Miracle-dz/UniFAR-FTUs huggingface dataset:
Scalable Inference of Symbolic Adversarial Examples

We present a novel method for generating symbolic adversarial examples: input regions guaranteed to only contain adversarial examples for the given neural network. These regions can generate real-world adversarial examples as they summarize trillions of adversarial examples. We theoretically show that computing optimal symbolic adversarial examples is computationally expensive. We present a method for approximating optimal examples in a scalable manner. Our method first selectively uses adversarial attacks to generate a candidate region and then prunes this region with hyperplanes that fit points obtained via specialized sampling. It iterates until arriving at a symbolic adversarial example for which it can prove, via state-of-the-art convex relaxation techniques, that the region only contains adversarial examples. Our experimental results demonstrate that our method is practically effective: it only needs a few thousand attacks to infer symbolic summaries guaranteed to contain $\approx 10^{258}$ adversarial examples.
Production of monoclonal antibodies to potato virus YNTN strain and their use for strain differentiation.

Four mouse monoclonal antibodies (MAbs) against potato virus Y (PVY) were produced. MAb 4C1 reacted with four isolates of PVYNTN and only very weakly with one isolate of the necrotic strain of PVY (PVYN). It did not react with other isolates of the ordinary strain of PVY tested. MAb 2C9 reacted with all isolates tested and can be used to produce a specific diagnostic kit for routine PVY detection. Other MAbs had different specificities and reacted with isolates of various strains of PVY. MAbs did not react with seven other members of the Potyvirus group including potato virus A. A MAb-based ELISA, using MAb 4C1, was devised and shown to detect PVYNTN specifically.
R*-Grove: Balanced Spatial Partitioning for Large-Scale Datasets

The rapid growth of big spatial data urged the research community to develop several big spatial data systems. Regardless of their architecture, one of the fundamental requirements of all these systems is to spatially partition the data efficiently across machines. The core challenges of big spatial partitioning are building high spatial quality partitions while simultaneously taking advantages of distributed processing models by providing load balanced partitions. Previous works on big spatial partitioning are to reuse existing index search trees as-is, e.g., the R-tree family, STR, Kd-tree, and Quad-tree, by building a temporary tree for a sample of the input and use its leaf nodes as partition boundaries. However, we show in this paper that none of those techniques has addressed the mentioned challenges completely. This paper proposes a novel partitioning method, termed R*-Grove, which can partition very large spatial datasets into high quality partitions with excellent load balance and block utilization. This appealing property allows R*-Grove to outperform existing techniques in spatial query processing. R*-Grove can be easily integrated into any big data platforms such as Apache Spark or Apache Hadoop. Our experiments show that R*-Grove outperforms the existing partitioning techniques for big spatial data systems. With all the proposed work publicly available as open source, we envision that R*-Grove will be adopted by the community to better serve big spatial data research.
A new species of Bredia (Sonerileae, Melastomataceae) from Sichuan, China

Abstract Bredia hispida (Sonerileae, Melastomataceae), a species occurring in southeastern Sichuan, China, is newly described based on morphological and molecular data. The generic placement of B. hispida is well supported by phylogenetic analysis and morphological characters, including basally cordate, hairy leaf blade, cymose inflorescence, basally gibbous anthers and enlarged ovary crown enclosing an inverted frustum-shaped depression. Both molecular and morphological divergence showed that B. hispida is well separated from its close relatives, justifying its recognition as a distinct species. The new species resembles B. repens, B. changii and B. guidongensis in the prostrate habit and isomorphic stamens but differs markedly in the unequal opposed leaves, the 2–4 mm long, stout bristles on the adaxial surface of leaf blade and acuminate leaf apex. Bredia hispida co-occurs with B. esquirolii in the wild. No morphologically putative hybrids between them were observed despite their overlap in flowering season. The isolating mechanism remains unclear, pending further investigation.
Extended Rako\v{c}evi\'{c}'s property

