can be effectively used as a model system before the studies of multicomponent hydrogen storage alloys (e.g. AB5 alloys).
Graphical abstract
Continuum modelling of a just-saturated inertial column collapse: capturing fluid-particle interaction
Authors: Webb William , Turnbull Barbara , Johnson Chris 
Published: January 2024

Abstract
This work presents a simple two-phase flow model to analyse a series of axisymmetric granular column collapse tests conducted under elevated gravitational accelerations. These columns were prepared with a just-saturated condition, where the granular pores were filled with a Newtonian fluid up to the column’s free surface. In this configuration, unlike the fully submerged case, air-water-grain contact angles may be important to flow dynamics. The interaction between a Newtonian fluid phase and a monodispersed inertial particle phase was captured by an inter-phase interaction term that considers the drag between the two phases as a function of the particle phase porosity. While this experimental setup has broad applications in understanding various industrial processes and natural phenomena, the focus of this study is on its relevance to predicting the motion of debris flows. Debris flows are challenging to model due to their temporally evolving composition, which can lead to the development of complex numerical models that become intractable. The developed numerical scheme in this study reasonably reproduces the particle-size and gravitational acceleration dependencies observed within the experimental runout and basal fluid pressure dissipation data. However, discrepancies between the model and physical experiments primarily arise from the assumption of modelling the granular phase as a continuum, which becomes less appropriate as particle size increases.

Graphical Abstract
Individualized foveated rendering with eye-tracking head-mounted display
Authors: Kim Jihwan , Kim Jejoong , Jung Myeongul , Kwon Taesoo , Kim Kwanguk Kenny 
Published: January 2024

AbstractFoveated rendering (FR) technology is designed to improve the efficiency of graphical rendering processes. In rendering, individualized approaches can help to balance users’ experiences of visual quality and saving computational resource. However, previous studies have not rigorously examined it related with the FR techniques. To address this issue, we developed an individualized FR (IFR) method using different central vision sizes and peripheral vision resolutions across individuals in virtual reality. In three user studies with 88 participants who were divided into groups designated as “large central area (LCA)” and “small central area (SCA),” the effects of IFR were compared with those of using the full-resolution condition and the average FR condition. The results indicate that the LCA group experienced higher visual quality under the IFR and full-resolution conditions than under the average FR condition. In contrast, the SCA group exhibited comparable levels of dependent measures between the IFR and average FR conditions, but both were lower than those of the full-resolution condition. We also evaluated the computational benefits of the proposed IFR method, and the results demonstrated the effectiveness of our approach in saving resources across the two groups. Although lower-bound adjustments may be required for some users, our overall results suggest that IFR is a malleable technology for enhancing rendering efficiency in virtual reality.
Dural arteriovenous fistula presenting with recurrent focal status epilepticus and lateralised periodic epileptiform discharges
Authors: Dunbabin Isobel , Banez Ramon M. , de Souza Aaron 
Published: January 2024

Abstract
Background
Dural arteriovenous fistulae (dAVF) are relatively infrequently encountered, and status epilepticus (SE) and lateralised periodic discharges (LPDs) on electroencephalography (EEG) have only rarely been associated with these arteriovenous malformations.

Methods
We present a patient with recurrent presentations with focal SE, aphasia and other focal deficits of cortical function and ictal and peri-ictal LPDs on serial EEG, who was shown to have a left hemispheric dAVF associated with left transverse and sigmoid sinus thrombosis. Seizures proved refractory to four anti-seizure medications but became more amenable to control after successful embolisation of the dAVF, with subsequent resolution of the focal cortical deficits. We discuss the co-occurrence of SE and LPDs with dAVF and review previously reported cases with this rare association.

