Miracle-dz/UniFAR-FTUs huggingface dataset:
A Natural Language Processing (NLP) Framework for Embedded Systems to Automatically Extract Verification Aspects from Textual Design Requirements

Embedded systems requirements are significantly different with respect to general purpose systems due to the safety-critical nature and the presence of temporal aspects. Particularly, the design requirements of embedded systems, comprise several temporal conditions, are first identified. Subsequently, a test engineer / system engineer analyzes the design requirements manually to identify the verification characteristics and develops the verification assertions / constraints accordingly. However, the manual analysis of design requirements for verification is time consuming task. Furthermore, high level of domain expertise is required to develop the correct and complete verification assertions from the design requirements. This article presents a novel Natural Language Processing (NLP) framework for embedded systems to analyze and automatically extract verification aspects from the textual design requirements. This leads to considerably simplify and accelerate the development of verification assertions. As a part of research, a complete AR2AA (Automated Requirements 2 Assertions Analyzer) tool is developed in C# by utilizing the SharpNLP and regular expression libraries. The usefulness of proposed framework is demonstrated through Car Collision and Avoidance System (CCAS) case study. The initial results prove that the proposed framework is highly effective for the analysis and development of verification assertions from the textual design requirements.
Susceptibility-adjusted herd immunity threshold model and potential R0 distribution fitting the observed Covid-19 data in Stockholm

The reproduction number, R0, is commonly used, and sometimes misused, in conjunction with the classic Kermack and McKindrick theory based on the assumption of homogeneity, in order to estimate herd immunity threshold (HIT). This provides a crude first estimate of HIT, with more elaborate modelling required to arrive at a more realistic value. Early estimates of HIT for Covid-19 were based on this simplistic homogeneous approach, yielding high HIT values that have since been revised downwards with more sophisticated network modelling taking account of R0 heterogeneity and with reference to the low HIT found from serological sampling in Stockholm County. The aim of this paper is to describe a simple model in which host susceptibility is directly linked to the heterogeneous R0 distribution, to shed further light on the mechanisms involved and to arrive at a bimodal R0 distribution consistent with the Covid-19 HIT observed in Stockholm County.
Personal Attributes Identification based on Gait Recognition using Smart Phone Sensors

Every individual has a unique gait that can not only be used for identification but also when observed carefully, may reveal personal attributes like age, gender, weight etc. of a person. This information can then be used for a number of purposes like in biometric-access control, for marketing applications, for making systems more intelligent in its user's recognition and for fitness applications. Although a lot of research has been done on these attributes separately, but this paper proposes a novel approach to identify all of the above-mentioned personal attributes of a person in a single framework based on his gait patterns using smart phone sensors. Series of experiments have been performed to demonstrate its effectiveness.
Inhibition of cytokinin-induced plant growth by jasmonic acid and its methyl ester

Effects of jasmonic acid, methyl jasmonate and ABA on cytokinin-induced soybean (Glycine max Merrill cv. Kingen No. 1) callus growth and radish (Raphanus sativus L. cv. Comet) cotyledon growth were studied. Jasmonic acid and methyl jasmonate were powerful inhibitors of kinetin- or N-phenyl-N′-(2-chloro-4-pyridyl)urea-induced soybean callus growth, the former being more effective than the latter, especially at low concentrations (0.45 to 4.5 μM). These compounds could completely eliminate kinetin- or N-phenyl-N′-(2-chloro-4-pyridyl)urea-induced soybean callus growth at 45 μM. At low concentrations ABA had no effect but at 450 μM it completely eliminated callus growth induced by kinetin. Of the compounds tested ABA was the most powerful inhibitor of radish cotyledon growth in the presence or absence of kinetin. Jasmonic acid and methyl jasmonate were much less effective than ABA in this assay system.
Thunderstorm Downbursts and Wind Loading of Structures: Progress and Prospect

