Miracle-dz/UniFAR-FTUs huggingface dataset:
Normal High HbA1c a Risk Factor for Abnormal Pain Threshold in the Japanese Population

Purpose: Small fiber dysfunction is common in subjects with diabetic polyneuropathy (DPN). It is unsettled, however, whether marginal glucose intolerance is implicated in the onset and progression of small fiber dysfunction. Herein, we explored the relationship between glycated hemoglobin levels (HbA1c) and pain sensation in the Japanese population. Methods: A population-based study of 894 individuals (352 men, 542 women; average age 53.8 ± 0.5 years) and 55 subjects with impaired fasting glucose (IFG) in the 2017 Iwaki project were enrolled in this study. Individuals with diabetes were excluded. Relationships between pain threshold for intraepidermal electrical stimulation (P-IES) and parameters associated with metabolic syndrome were examined. Results: P-IES was elevated with increasing of age in women but not in men. Average P-IES (mA) was increased in IFG subjects (n = 55, 0.20 ± 0.03) compared with normoglycemic/non-IFG individuals (n = 894, 0.15 ± 0.01) (p < 0.01). It was comparable between IFG and a group of normal high HbA1c (5.9–6.4%). Univariate linear regression analyses showed no influence of sex, triglyceride, or cholesterol on the value of P-IES. In contrast, there were significant correlations between P-IES and serum HbA1c level (ß = 0.120, p < 0.001) Adjustments for the multiple clinical measurements confirmed positive correlation of P-IES with HbA1c (ß = 0.077, p = 0.046). Conclusion: Individuals with normal high HbA1c exhibited an elevated P-IES in a healthy Japanese population which may be useful for the screening of subclinical DPN.
Predicting species occurrences with habitat network models

Abstract Biodiversity conservation requires modeling tools capable of predicting the presence or absence (i.e., occurrence‐state) of species in habitat patches. Local habitat characteristics of a patch (lh), the cost of traversing the landscape matrix between patches (weighted connectivity [wc]), and the position of the patch in the habitat network topology (nt) all influence occurrence‐state. Existing models are data demanding or consider only local habitat characteristics. We address these shortcomings and present a network‐based modeling approach, which aims to predict species occurrence‐state in habitat patches using readily available presence‐only records. For the tree frog Hyla arborea in the Swiss Plateau, we delineated habitat network nodes from an ensemble habitat suitability model and used different cost surfaces to generate the edges of three networks: one limited only by dispersal distance (Uniform), another incorporating traffic, and a third based on inverse habitat suitability. For each network, we calculated explanatory variables representing the three categories (lh, wc, and nt). The response variable, occurrence‐state, was parametrized by a sampling intensity procedure assessing observations of comparable species over a threshold of patch visits. The explanatory variables from the three networks and an additional non‐topological model were related to the response variable with boosted regression trees. The habitat network models had a similar fit; they all outperformed the non‐topological model. Habitat suitability index (lh) was the most important predictor in all networks, followed by third‐order neighborhood (nt). Patch size (lh) was unimportant in all three networks. We found that topological variables of habitat networks are relevant for the prediction of species occurrence‐state, a step‐forward from models considering only local habitat characteristics. For any habitat patch, occurrence‐state is most prominently influenced by its habitat suitability and then by the number of patches in a wide neighborhood. Our approach is generic and can be applied to multiple species in different habitats.
Surprising spatiotemporal stability and frequency-independence across multiple fitness peaks driving adaptive radiation in the wild