Conclusions
Our report supports a causative relationship between dAVF and focal SE, manifesting as ictal LPDs on EEG, and highlights the importance of active dAVF management in achieving seizure control. The relatively good patient outcome contrasts to the few similar case reports. Whilst rare, it is important to consider dAVF as a potentially treatable condition underlying new-onset seizures, including SE.
Transcriptomic Response of the Atlantic Surfclam (Spisula solidissima) to Acute Heat Stress
Authors: Acquafredda Michael , Guo Ximing , Munroe Daphne 
Published: January 2024

AbstractThere is clear evidence that the oceans are warming due to anthropogenic climate change, and the northeastern coast of USA contains some of the fastest warming areas. This warming is projected to continue with serious biological and social ramifications for fisheries and aquaculture. One species particularly vulnerable to warming is the Atlantic surfclam (Spisula solidissima). The surfclam is a critically important species, linking marine food webs and supporting a productive, lucrative, and sustainable fishery. The surfclam is also emerging as an attractive candidate for aquaculture diversification, but the warming of shallow coastal farms threatens the expansion of surfclam aquaculture. Little is known about the adaptive potential of surfclams to cope with ocean warming. In this study, the surfclam transcriptome under heat stress was examined. Two groups of surfclams were subjected to heat stress to assess how artificial selection may alter gene expression. One group of clams had been selected for greater heat tolerance (HS) and the other was composed of random control clams (RC). After a 6-h exposure to 16 or 29 °C, gill transcriptome expression profiles of the four temperature/group combinations were determined by RNA sequencing and compared. When surfclams experienced heat stress, they exhibited upregulation of heat shock proteins (HSPs), inhibitors of apoptosis (IAPs), and other stress-response related genes. RC clams differentially expressed 1.7 times more genes than HS clams, yet HS clams had a stronger response of key stress response genes, including HSPs, IAPs, and genes involved with mitigating oxidative stress. The findings imply that the HS clams have a more effective response to heat stress after undergoing the initial selection event due to genetic differences created by the selection, epigenetic memory of the first heat shock, or both. This work provides insights into how surfclams adapt to heat stress and should inform future breeding programs that attempt to breed surfclam for greater heat tolerance, and ultimately bring greater resiliency to shellfish farms.
Urine albumin-to-creatinine ratio diurnal variation rate predicts outcomes in idiopathic membranous nephropathy
Authors: Chen Xiaoqing , Zhang Yong , Yan Liqun , Xie Yangbin , Li Shujing , Zhuang Yongze , Wang Liping 
Published: January 2024

Abstract
Background
Idiopathic membranous nephropathy (IMN) is a leading cause of end-stage renal disease (ESRD). The purpose of this study was to evaluate whether urinary albumin-to-creatinine ratio (UACR) diurnal variation rate calculated by spot urinary protein test predicts 1-year nephrotic outcomes as a biomarker of proteinuria severity in patients with IMN.

Methods
Patients’ baseline demographics, blood and urinary biomarkers, and clinical and pathological characteristics were collected retrospectively. Urine samples were collected at 7:00 (before breakfast) and 19:00 (after dinner) to calculate the UACR diurnal variation rate. A prediction model for no remission (NR) was developed statistically based on differences between prognosis groups. Receiver operating characteristic curve (ROC) analysis was performed to evaluate prediction abilities and determine optimal cut-off points of the model and UACR diurnal variation rate alone.

Results
The formula for calculating the probability of NR was exp(L)/(1 + exp(L)), where the linear predictor L =  – 22.038 + 0.134 × Age (years) + 0.457 × 24-h urinary protein + 0.511 × blood urea nitrogen (BUN) + 0.014 × serum uric acid (SUA) + 2.411 if glomerular sclerosis + 0.816 × fasting blood glucose (FBG)-0.039 × UACR diurnal variation rate (%). Optimal cut-off points for NR prediction by the final model and UACR diurnal variation rate alone were 0.331 and 58.5%, respectively. Sensitivity and specificity were 0.889 and 0.859 for the final model, and 0.926 and 0.676 for UACR diurnal variation rate alone.

Conclusion
UACR diurnal variation using spot urinary protein is a simpler way to predict nephrotic outcomes and is a highly sensitive screening tool for identifying patients who should undergo further comprehensive risk assessment.
Recent nanotheranostic approaches in cancer research
Authors: Gupta Deepshikha , Roy Priyanka , Sharma Rishabh , Kasana Richa , Rathore Pragati , Gupta Tejendra Kumar 
Published: January 2024