The purpose of this paper is to introduce and study new extension of Rakocevic's property $(w)$ and property $(b)$ introduced by Berkani--Zariouh in \cite{berkani-zariouh1}, in connection with other Weyl type theorems and recent properties. We prove in particular, the two following results: 1. A bounded linear operator $T$ satisfies property $(w_{\pi_{00}})$ if and only if $T$ satisfies property $(w)$ and $\sigma_{uf}(T)=\sigma_{uw}(T). $ 2. $T$ satisfies property $(gw_{\pi_{00}})$ if and only if $T$ satisfies property $(w_{\pi_{00}})$ and $\pi_{0}(T)=p_{0}^a(T). $ Classes of operators are considered as illustrating examples.
Physicochemical properties of water‐soluble myofibrillar proteins prepared from chicken breast muscle

The solubility of skeletal muscle myofibrillar proteins in water was examined. The solubility of the proteins was found to be sensitive to ionic strength and pH of the solution. At the ionic strength of less than 12 mM and neutral pH, more than 80% of myofibrillar proteins were solubilized. Heating at a temperature of more than 70°C was required for the proteins to retain their solubility. The solubility of freeze-dried protein powder prepared from water-soluble myofibrillar proteins was also examined, and it was found that addition of trehalose and heating were essential for re-solubilization in water. Amino acid composition of water-soluble myofibrillar proteins was found to be almost the same as that of myofibrillar proteins.
Mesenchymal Stem Cell Therapy Using Human Umbilical Cord in a Rat Model of Autoimmune-Induced Premature Ovarian Failure

Premature ovarian failure (POF) is one of the principal causes of female infertility, and although its causes are complex and diverse, autoimmune deficiency may be involved. Human umbilical cord mesenchymal stem cells (UCMSCs) can be used for tissue regeneration and repair. Therefore, the present study was designed to determine the role of UCMSCs in immune factor-induced POF in rats. In this study, different concentrations of UCMSCs were injected into induced POF rats. Ovarian functions were examined by evaluating the estrus cycle, follicular morphology, hormonal secretion, and the proliferation and apoptosis of granulosa cells. Our results showed that the estrus cycle of rats returned to normal and follicular development was significantly improved after transplantation of UCMSCs. In addition, serum concentrations of 17-estradiol (E2), progesterone (P4), and anti-Müllerian hormone (AMH) increased significantly with treatment. Transplantation of UCMSCs also reduced the apoptosis of granulosa cells and promoted the proliferation of granulosa cells. All of these improvements were dose dependent. Furthermore, the results of related gene expression showed that transplanted human UCMSCs upregulated the expression of Bcl-2, AMH, and FSHR in the ovary of POF rats and downregulated the expression of caspase-3. These results further validated the potential mechanisms of promoting the release of cell growth factors and enhancing tissue regeneration and provide a theoretical basis for the clinical application of stem cells in the treatment of premature ovarian failure.
Physical Frailty and Fall Risk in Community-Dwelling Older Adults: A Cross-Sectional Study

Introduction Frailty is a condition in older adults with decreased physical and cognitive performance that can affect health outcomes associated with fracture, disability, and falls. The aim of this study was to compare fall risk with different physical frailty statuses and investigate factors associated with fall risk in community-dwelling older adults. Methods The population studied included 367 older adults (mean age = 73.2 years ± 7.0; 237 females (64.6%) and 130 males (35.4%)) who live in Chiang Mai, Thailand. This study was of cross-sectional design. Fried's phenotype was used to screen the physical frailty status. The physiological profile assessment (PPA) was used to screen for fall risk. One-way ANOVA analysis was used to compare the fall risk between the different levels of frailty status. Linear regression analysis was used to assess the association between frailty status and fall risk. Results The prevalence of the frailty group was 8.7% and that of the prefrailty group was 76.8%. The three statuses of frailty identified were found to have different levels of risk of falling. The frailty group had a higher fall risk than the nonfrailty group and the prefrailty group. In addition, the nonfrailty group had a lower fall risk than the prefrailty group. Conclusion The frailty group had the highest fall risk in this cohort of older adults living in a community-dwelling facility. Therefore, it is important to assess the frailty status among older adults as it can be a predictor for fall risk. This assessment will therefore lead to a reduction in the rate of disability and death in the community.
Draft Genome Sequence of Bacillus velezensis BZR 336g, a Plant Growth-Promoting Antifungal Biocontrol Agent Isolated from Winter Wheat

