Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Crop Rotation on Spring Wheat Yield and Pest Occurrence in Different Tillage Systems: A Multi-Year Experiment in Finnish Growing Conditions

Crop rotation and soil tillage are among key factors impacting cropping system productivity, pest management and soil health. To assess their role in northern cropping systems, we quantified the effects of crop rotation on spring wheat yield in different tillage systems based on a long-term (2005–2017) field experiment in southwestern Finland. In addition, effects of crop rotation on weeds, plant pathogens, and pest insects were assessed. Three types of crop rotation were compared: monoculture (spring wheat), 2-year rotation (spring wheat—turnip rape—spring wheat—barley) and 4-year rotation (spring wheat—turnip rape—barley—pea) under no-tillage and plowing. A diversified crop rotation improved spring wheat yield by up to 30% in no-tillage and by 13% under plowing compared with monoculture. Overall, the yield quantity and quality differences between crop rotations were higher in no-tillage plots than in plowed plots. The occurrence of weed species in spring wheat before herbicide control was highest in the four-year crop rotation and lowest in the wheat monoculture. For plant diseases, wheat leaf blotch disease severity, mainly caused by Pyrenophora tritici-repentis, was lowest in the most diverse crop rotation. On average, wheat leaf blotch disease severity was 20% less when wheat was grown every fourth year compared with wheat monoculture. The effect of crop rotation on stem and root diseases became apparent after 6 years of rotation and the disease index was lowest in the most diverse crop rotation. Neither rotation nor tillage affected the control need of wheat midge (Sitodiplosis mosellana). Based on our results, diverse crop rotations including cereals, oilseed crops, and legumes increase yield and reduce plant disease severity of spring wheat in Finland, with the magnitude being larger in no-tillage systems.
Mechanisms for Maintaining Eukaryotic Replisome Progression in the Presence of DNA Damage

The eukaryotic replisome coordinates template unwinding and nascent-strand synthesis to drive DNA replication fork progression and complete efficient genome duplication. During its advancement along the parental template, each replisome may encounter an array of obstacles including damaged and structured DNA that impede its progression and threaten genome stability. A number of mechanisms exist to permit replisomes to overcome such obstacles, maintain their progression, and prevent fork collapse. A combination of recent advances in structural, biochemical, and single-molecule approaches have illuminated the architecture of the replisome during unperturbed replication, rationalised the impact of impediments to fork progression, and enhanced our understanding of DNA damage tolerance mechanisms and their regulation. This review focusses on these studies to provide an updated overview of the mechanisms that support replisomes to maintain their progression on an imperfect template.
Crop Area Mapping in Southern and Central Malawi With Google Earth Engine

Agriculture in sub-Saharan Africa consists primarily of smallholder farms of rainfed crops. Historically, satellite data were too coarse to account for the heterogeneity in these landscapes. Sentinel-2 data have improved spectral resolution and much higher spatial resolution (10 m) than previously available satellites with global coverage, such as Landsat or MODIS, making mapping smallholder farms possible. Spectral mixture analysis was used to convert the Sentinel-2 signal into fractions of green vegetation, non-photosynthetic vegetation, soil, and shade endmembers. Very high spatial resolution imagery in Google Earth Pro was used to identify locations of crop and natural vegetation classes, with over 20,000 reference points interpreted. The high temporal resolution of Sentinel-2 (5 days repeat) allows for classification of landcover based on the phenological signal, with natural areas having smoothly varying amounts of photosynthetic vegetation annually, while cropped areas show more abrupt changes, and also the presence of bare soil due to agricultural activity at some point during the year. We summarized the endmember values using monthly medians, extracted values for the reference data points, randomly split them into training and test data sets, and input the training data into the random forests algorithm in Google Earth Engine to map crop area. We divided southern and central Malawi into tiles, and found crop/no crop classification accuracies on the test data for each tile to be between 87 and 93%. The 10 m map of crop area was aggregated to the district level and showed an R2 of 0.74 with ground-based statistics from the Malawi government and 0.79 with a remotely sensed product developed by the USGS.
Steam Reforming of Ethanol on Copper Catalysts Derived from Hydrotalcite-like Materials