In 1961, Davenport published a paper, considered by most to be a critical work in the study of wind engineering, in which meteorology, micrometeorology, climatology, aerodynamics, and structural dynamics were embedded in a homogeneous framework of the wind loading of structures. This framework, known as Davenport chain and based on a wind model coherent with synoptic-scale extra-tropical cyclones, is so limpid as to become a sort of axiom. In 1977, Gomes and Vickery separated thunderstorm from non-thunderstorm winds, evaluated their extreme wind speed marginal distributions, and from them obtained a mixed statistical model later generalized to other wind types. This viewpoint, dealt with as a milestone in the emerging issue of mixed climatology, pointed out the difficulty of labeling a heterogeneous set of phenomena endowed with different velocity fields, frequencies, durations, and sizes by the generic term “wind. ” Many wind types, in particular tropical cyclones, tornadoes, and downslope winds are typical of limited and well-known areas. Extra-tropical depressions and thunderstorms are natural hazards that affect the whole planet. This paper provides a state-of-the-art discussion of thunderstorm downburst, one of the most spectacular and damaging events caused by nature, and its wind loading of structures. Also, in light of the planet's climatology evolution, this topic is a key issue of structural safety and sustainability.
The Coronavirus PEDV Evades Type III Interferon Response Through the miR-30c-5p/SOCS1 Axis

Porcine epidemic diarrhea virus (PEDV) is an economically important pathogen that has evolved several mechanisms to evade type I IFN responses. Type III interferon (IFN-λ), an innate cytokine that primarily targets the mucosal epithelia, is critical in fighting mucosal infection in the host and has been reported to potently inhibit PEDV infection in vitro. However, how PEDV escapes IFN-λ antiviral response remains unclear. In this study, we found that PEDV infection induced significant IFN-λ expression in type I IFN-defective Vero E6 cells, but virus-induced endogenous IFN-λ did not reduce PEDV titers. Moreover, we demonstrated that PEDV escaped IFN-λ responses by substantially upregulating the suppressor of cytokine signaling protein 1 (SOCS1) expression, which impaired the induction of IFN-stimulated genes (ISGs) and dampened the IFN-λ antiviral response and facilitated PEDV replication in Vero E6 cells. We further showed that PEDV infection increased SOCS1 expression by decreasing host miR-30c-5p expression. MiR-30c-5p suppressed SOCS1 expression through targeting the 3′ untranslated region (UTR) of SOCS1. The inhibition of IFN-λ elicited ISGs expression by SOCS1 was specifically rescued by overexpression of miR-30c-5p. Collectively, our findings identify a new strategy by PEDV to escape IFN-λ-mediated antiviral immune responses by engaging the SOCS1/miR-30c axis, thus improving our understanding of its pathogenesis.
A Novel Multi-period Multivariate Multi-scale Phase Locking Value and its Application

Motor Imagery EEG or ECoG is the most popular driving signal in brain computer interface based rehabilitation system. Empirical Mode Decomposition (EMD) can be employed in feature extraction, which only a single scale IMF is considered by using Phase Locking Value (PLV), leading to the loss of phase information. In this paper, a Multi-period Multivariate Multi-scale PLV (MMMPLV) is proposed based on Noise-Assisted Multivariate EMD (NAMEMD). The selected multi-channel MI-ECoG are decomposed simultaneously by NAMEMD to obtain the multivariate multi-scale IMFs, and their length are divided into many periods. Then the PLV of pair-wise IMFs at the same scale are calculated in each time period for any two-channel MI-ECoG signals. The resulted MMMPLV are constructed as phase features. Furthermore, the phase features generated by MMMPLV and the spatial features extracted by Common Spatial Subspace Decomposition (CSSD) algorithm are fused in series, yielding a new feature extraction method, denoted as MMMPC. Experiments were conducted on a public database, and the Support Vector Machine (SVM) is used to classify the combined features. The experiment results of 9-fold Cross Validation (CV) show that the proposed method yields relative higher classification accuracy and better stability compared with the other synchronization methods and classical feature extraction methods.
SPARC Negatively Correlates With Prognosis After Transarterial Chemoembolization and Facilitates Proliferation and Metastasis of Hepatocellular Carcinoma via ERK/MMP Signaling Pathways