Bacillus velezensis strain BZR 336g is a plant growth-promoting rhizobacterium isolated from a winter wheat rhizoplane from the Krasnodar region in Russia. In this study, we report the genome, including genes with known phenotypic function, i.e., the biosynthesis of secondary metabolites with fungicidal and plant growth-promoting activities. We sequenced and analyzed the complete BZR 336g genome using two different DNA preparation methods to help us better understand the origin of the antimicrobial and antifungal abilities and to weigh the biocontrol properties of this strain. ABSTRACT Bacillus velezensis strain BZR 336g is a plant growth-promoting rhizobacterium isolated from a winter wheat rhizoplane from the Krasnodar region in Russia. In this study, we report the genome, including genes with known phenotypic function, i.e., the biosynthesis of secondary metabolites with fungicidal and plant growth-promoting activities. We sequenced and analyzed the complete BZR 336g genome using two different DNA preparation methods to help us better understand the origin of the antimicrobial and antifungal abilities and to weigh the biocontrol properties of this strain.
An evolution-based model for designing chorismate mutase enzymes

Learning from evolution Protein sequences contain information specifying their three-dimensional structure and function, and statistical analysis of families of sequences has been used to predict these properties. Building from sequence data, Russ et al. used statistical models that take into account conservation at amino acid positions and correlations in the evolution of pairs of amino acids to predict new artificial sequences that will have the properties of the protein family. For the chorismate mutase family of metabolic enzymes, the authors demonstrate experimentally that the artificial sequences display natural-like catalytic function. Because the models access an enormous space of diverse sequences, such evolution-based statistical approaches may guide the search for functional proteins with altered chemical activities. Science, this issue p. 440 An evolution-based, data-driven engineering process can build artificial functional enzymes. The rational design of enzymes is an important goal for both fundamental and practical reasons. Here, we describe a process to learn the constraints for specifying proteins purely from evolutionary sequence data, design and build libraries of synthetic genes, and test them for activity in vivo using a quantitative complementation assay. For chorismate mutase, a key enzyme in the biosynthesis of aromatic amino acids, we demonstrate the design of natural-like catalytic function with substantial sequence diversity. Further optimization focuses the generative model toward function in a specific genomic context. The data show that sequence-based statistical models suffice to specify proteins and provide access to an enormous space of functional sequences. This result provides a foundation for a general process for evolution-based design of artificial proteins.
A New Species of Pseudoeurycea (Amphibia: Caudata) from the Mountains of Central Veracruz, Mexico

Abstract. We describe a new species of plethodontid salamander of the genus Pseudoeurycea from the mountains of central Veracruz, Mexico. This species can be distinguished from its congeners by color pattern and morphological characters. The molecular phylogenetic analysis indicates that Pseudoeurycea granitum sp. nov. is part of the Pseudoeurycea leprosa subclade and is closely related to Pseudoeurycea nigromaculata, Pseudoeurycea firscheini, and Pseudoeurycea lynchi. Known localities for P. granitum sp. nov. are mostly located in cloud forest fragments, with one from a shaded coffee plantation and one from an ecotone between cloud forest and pine–oak forest, all immersed in highly modified landscapes. This suggests the need to implement a conservation strategy in order to preserve the limited remaining habitat for this species.
Severe COVID-19 is associated with elevated serum IgA and antiphospholipid IgA-antibodies