AbstractHumanity is suffering from cancer which has become a root cause of untimely deaths of individuals around the globe in the recent past. Nanotheranostics integrates therapeutics and diagnostics to monitor treatment response and enhance drug efficacy and safety. We hereby propose to discuss all recent cancer imaging and diagnostic tools, the mechanism of targeting tumor cells, and current nanotheranostic platforms available for cancer. This review discusses various nanotheranostic agents and novel molecular imaging tools like MRI, CT, PET, SPEC, and PAT used for cancer diagnostics. Emphasis is given to gold nanoparticles, silica, liposomes, dendrimers, and metal-based agents. We also highlight the mechanism of targeting the tumor cells, and the limitations of different nanotheranostic agents in the field of research for cancer treatment. Due to the complexity in this area, multifunctional and hybrid nanoparticles functionalized with targeted moieties or anti-cancer drugs show the best feature for theranostics that enables them to work on carrying and delivering active materials to the desired area of the requirement for early detection and diagnosis. Non-invasive imaging techniques have a specificity of receptor binding and internalization processes of the nanosystems within the cancer cells. Nanotheranostics may provide the appropriate medicine at the appropriate dose to the appropriate patient at the appropriate time.
Graphical abstract
Evaluation of NTRK expression and fusions in a large cohort of early-stage lung cancer
Authors: Dyrbekk Anne Pernille Harlem , Warsame Abdirashid Ali , Suhrke Pål , Ludahl Marianne Odnakk , Zecic Nermin , Moe Joakim Oliu , Lund-Iversen Marius , Brustugun Odd Terje 
Published: January 2024

AbstractTropomyosin receptor kinases (TRK) are attractive targets for cancer therapy. As TRK-inhibitors are approved for all solid cancers with detectable fusions involving the Neurotrophic tyrosine receptor kinase (NTRK)-genes, there has been an increased interest in optimizing testing regimes. In this project, we wanted to find the prevalence of NTRK fusions in a cohort of various histopathological types of early-stage lung cancer in Norway and to investigate the association between TRK protein expression and specific histopathological types, including their molecular and epidemiological characteristics. We used immunohistochemistry (IHC) as a screening tool for TRK expression, and next-generation sequencing (NGS) and fluorescence in situ hybridization (FISH) as confirmatory tests for underlying NTRK-fusion. Among 940 cases, 43 (4.6%) had positive TRK IHC, but in none of these could a NTRK fusion be confirmed by NGS or FISH. IHC-positive cases showed various staining intensities and patterns including cytoplasmatic or nuclear staining. IHC-positivity was more common in squamous cell carcinoma (LUSC) (10.3%) and adenoid cystic carcinoma (40.0%), where the majority showed heterogeneous staining intensity. In comparison, only 1.1% of the adenocarcinomas were positive. IHC-positivity was also more common in men, but this association could be explained by the dominance of LUSC in TRK IHC-positive cases. Protein expression was not associated with differences in time to relapse or overall survival. Our study indicates that NTRK fusion is rare in early-stage lung cancer. Due to the high level of false positive cases with IHC, Pan-TRK IHC is less suited as a screening tool for NTRK-fusions in LUSC and adenoid cystic carcinoma.
Second-line tislelizumab versus chemotherapy in Japanese patients with advanced or metastatic esophageal squamous cell carcinoma: subgroup analysis from RATIONALE-302
Authors: Hara Hiroki , Satoh Taroh , Kojima Takashi , Tsushima Takahiro , Sunakawa Yu , Okada Morihito , Ding Ningning , Wu Hongqian , Li Liyun , Yu Tian , Barnes Gisoo , Kato Ken 
Published: January 2024

Abstract
Background
Esophageal squamous cell carcinoma (ESCC) has a poor prognosis, with limited second-line systemic therapy options, and represents an increasing disease burden in Japan. In the phase 3 RATIONALE-302 study, the anti-programmed cell death protein 1 antibody, tislelizumab, significantly improved overall survival (OS) versus chemotherapy as second-line treatment for advanced/metastatic ESCC. Here, we report the Japanese patient subgroup results.

Methods
Patients with advanced/metastatic ESCC, with disease progression during/after first-line systemic therapy were randomized 1:1 to open-label tislelizumab 200 mg every 3 weeks or investigator’s choice of chemotherapy (paclitaxel/docetaxel). Efficacy and safety were assessed in all randomized Japanese patients.