Background: Transarterial chemoembolization (TACE) represents a widely accepted treatment procedure for intermediate stage or unresectable hepatocellular carcinoma (HCC). However, few studies have evaluated serologic prognosis factors in patients with HCC before TACE. Secreted protein acidic and rich in cysteine (SPARC) is a matricellular glycoprotein affecting tumorigenesis and metastasis, and leading to poor prognosis in HCC. Therefore, to further explore the potential prognosis value of SPARC, the expression levels in the plasma of patients and its potential molecular mechanisms underlying the regulation of HCC were investigated in this study. Materials and Methods: The study population included 43 patients with HCC who underwent TACE. To evaluate the expression of SPARC in different grades of pathological tissues, the immunohistochemistry was performed on tissues from 89 patients with HCC. Lentiviral vectors carrying interference sequences, as well as vectors harboring the complete open reading frame of SPARC for the knockdown or overexpression of SPARC in HuH-7 or HepG2 cells, respectively, allowed us to determine the biological functions of SPARC in vitro and in vivo. We also evaluated the levels of phosphorylated extracellular signal-regulated kinases 1/2 (p-ERK1/2) and matrix metalloproteinases 2/9 (MMP2/9) activation. Results: The association between serum levels of SPARC and the survival at different TNM and Barcelona-Clinic Liver Cancer (BCLC) stages in patients with HCC undergoing TACE were evaluated. We observed a significant upregulation of SPARC in high grade HCC tissues, predicting unfavorable prognosis, and suggesting an important tumor-promoting effect of SPARC. Functional studies indicated that downregulation of SPARC contributed to the inhibition of proliferation and metastasis of HuH-7 cells in vitro, whereas its overexpression led to opposite phenotypes. Mechanistically, decreased expression of SPARC resulted in dephosphorylation of ERK1/2 and deactivation of MMP2/9, thereby inhibiting growth and metastasis of HCC. Importantly, low expression levels of SPARC inhibited the formation of subcutaneous tumors in nude mice. Conclusions: SPARC was found to facilitate proliferation and metastasis of HCC via modulation of the ERK1/2-MMP2/9 signaling pathways. Our research has provided a glimpse on the biological mechanism of SPARC and might contribute to the eventual treatment of liver cancer.
Object-based Place Recognition for Mobile Robots using Laplace's Rule of Succession

Place recognition estimating a robot's location from various sensor data is one of the most active research field in robotics, as it is a prerequisite step for robots to perform more intelligent and complex tasks. In this paper, we present an object-based place recognition method using objects as a key intermediate representation of places. Objects are detected by a mobile robot equipped with a camera, and object map is constructed to contain object information of places. Then, locations are recognized by object information located at places. As the proposed method considers not only the type of the object but also the number of occurrences of objects, it is possible to distinguish places that could not be distinguished from the existing method. Simulation and experimental results are presented to verify the proposed method.
Practicality of Biochar Additions to Enhance Soil and Crop Productivity

The benefits of biochar to soils for agricultural purposes are numerous. Biochar may be added to soils with the intention to improve the soil, displace an amount of conventional fossil fuel based fertilizers, and sequester carbon. However, the variable application rates, uncertain feedstock effects, and initial soil state provide a wide range of cost for marginally improved yield from biochar additions, which is often economically impracticable. The need for further clarity on optimizing biochar application to various crop yields is necessary if it is to gain widespread acceptance as a soil amendment.
New Therapies for Advanced Thyroid Cancer

Thyroid cancer is the most common endocrine cancer. The discovery of new biomarkers for thyroid cancer has significantly improved the understanding of the molecular pathogenesis of thyroid cancer, thus allowing more personalized treatments for patients with thyroid cancer. Most of the recently discovered targeted therapies inhibit the known oncogenic mechanisms in thyroid cancer initiation and progression such as MAPK pathway, PI3K/Akt-mTOR pathways, or VEGF. Despite the significant advances in molecular testing and the discoveries of new and promising therapeutics, effective treatments for advanced and metastatic, iodine-refractory thyroid cancer are still lacking. Here, we aim to summarize the current understanding of the genetic alterations and the dysregulated pathways in thyroid cancer and to discuss the most recent targeted therapies and immunotherapy for advanced thyroid cancer with a promising anti-tumor activity and clinical benefit.
Antineoplastic Agents Targeting Sphingolipid Pathways

