Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Diversity and Selection Footprints in the Genome of Brazilian Soybean Cultivars

Although Brazil is currently the largest soybean producer in the world, only a small number of studies have analyzed the genetic diversity of Brazilian soybean. These studies have shown the existence of a narrow genetic base. The objectives of this work were to analyze the population structure and genetic diversity, and to identify selection signatures in the genome of soybean germplasms from different companies in Brazil. A panel consisting of 343 soybean lines from Brazil, North America, and Asia was genotyped using genotyping by sequencing (GBS). Population structure was assessed by Bayesian and multivariate approaches. Genetic diversity was analyzed using metrics such as the fixation index, nucleotide diversity, genetic dissimilarity, and linkage disequilibrium. The software BayeScan was used to detect selection signatures between Brazilian and Asian accessions as well as among Brazilian germplasms. Region of origin, company of origin, and relative maturity group (RMG) all had a significant influence on population structure. Varieties belonging to the same company and especially to the same RMG exhibited a high level of genetic similarity. This result was exacerbated among early maturing accessions. Brazilian soybean showed significantly lower genetic diversity when compared to Asian accessions. This was expected, because the crop’s region of origin is its main genetic diversity reserve. We identified 7 genomic regions under selection between the Brazilian and Asian accessions, and 27 among Brazilian varieties developed by different companies. Associated with these genomic regions, we found 96 quantitative trait loci (QTLs) for important soybean breeding traits such as flowering, maturity, plant architecture, productivity components, pathogen resistance, and seed composition. Some of the QTLs associated with the markers under selection have genes of great importance to soybean’s regional adaptation. The results reported herein allowed to expand the knowledge about the organization of the genetic variability of the Brazilian soybean germplasm. Furthermore, it was possible to identify genomic regions under selection possibly associated with the adaptation of soybean to Brazilian environments.
Integrating Effective 'Writing to Communicate' Experiences in Engineering Courses: Guidelines and Examples*

Incorporating writing into the curriculum is a challenge for engineering faculty. Constructivist and knowledge transformation frameworks of how writing helps build knowledge suggest that successful writing experiences in engineering are `writing to communicate'. Drawing from that literature, the author advocates five guidelines for integrating effective `writing to communicate' experience into undergraduate engineering courses: authentic investigation, tying the writing to the technical content, an authentic welldefined audience, providing useful practice for an engineering career and not being overly burdensome to the engineering faculty instructor. Specific examples of activities based on these guidelines, from classroom, homework and laboratory activities in sophomore, junior and senior-level classes serve as suggestions for faculty seeking to creatively incorporate writing throughout the engineering curriculum.
Epidemiological, Radiographical, and Laboratorial Characteristics of Chinese Asymptomatic Cases With COVID-19: A Systematic Review and Meta-Analysis

The comprehensive understanding of the characteristics of asymptomatic cases are helpful for the identification and management of patients with asymptomatic COVID-19 infection. Four electronic databases were searched from December 1, 2019 to February 8, 2022 for relevant articles. Data synthesis, subgroup analysis, and sensitivity analysis were performed on the included studies. I2 and Q tests were applied to evaluate heterogeneity across studies. The risk of publication bias was assessed and visualized using a funnel plot. A total of 45 studies consisting of 2,655 patients with no symptoms at the screening point were included. Pooled results showed that in China, 65% of initial no-symptoms COVID-19 patients did not present any COVID-19-related symptom during follow-up or by end of disease course (asymptomatic infections). High proportions of initial no-symptoms COVID-19 patients (76%) and patients with asymptomatic infection (55%) had abnormal CT features at the screening point. High proportion of patients with asymptomatic infection had been detected Ig G+ (72%) and/or Ig M+ (57%) at the screening point. The chest CT scan and SARS-CoV-2-specific antibody testing could serve as effective supplementary methods to identify asymptomatic cases in the early stage of SARS-CoV-2 infection. However, the chest CT scan and the SARS-CoV-2-specific IgM and IgG testing should not replace reverse transcription–polymerase chain reaction (RT-PCR) for screening in asymptomatic patients. The combination of repeated RT-PCR, chest CT scans, and the SARS-CoV-2-specific IgM and IgG testing should be performed for those highly suspected SARS-CoV-2 infections. Systematic Review Registration https://www.crd. york.ac. uk/PROSPERO/#recordDetails, identifier: CRD 42021261130.
Relationships Between Climate Mitigation Actions and Mental Health: A Systematic Review of the Research Landscape

