Miracle-dz/UniFAR-FTUs huggingface dataset:
Observed and estimated prevalence of Covid-19 in Italy: Is it possible to estimate the total cases from medical swabs data?

During the current Covid-19 pandemic in Italy, official data are collected with medical swabs following a pure convenience criterion which, at least in an early phase, has privileged the exam of patients showing evident symptoms. However, there are evidences of a very high proportion of asymptomatic patients (e. g. Aguilar et al., 2020; Chugthai et al, 2020; Li, et al., 2020; Mizumoto et al., 2020a, 2020b and Yelin et al., 2020). In this situation, in order to estimate the real number of infected (and to estimate the lethality rate), it should be necessary to run a properly designed sample survey through which it would be possible to calculate the probability of inclusion and hence draw sound probabilistic inference. Some researchers proposed estimates of the total prevalence based on various approaches, including epidemiologic models, time series and the analysis of data collected in countries that faced the epidemic in earlier time (Brogi et al., 2020). In this paper, we propose to estimate the prevalence of Covid-19 in Italy by reweighting the available official data published by the Istituto Superiore di Sanita so as to obtain a more representative sample of the Italian population. Reweighting is a procedure commonly used to artificially modify the sample composition so as to obtain a distribution which is more similar to the population (Valliant et al., 2018). In this paper, we will use post-stratification of the official data, in order to derive the weights necessary for reweighting them using age and gender as post-stratification variables thus obtaining more reliable estimation of prevalence and lethality.
A Multi-strategy LSHADE Algorithm and its Applications on Temporal Alignment

This document outlines how at FabFitFun we have developed a bundle of machine learning models that enabled us algorithmically assemble future boxes that are shipped to our members. FabFitFun is a technology and e-commence startup that works with small vendors to discover cool products in a similar fashion to Amazon marketplace. The team of data scientists utilize our historical data which includes details of our customers and products we have sold and are planning to sell, programmatically discover new products. We use classical machine learning supervised models to classify our products and latest technologies like genetic programming, linear optimization to help business to curate products to members in a new era. Genetic programming allows us to spot repetitive features for our supervised learning models, provide product diversity via measuring how far away a newly generated collection of products are from the historically seen and the optimal solution. Our paper demonstrates novel way to evaluate algorithmically created boxes using Sharpe Ratio Concept from finance. Thus, we discover novel products based on the distance threshold from the optimal solutions and adapted way to evaluate boxes with Sharpe Scores. Utilize genetic programming to generate synthetic data, provide diversity, novelty across our products.
EFFECTS OF BREEDING FOR QUALITY ON ALFALFA ENSILABILITY

Eight alfalfa (Medicago sativa L.) populations were cut at early and late maturities in primary growth and in regrowth, wilted to 350 g dry matter (DM)/kg, and ensiled to determine if breeding for high quality affects the ensilability of the alfalfa. Two populations were of standard quality, two were of improved quality, and four were of high quality. The high–quality lines were approximately 30 g/kg DM higher in crude protein and 35 and 30 g/kg DM lower in neutral and acid detergent fiber, respectively, than the standard lines at ensiling. In contrast, there were no significant differences among populations regarding ensiling characteristics [water–soluble carbohydrate (WSC) concentration, buffering capacity (BC), and WSC/BC ratio] in the unensiled forage. However, the three highest BC values were in three of the four high–quality lines, but the other high–quality line had the highest WSC/BC ratio of the eight lines. Silage pH and lactic and acetic acid concentrations varied significantly by population. The population with the best fermentation (lowest pH and acetic acid, highest lactic acid) was a high–quality line. The other three high–quality lines were numerically worse (0.03 to 0.09) than the standard lines in pH, although only one was significant. Overall, the magnitudes of these differences were small practically and not necessarily in an adverse direction for all high–quality populations. These results suggest that present efforts in breeding for high quality are not having a substantial negative effect on ensiling.
Weighted vs. Unweighted Mean Performance of Varieties across Environments

If within-environment error and variety × environment interaction variances are heterogeneous across environments, weighted means may provide more precise estimates of varietal mean performance than the arithmetic (unweighted) mean. The objective of this study was to compare the arithmetic mean (Y A ) and two types of weighted means (Y R and Y E ) as estimators of varietal performance(.)
Uses of tree species producing gum arabic in Karamoja, Uganda

