Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-wide association analysis for emergence of deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes for adaptation to dry-direct seeding in the field

Dry direct-seeded rice (dry-DSR) is typically sown deeply to circumvent the need for irrigation, and thus seedling emergence is a crucial trait affecting plant stand and yield. To breed elite cultivars that use less water and are climate-resilient, an understanding of the genomic regions and underlying genes that confer emergence in deeply sown dry-DSR would be highly advantageous. A combined diversity panel of 470 rice accessions (RDP1 plus aus subset of 3K RGP) was evaluated with 2.9 million single nucleotide polymorphisms (SNPs) to identify associations with dry-DSR traits in the field and component traits in a controlled-environment experiment. Using genome-wide association study (GWAS) analyses, we identified 18 unique QTLs on chromosomes 1, 2, 4, 5, 6, 7, 9, 10, and 11, explaining phenotypic variance ranging from 2.6% to 17.8%. Three QTLs, namely, qSOE-1.1, qEMERG-AUS-1.2, and qEMERG-AUS-7.1, were co-located with previously reported QTLs for mesocotyl length. Among the identified QTLs, half were associated with the emergence of aus, and six were unique to the aus genetic group. Based on functional annotation, we identified eleven compelling candidate genes that primarily regulate phytohormone pathways such as cytokinin, auxin, gibberellic acid, and jasmonic acid. Prior studies indicated that these phytohormones play a critical role in mesocotyl length under deep sowing. This study provides new insight into the importance of aus and indica as desirable genetic resources to mine favorable alleles for deep-sowing tolerance in rice. The candidate genes and marker-tagged desirable alleles identified in this study should benefit rice breeding programs directly.
Extreme heat alters the performance of hosts and pathogen

The frequency and intensity of extreme heat in the environment have increased in the last decade. Extreme heating events (EHE) have wide-ranging impacts on biological systems from the molecular to the community level. However, the impacts of EHE have been poorly studied in pathogen–host systems. Here, we explore how EHE affects the interaction among the insect hosts, Osmia cornifrons and Osmia lignaria, and a protozoan pathogen, Crithidia mellificae. We compared changes in the upper limit for locomotion of hosts (Ctmax), thermal boldness (voluntary exposure to Extreme Temperature Zones – ETZ) between healthy and infected host exposed to EHE, and the effect of host Ctmax on pathogen growth rate. Our results showed that 1-day EHE significantly reduced the upper limit for locomotion of hosts by an average of 4 °C in healthy and 7 °C in infected hosts. Further, EHE significantly reduced the protozoan pathogen growth rate. EHE also reduced the hosts’ voluntary exposure to (or transit across) extreme (hot or cold) temperature zones (ETZ). Our results show that EHE reduces both hosts’ heat tolerance and pathogen fitness, and shed light on the implications of EHE on host–pathogen dynamics under warmer world.
Risk prediction in patients with classical low-flow, low-gradient aortic stenosis undergoing surgical intervention

Introduction Classical low-flow, low-gradient aortic stenosis (LFLG-AS) is an advanced stage of aortic stenosis, which has a poor prognosis with medical treatment and a high operative mortality after surgical aortic valve replacement (SAVR). There is currently a paucity of information regarding the current prognosis of classical LFLG-AS patients undergoing SAVR and the lack of a reliable risk assessment tool for this particular subset of AS patients. The present study aims to assess mortality predictors in a population of classical LFLG-AS patients undergoing SAVR. Methods This is a prospective study including 41 consecutive classical LFLG-AS patients (aortic valve area ≤1.0 cm2, mean transaortic gradient <40 mmHg, left ventricular ejection fraction <50%). All patients underwent dobutamine stress echocardiography (DSE), 3D echocardiography, and T1 mapping cardiac magnetic resonance (CMR). Patients with pseudo-severe aortic stenosis were excluded. Patients were divided into groups according to the median value of the mean transaortic gradient (≤25 and >25 mmHg). All-cause, intraprocedural, 30-day, and 1-year mortality rates were evaluated. Results All of the patients had degenerative aortic stenosis, with a median age of 66 (60–73) years; most of the patients were men (83%). The median EuroSCORE II was 2.19% (1.5%–4.78%), and the median STS was 2.19% (1.6%–3.99%). On DSE, 73.2% had flow reserve (FR), i.e., an increase in stroke volume ≥20% during DSE, with no significant differences between groups. On CMR, late gadolinium enhancement mass was lower in the group with mean transaortic gradient >25 mmHg [2.0 (0.0–8.9) g vs. 8.5 (2.3–15.0) g; p = 0.034), and myocardium extracellular volume (ECV) and indexed ECV were similar between groups. The 30-day and 1-year mortality rates were 14.6% and 43.8%, respectively. The median follow-up was 4.1 (0.3–5.1) years. By multivariate analysis adjusted for FR, only the mean transaortic gradient was an independent predictor of mortality (hazard ratio: 0.923, 95% confidence interval: 0.864–0.986, p = 0.019). A mean transaortic gradient ≤25 mmHg was associated with higher all-cause mortality rates (log-rank p = 0.038), while there was no difference in mortality regarding FR status (log-rank p = 0.114). Conclusions In patients with classical LFLG-AS undergoing SAVR, the mean transaortic gradient was the only independent mortality predictor in patients with LFLG-AS, especially if ≤25 mmHg. The absence of left ventricular FR had no prognostic impact on long-term outcomes.
The relationship between working in the “gig” economy and perceived subjective well-being in Western Balkan countries