The impacts of climate change-related events on mental health and emotional wellbeing have gained increased attention in recent years. However, research exploring how climate mitigation action, i.e., moving toward more sustainable lifestyles, interrelates with mental health is arguably a more hidden body of work. This research is scattered across fields and uses a variety of concepts to explore both the role that emotional and mental health management skills may play in enabling personal climate mitigation actions, as well as the ways in which accelerated transitions toward lower carbon emitting ways of life may impact on mental wellbeing at both an individual and societal level. Our systematic review therefore aims to bring together for the first time research which has been undertaken in the emerging area of mental health and climate mitigation action. To facilitate this exploration, systematic Web of Science searches were undertaken which: (1) identified 165 publications exploring climate change and mental health issues broadly, and (2) identified 26 publications relating climate mitigation actions with specific mental health impacts (anxiety, trauma, suicide, OCD). We find that mental health is primarily being seen as an outcome of climate change impacts, not a factor in our ability to work to avoid them. The limited work which does exist around mental health and climate mitigation action focusses on anxiety and trauma and spans the psychological, psychosocial, public health and wider social sciences. Anxiety and trauma-avoidance has been found to both stimulate and stifle action in different circumstances. One explanation may be the role organizations (and other social structures like family or gender identities) play in maintaining cultures which either support social defenses against mitigation action or provide emotionally-safe spaces for building climate commitment. Anticipating potential mental health impacts during policy planning—and putting in place appropriate support measures—will be vital to successfully meeting climate targets. We therefore conclude with implications for policy and practice, including the need to: build appropriate psychological support into behavior change interventions, work with groups who can provide each other with emotional peer support, and ensure health and social care professionals are given adequate training.
Emotional (dys)Regulation and Family Environment in (non)Clinical Adolescents’ Internalizing Problems: The Mediating Role of Well-Being

Adolescence is a period of several changes and a time when young people are confronted with some difficult tasks of dealing with a diversity of emotions and building their own identity. Therefore, it is a period of higher vulnerability for the development of internalizing problems. The present paper aims to study some constructs considered relevant to adolescents’ adjustment and/or internalizing disorders, emphasizing the role of well-being, emotional regulation and family environment. Therefore, this research aims to (1) test the mediating role of well-being in the relationship between emotional regulation difficulties, the family environment, and internalizing problems, and (2) understand the differences between adolescents with a higher and lower risk of presenting internalizing problems. In the study, 723 adolescents of both sexes (12–18 years old) from middle to high school completed self-report questionnaires. The results indicated that the mediating role of well-being was partially established between emotional regulation difficulties and internalizing problems, explaining 31% of the variance in these problems. Well-being was also considered a partial mediator between family environment (cohesion and support and conflict) and internalizing problems, explaining 19 and 26% of the variance, respectively. Furthermore, the group with a higher risk of developing internalizing problems (n = 130) revealed higher levels of emotional regulation difficulties and family conflict. In contrast, this group reported less family cohesion and support and lower levels of well-being. The main results of the present study provide relevant data in the context of clinical practice. Important implications are also discussed for the design of psychopathology prevention programs and the promotion of global well-being with adolescents. Considering the limitations of the present study, such as the nonrandom sampling process and the reduced number of participants included in the clinical group, these results need to be deepened in future research in this area.
In Vitro Characterization of 177Lu-DOTA-M5A Anti-Carcinoembryonic Antigen Humanized Antibody and HSP90 Inhibition for Potentiated Radioimmunotherapy of Colorectal Cancer