The effect of the environment on fitness in natural populations is a fundamental question in evolutionary biology. However, most empirical field studies of fitness do not experimentally manipulate phenotypes or environmental conditions and rarely investigate more than a single species or population. Thus, the relative importance of the competitive environment versus intrinsic organismal performance in shaping the location, height, and fluidity of fitness peaks on the adaptive landscape remains largely unknown. We experimentally tested the effect of competitive environment on a multi-peak fitness landscape driving a microendemic adaptive radiation of generalist and trophic specialist pupfishes on San Salvador Island, Bahamas. We manipulated phenotypes, by generating lab-reared hybrid crosses, and competitive environment, by altering the frequency of rare phenotypes within field enclosures in their natural hypersaline lake environments on San Salvador. We tracked the growth and survival of 2,611 F4/F5 hybrids for 3 to 11 months in high- and low-frequency treatments replicated across two lake populations. We found strong evidence for frequency-dependent growth rates within and between enclosures, but no evidence for frequency-dependent survival differences. However, both fitness proxies supported a complex fitness landscape isolating generalist phenotypes on a local fitness peak separated by a small fitness valley from a higher fitness peak for molluscivores and a large fitness valley isolating the scale-eating phenotype in all trait dimensions. The striking consistency of this multi-peak fitness landscape across competitive environments, multivariate trait axes, and a previous field experiment provides experimental evidence for stasis, possibly due to fixed biomechanical constraints on organismal performance. These results challenge existing theory and highlight the interplay of organism and environment underlying the static and dynamic features of fitness landscapes.
Human oocytes harbouring damaged dna can complete meiosis-i

Chromosomal abnormalities such as aneuploidies and DNA damage are considered a major threat to the establishment of healthy eggs and embryos. Recent landmark studies showed that mouse oocytes with damaged DNA can resume meiosis and undergo Germinal Vesicle Breakdown (GVBD), but then arrest in metaphase of meiosis-I in a process involving Spindle Assembly Checkpoint (SAC) signalling. Such a mechanism could help prevent the generation of metaphase-II (Met-II) eggs with damaged DNA. However we report that this is not the case in the human oocyte. DNA damage prevents human oocytes from undergoing GVBD in some cases. Strikingly however, most oocytes harbouring DNA damage progress through meiosis-I and subsequently extrude the first polar body (PB1) to form a metaphase-II egg, revealing the absence of a DNA-damage-induced SAC response. Analysis of the resulting metaphase-II eggs revealed highly disorganised spindles with misaligned and heavily damaged chromosomes. Our results suggest that DNA damage accumulated in meiosis-I, such as could occur during in vitro maturation procedures, does not prevent polar body extrusion and therefore could persist in morphologically normal looking metaphase-II eggs.
Residual efficacy of methoxyfenozide applied on different grain commodities for the control of three stored-product insect pests

Laboratuvar kosullarinda 1, 2 ve 4 mg kg -1 aktif madde konsantrasyonlarinda uygulama yapilmis (bugday, misir, celtik ve yulaf) urunlerde, Oryzaephilus surinamensis (Linnaeus, 1758) (Coleoptera: Silvanidae), Tribolium castaneum Herbst, 1797 (Coleoptera: Tenebrionidae) ve Trogoderma granarium Everts, 1898 (Coleoptera: Dermestidae)'un son donem larvalari uzerinde metoksifenozidin kalinti etkinligi degerlendirilmistir. Bu deneme, Ziraat Universitesi, Entomoloji Bolumu (Faisalabad, Pakistan)’nde 2018 yilinda gerceklestirilmistir. Uygulama yapilmis urunlere zararli bocekler birakildiktan farkli sureler (0, 2, 4, 8, 12 ve 16 hafta) sonrasinda, alti biyolojik analiz yapilmistir. Uygulama yapilmis urunlerdeki larvalarin ergin olma orani, 4 mg kg -1 'de 0. haftada %15'i gecmezken, test edilen tum urunlerde ve tum bocek turlerinde 12. haftada %36'dan daha az olarak saptanmistir. Metoksifenozid, genellikle yulaf uzerinde sirasiyla bugday, misir ve pirince gore T. granarium 'a gore O. surinamensis ve T. castaneum acisindan daha fazla etkiliyken; T. granarium 'a karsi ise yulaf, misir ve pirince gore bugday uzerinde daha etkili olmustur. Sonuclar, O. surinamensis , T. castaneum ve T. granarium acisindan metoksifenozidin kalinti kontrolu icin buyuk potansiyele sahip oldugunu ve geleneksel sinir sistemi insektisitlerinin yerini alabilecegini gostermektedir.
FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds

Methods to predict RNA 3D structures from sequence are needed to understand the exploding number of RNA molecules being discovered across biology. As assessed during community-wide RNA-Puzzles trials, Rosetta’s Fragment Assembly of RNA with Full-Atom Refinement (FARFAR) enables accurate prediction of complex folds, but it remains unclear how much human intervention and experimental guidance is needed to achieve this performance. Here, we present FARFAR2, a protocol integrating recent innovations with updated RNA fragment libraries and helix modeling. In 16 of 21 RNA-Puzzles revisited without experimental data or expert intervention, FARFAR2 recovers structures that are more accurate than the original models submitted by our group and other participants during the RNA-Puzzles trials. In five prospective tests, pre-registered FARFAR2 models for riboswitches and adenovirus VA-I achieved 3–8 Å RMSD accuracies. Finally, we present a server and three large model archives (FARFAR2-Classics, FARFAR2-Motifs, and FARFAR2-Puzzles) to guide future applications and advances.
[Alternative means of drug therapy in cancer: letril].

: Letril (amygdaline) is one of drugs of alternative therapy for cancer that is used over three decades and relates to cyanogenic glycosides received from kernels of various fruits (almonds, apricots, peaches, etc. The basis of suggestion of letril as antitumor agent is hypotheses about selective fermentative splitting of amygdaline in tumor cells with developing of cyanide that should cause to apoptosis as a result of aerobic glycolysis suppression. None of these assumptions found their experimental confirmation. In clinical trials there was established inefficiency of letril with a very high probability to develop severe cyanide intoxication. Despite obtained scientific data and absence of permission from the supervising institutions (FDA) letril is still advertised, produced and distributed as anti-tumor drug.
Mechanisms of distributed working memory in a large-scale model of the macaque neocortex

Working memory, the brain’s ability to retain and manipulate information internally, has been traditionally associated with persistent neural firing in localized brain areas such as those in the frontal cortex (Fuster 1973, Funahashi et al., 1989; Goldman-Rakic 1995; Romo et al., 1999; Rigotti et al., 2013; Kopec et al., 2015; Inagaki et al., 2019). However, self-sustained neural persistent activity during working memory is present in multiple brain regions (Romo et al., 2004; Christophel et al., 2017; Leavitt et al., 2017; Sreenivasan and D’Esposito, 2019), the underlying mechanism is unknown. We developed an anatomically constrained large-scale computational model of the macaque cortex endowed with a macroscopic gradient of synaptic excitation, to investigate the origin of distributed working memory representation. We found that long-range inter-areal reverberation can support the emergence of persistent activity patterns across multiple cortical regions, by virtue of a robust bifurcation in space, even when none of isolated local areas is capable of generating persistent activity. The model uncovered a host of distinct persistent activity patterns (attractor states), and provides experimentally testable predictions that cannot be explained in local circuit models. Simulating cortical lesions reveals that distributed activity patters are resilient against simultaneous lesions of multiple cortical areas, but depend on areas that form the core of the entire cortex. This work provides a theoretical framework for identifying large-scale brain mechanisms and computational principles of distributed cognitive processes.
Species identification and antimicrobial susceptibility profile of bacteria causing subclinical mastitis in buffalo