This article presents an inventory of the uses of the tree species producing gum arabic by the local community in the Karamoja region. The study was conduced in 2000 using semi-structured interviews, focal group discussions and participants' observation. There were three tree genera with a total of six species that produced gum arabic. These were Balanites aegyptica, Acacia senegal, A. seyal, A. sieberiana, A. gerrardii and Lanea humilis. The dominant species producing gum arabic were A. senegal (85%), A. seyal (87%) and A. sieberiana (70.5%). Other uses by the local people included fencing, fuel wood, poles, crafts, medicine, intercropping, fibre and extraction of tannin. The intensity of utilization for fencing, fuel wood and poles was higher than that of gum arabic production. The local uses of gum arabic were food, gumming spears, gumming pots, gluing arrows, gluing broken stools, calabashes and joining leather. Establishing and facilitating the conservation status of these tree species are important for maintaining and even increasing the provisions for the local uses by the local community in Karamoja.
Invasion by the amphipod Gammarus pulex alters community composition of native freshwater macroinvertebrates

Assessing the effects of invading species on native community structure is often confounded by environmental factors and weakened by lack of replicated, long‐term pre‐ and post‐invasion monitoring. Here, we uncouple the community effects of a freshwater amphipod invader from environmental differences. In Irish rivers, the introduced Gammarus pulex replaces the native Gammarus duebeni celticus. However, the River Lissan in Northern Ireland is dissected by a weir that has slowed the upstream invasion by G. pulex. This allowed us in 2000 to sample three contiguous 150‐m reaches that were (1) G. pulex dominated; (2) mixed Gammarus spp. ; and (3) G. duebeni celticus only. In 2003, we resampled these reaches and one additional of mixed Gammarus species and one with only G. duebeni celticus further upstream. In temperature, conductivity, and pH, there were statistically significant but no biologically relevant differences among the five reaches of 2003, and between the three reaches surveyed in both years. Although there was evidence of recovery in macroinvertebrate diversity and richness in invaded reaches between years, continued upstream invasion was associated with sustained reductions in these community metrics as compared to un‐invaded sites. Community ordination indicated (1) different associations of community composition attributed to the distribution, abundance, and biomass of the invader; and (2) increasing similarity of invaded communities over time. The impact mechanisms of G. pulex on macroinvertebrate community composition may include predation and competition. The consequences of the observed community changes for ecosystem functioning require further investigation.
Microsatellite Genetic Diversity Analysis and Allelic Variation Comparison of Obsolete and Modern Bulgarian Bread Wheat (Triticum aestivum L.) Varieties

A set of 24 microsatellite markers was used for assessing the genetic diversity of 40 obsolete and modern Bulgarian winter wheat (Triticum aestivum L.) varieties. The total number of alleles detected was 215 with the average per locus 8.96 and varying from 4 (Xgwm480, Xgwm333) to 15 (Xgwm291). The obsolete varieties of interest were created in the period between 1911 and 1938 through selection of local populations, originating from three Bulgarian regions. The number of alleles detected in those old varieties was 182 with an average of 7.58, out of which 2.67 were rare. Regional differences in the allelic richness and diversity were also observed. Greater number of alleles was found in the old varieties, originating from South Bulgarian and Northeast landraces. Modern wheat breeding in Bulgaria has led to a decrease in the alleles per locus ratio and an increase in the allelic frequency. The same process has invalidated 44.2% of the old wheat alleles, preserved 40.9% and made possible an inflow of 14.9% n.
Characterization of a Glutamate Biosensor Based on a Novel Glutamate Oxidase Integrated into a Redox Hydrogel

