Miracle-dz/UniFAR-FTUs huggingface dataset:
A genetic screen for dominant chloroplast reactive oxygen species signaling mutants reveals life stage-specific singlet oxygen signaling networks

Plants employ intricate molecular mechanisms to respond to abiotic stresses, which often lead to the accumulation of reactive oxygen species (ROS) within organelles such as chloroplasts. Such ROS can produce stress signals that regulate cellular response mechanisms. One ROS, singlet oxygen (1O2), is predominantly produced in the chloroplast during photosynthesis and can trigger chloroplast degradation, programmed cell death (PCD), and retrograde (organelle-to-nucleus) signaling. However, little is known about the molecular mechanisms involved in these signaling pathways or how many different signaling 1O2 pathways may exist. The Arabidopsis thaliana plastid ferrochelatase two (fc2) mutant conditionally accumulates chloroplast 1O2, making fc2 a valuable genetic system for studying chloroplast 1O2-initiated signaling. Here, we have used activation tagging in a new forward genetic screen to identify eight dominant fc2 activation-tagged (fas) mutations that suppress chloroplast 1O2-initiated PCD. While fc2 fas mutants all block 1O2-triggered PCD in the adult stage, only two fc2 fas mutants block such cellular degradation at the seedling stage, suggesting that life-stage-specific 1O2-response pathways exist. In addition to PCD, fas mutations generally reduce 1O2-induced retrograde signals. Furthermore, fas mutants have enhanced tolerance to excess light, a natural mechanism to produce chloroplast 1O2. However, general abiotic stress tolerance was only observed in one fc2 fas mutant (fc2 fas2). Together, this suggests that plants can employ general stress tolerance mechanisms to overcome 1O2 production but that this screen was mostly specific to 1O2 signaling. We also observed that salicylic acid (SA) and jasmonate (JA) stress hormone response marker genes were induced in 1O2-stressed fc2 and generally reduced by fas mutations, suggesting that SA and JA signaling is correlated with active 1O2 signaling and PCD. Together, this work highlights the complexity of 1O2 signaling by demonstrating that multiple pathways may exist and introduces a suite of new 1O2 signaling mutants to investigate the mechanisms controlling chloroplast-initiated degradation, PCD, and retrograde signaling.
Untangling the Role of Pathobionts from Bacteroides Species in Inflammatory Bowel Diseases

Inflammatory bowel diseases (IBD) arise from a convergence of underlying genetic susceptibility, environmental factors, and shifts in gut microbiota function and membership. Although the latter may trigger and contribute to IBD, there is little consensus on a specific causative pathogen. In this study, we demonstrate that commensal Bacteroides fragilis strains from ulcerative colitis (UC) patients before and during the development of ileal pouchitis engraft and promote colitis in specific pathogen free (SPF) IL-10 deficient (IL-10-/-) mice, but not in wild type SPF mice or when mono-associated in germ free mice. The colitis in IL-10-/- mice was also associated with significant alterations in commensal microbiota potentially important for maintaining intestinal and immune homeostasis. UC pouchitis B. fragilis also engrafts in DSS-induced colitis in WT SPF mice, indicating a fitness advantage under conditions of mucosal inflammation over other commensals in the gut microbiota. These findings show that gut inflammation promotes the expansion and fitness of UC-derived Bacteroides species that is associated with changes in the SPF gut microbiota and may be promote colitis in genetically susceptible hosts. Importance This study supports the notion that human inflammatory bowel diseases arise from the emergence of indigenous pathobionts in genetically-prone subjects. Colitis-promoting pathobionts are well-suited to establish themselves in the host inflammatory environment and outcompete endogenous microbiota. Once engrafted, the pathobiont can further aggravate inflammation in a genetically-susceptible host. Such complex interplay among several factors creates a vicious pro-inflammatory cycle and promotes disease development. These findings are consistent with our previous clinical observation that B. fragilis, an otherwise low-abundance commensal species, expands prior to the development of UC pouchitis. We believe these findings are relevant to the pathogenesis of UC pouchitis and possibly human inflammatory bowel diseases in general, underscoring the role of commensal to pathobiont transitions, rather than classical pathogens, in promoting and exacerbating the onset of human IBD.
Diversity of RNA viruses in declining Mediterranean forests