Vásquez-García A. , Silva T.S. , Almeida-Queiroz S.R. , Godoy S.H. S. , Fernandes A.M., Sousa R.L. M. & Franzolin R. 2017. Species identification and antimicrobial profile of bacteria causing subclinical mastitis in buffalo. Pesquisa Veterinária Brasileira 37(5):447-452. Departamento de Zootecnia, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte 225, Pirassununga, SP 13635-900, Brazil. E-mail: rfranzol@usp.br Microorganisms causing subclinical mastitis in water buffalo were isolated from 20 buffalo milk samples at four dairy farms located in central region of São Paulo State, Brazil, through testing of somatic cell count (SCC), standard plate count (SPC), biochemical, PCR assays and antimicrobial profile. The SCC showed average of 721,000 cells/mL in the milk, indicating the presence of subclinical mastitis. The overall average for SPC was 1.8 x 104 CFU/mL. The microorganism most frequently isolation according to biochemical tests were: Staphylococcus epidermidis (17%), Staphylococcus aureus (15%), Bacillus spp. (14%), Acinetobacter spp. (12.5%); with intermediate frequency: Pseudomonas aeruginosa (9.5%); Shigella flexneri (7.0%), Streptococcus spp. (5.5%), Corynebacterium spp. (5.0%), Escherichia coli (4.5%), Serratia marcescens (4.0%), Stenotrophomonas maltophilia (4.0%), and low incidence: Klebsiella rhinoscleromatis (0.5%), Klebsiella ozaenae (0.5%), Tatumella ptyseos (0.5%), Enterobacter cloacae (0.5%). The molecular analysis indicated that samples positive by culture method of the genera Staphylococcus, Streptococcus and E. coli were positive by PCR. Para S. aureus and S. epidermidis the highest percentages of observed sensitivity were gentamicin (100%) and vancomycin (100%); for the genus Streptococcus to gentamicin and oxacillin and E. coli to Ampicilin. These findings may help in the control and treatment of subclinical mastitis in buffaloes and contribute to improving the efficiency and quality of the milk produced.
Development Model and Spatial Reconstruction of Rural Tourism in Hainan from the Perspective of Agricultural Sustainable Development

Rural tourism projects are mainly concentrated in rural areas, and its core factors and unique selling points are rural, that is, rural unique local flavor and rural customs. In view of the current situation of rural tourism development in Hainan, this paper makes a concrete analysis of the existing problems in the development of rural tourism in Hainan, and puts forward corresponding countermeasures, with a view to benefiting the continuous development of rural tourism in Hainan. Furthermore, it provides a good reference for contemporary rural space, planning and design, avoids the waste and excessive development of resource elements in the process of rural space construction and development, and promotes the optimal utilization of tourism resources. Hainan's rural tourism began to upgrade and rural tourism promoted the adjustment of Hainan's industrial structure. Design corresponding development models, business models, provide policy support, strengthen human resources training, upgrade market demand, accelerate industrial integration based on civilized ecological construction, and promote rural tourism to a formal, orderly and sustainable development path. Agricultural multi-function refers to the economic function of agriculture in addition to providing food and other commodity output, but also has the environmental and social functions related to rural environment, rural agricultural landscape, Rural Agricultural Cultural Inheritance and another non-commodity output. He emphasizes the sustainable development of agriculture, which is the inevitable trend of agricultural development in the post-industrial era. Rural tourism is a kind of tourism development which combines agricultural production, rural life and ecological environment. In recent years, rural tourism has brought opportunities for rural development and promoted the development of rural economy, but most products lack innovative consciousness and humanistic care. It does not meet the needs of the times to develop multi-functional agriculture.
Mapping of Genetic Loci Conferring Resistance to Leaf Rust From Three Globally Resistant Durum Wheat Sources

Genetic resistance in the host plant is the most economical and environmentally friendly strategy for controlling wheat leaf rust, caused by Puccinia triticina Eriks. The durum wheat lines Gaza (Middle East), Arnacoris (France) and Saragolla (Italy) express high levels of resistance to the Mexican races of P. triticina. Three recombinant inbred line (RIL) populations, derived from crosses of each of these resistance sources to the susceptible line ATRED #2, were evaluated for leaf rust reactions at CIMMYT’s leaf rust nurseries in Mexico. Genetic analyses of host reactions suggested oligogenic control of resistance in all populations. The F8 RILs from each cross were genotyped using the Illumina iSelect 90K array, and high-density genetic maps were constructed for each population. Using composite interval mapping, a total of seven quantitative trait loci (QTL) that provide resistance to leaf rust were identified. Two QTL designated as QLr.usw-6BS and QLr.usw-6BL were identified on chromosome 6B in Gaza, which explained up to 78.5% and 21.3% of the observed leaf rust severity variance, respectively. A major QTL designated as QLr.usw-7BL was detected on the long arm of chromosome 7B in Arnacoris, which accounted for up to 65.9% of the disease severity variance. Arnacoris also carried a minor QTL on chromosome 1BL, designated as QLr.usw-1BL.1 that explained up to 17.7% of the phenotypic variance. Three QTL conferred leaf rust resistance in Saragolla, namely QLr.usw-2BS, QLr.usw-3B, and QLr.usw-1BL.2, which accounted for up to 42.3, 9.4, and 7.1% of the phenotypic variance, respectively. Markers flanking each QTL were physically mapped against the durum wheat reference sequence and candidate genes involved in disease resistance were identified within the QTL intervals. The QTL identified in this study and their closely linked markers are useful resources for gene pyramiding and breeding for durable leaf rust resistance in durum wheat.
Membrane composition influences the conformation and function of the dopamine transporter in vivo