A newly isolated and purified glutamate oxidase was used to construct amperometric biosensors for glutamate monitoring. The enzyme-producing microorganism belongs to the genus of Streptomyces - Streptomyces sp. Z-11-6 - and is capable of producing extracellular L-glutamate oxidase. The microorganism was obtained by mutagenesis with HNo2 from a parent strain isolated from soil of Lypetskaya region, Russia, followed by conventional screening methods. The developed biosensor is based on a coupled enzyme system (glutamate oxidase and horseradish peroxidase), the enzymes being crosslinked to a redox polymer (PVI19-dmeOs) using poly(ethylene glycol) diglycidyl ether as crosslinker. ne characteristics of the obtained biosensors were compared with those obtained for similarly constructed electrodes based on a commercially available glutamate oxidase from Yamasa Corp., Japan. The biosensors were operated at - 50 mV (vs. Ag/AgCl 0.1 M KCl) in a flow injection system. Special attention has been focused on the selectivity of the biosensors, evaluating their responses in the presence of several potentially interfering substances, possibly present in brain microdialysates (ascorbic acid, aspartate, cysteine, dopamine, DOPAC, GABA, glutamine, glycine, 5-HIAA, HMPG, HVA, serotonin, tryptophan, tyrosine and uric acid). The biosensors based on the two enzymes displayed similar bioanalytical characteristics but different selectivity patterns. (Less)
SORBS2 is a genetic factor contributing to cardiac malformation of 4q deletion syndrome

Chromosome 4q deletion is one of the most frequently detected genomic imbalance events in congenital heart disease (CHD) patients. However, a portion of CHD-associated 4q deletions do not include known CHD genes. Alignment of those 4q deletions defined a minimal overlapping region including only one gene-SORBS2. Histological analysis of Sorbs2-/- heart revealed atrial septal hypoplasia/aplasia or double atrial septum. Mechanistically, SORBS2 had a dual role in maintaining sarcomeric integrity of cardiomyocytes and specifying the fate of second heart field (SHF) progenitors through c-ABL/NOTCH/SHH axis. In a targeted sequencing of a panel of known and candidate CHD genes on 300 CHD cases, we found that rare SORBS2 variants were significantly enriched in CHD patients. Our findings indicate that SORBS2 is a regulator of cardiac development and its haploinsufficiency may contribute to cardiac phenotype of 4q deletion syndrome. The presence of double atrial septum in Sorbs2-/- hearts reveals the first molecular etiology of this rare anomaly linked to paradoxical thromboembolism.
Genome-wide identification of Aedes albopictus long noncoding RNAs and their association with dengue and zika virus infection

The Asian tiger mosquito, Aedes albopictus (Ae. albopictus), is an important vector that transmits arboviruses such as dengue (DENV), Zika (ZIKV) and Chikungunya virus (CHIKV). On the other hand, long noncoding RNAs (lncRNAs) are known to regulate various biological processes. Knowledge on Ae. albopictus lncRNAs and their functional role in virus-host interactions are still limited. Here, we identified and characterized the lncRNAs in the genome of an arbovirus vector, Ae. albopictus, and evaluated their potential involvement in DENV and ZIKV infection. We used 148 public datasets, and identified a total of 10, 867 novel lncRNA transcripts, of which 5,809, 4,139, and 919 were intergenic, intronic and antisense respectively. The Ae. albopictus lncRNAs shared many characteristics with other species such as short length, low GC content, and low sequence conservation. RNA-sequencing of Ae. albopictus cells infected with DENV and ZIKV showed that the expression of lncRNAs was altered upon virus infection. Target prediction analysis revealed that Ae. albopictus lncRNAs may regulate the expression of genes involved in immunity and other metabolic and cellular processes. To verify the role of lncRNAs in virus infection, we generated mutation in lncRNA loci using CRISPR-Cas9, and discovered that two lncRNA loci mutations, namely XLOC_029733 (novel lncRNA transcript id: lncRNA_27639.2) and LOC115270134 (known lncRNA transcript id: XR_003899061.1) resulted in enhancement of DENV and ZIKV replication. The results presented here provide an important foundation for future studies of lncRNAs and their relationship with virus infection in Ae. albopictus. Author summary Ae. albopictus is an important vector of arboviruses such as dengue and Zika. Studies on virus-host interaction at gene expression and molecular level are crucial especially in devising methods to inhibit virus replication in Aedes mosquito. Previous reports showed that, besides protein-coding genes, noncoding RNAs such as lncRNAs are also involved in virus-host interaction. In this study, we report a comprehensive catalog of novel lncRNA transcripts in the genome of Ae. albopictus. We also show that the expression of lncRNAs was altered upon infection with dengue and Zika. Additionally, depletion of certain lncRNAs resulted in increased replication of dengue and Zika; hence, suggesting potential association of lncRNAs in virus infection. Results of this study provide a new avenue to the investigation of mosquito-virus interactions that may potentially pave way to the development of novel methods in vector control.
Cerebellar Golgi cell models predict dendritic processing and mechanisms of synaptic plasticity