The combination of accelerated digitalization and the recent COVID-19 crisis has increased the number of remote workers worldwide to unimaginable proportions. Among the large number of remote workers that execute their projects from home, there is a significant number of permanently self-employed remote workers, usually referred to as freelancers. Despite the importance of this kind of business activity for modern project management society, perceived drivers of freelancing are still unknown. The goal of this paper was to shed some light on the general subjective well-being of freelancing activity and investigate differences concerning gender, age, and education. The study was performed in late 2020 and included 471 freelancers from Serbia, Bosnia and Herzegovina, Macedonia, and Montenegro that participated in an online questionnaire evaluating their subjective well-being while participating in the “gig” economy. Factor analysis was used as a primary statistical method and two major groups were identified: (1) Impact of working from home on a freelancer’s personal life and health and (2) Fulfillment of expectations in the economic and professional sense. Gender was found not to be significant for overall work satisfaction. However, older freelancers proved to be more satisfied with the fulfillment of economic and professional expectations, which correlate with years of professional experience. Another conclusion is that more educated freelancers are generally less satisfied with both groups of drivers - fulfillment of personal life and professional expectations. Understanding how the combination of occupations, technological infrastructure, and demographic characteristics in the region has affected the well-being of freelancers may help policymakers and organization owners, as well as future entrepreneurs, better prepare for this model of work in the future. It also increases the possibility of exploring individual dimensions of wellbeing useful for targeting interventions at the level of each country separately. In line with this, the present study contributes to the existing body of knowledge and the impact of hybrid models of work on the subjective well-being of workers in the “gig” economy.
Safety profile of vascular endothelial growth factor receptor tyrosine-kinase inhibitors in pediatrics: a pharmacovigilance disproportionality analysis

Introduction: existing research on children consists primarily of phase I/II clinical trials for VEGFR-TKI. System reports of safety on the use of VEGFR-TKI in pediatrics are lacking. Aim: to investigate the safety profiles of VEGFR-TKI in pediatrics via the FDA Adverse Event Reporting System (FAERS). Method: data regarding VEGFR-TKIs were extracted from the FAERS between 2004Q1 to 2022Q3 and categorized by the Medical Dictionary for Regulatory Activities (MedDRA). Population characteristics were analyzed, and reporting odds ratio (ROR) was performed to identify risk signals associated with VEGFR-TKI. Results: 53,921 cases containing 561 children were identified in the database from 18 May 2005, to 30 September 2022. Among those in the system organ class, skin, subcutaneous tissue disorders, and blood and lymphatic system disorders in pediatrics contributed to over 140 cases. Palmar-plantar eythrodysesthesia syndrome (PPES) in VEGFR-TKI presented the most significant 340.9 (95% 229.2–507.0). And pneumothorax also gave a high reporting odds ratio of 48.9 (95% 34.7–68.9). For a specific drug, musculoskeletal pain gave a ROR of 78.5 (95% 24.4–252.6) in cabozantinib and oesophagitis in lenvatinib with a ROR of 95.2 (95% 29.5–306.9). Additionally, hypothyroidism presented a high signal, especially sunitinib, with a ROR of 107.8 (95% 37.6–308.7). Conclusion: the present study explored the safety profile of VEGFR-TKI in pediatrics using the FAERS database. Multiple skin and subcutaneous tissue disorders, as well as blood and lymphatic system disorders, were common VEGFR-TKI-related AEs in system organ class. No serious hepatobiliary AEs were detected. For the specific AEs, PPES and pneumothorax were VEGFR-TKI-related AEs that presented significantly higher signals than those in the general population.
Coexistence of blaIMP-4, blaNDM-1 and blaOXA-1 in blaKPC-2-producing Citrobacter freundii of clinical origin in China