Carcinoembryonic antigen (CEA) is an antigen that is highly expressed in colorectal cancers and widely used as a tumor marker. 131I and 90Y-radiolabeled anti-CEA monoclonal antibodies (mAbs) have previously been assessed for radioimmunotherapy in early clinical trials with promising results. Moreover, the heat shock protein 90 inhibitor onalespib has previously demonstrated radiotherapy potentiation effects in vivo. In the present study, a 177Lu-radiolabeled anti-CEA hT84.66-M5A mAb (M5A) conjugate was developed and the potential therapeutic effects of 177Lu-DOTA-M5A and/or onalespib were investigated. The 177Lu radiolabeling of M5A was first optimized and characterized. Binding specificity and affinity of the conjugate were then evaluated in a panel of gastrointestinal cancer cell lines. The effects on spheroid growth and cell viability, as well as molecular effects from treatments, were then assessed in several three-dimensional (3D) multicellular colorectal cancer spheroid models. Stable and reproducible radiolabeling was obtained, with labeling yields above 92%, and stability was retained at least 48 h post-radiolabeling. Antigen-specific binding of the radiolabeled conjugate was demonstrated on all CEA-positive cell lines. Dose-dependent therapeutic effects of both 177Lu-DOTA-M5A and onalespib were demonstrated in the spheroid models. Moreover, effects were potentiated in several dose combinations, where spheroid sizes and viabilities were significantly decreased compared to the corresponding monotherapies. For example, the combination treatment with 350 nM onalespib and 20 kBq 177Lu-DOTA-M5A resulted in 2.5 and 2.3 times smaller spheroids at the experimental endpoint than the corresponding monotreatments in the SNU1544 spheroid model. Synergistic effects were demonstrated in several of the more effective combinations. Molecular assessments validated the therapy results and displayed increased apoptosis in several combination treatments. In conclusion, the combination therapy of anti-CEA 177Lu-DOTA-M5A and onalespib showed enhanced therapeutic effects over the individual monotherapies for the potential treatment of colorectal cancer. Further in vitro and in vivo studies are warranted to confirm the current study findings.
ALSA: Associative Learning Based Supervised Learning Algorithm for SNN

Spiking neural network (SNN) is considered to be the brain-like model that best conforms to the biological mechanism of the brain. Due to the non-differentiability of the spike, the training method of SNNs is still incomplete. This paper proposes a supervised learning method for SNNs based on associative learning: ALSA. The method is based on the associative learning mechanism, and its realization is similar to the animal conditioned reflex process, with strong physiological plausibility and rationality. This method uses improved spike-timing-dependent plasticity (STDP) rules, combined with a teacher layer to induct spikes of neurons, to strengthen synaptic connections between input spike patterns and specified output neurons, and weaken synaptic connections between unrelated patterns and unrelated output neurons. Based on ALSA, this paper also completed the supervised learning classification tasks of the IRIS dataset and the MNIST dataset, and achieved 95.7 and 91.58% recognition accuracy, respectively, which fully proves that ALSA is a feasible SNNs supervised learning method. The innovation of this paper is to establish a biological plausible supervised learning method for SNNs, which is based on the STDP learning rules and the associative learning mechanism that exists widely in animal training.
Adaptation to Varying Salinity in Halomonas elongata: Much More Than Ectoine Accumulation