Background: While the pathogenesis of coronavirus disease 2019 (COVID-19) is becoming increasingly clear, there is little data on IgA response, the first line of bronchial immune defense. Objective: To determine, whether COVID-19 is associated with a vigorous total IgA response and whether IgA autoantibodies are associated with complications of severe illness. Since thrombotic events are frequent in severe COVID-19 and resemble hypercoagulation of antiphospholipid syndrome (APS), our approach focused on antiphospholipid antibodies (aPL). Materials and methods: In this retrospective cohort study we compared clinical data and aPL from 64 patients with COVID-19 from three independent centers (two in Switzerland, one in Liechtenstein). Samples were collected from April 9, 2020 to May 1, 2020. Total IgA and aPL were measured with FDA-approved commercially available clinical diagnostic kits. Results: Clinical records of the 64 patients with COVID-19 were reviewed and divided into a cohort with mild illness (mCOVID, n=26 [41%]), a discovery cohort with severe illness (sdCOVD, n=14 [22%]) and a confirmation cohort with severe illness (scCOVID, n=24 [38%]). Severe illness was significantly associated with increased total IgA (sdCOVID, P=0.01; scCOVID, P<0.001). Total IgG levels were similar in both cohorts. Among aPL, both cohorts with severe illness significantly correlated with elevated anti-Cardiolipin IgA (sdCOVID and scCOVID, P<0.001), anti-Cardiolipin IgM (sdCOVID, P=0.003; scCOVID, P<0.001), and anti-Beta2 Glycoprotein-1 IgA (sdCOVID and scCOVID, P<0.001). Systemic lupus erythematosus was excluded from all patients as a potential confounder of APS. Conclusions: Higher total IgA and IgA-aPL were consistently associated with severe illness. These novel data strongly suggest that a vigorous antiviral IgA-response triggered in the bronchial mucosa induces systemic autoimmunity.
Dynamic Viscoelastic Properties of Heated Gluten/Soy Protein Gels

Hydrated gluten, soy concentrate, and mixtures of both were heated at 90 8 88 88C for 0.5 to 6 h. All heated samples were analyzed for viscoelastic properties and SDS-PAGE electrophoretograms. Results of the rheological analysis showed storage (G9) and loss (G0 00 0 0) moduli of gluten increased sharply as a result of heating and the shapes of both shear moduli were significantly different from the unheated samples. In the soy system, both shear moduli increased slightly upon heating and the shapes were similar to the unheated samples. The linkages found in the heated systems were disulfide bonds as shown by the electrophoretograms.
Forecasting French GDP with Dynamic Factor Models : a pseudo-real time experiment using Factor-augmented Error Correction Models

Dynamic Factor Models (DFMs) allow to take advantage of the information provided by a large dataset, which is summarized by a small set of unobservable latent variables, and they have proved to be very useful for short-term forecasting. Since most of their properties rely on the stationarity of the series, these models have been mainly used on data which have been di_erenciated to achieve stationarity. However estimation procedures for DFMs with I(1) common factors have been proposed by Bai (2004) and Bai and Ng(2004). Further, Banerjee and Marcellino (2008) and Banerjee, Marcellino and Masten (2014) have proposed to extend stationary Factor Augmented VAR models to the non-stationary case, and introduced Factor augmented Error Correction Models (FECM). We rely on this approach and conduct a pseudoreal time forecasting experiment, in which we compare short term forecasts of French GDP based on stationary and non-stationary DFMs. We mimic the timeliness of data, and use in the non-stationary framework the 2-step estimator proposed by Doz, Giannone and Reichlin(2011). In our study, forecasts based on stationary or non-stationary DFMs have a similar precision.
Simple and hydrolyzable phenolic compounds in virgin olive oil. 1. Their extraction, separation, and quantitative and semiquantitative evaluation by HPLC

Phenolic compounds have a fundamental importance in the nutritional and sensory characteristics of virgin olive oil. Problems regarding their qualitative and quantitative evaluation have not been completely solved; hence, in this paper the extractive and HPLC methods of analysis are examined and some modifications are presented. By means of these techniques, elenolic acid and four unknown compounds having phenolic behavior were separated from virgin olive oil. Four of them were correlated with total phenols evaluated by means of the Folin-Ciocalteu reagent, and two of them were correlated with olive oil autoxidation stability
Evaluation of noise and clutter induced relocation errors in SAR MTI