Purpose To explore the genetic characteristics of the IMP-4, NDM-1, OXA-1, and KPC-2 co-producing multidrug-resistant (MDR) clinical isolate, Citrobacter freundii wang9. Methods MALDI-TOF MS was used for species identification. PCR and Sanger sequencing analysis were used to identify resistance genes. In addition to agar dilution, broth microdilution was used for antimicrobial susceptibility testing (AST). We performed whole genome sequencing (WGS) of the strains and analyzed the resulting data for drug resistance genes and plasmids. Phylogenetic trees were constructed with maximum likelihood, plotted using MAGA X, and decorated by iTOL. Results Citrobacter freundii carrying blaKPC-2, blaIMP-4, blaOXA-1, and blaNDM-1 are resistant to most antibiotics, intermediate to tigecycline, and only sensitive to polymyxin B, amikacin, and fosfomycin. The blaIMP-4 coexists with the blaNDM-1 and the blaOXA-1 on a novel transferable plasmid variant pwang9-1, located on the integron In1337, transposon TnAS3, and integron In2054, respectively. The gene cassette sequence of integron In1337 is IntI1-blaIMP-4-qacG2-aacA4′-catB3Δ, while the gene cassette sequence of In2054 is IntI1-aacA4cr-blaOXA-1-catB3-arr3-qacEΔ1-sul1. The blaNDM-1 is located on the transposon TnAS3, and its sequence is IS91-sul-ISAba14-aph (3′)-VI-IS30-blaNDM-1-ble-trpF-dsbD-IS91. The blaKPC-2 is located on the transposon Tn2 of plasmid pwang9-1, and its sequence is klcA-korC-ISkpn6-blaKPC-2-ISkpn27-tnpR-tnpA. Phylogenetic analysis showed that most of the 34\u00B0C. freundii isolates from China were divided into three clusters. Among them, wang1 and wang9 belong to the same cluster as two strains of C. freundii from environmental samples from Zhejiang. Conclusion We found C. freundii carrying blaIMP–4, blaNDM–1, blaOXA-1, and blaKPC-2 for the first time, and conducted in-depth research on its drug resistance mechanism, molecular transfer mechanism and epidemiology. In particular, we found that blaIMP-4, blaOXA-1, and blaNDM-1 coexisted on a new transferable hybrid plasmid that carried many drug resistance genes and insertion sequences. The plasmid may capture more resistance genes, raising our concern about the emergence of new resistance strains.
Long non-coding RNAs in intracerebral hemorrhage

Intracerebral hemorrhage (ICH), a subtype of stroke, can lead to long-term disability and is one of the leading causes of death. Unfortunately, the effectiveness of pharmacological therapy for ICH is still uncertain. Long non-coding RNA (lncRNA) was defined as an RNA molecule that consists of more than 200 nt without translational activity. As a vital class of diverse molecules, lncRNAs are involved in developmental and pathological processes and have been attractive for decades. LncRNAs have also become potential targets for therapies, as they were massively identified and profiled. In particular, emerging evidence has revealed the critical role of lncRNAs in ICH while attempts were made to treat ICH via regulating lncRNAs. But the latest evidence remains to be summarized. Thus, in this review, we will summarize the recent advances in lncRNA in ICH, highlighting the regulatory role of lncRNAs and their potential as therapeutic targets.
The role of MRI after neochemoradiotherapy in predicting pathological tumor regression grade and clinical outcome in patients with locally advanced rectal adenocarcinoma