Global change alters forestry habitats and facilitates the entry of new pathogens that don’t share a co-evolution history with the forest, leading them into a spiral of decline. As a result, relationships between forests’ organisms get disbalanced. Under this scenario, RNA viruses are of particular interest, as they participate in many of such relationships thanks to their ability to infect a wide range of hosts, even from different kingdoms of life. For this reason, the study of RNA viruses is essential to understand how viral flow across different hosts might occur, and to prevent possible outbreaks of diseases in the future. In this work the RNA virus diversity found in trees, arthropods and fungi from declining Mediterranean forests is described. To this extent, three habitats (Quercus ilex, Castanea sativa and Pinus radiata) were sampled and RNAseq was performed on tree tissues, arthropods and fungi. 146 viral sequences were detected by searching for matches to conserved motifs of the RNA-dependent RNA polymerase (RdRP) using Palmscan. Up to 15 viral families were identified, with Botourmiaviridae (28.7%) and Partitiviridae (9.6%) being the most abundant. In terms of genome type, ssRNA(+) viruses were the most represented (83.5%), followed by dsRNA (15%) and two ssRNA(-) representatives. Viruses belonging to families with cross-kingdom capabilities such as Hypoviridae (1), Mitoviridae (6) and Narnaviridae (5) were also found. Distribution of viruses across ecosystems was: Q.ilex (57.5%), P.radiata (26.7%) and C.sativa (15.8%). Interestingly, two RdRP sequences had no matches in available viral databases. This work constitutes a starting point to gain insight into virus evolution and diversity occurring in forests affected by decline, as well as searching for novel viruses that might be participating in unknown infectious pathways.
Real-Time Computation of Brain E-Field for Enhanced Transcranial Magnetic Stimulation Neuronavigation and Optimization

Transcranial Magnetic Stimulation (TMS) coil placement and pulse wave-form current are often chosen to achieve a specified E-field dose on targeted brain regions. TMS neuronavigation could be improved by including real-time accurate distributions of the E-field dose on the cortex. We introduce a method and develop software for computing brain E-field distributions in real-time enabling easy integration into neuronavigation and with the same accuracy as 1st-order finite element method (FEM) solvers. Initially, a spanning basis set (< 400) of E-fields generated by white noise magnetic currents on a surface separating the head and permissible coil placements are orthogonalized to generate the modes. Subsequently, Reciprocity and Huygens’ principles are utilized to compute fields induced by the modes on a surface separating the head and coil by FEM, which are used in conjunction with online (real-time) computed primary fields on the separating surface to evaluate the mode expansion. We conducted a comparative analysis of E-fields computed by FEM and in real-time for eight subjects, utilizing two head model types (SimNIBS’s ‘headreco’ and ‘mri2mesh’ pipeline), three coil types (circular, double-cone, and Figure-8), and 1000 coil placements (48,000 simulations). The real-time computation for any coil placement is within 4 milliseconds (ms), for 400 modes, and requires less than 4 GB of memory on a GPU. Our solver is capable of computing E-fields within 4 ms, making it a practical approach for integrating E-field information into the neuronavigation systems without imposing a significant overhead on frame generation (20 and 50 frames per second within 50 and 20 ms, respectively).
Quickest Change Detection With Controlled Sensing