A synthetic aperture radar (SAR) is a side looking airborne radar designed to produce two dimensional high resolution radar images. Moving targets are displaced in azimuth on a SAR map. A separate SAR-MTI process is therefore used for the detection and relocation of moving targets. Errors in estimating the angular positions of the detected moving targets are referred to as relocation errors. A two port interferometer antenna whose baseline lies along the flight direction allows the detection of slow moving targets that are otherwise masked by main lobe clutter. A model for evaluating relocation errors in a two port interferometer SAR-MTI scheme is developed. The effects of various parameters such as aircraft speed, antenna beamwidth, squint angle, radar PRF and the target to noise and clutter ratios are evaluated.
Effect of electrical stimulation, delayed chilling and post‐mortem aging on the quality of M. longissimus dorsi and M. biceps femoris of grass‐fed steers

BACKGROUND: Roughage-based low-input beef production systems are gaining increasing interest owing to the perceived ecological advantages and potential health benefits associated with the favourable fatty acid composition of such beef. The low plane of nutrition may on the other hand yield less tender beef by affecting growth, carcass weight and fatness and therefore, indirectly, early post-mortem (p.m.) proteolytic enzyme activity and sarcomere shortening. This study aimed to examine delayed chilling and electrical stimulation as promising techniques to control early p.m. muscle metabolism in a way that improves the tenderness of beef from purely grass-fed steers in comparison with that from steers receiving a finishing diet with concentrates. RESULTS: Electrical stimulation decreased the pH at 1.5 and 3 h p.m. in the M. longissimus dorsi (LD) and M. biceps femoris (BF) of the treated carcass sides as well as the maximum shear force in the LD, while delayed chilling had no effect on pH or texture. The interactions of carcass fatness with electrical stimulation (P = 0.025) and delayed chilling (P = 0.089) indicated more pronounced effects of the p.m. treatments on beef texture in leaner carcasses. CONCLUSION: Electrical stimulation, but not delayed chilling, could markedly improve pasture beef texture and reduce the aging period needed for proper tenderisation. Copyright © 2008 Society of Chemical Industry
Risk Measures for Natural Resource Management: Description, Simulation Testing, and R Code With Fisheries Examples

Abstract Traditional measures that quantify variation in natural resource systems include both upside and downside deviations as contributing to variability, such as standard deviation or the coefficient of variation. Here we introduce three risk measures from investment theory, which quantify variability in natural resource systems by analyzing either upside or downside outcomes and typical or extreme outcomes separately: semideviation, conditional value-at-risk, and probability of ruin. Risk measures can be custom tailored to frame variability as a performance measure in terms directly meaningful to specific management objectives, such as presenting risk as harvest expected in an extreme bad year, or by characterizing risk as the probability of fishery escapement falling below a prescribed threshold. In this paper, we present formulae, empirical examples from commercial fisheries, and R code to calculate three risk measures. In addition, we evaluated risk measure performance with simulated data, and we .
Cre/LoxP-HBV plasmids generating recombinant covalently closed circular DNA genome upon transfection

New therapies against hepatitis B virus (HBV) require the elimination of covalently closed circular DNA (cccDNA), the episomal HBV genome. HBV plasmids containing an overlength 1.3-mer genome and bacterial backbone (pHBV1.3) are used in many different models, but do not replicate the unique features of cccDNA. Since the stable cccDNA pool is a barrier to HBV eradication in patients, we developed a recombinant circular HBV genome (rcccDNA) to mimic the cccDNA using Cre/LoxP technology. We validated four LoxP insertion sites into the HBV genome using hydrodynamic tail vein injection into murine liver, demonstrating high levels of HBV surface antigen (HBsAg) and HBV DNA expression with rcccDNA formation. HBsAg expression from rcccDNA was >30,000 ng/mL over 78 days, while HBsAg-expression from pHBV1.3 plasmid DNA declined from 2,753 ng/mL to 131 ng/mL over that time in immunodeficient mice (P<0.001), reflective of plasmid DNA silencing. We then cloned Cre-recombinase in cis on the LoxP-HBV plasmids, achieving plasmid stability in bacteria with intron insertion into Cre and demonstrating rcccDNA formation after transfection in vitro and in vivo. These cis-Cre/LoxP-HBV plasmids were then used to create HBx-mutant and GFP reporter plasmids to further probe cccDNA biology and antiviral strategies against cccDNA. Overall, we believe these auto-generating rcccDNA plasmids will be of great value to model cccDNA for testing new therapies against HBV infection.