The Golgi cells are the main inhibitory interneurons of the cerebellar granular layer. Although recent works have highlighted the complexity of their dendritic organization and synaptic inputs, the mechanisms through which these neurons integrate complex input patterns remained unknown. Here we have used 8 detailed morphological reconstructions to develop multicompartmental models of Golgi cells, in which Na, Ca, and K channels were distributed along dendrites, soma, axonal initial segment and axon. The models faithfully reproduced a rich pattern of electrophysiological and pharmacological properties and predicted the operating mechanisms of these neurons. Basal dendrites turned out to be more tightly electrically coupled to the axon initial segment than apical dendrites. During synaptic transmission, parallel fibers caused slow Ca-dependent depolarizations in apical dendrites that boosted the axon initial segment encoder and Na-spike backpropagation into basal dendrites, while inhibitory synapses effectively shunted backpropagating currents. This oriented dendritic processing set up a coincidence detector controlling voltage-dependent NMDA receptor unblock in basal dendrites, which, by regulating local calcium influx, may provide the basis for spike-timing dependent plasticity anticipated by theory. Author Summary The Golgi cells are the main inhibitory interneurons of the cerebellum granular layer and play a fundamental role in controlling cerebellar processing. However, it was unclear how spikes are processed in the dendrites by specific sets of ionic channels and how they might contribute to integrate synaptic inputs and plasticity. Here we have developed detailed multicompartmental models of Golgi cells that faithfully reproduced a large set of experimental findings and revealed the nature of signal interchange between dendrites and axo-somatic compartments. A main prediction of the models is that synaptic activation of apical dendrites can effectively trigger spike generation in the axonal initial segment followed by rapid spike backpropagation into basal dendrites. Here, incoming mossy fiber inputs and backpropagating spikes regulate the voltage-dependent unblock of NMDA channels and the induction of spike timing-dependent plasticity (STDP). STDP, which was predicted by theory, may therefore be controlled by contextual information provided by parallel fibers and integrated in apical dendrites, supporting the view that spike timing is fundamental to control synaptic plasticity at the cerebellar input stage.
Antibody repertoire induced by SARS-CoV-2 spike protein immunogens

Multiple vaccine candidates against SARS-CoV-2 based on viral spike protein are under development. However, there is limited information on the quality of antibody response generated following vaccination by these vaccine modalities. To better understand antibody response induced by spike protein-based vaccines, we immunized rabbits with various SARS-CoV-2 spike protein antigens: S-ectodomain (S1+S2) (aa 16-1213), which lacks the cytoplasmic and transmembrane domains (CT-TM), the S1 domain (aa 16-685), the receptor-binding domain (RBD) (aa 319-541), and the S2 domain (aa 686-1213 as control). Antibody response was analyzed by ELISA, Surface Plasmon Resonance (SPR) against different Spike proteins in native conformation, and a pseudovirion neutralization assay to measure the quality and function of the antibodies elicited by the different Spike antigens. All three antigens (S1+S2 ectodomain, S1 domain, and RBD) generated strong neutralizing antibodies against SARS-CoV-2. Vaccination induced antibody repertoire was analyzed by SARS-CoV-2 spike Genome Fragment Phage Display Libraries (SARS-CoV-2 GFPDL), which identified immunodominant epitopes in the S1, S1-RBD and S2 domains. Furthermore, these analyses demonstrated that surprisingly the RBD immunogen elicited a higher antibody titer with 5-fold higher affinity antibodies to native spike antigens compared with other spike antigens. These findings may help guide rational vaccine design and facilitate development and evaluation of effective therapeutics and vaccines against COVID-19 disease. One Sentence Summary SARS-CoV-2 Spike induced immune response
Fibroscan as a non-invasive predictor of hepatic steatosis in women with polycystic ovary syndrome