The biophysical and biochemical properties of membrane lipids can alter the conformation and function of membrane-spanning proteins, yet the specific, physiological consequence in vivo of changing the membrane milieu for a specific protein has been rarely investigated. Using various genetic approaches to eliminate expression of the membrane-associated protein Flotillin-1, we have found that the lipid environment of the dopamine transporter (DAT) is necessary for mice to respond to amphetamine but not cocaine, because the localization of DAT to cholesterol-rich membranes is required for a DAT conformation that is essential for reverse transport of dopamine. Furthermore, a conditional rather than constitutive loss-of-function approach was necessary to reveal this phenotype, indicating a broader role for membrane-protein interactions that are modulated by Flotillin-1. Taken together, these findings demonstrate how interaction of a transmembrane protein with its membrane environment can regulate distinct events in the vertebrate brain that give rise to specific behavioral outcomes.
Methyl Jasmonate and Salinity Increase Anthocyanin Accumulation in Radish Sprouts

Plant secondary metabolites with antioxidant properties, such as anthocyanins, are considered to have an important commercial value for some crops. Although anthocyanin concentration increases in response to various stimuli in plants, the mechanism of anthocyanin accumulation under multiple stimuli is not yet well understood. Here, we examined the effects of methyl jasmonate (MJ) and salinity on anthocyanin accumulation in radish (Raphanus sativus) sprouts. MJ treatments induced anthocyanin accumulation, which was enhanced by simultaneous treatment with salinity (200 mM NaCl), accompanied by growth restrictions. Sprouts treated with salinity alone did not induce anthocyanin accumulation, although sprout growth was restricted. Co-treatment with MJ and salinity increased hydrogen peroxide, total phenol content, and radical scavenging capacity more strongly than was achieved when each treatment was applied singly. Accumulation of anthocyanin was dependent on NaCl concentration and light intensity. Changing MJ and salinity treatment periods had different effects on anthocyanin accumulation and growth restriction, indicating that these phenomena might be differentially regulated. These results may provide an effective anthocyanin accumulation method without reducing plant biomass.
Investigation of dormancy and storage potential of seeds of yellow passion fruit

Abstract: Passiflora actinia Hooker is a passion fruit species native to Brazil, typically found in the Atlantic and Araucaria Forests. It has economic relevance (edible fruit) and medicinal value (sedative and anxiolytic properties), in addition to being used for vegetative propagation, as rootstock for other Passiflora species. This study aimed at investigating the occurrence of dormancy in P. actinia seeds, and at evaluating their storage potential. The germination test considered different combinations of temperature and lighting regimes, whereas seed dormancy was assessed using different germination-inducing treatments (tegument cutting, warm water immersion, and gibberellin application). Seed viability during storage was also appraised. The results showed that seed germination should be conducted on paper at the alternating temperature of 20-30 °C, without lighting. Also, newly-harvested seeds presented physical and physiological dormancies. The immersion of seeds in water at 40 °C or 50 °C (for 5 or 10 minutes) proved to be efficient in breaking the physical dormancy. Physiological dormancy, in turn, was successfully interrupted by applying 100 mg. L-1 of gibberellic acid on the substrate paper. The storage of seeds under refrigeration, inside hermetically sealed polyethylene packaging, preserved their physiological quality for up to nine months.