Results
The Japanese subgroup comprised 50 patients (n = 25 per arm). Tislelizumab improved OS versus chemotherapy (median: 9.8 vs. 7.6 months; HR 0.59; 95% CI 0.31, 1.12). Among patients with programmed death-ligand 1 score ≥ 10%, median OS was 12.5 months with tislelizumab (n = 10) versus 2.9 months with chemotherapy (n = 6) (HR 0.31; 95% CI 0.09, 1.03). Tislelizumab improved progression-free survival versus chemotherapy (median: 3.6 vs. 1.7 months, respectively; HR 0.50; 95% CI 0.27, 0.95). Objective response rate was greater with tislelizumab (32.0%) versus chemotherapy (20.0%), and responses were more durable (median duration of response: 8.8 vs. 2.6 months, respectively). Fewer patients experienced ≥ grade 3 treatment-related adverse events with tislelizumab (24.0%) versus chemotherapy (47.8%). Tislelizumab demonstrated an improvement in health-related quality of life versus chemotherapy.

Conclusions
As second-line therapy for advanced/metastatic ESCC, tislelizumab improved OS versus chemotherapy, with a favorable safety profile, in the Japanese patient subgroup, consistent with the overall population.

Clinical trial registry
ClinicalTrials.gov: NCT03430843.
Using recent genetic history to inform conservation options of two Lesser Caymans iguana (Cyclura nubila caymanensis) populations
Authors: Rogers Thea F. , Stenhouse Ewan H. , Wilson Hannah , Pendaries Morgan , Bruford Michael W. , Goetz Matthias , Orozco-terWengel Pablo 
Published: January 2024

AbstractThe Sister Islands rock iguana (Cyclura nubila caymanensis) is critically endangered and endemic to the Caribbean islands Little Cayman and Cayman Brac. The Cayman Brac population and indeed the entire species is under threat from habitat destruction, invasive species, and anthropogenic impacts on the island. We assessed the genetic diversity, estimated effective population sizes, and tested for differentiation of populations between these two islands to inform potential future translocation should this be needed for the Cayman Brac population. Two mitochondrial DNA markers (cytochrome b and NADH subunit 4) and seven DNA microsatellite markers were used to assess the genetic diversity, genetic structure, demographic history, and effective population size of the two iguana populations. Mitochondrial DNA showed no genetic differentiation between populations; however, we found little to moderate divergence with microsatellites. We compared multiple demographic scenarios and revealed that ongoing gene flow is likely. The demographic history implied a significant genetic bottleneck around 10,000 years ago, coinciding with the sea level rise at the close of the last glacial period, and the start of the Holocene. Estimates of current effective population sizes indicate a small-scale number of breeders on each island of similar magnitude to the census mature population size (between 100 and 800 individuals). The relatively low differentiation between populations supports the possible development of active genetic management plans to manage the declining populations of the Sister Islands rock iguana.
Research Avenues Supporting Embodied Cognition in Learning and Instruction
Authors: Castro-Alonso Juan C. , Ayres Paul , Zhang Shirong , de Koning Björn B. , Paas Fred 
Published: January 2024

AbstractResearch on embodied cognition acknowledges that cognitive processing is tightly coupled with bodily activities and the environment. An important implication for education is that learning can be enhanced when the brain, body, and environment mutually influence each other, such as when making or observing human actions, especially those involving hand gestures and manipulation of objects. In this narrative review article, we describe the evidence from six research avenues that can help explain why embodied cognition can enhance learning and instruction. Through the exploration of these six interconnected research pathways, we aim to make a significant contribution by proposing innovative directions for learning and instruction research, all rooted in the principles of embodied cognition. We establish a direct link between the six research pathways and embodied phenomena, both in the contexts of making and observing human movements. When making human movements, the research avenues explaining the learning benefits due to these movements are physical activity, generative learning, and offloaded cognition. When observing human movements, the avenues researching these phenomena are specialized processor and signaling. Lastly, the research avenue social cognition is integral to both making and observing human movements. With originality in focus, we also include research that has not been traditionally associated with embodied cognition or embodiment. This article offers comprehensive discussions, substantiated with evidence and influencing features, for each of these research avenues. We conclude by outlining the implications of these findings for instruction and charting potential directions for future investigation.