Objective To evaluate the predictive value of tumor regression grade assessed by MRI (mr-TRG) after neoadjuvant chemoradiotherapy (neo-CRT) for postoperative pathological TRG (pTRG) and prognosis in patients with locally advanced rectal adenocarcinoma (LARC). Materials and methods This was a retrospective study from a single center experience. The patients who were diagnosed with LARC and received neo-CRT in our department between January 2016 and July 2021 were enrolled. The agreement between mrTRG and pTRG was assessed with the weighted κ test. Overall survival (OS), progress-free survival (PFS), local recurrence-free survival (LRFS), and distant metastasis-free survival (DMFS) were calculated by Kaplan-Meier analysis and log-rank test. Results From January 2016 to July 2021, 121 LARC patients received neo-CRT in our department. Among them, 54 patients had complete clinical data, including MRI of pre- and post-neo-CRT, postoperative tumor samples, and follow-up. The median follow-up time was 34.6 months (range: 4.4-70.6 months). The estimated 3-year OS, PFS, LRFS and DMFS were 78.5%, 70.7%, 89.0%, and 75.2%, respectively. The median time from the completion of neo-CRT to preoperative MRI and surgery was 7.1 weeks and 9.7 weeks, respectively. Out of 54 patients, 5 patients achieved mrTRG1 (9.3%), 37 achieved mrTRG2 (68.5%), 8 achieved mrTRG3 (14.8%), 4 achieved mrTRG4 (7.4%), and no patient achieved mrTRG5 after neo-CRT. Regarding pTRG, 12 patients achieved pTRG0 (22.2%), 10 achieved pTRG1 (18.5%), 26 achieved pTRG2 (48.1%), and 6 achieved pTRG3 (11.1%). The agreement between three-tier mrTRG (mrTRG1 vs. mrTRG2-3 vs. mrTRG4-5) and pTRG (pTRG0 vs. pTRG1-2 vs. pTRG3) was fair (weighted kappa=0.287). In a dichotomous classification, the agreement between mrTRG(mrTRG1 vs. mrTRG2-5)and pTRG(pTRG0 vs. pTRG1-3) also resulted in fair agreement (weighted kappa=0.391). The sensitivity, specificity, positive, and negative predictive values of favorable mrTRG (mrTRG 1-2) for pathological complete response (PCR) were 75.0%, 21.4%, 21.4%, and 75.0%, respectively. In univariate analysis, favorable mrTRG (mrTRG1-2) and downstaging N were significantly associated with better OS, while favorable mrTRG (mrTRG1-2), downstaging T, and downstaging N were significantly associated with superior PFS (p<0.05). In multivariate analysis, downstaging N was an independent prognostic factor for OS. Meanwhile, downstaging T and downstaging N remained independent prognostic factors for PFS. Conclusions Although the consistency between mrTRG and pTRG is only fair, favorable mrTRG after neo-CRT may be used as a potential prognostic factor for LARC patients.
Plant protection from virus: a review of different approaches

This review analyzes methods for controlling plant viral infection. The high harmfulness of viral diseases and the peculiarities of viral pathogenesis impose special requirements regarding developing methods to prevent phytoviruses. The control of viral infection is complicated by the rapid evolution, variability of viruses, and the peculiarities of their pathogenesis. Viral infection in plants is a complex interdependent process. The creation of transgenic varieties has caused much hope in the fight against viral pathogens. The disadvantages of genetically engineered approaches include the fact that the resistance gained is often highly specific and short-lived, and there are bans in many countries on the use of transgenic varieties. Modern prevention methods, diagnosis, and recovery of planting material are at the forefront of the fight against viral infection. The main techniques used for the healing of virus-infected plants include the apical meristem method, which is combined with thermotherapy and chemotherapy. These methods represent a single biotechnological complex method of plant recovery from viruses in vitro culture. It widely uses this method for obtaining non-virus planting material for various crops. The disadvantages of the tissue culture-based method of health improvement include the possibility of self-clonal variations resulting from the long-term cultivation of plants under in vitro conditions. The possibilities of increasing plant resistance by stimulating their immune system have expanded, which results from the in-depth study of the molecular and genetic bases of plant resistance toward viruses and the investigation of the mechanisms of induction of protective reactions in the plant organism. The existing methods of phytovirus control are ambiguous and require additional research. Further study of the genetic, biochemical, and physiological features of viral pathogenesis and the development of a strategy to increase plant resistance to viruses will allow a new level of phytovirus infection control to be reached.
Large Eddy Simulations of Particle Dispersion and Deposition in a Turbulent Square Duct Flow