The halophilic γ-proteobacterium Halomonas elongata DSM 2581T thrives at salt concentrations well above 10 % NaCl (1.7 M NaCl). A well-known osmoregulatory mechanism is the accumulation of the compatible solute ectoine within the cell in response to osmotic stress. While ectoine accumulation is central to osmoregulation and promotes resistance to high salinity in halophilic bacteria, ectoine has this effect only to a much lesser extent in non-halophiles. We carried out transcriptome analysis of H. elongata grown on two different carbon sources (acetate or glucose), and low (0.17 M NaCl), medium (1 M), and high salinity (2 M) to identify additional mechanisms for adaptation to high saline environments. To avoid a methodological bias, the transcripts were evaluated by applying two methods, DESeq2 and Transcripts Per Million (TPM). The differentially transcribed genes in response to the available carbon sources and salt stress were then compared to the transcriptome profile of Chromohalobacter salexigens, a closely related moderate halophilic bacterium. Transcriptome profiling supports the notion that glucose is degraded via the cytoplasmic Entner-Doudoroff pathway, whereas the Embden-Meyerhoff-Parnas pathway is employed for gluconeogenesis. The machinery of oxidative phosphorylation in H. elongata and C. salexigens differs greatly from that of non-halophilic organisms, and electron flow can occur from quinone to oxygen along four alternative routes. Two of these pathways via cytochrome bo' and cytochrome bd quinol oxidases seem to be upregulated in salt stressed cells. Among the most highly regulated genes in H. elongata and C. salexigens are those encoding chemotaxis and motility proteins, with genes for chemotaxis and flagellar assembly severely downregulated at low salt concentrations. We also compared transcripts at low and high-salt stress (low growth rate) with transcripts at optimal salt concentration and found that the majority of regulated genes were down-regulated in stressed cells, including many genes involved in carbohydrate metabolism, while ribosome synthesis was up-regulated, which is in contrast to what is known from non-halophiles at slow growth. Finally, comparing the acidity of the cytoplasmic proteomes of non-halophiles, extreme halophiles and moderate halophiles suggests adaptation to an increased cytoplasmic ion concentration of H. elongata. Taken together, these results lead us to propose a model for salt tolerance in H. elongata where ion accumulation plays a greater role in salt tolerance than previously assumed.
Effect of Long-Term Agricultural Management on the Soil Microbiota Influenced by the Time of Soil Sampling

Application of agrochemicals and mechanization enabled increasing agricultural productivity yet caused various environmental and soil health-related problems. Agricultural practices affect soil microorganisms, which are the key players of many ecosystem processes. However, less is known about whether this effect differs between time points. Therefore, soil was sampled in winter (without crop) and in summer (in the presence of maize) from a long-term field experiment (LTE) in Bernburg (Germany) managed either under cultivator tillage (CT) or moldboard plow (MP) in combination with either intensive nitrogen (N)-fertilization and pesticides (Int) or extensive reduced N-fertilization without fungicides (Ext), respectively. High-throughput sequencing of 16S rRNA gene and fungal ITS2 amplicons showed that changes in the microbial community composition were correlated to differences in soil chemical properties caused by tillage practice. Microbial communities of soils sampled in winter differed only depending on the tillage practice while, in summer, also a strong effect of the fertilization intensity was observed. A small proportion of microbial taxa was shared between soils from the two sampling times, suggesting the existence of a stable core microbiota at the LTE. In general, taxa associated with organic matter decomposition (such as Actinobacteria, Bacteroidetes, Rhizopus, and Exophiala) had a higher relative abundance under CT. Among the taxa with significant changes in relative abundances due to different long-term agricultural practices were putative pathogenic (e.g., Gibellulopsis and Gibberella) and beneficial microbial genera (e.g., Chitinophagaceae, Ferruginibacter, and Minimedusa). In summary, this study suggests that the effects of long-term agricultural management practices on the soil microbiota are influenced by the soil sampling time, and this needs to be kept in mind in future studies for the interpretation of field data.
Therapeutic Targeting Hypoxia-Inducible Factor (HIF-1) in Cancer: Cutting Gordian Knot of Cancer Cell Metabolism

