Miracle-dz/UniFAR-FTUs huggingface dataset:
CryoWire: wire-driven microarchitecture designs for cryogenic computing

Cryogenic computing, which runs a computer device at an extremely low temperature, is promising thanks to its significant reduction of wire resistance as well as leakage current. Recent studies on cryogenic computing have focused on various architectural units including the main memory, cache, and CPU core running at 77K. However, little research has been conducted to fully exploit the fast cryogenic wires, even though the slow wires are becoming more serious performance bottleneck in modern processors. In this paper, we propose a CPU microarchitecture which extensively exploits the fast wires at 77K. For this goal, we first introduce our validated cryogenic-performance models for the CPU pipeline and network on chip (NoC), whose performance can be significantly limited by the slow wires. Next, based on the analysis with the models, we architect CryoSP and CryoBus as our pipeline and NoC designs to fully exploit the fast wires. Our evaluation shows that our cryogenic computer equipped with both microarchitectures achieves 3.82 times higher system-level performance compared to the conventional computer system thanks to the 96% higher clock frequency of CryoSP and five times lower NoC latency of CryoBus.
Using landscape genomics to infer genomic regions involved in environmental adaptation of soybean genebank accessions

Understanding how crops adapt to specific environmental conditions is becoming increasingly important in the face of accelerating climate change, but the genetics of local adaptation remain little understood for many crops. Landscape genomics can reveal patterns of genetic variation that indicate adaptive diversification during crop evolution and dispersal. Here, we examine genetic differentiation and association signatures with environmental gradients in soybean (Glycine max) germplasm groups from China that were inferred from the USDA Soybean Germplasm Collection (N = 17,019 accessions) based on population structure and passport information. We recover genes previously known to be involved in soybean environmental adaptation and report numerous new candidate genes in selection signatures implicated by genomic resources such as the genome annotation and gene expression datasets to function in flowering regulation, photoperiodism and stress reaction cascades. Linkage disequilibrium network analysis suggested functional relationships between genomic regions with selection signatures, consistent with the polygenic nature of environmental adaptation. We tested whether haplotypes associated with environmental adaptation in China were present in 843 North American and 160 European soybean cultivars and found that haplotypes in major genes for early maturity have been selected during breeding, but also that a large number of haplotypes exhibiting putative adaptive variation for cold regions at high latitudes are underrepresented in modern cultivars. Our results demonstrate the value of landscape genomics analysis in genebank germplasm as a starting point for the study of crop environmental adaptation and have the potential to inform future research efforts focused on improved soybean adaptation. Functional validation of candidate genes will support understanding of their adaptive roles and likely enable the transfer of beneficial adaptive variation into modern breeding germplasm.
Cardiac myosin filaments are directly regulated by calcium

Contraction of cardiac and skeletal muscle is initiated by calcium (Ca2+) binding to regulatory proteins on actin-containing thin filaments. During muscle contraction, structural changes in Ca2+-dependent thin filament allow the binding of myosin motors to drive muscle contraction1. The dynamic switching between the resting off states and the active on states of myosin is also critical in regulating muscle contractility2–4. However, the molecular switch on the myosin-containing thick filament that drives this process is not understood. Here we show that cardiac thick filaments are directly Ca2+-regulated. We find that Ca2+ progressively moves the myosin heads from ordered off states close to the thick filament backbone to disordered on states closer to the thin filaments. This Ca2+-dependent structural shift of myosin is accompanied by a biochemically defined transition from the inactive super-relaxed state(s) to the active disordered relaxed state(s)3. Furthermore, we find that this Ca2+-mediated molecular switching is an intrinsic property of cardiac myosin but only when assembled into thick filaments. This novel concept of Ca2+ as a regulatory modulator of the thick filament provides a fresh perspective on cardiac muscle regulation, which may be particularly valuable for devising restorative treatments for pathologies altering the Ca2+ sensitivity of the sarcomere.
Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees

Phylogenomic analyses routinely estimate species trees using methods that account for gene tree discordance. However, the most scalable species tree inference methods, which summarize independently inferred gene trees to obtain a species tree, are sensitive to hard-to-avoid errors introduced in the gene tree estimation step. This dilemma has created much debate on the merits of concatenation versus summary methods and practical obstacles to using summary methods more widely and to the exclusion of concatenation. The most successful attempt at making summary methods resilient to noisy gene trees has been contracting low support branches from the gene trees. Unfortunately, this approach requires arbitrary thresholds and poses new challenges. Here, we introduce threshold-free weighting schemes for the quartet-based species tree inference, the metric used in the popular method ASTRAL. By reducing the impact of quartets with low support or long terminal branches (or both), weighting provides stronger theoretical guarantees and better empirical performance than the original ASTRAL. More consequentially, weighting dramatically improves accuracy in a wide range of simulations and reduces the gap with concatenation in conditions with low gene tree discordance and high noise. On empirical data, weighting improves congruence with concatenation and increases support. Together, our results show that weighting, enabled by a new optimization algorithm we introduce, dramatically improves the utility of summary methods and can reduce the incongruence often observed across analytical pipelines.
Quantitative sequence basis for the E. coli transcriptional regulatory network