In the problem of quickest change detection, a change occurs at some unknown time in the distribution of a sequence of random vectors that are monitored in real time, and the goal is to detect this change as quickly as possible subject to a certain false alarm constraint. In this work we consider this problem in the presence of parametric uncertainty in the post-change regime and controlled sensing. That is, the post-change distribution contains an unknown parameter, and the distribution of each observation, before and after the change, is affected by a control action. In this context, in addition to a stopping rule that determines the time at which it is declared that the change has occurred, one also needs to determine a sequential control policy, which chooses the control action at each time based on the already collected observations. We formulate this problem mathematically using Lorden’s minimax criterion, and assuming that there are finitely many possible actions and post-change parameter values. We then propose a specific procedure for this problem that employs an adaptive CuSum statistic in which (i) the estimate of the parameter is based on a fixed number of the more recent observations, and (ii) each action is selected to maximize the Kullback-Leibler divergence of the next observation based on the current parameter estimate, apart from a small number of exploration times. We show that this procedure, which we call the Windowed Chernoff-CuSum (WCC), is first-order asymptotically optimal under Lorden’s minimax criterion, for every possible value of the unknown post-change parameter, as the mean time to false alarm goes to infinity. We also provide simulation results to illustrate the performance of the WCC procedure.
A New Alluaudite-like Phosphate, Na 1.67 Co 2.45 Cr

The development of new phosphate materials has attracted huge attention because of their promising applications as electrode materials and solid-state electrolytes for next-generation batteries. Several phosphates were elaborated and structurally investigated, such as the NASICON and alluaudite families, which show promising structural features permitting electrochemical activity as electrodes for rechargeable Li/Na batteries. In the context of the elaboration and structural investigation of novel alluaudite phosphates, we report on the crystal growth and the structural investigation of a new sodium, cobalt, and chromi-um-based phosphate, Na 1.67 Co 2.45 Cr 0.78 (PO 4 ) 3 , with an alluaudite-type structure. This phosphate has been produced using a solid-state technique and its structure has been elucidated thanks to single-crystal X-ray diffraction (XRD) data. The title compound crystallizes in space group C2/c of the monoclinic system with the lattice parameters a = 11.7538 (3) Å, b = 12.3671 (3) Å, c = 6.4180 (2) Å, and β = 114.022 (10)°. Its structure is formed by infinite chains, which are in turn created from edge-sharing (Co1,Cr1) 2 O 10 units and Co2O 6 octahedra. These infinite chains are bonded together by the PO 4 tetrahedra, resulting in a three-dimensional framework with two different kinds of hexagonal tunnels where Na + and Na + /Co 2+ cations can be found.
whole slide imaging in pathology: advantages, limitations, and emerging perspectives

: Significant technologic gains have led to the adoption of innovative digital imaging solutions in pathology. Whole slide imaging (WSI), which refers to scanning of conventional glass slides in order to produce digital slides, is the most recent imaging modality being employed by pathology departments worldwide. WSI continues to gain traction among pathologists for diagnostic, educational, and research purposes. This article provides a technologic review of WSI platforms and covers clinical and nonclinical pathology applications of these imaging systems. Barriers to adoption of WSI include limiting technology, image quality, problems with scanning all materials (eg, cytology slides), cost, digital slide storage, inability to handle high-throughput
THEORIES AND HYPOTHESIS THAT EXPLAIN THE USAGE OF E-DELIVERY SERVICES

In the new digital era, electronic commerce is a modern industry with an increasing number of Internet users worldwide. The technological development of the Internet as a prerequisite for ecommerce certainly took place quickly and robustly. E-commerce is regarded as the most effective form of trade because of its low cost and simplicity. It should be noted that, as the Internet increases competition, lower prices and more meaningful options are available to consumers. This research aims to identify theories that explain THE USAGE OF E-DELIVERY SERVICES , And from that he reached In particular, theories which cover IT issues and IT issues, and the importance of information technology, have been clarified.
Orbit Classiﬁcation and Sensitivity Analysis in Dynamical Systems Using Surrogate Models †