Background & objectives: There is limited data on non-alcoholic fatty liver disease (NAFLD) among Indian women with polycystic ovary syndrome (PCOS), and there are no data on the utility of fibroscan in its assessment. The objective of this study was thus to investigate the frequency of hepatic steatosis in young women with PCOS and evaluate the utility of transient elastography (TE) in its assessment. Methods: Seventy women diagnosed with PCOS and 60 apparently healthy women (controls) were enrolled in this pilot study. These women were evaluated for clinical, biochemical and hormonal parameters, transabdominal ultrasonography, dual-energy X-ray absorptiometry and fibroscan assessing liver stiffness measure (LSM) and controlled attenuation parameter (CAP). Other indices such as liver fat score (LFS), lipid accumulation product (LAP), fibrosis-4 (FIB-4) and aspartate aminotransferase to platelet ratio index, hepatic steatosis index (HIS) scores were also calculated. The main outcome measures were the presence of NAFLD in women with PCOS and its correlation with CAP and LSM on TE. Results: Women with PCOS had higher frequency (38.57 vs. 6.67%) of hepatic steatosis than control women as determined by abdominal sonography. The aminotransferases were higher in PCOS group (14.28 vs. 1.7%, P=0.03) even after adjusting for body mass index implying higher non-alcoholic steatohepatitis among young PCOS patients. PCOS women had significantly higher CAP on TE compared to controls (210 vs. 196). CAP had a significant correlation with LFS, LAP and HIS. Interpretation & conclusions: NAFLD is common in young women with PCOS, and fibroscan using TE may be considered as a promising non-invasive diagnostic modality in its early detection.
Localization and Characterization of the Calsequestrin-binding Domain of Triadin 1

Triadin is an integral membrane protein of the junctional sarcoplasmic reticulum that binds to the high capacity Ca2+-binding protein calsequestrin and anchors it to the ryanodine receptor. The lumenal domain of triadin contains multiple repeats of alternating lysine and glutamic acid residues, which have been defined as KEKE motifs and have been proposed to promote protein associations. Here we identified the specific residues of triadin responsible for binding to calsequestrin by mutational analysis of triadin 1, the major cardiac isoform. A series of deletional fusion proteins of triadin 1 was generated, and by using metabolically labeled calsequestrin in filter-overlay assays, the calsequestrin-binding domain of triadin 1 was localized to a single KEKE motif comprised of 25 amino acids. Alanine mutagenesis within this motif demonstrated that the critical amino acids of triadin binding to calsequestrin are the even-numbered residues Lys210, Lys212, Glu214, Lys216, Gly218, Gln220, Lys222, and Lys224. Replacement of the odd-numbered residues within this motif by alanine had no effect on calsequestrin binding to triadin. The results suggest a model in which residues 210–224 of triadin form a β-strand, with the even-numbered residues in the strand interacting with charged residues of calsequestrin, stabilizing a “polar zipper” that links the two proteins together. This small, highly charged β-strand of triadin may tether calsequestrin to the junctional face membrane, allowing calsequestrin to sequester Ca2+ in the vicinity of the ryanodine receptor during Ca2+ uptake and Ca2+ release.
Export Competitiveness of Fresh Vegetables in India

Total vegetable exports from India were around US$464 million in 2010–2011, including 2.12% of agricultural exports and 12.8% of horticultural exports. India is the second largest producer of vegetables in the world and 24th in export of vegetables. Major destinations of India’s fresh vegetable exports are the United Arab Emirates (UAE), Nepal, Sri Lanka, the United Kingdom, and Saudi Arabia, together accounting for 55% of total vegetable exports from India. This study was undertaken to determine export competitiveness, comparative advantage in exports, and market share of selected Indian-grown fresh vegetables. India has a comparative advantage in exporting onion (Allium cepa L.) and peas (Pisum sativum L.) compared to other vegetables. Tomato (Solanum lycopersicum L.), onion, and potato (S. tuberosum L.) formed the major portion of exported vegetables, constituting 45% of total area under vegetable cultivation and 50% of total vegetable production in India. Bangladesh was the most stable market for export of tomatoes from India. Maldives, Nepal, and Mauritius were stable markets for export of potato. The UAE and Bangladesh were stable markets for onion exports from India. India still has a huge potential to be utilized in fresh vegetable exports, particularly for cabbage (Brassica oleracea L. var. capitata), cauliflower (B. oleracea L. var. botrytis), tomato, and eggplant (S. melongena L.). New emerging markets can be encouraged and existing markets in Singapore, Pakistan, Sri Lanka, Bangladesh, and Mauritius strengthened.