The transcriptional regulatory network (TRN) of E. coli consists of thousands of interactions between regulators and DNA sequences. Inherently the DNA sequence is the primary determinant of the TRN; however, it is well established that the presence of a DNA binding motif does not guarantee a functional regulatory protein binding site. Thus, the extent to which the TRN architecture can be predicted by the genome DNA sequence alone remains unclear. Here, we developed machine learning models that predict the TRN structure of E. coli based on genome sequence. Models were constructed successfully (cross-validation AUROC >= 0.8) for 84% (57/68) of valid E. coli regulons identified from top-down analysis of RNA-seq data. We found that: 1) While regulatory motif strength is the most important sequence feature for determining regulon membership, additional features such as DNA shape substantially influence membership; 2) complex regulons involving multiple interacting regulators could be unraveled by machine learning; 3) investigating regulons where initial ML models failed revealed new regulator-specific sequence features that improved model accuracy. Finally, while regulon structure can appear to be variable across estimation methods and strains, we found that strong regulatory sequence features underlie both the genes that appear most consistently in regulons across estimation methods as well as the core regulon genes in the Fur pan-regulon. This work develops a quantitative understanding of the sequence basis of the TRN and suggests a path towards computationally-guided control of transcriptional regulation for synthetic biology applications.
Candidate Biomarkers for the Prediction and Monitoring of Partial Remission in Pediatric Type 1 Diabetes

The partial remission (PR) phase, a period experienced by most patients with type 1 diabetes (T1D) soon after diagnosis, is characterized by low insulin requirements and improved glycemic control. Given the great potential of this phase as a therapeutic window for immunotherapies because of its association with immunoregulatory mechanisms and β-cell protection, our objective was to find peripheral immunological biomarkers for its better characterization, monitoring, and prediction. The longitudinal follow-up of 17 pediatric patients with new-onset T1D over one year revealed that, during the PR phase, remitter patients show increased percentages of effector memory (EM) T lymphocytes, terminally differentiated EM T lymphocytes, and neutrophils in comparison to non-remitter patients. On the contrary, remitter patients showed lower percentages of naïve T lymphocytes, regulatory T cells (TREG), and dendritic cells (DCs). After a year of follow-up, these patients also presented increased levels of regulatory B cells and transitional T1 B lymphocytes. On the other hand, although none of the analyzed cytokines (IL-2, IL-6, TGF-β1, IL-17A, and IL-10) could distinguish or predict remission, IL-17A was increased at T1D diagnosis in comparison to control subjects, and remitter patients tended to maintain lower levels of this cytokine than non-remitters. Therefore, these potential monitoring immunological biomarkers of PR support that this stage is governed by both metabolic and immunological factors and suggest immunoregulatory attempts during this phase. Furthermore, since the percentage of TREG, monocytes, and DCs, and the total daily insulin dose at diagnosis were found to be predictors of the PR phase, we next created an index-based predictive model comprising those immune cell percentages that could potentially predict remission at T1D onset. Although our preliminary study needs further validation, these candidate biomarkers could be useful for the immunological characterization of the PR phase, the stratification of patients with better disease prognosis, and a more personalized therapeutic management.
Feeding Bacillus subtilis ATCC19659 to Broiler Chickens Enhances Growth Performance and Immune Function by Modulating Intestinal Morphology and Cecum Microbiota