Steam reforming of ethanol (SRE) and sorption enhanced steam reforming of ethanol (SE-SRE) on Cu,Zn,Al materials was studied in the temperature range between 200 and 600 °C for hydrogen production. Precursors with different structures, such as a hydrotalcite-like compound (CuZnAl-HT), zincian malachite derivative (CuZnAl-REF, a reference catalyst precursor for the synthesis of methanol) and amorphous material with embedded copper particles (CuZnAl-ECP), were employed to obtain the active phases. Among the three samples used, the CuZnAl-HT catalyst shows the highest activity (ethanol and water conversion) and selectivity (hydrogen yield). This material also shows a satisfying stability, as the ethanol conversion only decreases around 20% at 400 °C during 12 h of lifetime test. In addition, carbon dioxide uptake during the transient period of SRE was found on the CuZnAl based materials. Especially for the CuZnAl-HT catalyst a SE-SRE phenomena was perfectly observed at 400 °C due to a relative good interacti.
Targeting Myeloid-Derived Suppressor Cells to Enhance a Trans-Sialidase-Based Vaccine Against Trypanosoma cruzi

Trypanosoma cruzi (T. cruzi) is a hemoflagellate protozoan parasite that causes Chagas disease, a neglected tropical disease that affects more than 6 million people around the world, mostly in Latin America. Despite intensive research, there is no vaccine available; therefore, new approaches are needed to further improve vaccine efficacy. It is well established that experimental T. cruzi infection induces a marked immunosuppressed state, which includes notably increases of CD11b+ GR-1+ myeloid-derived suppressor cells (MDSCs) in the spleen, liver and heart of infected mice. We previously showed that a trans-sialidase based vaccine (TSf-ISPA) is able to confer protection against a virulent T. cruzi strain, stimulating the effector immune response and decreasing CD11b+ GR-1+ splenocytes significantly. Here, we show that even in the immunological context elicited by the TSf-ISPA vaccine, the remaining MDSCs are still able to influence several immune populations. Depletion of MDSCs with 5 fluorouracil (5FU) at day 15 post-infection notably reshaped the immune response, as evidenced by flow cytometry of spleen cells obtained from mice after 21 days post-infection. After infection, TSf-ISPA-vaccinated and 5FU-treated mice showed a marked increase of the CD8 response, which included an increased expression of CD107a and CD44 markers in CD8+ cultured splenocytes. In addition, vaccinated and MDSC depleted mice showed an increase in the percentage and number of CD4+ Foxp3+ regulatory T cells (Tregs) as well as in the expression of Foxp3+ in CD4+ splenocytes. Furthermore, depletion of MDSCs also caused changes in the percentage and number of CD11chigh CD8α+ dendritic cells as well as in activation/maturation markers such as CD80, CD40 and MHCII. Thus, the obtained results suggest that MDSCs not only play a role suppressing the effector response during T. cruzi infection, but also strongly modulate the immune response in vaccinated mice, even when the vaccine formulation has a significant protective capacity. Although MDSC depletion at day 15 post-infection did not ameliorated survival or parasitemia levels, depletion of MDSCs during the first week of infection caused a beneficial trend in parasitemia and mice survival of vaccinated mice, supporting the possibility to target MDSCs from different approaches to enhance vaccine efficacy. Finally, since we previously showed that TSf-ISPA immunization causes a slight but significant increase of CD11b+ GR-1+ splenocytes, here we also targeted those cells at the stage of immunization, prior to T. cruzi challenge. Notably, 5FU administration before each dose of TSf-ISPA vaccine was able to significantly ameliorate survival and decrease parasitemia levels of TSf-ISPA-vaccinated and infected mice. Overall, this work supports that targeting MDSCs may be a valuable tool during vaccine design against T. cruzi, and likely for other pathologies that are characterized by the subversion of the immune system.
Polydimensional Structure and Psychosocial Functions of the Direct Address in TV Series