Emerging studies in the enigmatic area of bioactive lipids have made many exciting new discoveries in recent years. Once thought to play a strictly structural role in cellular function, it has since been determined that sphingolipids and their metabolites perform a vast variety of cellular functions beyond what was previously believed. Of utmost importance is their role in cellular signaling, for it is now well understood that select sphingolipids serve as bioactive molecules that play critical roles in both cancer cell death and survival, as well as other cellular responses such as chronic inflammation, protection from intestinal pathogens, and intrinsic protection from intestinal contents, each of which are associated with oncogenesis. Importantly, it has been demonstrated time and time again that many different tumors display dysregulation of sphingolipid metabolism, and the exact profile of said dysregulation has been proven to be useful in determining not only the presence of a tumor, but also the susceptibility to various chemotherapeutic drugs, as well as the metastasizing characteristics of the malignancies. Since these discoveries surfaced it has become apparent that the understanding of sphingolipid metabolism and profile will likely become of great importance in the clinic for both chemotherapy and diagnostics of cancer. The goal of this paper is to provide a comprehensive review of the current state of chemotherapeutic agents that target sphingolipid metabolism that are undergoing clinical trials. Additionally, we will formulate questions involving the use of sphingolipid metabolism as chemotherapeutic targets in need of further research.
Identifying a Molecular Mechanism That Imparts Species-Specific Toxicity to YoeB Toxins

The ribosome-dependent E. coli (Ec) mRNase toxin YoeB has been demonstrated to protect cells during thermal stress. Agrobacterium tumefaciens (At), a plant pathogen, also encodes a YoeB toxin. Initial studies indicated that AtYoeB does not impact the growth of Ec, but its expression is toxic to the native host At. The current work examines this species-specific effect. We establish the highly similar structure and function of Ec and AtYoeB toxins, including the ability of the AtYoeB toxin to inhibit Ec ribosomes in vitro. Comparison of YoeB sequences and structures highlights a four-residue helix between β-strands 2 and 3 that interacts with mRNA bases within the ribosome. This helix sequence is varied among YoeB toxins, and this variation correlates with bacterial classes of proteobacteria. When the four amino acid sequence of this helix is transplanted from EcYoeB onto AtYoeB, the resulting chimera gains toxicity to Ec cells and lessens toxicity to At cells. The reverse is also true, such that EcYoeB with the AtYoeB helix sequence is less toxic to Ec and gains toxicity to At cultures. We suggest this helix sequence directs mRNA sequence-specific degradation, which varies among proteobacterial classes, and thus controls growth inhibition and YoeB toxicity.
The low complexity motif of cytoplasmic polyadenylation element binding protein 3 (CPEB3) is critical for the trafficking of its targets in neurons

Biomolecular condensates, membraneless organelles found throughout the cell, play critical roles in many aspects of cellular function. Ribonucleoprotein granules (RNPs), a type of biomolecular condensate found in neurons that are necessary for local protein synthesis and are involved in long-term potentiation (LTP). Several RNA-binding proteins present in RNPs are necessary for the synaptic plasticity involved in LTP and long-term memory. Most of these proteins possess low complexity motifs, allowing for increased promiscuity. We explore the role the low complexity motif plays for RNA binding protein cytoplasmic polyadenylation element binding protein 3 (CPEB3), a protein necessary for long-term memory persistence. We found that RNA binding and SUMOylation are necessary for CPEB3 localization to the P body, thereby having functional implications on translation. Here, we investigate the role of the low complexity motif of CPEB3 and find that it is necessary for P body localization and downstream targeting for local protein synthesis.
Quantifying acceptable levels of visitor use on Red Sea reef flats