: Dynamics of many classical physics systems are described in terms of Hamilton’s equations. Commonly, initial conditions are only imperfectly known. The associated volume in phase space is preserved over time due to the symplecticity of the Hamiltonian ﬂow. Here we study the propagation of uncertain initial conditions through dynamical systems using symplectic surrogate models of Hamiltonian ﬂow maps. This allows fast sensitivity analysis with respect to the distribution of initial conditions and an estimation of local Lyapunov exponents (LLE) that give insight into local predictability of a dynamical system. In Hamiltonian systems, LLEs permit a distinction between regular and chaotic orbits. Combined with Bayesian methods we provide a statistical analysis of local stability and sensitivity in phase space for Hamiltonian systems. The intended application is the early classiﬁcation of regular and chaotic orbits of fusion alpha particles in stellarator reactors. The degree of stochastization during a given time period is used as an estimate for the probability that orbits of a speciﬁc region in phase space are lost at the plasma boundary. Thus, the approach offers a promising way to accelerate the computation of fusion alpha particle losses.
De ﬁ ning and managing incidental ﬁ ndings in genetic and genomic practice

The rapidly declining costs and increasing speeds of whole-genome analysis mean that genetic testing is undergoing a shift from targeted approaches to broader ones that look at the entire genome. As whole-genome technologies gain widespread use, questions about the management of so-called incidental ﬁ ndings — those unrelated to the question being asked — need urgent consideration. In this review, we bring together current understanding and arguments about (1) appropriate terminology, (2) the determination of clinical utility and when to disclose incidental ﬁ ndings, (3) the differences in management and disclosure in clinical, research and commercial contexts and (4) ethical and practical issues about familial implications and recontacting those tested. We recommend that greater international consensus is developed around the disclosure and management of incidental ﬁ ndings, with particular attention to when, and how, less clear-cut results should be communicated. We suggest that there is no single term that captures all the issues around these kinds of ﬁ ndings and that different terms may, therefore, need to be used in different settings. We also encourage the use of clear consent processes, but suggest that the absence of consent should not always preclude disclosure. Finally, we recommend further research to identify ways to implement the use of a genome output as a resource, accessible over time, to facilitate appropriate disclosure and recontact when the signi ﬁ cance of a previously unclear incidental ﬁ nding is clari
Using Front Lines to Predict Deaths in the Bosnian Civil War

What static, readily observable indicators might help us predict levels of killing in civil wars? Research using disaggregated event data and spatial models has reported strong relationships between various indicators of ethnic diversity and violent conflict during the Bosnian War (1992-1995). Bosnia is a rare case for empirical research on ethnic violence in civil wars: a census was conducted a few months before violence broke out in a country which recognized and recorded ethnic group membership, and extensively documented post-war fact-finding has recorded over 75,000 deaths and their location. Applying the resulting ethnic conflict models to other conflicts that lack such data will be difficult. This paper examines the relative fit of an alternative model based on distance to front lines and other factors that can be obtained through remote sensing, and which hence are more generalizable. Results from a spatial negative binomial count model estimated with Markov Chain Monte Carlo (MCMC) methods show that front lines model performs similarly to the ethnic conflict model in terms of fit, and both are improvements over a base model which accounts for spatial diffusion of violence and local population size only.
Evolution of animal welfare in Europe and its role for safeguarding animal health (Evolução do bem-estar animal na Europa e o seu papel na salvaguarda da saúde animal)

From farm animal husbandry to farm animal production some examples of the consequences for animal health and welfare. The radical changes in agriculture from 1950s onwards, when traditional animal husbandry successively became intense animal production, involved changes of animals and changes of their environment and thereby change of the relationship between animal and environment. The changes of the animals can be described as follows: The animal breeding in traditional animal husbandry had several goals, like good health, good temperament, and long life. It became from the 1950s concentrated on one goal: high production, it may be milk, eggs or faster growth. Also the feeding became more intense, aiming at high production. As example of this the development in Sweden might be a good example, table 1 and figure 1.
In�uencing factors of incision healing in HIV positive patients with giant cell tumor of long bone in extremities