This study investigated dietary supplementation with Bacillus subtilis (BS) ATCC19659 on growth performance, biochemical indices, intestinal morphology, and cecum microflora in broiler chicks. A total of 600 Arbor 1-day Acres broilers of either sex were allotted to 5 treatments: chicks were fed a corn- and soybean-based diet (CON); chicks were fed basal diet containing 500 mg ZnB/kg (ZnB); chicks were fed basal diet containing 1 × 108 CFU/g feed of BS-ATCC19659 (BS-1); chicks were fed basal diet containing 3 × 108 CFU/g feed of BS-ATCC19659 (BS-3); and chicks were fed basal diet containing 5 × 108 CFU/g feed of BS-ATCC19659 (BS-5). Each treatment comprised 6 replicates with 20 birds for each replicate pen. Chicks in the BS-5 and BS-3 groups had higher body weight at the 21st and 42nd days and average daily gain from 1 to 21 days than that in the CON group (p < 0.05). Chicks in the BS-5 and ZnB groups had higher serum antioxidant activities and immunity response than those in the CON group (p < 0.05). Compared with the CON group, the liver mRNA abundance of GHR, TGF-β, IGF-1, IFN-γ, SOD, CAT, and GPX of chicks in three BS groups and the ileum villus length (μm) of chicks in BS-3 and ZnB groups was increased (p < 0.05). Compared with the CON group, the villus height-to-crypt depth ratio of the ileum of chicks in the BS-5 and BS-3 groups and the crypt depth and villus height-to-crypt depth ratio of the jejunum in the BS-5 and ZnB groups were increased (p < 0.05). The abundance of the Cyanobacteria phyla in the cecum decreased in response to treatment with both BS-ATCC19659 and ZnB groups (p < 0.05). Compared with the CON group, the cecum abundance of genera GCA-900066575 (Lachnospiraceae), Anaerofustis, and Papillibacter (Firmicutes phylum) in three BS groups were increased (p < 0.05); The abundance of genus Escherichia–Shigella reduced in the BS-3 group (p < 0.05). Compared with the CON group, the cecum abundance of genus Clostridia_unclassified in ZnB and BS-5 groups was decreased (p < 0.05) of broilers. Generally, Bacillus subtilis ATCC19659 as feed additive positively affected growth performance, immunity response, and cecal microflora of broilers.
Exploring the Impact of the Somatic Method ‘Timani’ on Performance Quality, Performance-Related Pain and Injury, and Self-Efficacy in Music Students in Norway: An Intervention Study

The importance of including performance-related body mechanics into music education to improve performance quality and prevent performance-related injuries has been stressed by many researchers recently. However, it is unclear how this information could be delivered most effectively. The somatic method ‘Timani’ provides a practical solution by combining expertise in music performance and functional body mechanics with the goal of achieving a more efficient playing technique. Since no in-depth study has been conducted to assess the method before, we explored the impact of this method on young musicians’ performance through an online, 4-week-long Timani intervention with a mixed-methodology design. 17 students (mean age = 19.17 years) were recruited from the Norwegian Academy of Music. They participated in two group workshops at the beginning and the end of the project and received four individual Timani sessions administered by certified teachers. We collected survey data at the workshops about performance-related pain and self-efficacy, and qualitative feedback after each session. In addition, all sessions were observed by the researcher and semi-structured interviews were conducted with the teachers about the perceived outcomes and their experiences with teaching the method online. Our findings show that the intervention had a positive impact on a physical, professional, and to some extent, psychological and behavioral level. The improvements included better posture when playing, enhanced control and dexterity in the upper extremities, and improved breathing mechanisms. The seven students who had performance-related pain pre-intervention reported a reduction in the discomfort. The positive results were achieved by the dual expertise of the teachers in music performance and functional body mechanics, the structure of the sessions, the communication, and the pedagogical tools used. Both students and teachers felt that administering the sessions online was satisfactory and produced good results. Timani is a promising method to establish healthy playing and singing habits thus improving performance quality and preventing performance-related problems and has great potential in reducing pre-existing injuries and pain. Also, it can be effectively taught online which has further implications for the logistics of delivery.
Comparative Genomics Reveals Evolutionary Traits, Mating Strategies, and Pathogenicity-Related Genes Variation of Botryosphaeriaceae

Botryosphaeriaceae, as a major family of the largest class of kingdom fungi Dothideomycetes, encompasses phytopathogens, saprobes, and endophytes. Many members of this family are opportunistic phytopathogens with a wide host range and worldwide geographical distribution, and can infect many economically important plants, including food crops and raw material plants for biofuel production. To date, however, little is known about the family evolutionary characterization, mating strategies, and pathogenicity-related genes variation from a comparative genome perspective. Here, we conducted a large-scale whole-genome comparison of 271 Dothideomycetes, including 19 species in Botryosphaeriaceae. The comparative genome analysis provided a clear classification of Botryosphaeriaceae in Dothideomycetes and indicated that the evolution of lifestyle within Dothideomycetes underwent four major transitions from non-phytopathogenic to phytopathogenic. Mating strategies analysis demonstrated that at least 3 transitions were found within Botryosphaeriaceae from heterothallism to homothallism. Additionally, pathogenicity-related genes contents in different genera varied greatly, indicative of genus-lineage expansion within Botryosphaeriaceae. These findings shed new light on evolutionary traits, mating strategies and pathogenicity-related genes variation of Botryosphaeriaceae.
Wheat Breeding, Transcription Factories, and Genetic Interactions: New Perspectives