1. The effects of trampling by visitors walking over the reef flat to snorkel or swim along the reef edge were studied at Ras Um Sidd, a popular fringing reef site at Sharm El Sheikh, and in the Ras Mohammed National Park, South Sinai, Egypt. Twelve stations showed a sequence of events linked to increased frequency and extent of trampling, with the intensities of trampling ranging from 0.1 to 324 tramplers m−2 yr−1. 2. Heavily trampled stations had a reduced coral cover (in particular branching corals), higher amounts of coral damage, less old dead coral, less obligate corallivorous fishes and more herbivores. 3. Wave exposure was crucial in determining the susceptibility of coral communities to trampling. Exposed communities were dominated by branching corals and were mechanically more resistant, since wave stress had favoured stockier growth forms. 4. The applicability of the ‘carrying capacity concept’ was investigated as a management tool for determining how much use is sustainable. Examination of the relationship between hard coral cover and intensity of trampling suggested that carrying capacity could be set at approximately 50 tramplers m−2 yr−1. The actual amount of damage caused by trampling showed a linear increase with increasing trampling intensities, so that the carrying capacity concept, as defined in this study, was not applicable to the relationship since no threshold existed. Instead, the ‘limits of acceptable change’ approach would be more practicable, with managers deciding what amount of coral damage they permit before limiting access. To establish meaningful limits of change, more knowledge is required about ecological as well as social consequences (e.g. visitor satisfaction) of such limits. Copyright © 2007 John Wiley & Sons, Ltd.
T cells expanded from renal cell carcinoma are tumor-reactive but fail to produce IFN-γ, TNF-α or IL-2

Metastatic renal cell carcinoma (RCC) has a poor prognosis. Recent advances have shown beneficial responses to immune checkpoint inhibitors, such as anti-PD-1 or anti-PD-L1 antibodies. As only a subset of RCC patients respond, alternative strategies should be explored. Patients refractory to anti-PD-1 therapy may benefit from autologous tumor infiltrating lymphocyte (TIL) therapy. Even though efficient TIL expansion was reported from RCC lesions, it is not well established how many RCC TIL products are tumor-reactive, how well they produce pro-inflammatory cytokines in response to autologous tumors, and whether their response correlates with the presence of specific immune cells in the tumor lesions. We here compared the immune infiltrate composition of RCC lesions with that of autologous kidney tissue of 18 RCC patients. T cell infiltrates were increased in the tumor lesions, and CD8+ T cell infiltrates were primarily of effector memory phenotype. Nine out of 16 (56%) tested TIL products we generated were tumor-reactive, as defined by CD137 upregulation after exposure to autologous tumor digest. Tumor reactivity was found in particular in TIL products originating from tumors with a high percentage of infiltrated T cells compared to autologous kidney, and coincided with increased ex vivo CD25 expression on CD8+ T cells. Importantly, although TIL products had the capacity to produce the key effector cytokines IFN-γ, TNF-α or IL-2, they failed to do so in response to autologous tumor digests. In conclusion, TIL products from RCC lesions contain tumor-reactive T cells. Their lack of tumor-specific cytokine production requires further investigation of immunosuppressive factors in RCC and subsequent optimization of RCC-derived TIL culture conditions.
Assessment of Genetic Diversity, Mutation Drift Equilibrium and Mitochondrial D-Loop Variation in Toda buffalo—The Endangered Breed of South India

Abstract Kataria, R.S. , Kathiravan, P., Bulandi, S.S. , Yadav, N.K. , Dubey, P.K. and Mishra, B.P. 2009. Assessment of genetic diversity, mutation drift equilibrium and mitochondrial D-Loop variation in Toda buffalo—the endangered breed of South India. J. Appl. Anim. Res., 35: 67–72. The Toda buffalo of South India was evaluated for its genetic variability and mutation drift equilibrium using a set of 25 bovine specific heterologous microsatellite markers. A total of 105 alleles were detected across 25 loci with mean effective number of alleles being 2.661. The mean observed and expected heterozygosity were 0.570 and 0.598, respectively. The test for Hardy-Weinberg equilibrium (HWE) revealed significant deviations in many of the investigated loci. There were highly significant deviations from mutation drift equilibrium while the qualitative test of mode shift did not reveal any genetic bottleneck in the recent past. The mitochondrial DNA D-loop sequence analysis of 165 bp region in three buffalo breeds viz. Toda, Assamese and Murrah revealed a total of 12 haplotypes, of which five were unique and remaining seven were found to be shared among different breeds. The phylogenetic analysis indicated clustering of all the riverine buffalo haplotypes together in a single clade including Toda and Assamese while the swamp buffaloes formed a separate cluster.