Objective To evaluate the risk factors that affect wound healing after surgery of giant cell tumor in patients with human immunode�ciency virus (HIV). Methods 20 patients of giant cell tumor with HIV were recruited from June 2018 to June 2022, once diagnosed, 20 patients were receive timely HAART (Highly Active Antiretroviral Therapy) with China's �rst choice of national free HAART drug containing tenofovir disoproxil fumarate, lamivudine and efavirenz (TDF + 3TC + EFV, ). and 20 patients of giant cell tumor without HIV were enrolled as control at same time. All patients were underwent the same surgical method. Observe the incidence of infection at the surgical site and risk factors that affect wound healing were evaluated.
Arctic Precipitation and Evaporation: Model Results and Observational Estimates

Abstract Observational estimates of precipitation and evaporation over the Arctic Ocean and its terrestrial watersheds are compared with corresponding values from the climate model simulations of the Atmospheric Model Intercomparison Project (AMIP). Estimates of Arctic regional mean precipitation from several observational sources show considerable scatter, and the observational estimates based on gauge-adjusted station data are considerably larger than the other observational estimates. While the AMIP model simulations of precipitation also show scatter, the ensemble mean of the models’ precipitation exceeds even the higher (gauge-adjusted) observational estimates over the Arctic Ocean and its major watersheds. The difference between simulated precipitation and evaporation (P − E), representing the net freshwater gain (runoff) by the surface, also exceeds the observational estimates by 44%–83% over the Arctic Ocean and by generally smaller percentages over the terrestrial watersheds. The ensemble model m.
Catchment-wide erosion rates, glaciation, and topography of the central ladakh Range, India

Introduction Researchers have hypothesized that erosional unloading can influence rate and style of tectonic deformation, but this hypothesis remains controversial, and rates of erosion and sediment transfer need to be quantified to help test these models. The central Ladakh Range, located in the Transhimalaya of northern India, is an ideal setting to examine these models because the range has contrasting styles of deformation, unroofing history, and geomorphology on its northern and southern sides. The asymmetric topography and morphology of the Ladakh Range suggests that erosional unloading affects rock uplift on the northern side of the range. In this study, we aim to test this idea by comparing catchment-wide erosion rates, long valley profiles, equilibrium-line altitude‘s (ELAs), and basin statistics across the central Ladakh Range using Be TCN methods, and morphometric analysis.
Abacavir/lamivudine combination in the treatment of Hiv: a review

: Abacavir has been at the center of research and clinical interest in the last two years. The frequency of the associated abacavir hypersensitivity syndrome has decreased substantially since the introduction of routine testing for the HLA-B*5701 allele; the activity of the drug in HIV-infected persons with HIV RNA values more than 100,000 copies/mL has been questioned; the possible increased risk of myocardial infarction after recent exposure to abacavir has been debated; and the drug has been moved from the “recommended” category to the “alternative” category in several guidelines. Still, the drug remains a useful agent in combination with other drugs, including lamivudine, for the treatment of HIV infection. This review will focus on the pharmacokinetics, activity, side effects, and resistance profile of both abacavir and lamivudine, including a thorough review of all of the recent studies relevant to both drugs.
A Review study on Self-confidence of School students

: This paper records a review of studies conducted on Self-confidence of high school and higher secondary students. The ability to believe in oneself is crucial for academic success. Students who are confident in themselves are better able to push themselves to their limits, while those who lack confidence may find it difficult to take chances and try new things. Students who are self-assured are better able to face obstacles, tolerate criticism, and recover from failure and disappointment. Students who are self-assured are more likely to take initiative, manage stress, stay motivated, and create and achieve goals. Additionally, it can support the development of enduring bonds with mentors, teachers, and peers. Six Researchers’ research out put on Self-confidence reviewed for this article.