Epistatic interactions and negative heterosis have been shown to be associated with interchromosomal interactions in wheat. Physical gene-gene interactions between co-regulated genes clustered in “transcription factories” have been documented, and a genome-wide atlas of functionally paired, interacting regulatory elements and genes of wheat recently produced. Integration of these new studies on gene and regulatory element interactions, co-regulation of gene expression in “transcription factories,” and epigenetics generates new perspectives for wheat breeding and trait enhancement.
Relations Between Class Competition and Primary School Students’ Academic Achievement: Learning Anxiety and Learning Engagement as Mediators

This study aimed to analyze the relations between class competition and primary school students’ academic achievement, considering the possible mediating roles of learning anxiety and learning engagement. Participants were 1,479 primary school students from four primary schools in Zhejiang, China. We analyzed participants’ scores for class competition, learning anxiety, and learning engagement and their last two final exam scores. Class competition did not directly predict academic achievement, but indirectly affected academic achievement through learning anxiety and learning engagement. There were three effect paths: (1) class competition negatively predicted academic achievement by increasing learning anxiety; (2) class competition positively predicted academic achievement by promoting learning engagement; and (3) class competition affected academic achievement through multiple mediating effects of learning anxiety and learning engagement. This study highlights the important roles of learning anxiety and learning engagement in class competition and academic achievement, which have theoretical and practical significance.
Acute Symptomatic Seizures and Risk of Epilepsy in Autoimmune Encephalitis: A Retrospective Cohort Study

Purpose To investigate the clinical characteristics of acute symptomatic seizures and the predictors of the development of epilepsy in patients with anti-NMDAR, anti-LGI1, and anti-GABABR encephalitis. Methods We retrospectively screened the medical records of 86 hospitalized patients with confirmed autoimmune encephalitis (AE). The clinical characteristics of acute symptomatic seizures were analyzed. The predictors of the development of epilepsy were investigated using logistic regression analysis. Results A total of 86 patients with AE were finally included. Eighty-six percent of patients (n = 74) experienced acute symptomatic seizures, and 28.4% of patients developed epilepsy during follow-up. Abnormal EEG findings were more frequent in AE patients with acute symptomatic seizures. A greater number of anti-seizure medications (ASMs), abnormal EEG findings, and delayed immunotherapy were found to be independently associated with the development of epilepsy. Conclusion Acute symptomatic seizures are a common manifestation in AE patients. During follow-up, 28.4% of AE patients developed epilepsy. The independent factors that predicted the development of epilepsy after the acute phase included a larger number of ASMs, EEG abnormalities, and delayed immunotherapy. In clinical practice, we should prioritize immunotherapy to control acute seizures as soon as possible. For AE patients with an increased risk of developing epilepsy, early withdrawal of ASM is not recommended.
Infection-Derived Monocytic MDSCs Require TGF-β to Suppress Filarial-Specific IFN-γ But Not IL-13 Release by Filarial-Specific CD4+ T Cells In Vitro

Lymphatic filariasis (LF) remains a major health problem with severe economic repercussions in endemic communities of Sub-saharan Africa, South-East Asia and South America. The rodent-specific nematode Litomosoides sigmodontis (Ls) is used to study the immunomodulatory potential of filariae and research has elucidated pathways involving regulatory T cells (Tregs), IL-10 producing cells and alternatively activated macrophages (AAMs) and that CD4+ T cells play a paramount role during infection. Myeloid-derived suppressor cells (MDSCs) have been identified and characterised in man in cancer and other pathologies. The hallmark of MDSC populations is the suppression of T and B cell responses using various mechanisms, which are mostly specific to the pathology or setting. However, until now, it remains unclear whether they play a role in filarial-specific responses. We report here that monocytic MDSCs (Mo-MDSCs, CD11b+Ly6C+Ly6G-) and polymorphonuclear MDSCs (PMN-MDSCs, CD11b+Ly6Cint/loLy6G+) expanded in the thoracic cavity (TC, the site of infection) and correlated positively with filarial life-stages in Ls-infected BALB/c mice. In vitro, only infection-derived Mo-MDSCs showed a suppressive nature by preventing IL-13 and IFN-γ secretion from filarial-specific CD4+ T cells upon co-culture with soluble worm extract. This suppression was not mediated by IL-10, IL-6 or TNF-α, and did not require cell-contact, nitric oxide (NO), IL-4/IL-5 signalling pathways or CCR2. Interestingly, neutralizing TGF-β significantly rescued IFN-γ but not IL-13 production by filarial-specific CD4+ T cells. In comparison to naive cells, PCR array data showed an overall down-regulation of inflammatory pathways in both infection-derived Mo-MDSCs and PMN-MDSCs. In conclusion, these primary data sets show activity and expansion of MDSCs during Ls infection adding this regulatory cell type to the complex milieu of host responses during chronic helminth infections.