In the current dissertation work, the preferential concentration and deposition of heavy solid particles in a downward, fully developed turbulent square duct flow are studied using large eddy simulations. A second-order accurate, finite-volume based fractional step scheme, based on an unstructured Cartesian mesh, is used to integrate the unsteady, incompressible, three-dimensional Navier-Stokes equations. An algebraic multigrid solver is used to solve the Poisson equation resulting from the fractional step method. The subgrid stresses are modeled with a dynamic subgrid kinetic energy model. The particle equation of motion includes drag, lift and gravity forces and is integrated using the fourth-order accurate Runge-Kutta method. The Reynolds number for the square duct is 360, based on average friction velocity and duct width. The grid used is 80×80×128 in the two wall-normal and streamwise directions, respectively. The preferential concentration of particles is studied assuming that the particles do not modify the turbulence and that particle-particle collisions are insignificant. The continuous and the dispersed phases are treated using Eulerian and Lagrangian approaches, respectively. Four cross-sectional locations representative of the time mean secondary flow patterns and six particle response times were chosen to study the effect of location and particle inertia on preferential concentration. Variation of vorticity magnitude, swirling strength, strain-rate, and ∇u:∇u, and their probability distribution functions(PDF), with particle response time and location is shown to demonstrate preferential concentration. Particles are seen to accumulate in regions of high ∇u:∇u and strain-rate and in regions of low swirling strength. In general, particles accumulate in regions of low vorticity magnitude. However, near the wall, large particles accumulate in regions of high vorticity magnitude. In addition, instantaneous contours of the above statistics and scatter plots of particle positions in a near-wall plane are presented to illustrate preferential concentration. Deposition of particles in a square duct is the focus of the second set of simulations. Ten particle response times are studied. Simulations are carried out using one-way coupling as well as select cases using twoand fourway coupling. A particle -particle collision algorithm has been developed. PDFs of deposition location, average streamwise and wall-normal deposition velocities, and deposition rates are presented.
Ionic Liquids as Environmental Pollutants—Analysis of the Effect of Tetrabutylammonium Chloride on the Growth and Development of Wheat and Cucumber

Ionic liquids are a huge group of chemical compounds that have found, or may, in the future, find, applications in various industries. These compounds are characterized by excellent physical, chemical, and biological properties, but a big problem is their environmental impact. One of the representatives of this group of compounds is tetrabutylammonium chloride ([TBA][Cl]). In this present study, the effects of [TBA][Cl] were evaluated on two popular plant species—a monocotyledonous plant—wheat (Triticum aestivum L.) and a dicotyledonous plant—cucumber (Cucumis sativus L.). The results showed that the compound caused a pronounced inhibition of plant growth and roots, as well as plant fresh weight yield. An increase in plant dry weight was observed at the same time. Despite the decrease in the content of photosynthetic pigments, no major changes were observed in chlorophyll fluorescence. All observed changes were strongly related to the applied concentration of the compound.
Silane functionalization of WS2 nanotubes for interaction with poly(lactic acid).

Functionalisation of nanofillers is required for the promotion of strong interfacial interactions with polymers and is essential as a route for the preparation of (nano)composites with superior mechanical properties. Tungsten disulphide nanotubes (WS2 NTs) were functionalized using (3-aminopropyl) triethoxysilane (APTES) for preparation of composites with poly(lactic acid) (PLA). The WS2 NTs : APTES ratios used were 1 : 1, 1 : 2 and 1 : 4 WS2 NTs : APTES. The APTES formed siloxane networks bound to the NTs via surface oxygen and carbon moieties adsorbed on the WS2 NTs surface, detected by X-ray photoelectron spectroscopy (XPS) studies and chemical mapping using energy dispersive X-ray spectroscopy in the scanning transmission electron microscope (STEM-EDS). The successful silane modification of the WS2 NTs was clearly evident with both significant peak shifting by as much as 60 cm-1 for Si-O-Si vibrations (FTIR) and peak broadening of the A1g band in the Raman spectra of the WS2 NTs. The evolution of new bands was also observed and are associated with Si-CH2-CH2 and, symmetric and assymetric -NH3+ deformation modes (FTIR). Further evidence for functionalization was obtained from zeta potential measurements as there was a change in surface charge from negative for pure WS2 NTs to positive for APTES modified WS2 NTs. Additionally, the thermal stability of APTES was shifted to much higher temperatures as it was bound to the WS2 NTs. The APTES modified WS2 NTs were organophilic and readily dispersed in PLA, while presence of the pendant amine and hydroxyl groups resulted in strong interfacial interactions with the polymer matrix. The inclusion of as little as 0.5 wt% WS2 NTs modified with 2.0 wt% APTES resulted in an increase of 600% in both the elongation at break (a measure of ductility) and the tensile toughness relative to neat PLA, without impacting the stiffness or strength of the polymer.