Traditionally, in media studies research, the direct address or aside, i.e., a construction in which a speaker communicates a message directly to the audience breaking the continuity of the narrative flow, has been investigated mainly for its dramaturgical function. The present study aims to consider the direct address as a research object of the social psychology of communication to increase our understanding of this technique by going beyond the analysis of its dramaturgical function. In particular, the direct address will be examined through an integrated approach based on argumentative and conversational tools to highlight its less known polydimensional structure, i.e., diegetic and extra-diegetic dimensions and their interactions, and psychosocial functions, i.e., connecting the characters among each other within the show as well as with the audience. This objective will be achieved by analyzing two different direct addresses from the American TV series House of Cards. The analysis showed that the direct address performs its dramaturgical function by impacting both diegetic and extradiegetic levels. In the first case, as considered in previous studies, these plans are activated in parallel, aiming to build what we have defined as the “strategic subjectivity” of the character who employs this technique. Instead, in the second case—which comprises two direct addresses produced by two different characters—this technique involves the creation of what we will call “platforms of intersubjectivity. ” In this occurrence, the dramaturgical action establishes a “bridge” between the diegetic and extradiegetic plans that act synergistically. In conclusion, the present study shows how an integrated approach based on argumentative and conversational tools of analysis permits to enlarge the traditional media studies perspective, highlighting the less investigated polydimensional structure and analyzing the psychosocial functions of the direct address, here considered as a research object of the social psychology of communication examined in its diegetic and extra-diegetic dimensions. The integration of the pragma-dialectical approach to argumentation with the interlocutory logic theory has brought to light a new modality of use of the direct address that can be termed “intersubjective aside,” a type of aside that can be added to the three already known, i.e., aside ad spectatores, monological aside, and dialogical aside.
Quantitative Analysis of Morphometric Data of Pre-modern Birds: Phylogenetic Versus Ecological Signal

Birds are one of the most diverse clades of extant terrestrial vertebrates, a diversity that first arose during the Mesozoic as a multitude of lineages of pre-neornithine (stem) birds appeared but did not survive into the Cenozoic Era. Modern birds (Neornithes) inhabit an extensive array of ecologically distinct habitats and have specific and varied foraging strategies. Likewise, the morphological disparity among Mesozoic lineages appears to underscore a significant degree of ecological diversity, yet attempts to determine lineage-specific ecologies have mainly been limited to superficial narratives. In recent years, numerous studies have used various morphometric proxies to interpret the paleoecology of Mesozoic bird lineages, but largely without evaluating the interplay between ecological and phylogenetic signals. Moreover, most studies of this sort transform the original data into logarithms to control dimensionality, underestimating the biases induced upon such transformations. The goal of this study is to quantitatively address the ecomorphology of crown-group Neornithes using a dense sample of raw forelimb and hindlimb measurements, and to examine if such results can be used to infer the ecologies of Mesozoic bird lineages. To that end, scaling of limb measurements and ecological data from modern birds was assessed statistically using phylogenetic comparative methods, followed by the inclusion of fossil taxa. A strong relationship was recovered between humerus and hindlimb allometric scaling and phylogeny. Our results indicate that while some ecological classes of modern birds can be discriminated from each other, phylogenetic signature can overwhelm ecological signal in morphometric data, potentially limiting the inferences that can be made from ecomorphological studies. Furthermore, we found differential scaling of leg bones among Early Cretaceous enantiornithines and ornithuromorphs, a result hinting that habitat partitioning among different lineages could be a pervasive phenomenon in avian evolution.
Policy-Relevant Attitudes Toward COVID-19 Vaccination: Associations With Demography, Health Risk, and Social and Political Factors