Metabolic alterations are one of the hallmarks of cancer, which has recently gained great attention. Increased glucose absorption and lactate secretion in cancer cells are characterized by the Warburg effect, which is caused by the metabolic changes in the tumor tissue. Cancer cells switch from oxidative phosphorylation (OXPHOS) to aerobic glycolysis due to changes in glucose degradation mechanisms, a process known as “metabolic reprogramming”. As a result, proteins involved in mediating the altered metabolic pathways identified in cancer cells pose novel therapeutic targets. Hypoxic tumor microenvironment (HTM) is anticipated to trigger and promote metabolic alterations, oncogene activation, epithelial-mesenchymal transition, and drug resistance, all of which are hallmarks of aggressive cancer behaviour. Angiogenesis, erythropoiesis, glycolysis regulation, glucose transport, acidosis regulators have all been orchestrated through the activation and stability of a transcription factor termed hypoxia-inducible factor-1 (HIF-1), hence altering crucial Warburg effect activities. Therefore, targeting HIF-1 as a cancer therapy seems like an extremely rational approach as it is directly involved in the shift of cancer tissue. In this mini-review, we present a brief overview of the function of HIF-1 in hypoxic glycolysis with a particular focus on novel therapeutic strategies currently available.
Allocation of Credit Resources and “Borrow to Lend” Activities: Evidence From Chinese-Listed Companies

Credit distribution is uneven in the domestic financial market since it is relatively easy for listed companies, mainly state-owned enterprises, to obtain banks’ funds. Unbalanced credit distribution has caused some listed companies to participate in “Borrow to Lend” activities. Based on the traditional “financing priority” theory and credit rationing theory, this paper studies the “Borrow to Lend” shadow banking activities of China’s non-financial listed companies based on the 2007–2018 financial statement data of Chinese-listed companies and discusses the micro-level and macro-level related factors behind this activity. The empirical results show that China’s non-financial listed companies, especially the state-owned enterprises, are participating in obvious “Borrow to Lend” activities. The real economy’s rate of return shows a negative relationship with “Borrow to Lend” activities at the level of individual companies and their industries. This article uses the exogenous growth part of M2 growth to measure monetary policy tightness in terms of macro and credit policies. It uses the ratio of state-owned enterprise loans to total corporate loans as an approximate indicator of the credit distribution structure. The empirical results indicate that state-owned enterprises’ “Borrow to Lend” activities have shifted in the same direction as the tightening of monetary policy after the financial crisis. The proportion of state-owned enterprise loans positively correlates with state-owned enterprises’ “Borrow to Lend” activities.
Comparative Transcriptome Analysis Provides Insight into Spatio-Temporal Expression Characteristics and Genetic Regulatory Network in Postnatal Developing Subcutaneous and Visceral Fat of Bama Pig

The depot differences between Subcutaneous Fat (SAF) and Visceral Fat (VAF) are critical for human well-being and disease processes in regard to energy metabolism and endocrine function. Miniature pigs (Sus scrofa) are ideal biomedical models for human energy metabolism and obesity due to the similarity of their lipid metabolism with that of humans. However, the regulation of differences in fat deposition and development remains unclear. In this study, the development of SAF and VAF was characterized and compared in Bama pig during postnatal development (infancy, puberty and adulthood), using RNA sequencing techniques (RNA-Seq). The transcriptome of SAF and VAF was profiled and isolated from 1-, 3- and 6 months-old pigs and identified 23,636 expressed genes, of which 1,165 genes were differentially expressed between the depots and/or developmental stages. Upregulated genes in SAF showed significant function and pathway enrichment in the central nervous system development, lipid metabolism, oxidation-reduction process and cell adhesion, whereas genes involved in the immune system, actin cytoskeleton organization, male gonad development and the hippo signaling pathway were preferentially expressed in VAF. Miner analysis of short time-series expression demonstrated that differentiation in gene expression patterns between the two depots corresponded to their distinct responses in sexual development, hormone signaling pathways, lipid metabolism and the hippo signaling pathway. Transcriptome analysis of SAF and VAF suggested that the depot differences in adipose tissue are not only related to lipid metabolism and endocrine function, but are closely associated with sexual development and organ size regulation.