Background: Vaccination is considered to be a key public health intervention to end the COVID-19 pandemic. Yet, the success of the intervention is contingent on attitudes toward vaccination and the design of vaccination policies. Methods: We conduct cross-sectional analyses of policy-relevant attitudes toward COVID-19 vaccination using survey data of a representative sample of Austrian residents collected by the Austrian Corona Panel Project (ACPP). As outcomes, we examine the individual readiness to get vaccinated, the support for compulsory vaccinations, and the preference for making the vaccine available free of charge. The independent variables include demographics, objective and perceived health risks, and social and political factors. Results: Although there is broad public support for making the vaccine available free of charge, vaccine hesitancy and the opposition to a vaccine mandate are widespread. The protective function of the vaccine for the individual only motivates limited support for vaccinations. Opposition to COVID-19 vaccination also stems from a lack of sense of community and an ongoing politicization of the issue through conspiracy theories and party politics. Conclusion: We propose that overcoming the inherent free-rider problem of achieving sufficiently high vaccination rates poses a potential dilemma for policymakers: Given the politicized nature of the issue, they may find themselves having to choose between making vaccinations compulsory at political costs and a lingering pandemic at high costs for public health and the economy. We propose that promoting a sense of community and addressing potential practical constraints will be key in designing an effective COVID-19 vaccination policy.
A Conserved Role for Asrij/OCIAD1 in Progenitor Differentiation and Lineage Specification Through Functional Interaction With the Regulators of Mitochondrial Dynamics

Mitochondria are highly dynamic organelles whose activity is an important determinant of blood stem and progenitor cell state. Mitochondrial morphology is maintained by continuous fission and fusion and affects stem cell proliferation, differentiation, and aging. However, the mechanism by which mitochondrial morphology and dynamics regulate cell differentiation and lineage choice remains incompletely understood. Asrij/OCIAD1 is a conserved protein that governs mitochondrial morphology, energy metabolism and human embryonic stem cell (hESC) differentiation. To investigate the in vivo relevance of these properties, we compared hESC phenotypes with those of Drosophila hematopoiesis, where Asrij is shown to regulate blood progenitor maintenance by conserved mechanisms. In concordance with hESC studies, we found that Drosophila Asrij also localizes to mitochondria of larval blood cells and its depletion from progenitors results in elongated mitochondria. Live imaging of asrij knockdown hemocytes and of OCIAD1 knockout hESCs showed reduced mitochondrial dynamics. Since key regulators of mitochondrial dynamics actively regulate mitochondrial morphology, we hypothesized that mitochondrial fission and fusion may control progenitor maintenance or differentiation in an Asrij-dependent manner. Knockdown of the fission regulator Drp1 in Drosophila lymph gland progenitors specifically suppressed crystal cell differentiation whereas depletion of the fusion regulator Marf (Drosophila Mitofusin) increased the same with concomitant upregulation of Notch signaling. These phenotypes were stronger in anterior progenitors and were exacerbated by Asrij depletion. Asrij is known to suppress Notch signaling and crystal cell differentiation. Our analysis reveals that synergistic interactions of Asrij with Drp1 and Marf have distinct impacts on lymph gland progenitor mitochondrial dynamics and crystal cell differentiation. Taken together, using invertebrate and mammalian model systems we demonstrate a conserved role for Asrij/OCIAD1 in linking mitochondrial dynamics and progenitor differentiation. Our study sets the stage for deciphering how regulators of mitochondrial dynamics may contribute to functional heterogeneity and lineage choice in vertebrate blood progenitors.
Role of Th22 Cells in the Pathogenesis of Autoimmune Diseases

Upon antigenic stimulation, naïve CD4+T cells differentiate into different subsets and secrete various cytokines to exert biological effects. Th22 cells, a newly identified CD4+T cell subset,are distinct from the Th1, Th2 and Th17 subsets. Th22 cells secrete certain cytokines such as IL-22, IL-13 and TNF-α, but not others, such as IL-17, IL-4, or interferon-γ (IFN-γ), and they express chemokine receptors CCR4, CCR6 and CCR10. Th22 cells were initially found to play a role in skin inflammatory diseases, but recent studies have demonstrated their involvement in the development of various autoimmune diseases. Here, we review research advances in the origin, characteristics and effector mechanisms of Th22 cells, with an emphasis on the role of Th22 cells and their main effector cytokine IL-22 in the pathogenesis of autoimmune diseases. The findings presented here may facilitate the development of new therapeutic strategies for targeting these diseases.
m6A mRNA Methylation Regulates Epithelial Innate Antimicrobial Defense Against Cryptosporidial Infection

Increasing evidence supports that N6-methyladenosine (m6A) mRNA modification may play an important role in regulating immune responses. Intestinal epithelial cells orchestrate gastrointestinal mucosal innate defense to microbial infection, but underlying mechanisms are still not fully understood. In this study, we present data demonstrating significant alterations in the topology of host m6A mRNA methylome in intestinal epithelial cells following infection by Cryptosporidium parvum, a coccidian parasite that infects the gastrointestinal epithelium and causes a self-limited disease in immunocompetent individuals but a life-threatening diarrheal disease in AIDS patients. Altered m6A methylation in mRNAs in intestinal epithelial cells following C. parvum infection is associated with downregulation of alpha-ketoglutarate-dependent dioxygenase alkB homolog 5 and the fat mass and obesity-associated protein with the involvement of NF-кB signaling. Functionally, m6A methylation statuses influence intestinal epithelial innate defense against C. parvum infection. Specifically, expression levels of immune-related genes, such as the immunity-related GTPase family M member 2 and interferon gamma induced GTPase, are increased in infected cells with a decreased m6A mRNA methylation. Our data support that intestinal epithelial cells display significant alterations in the topology of their m6A mRNA methylome in response to C. parvum infection with the involvement of activation of the NF-кB signaling pathway, a process that modulates expression of specific immune-related genes and contributes to fine regulation of epithelial antimicrobial defense.
Topologically Associating Domains and Regulatory Landscapes in Development, Evolution and Disease

Animal genomes are folded in topologically associating domains (TADs) that have been linked to the regulation of the genes they contain by constraining regulatory interactions between cis-regulatory elements and promoters. Therefore, TADs are proposed as structural scaffolds for the establishment of regulatory landscapes (RLs). In this review, we discuss recent advances in the connection between TADs and gene regulation, their relationship with gene RLs and their dynamics during development and differentiation. Moreover, we describe how restructuring TADs may lead to pathological conditions, which explains their high evolutionary conservation, but at the same time it provides a substrate for the emergence of evolutionary innovations that lay at the origin of vertebrates and other phylogenetic clades.
Low-Dose Radiotherapy Versus Moderate-Dose Radiotherapy for the Treatment of Indolent Orbital Adnexal Lymphomas

Purpose Radiation therapy (RT) with doses ranging from 24 Gray (Gy) to 40 Gy is a proven treatment modality for indolent orbital adnexal lymphoma (IOAL), but recently the use of low dose RT (LDRT, defined as 2 Gy x 2 fractions) has become a notable alternative. However, limited data exists comparing outcomes following LDRT to moderate-dose RT (MDRT, RT dose 4 – 36 Gy). We present a single institution retrospective analysis comparing outcomes of patients with IOALs following LDRT or MDRT. Methods A total of 36 patients treated with 38 consecutive courses of RT were identified; LDRT was delivered for 14 courses and MDRT for 24 courses. Overall response rates (ORR) were recorded according to Deauville or RECIST criteria with a response characterized as a complete response (CR) or partial response. Local control (LC), orbital control (OC), and overall survival (OS) rates were estimated with the Kaplan-Meier method. RT toxicity was graded per CTCAEv5 and compared with the Fisher’s exact test. Results Median follow-up time was 29 months (m) (range, 4-129m), and median MDRT dose used was 24 Gy (range 21-36 Gy). Overall response rates (ORR) were 100% (CR 50%) and 87.5% (CR 58.3%) following LDRT and MDRT, respectively. OS at 2 years was 100% and 95% for the LDRT and MDRT groups, respectively (p=0.36). LC rates at 2 years was 100% for both LDRT and MDRT groups and at 4 years was 100% and 89% for the LDRT and MDRT groups, respectively (p=0.56). The 4-year OC rate (including both ipsilateral and contralateral relapses) was 80% and 85% for the LDRT and MDRT groups, respectively (p=0.79). No patient required treatment with RT to a previously irradiated orbit. Acute toxicities were reported following 6 LDRT courses compared to 20 MDRT courses (p=.014). No Grade 3 or higher acute toxicities occurred in either group. Late toxicities were reported following 2 LDRT courses compared to 10 MDRT courses (p=0.147). Conclusions LDRT produced similar ORR, LC, OC, and OS rates compared to MDRT with fewer acute and minimal late toxicities reported. Future multi-center studies with larger patient numbers are warranted to show significant associations.