Miracle-dz/UniFAR-FTUs huggingface dataset:
Fully-Dynamic All-Pairs Shortest Paths: Improved Worst-Case Time and Space Bounds

Given a directed weighted graph $G=(V,E)$ undergoing vertex insertions \emph{and} deletions, the All-Pairs Shortest Paths (APSP) problem asks to maintain a data structure that processes updates efficiently and returns after each update the distance matrix to the current version of $G$. In two breakthrough results, Italiano and Demetrescu [STOC '03] presented an algorithm that requires $\tilde{O}(n^2)$ \emph{amortized} update time, and Thorup showed in [STOC '05] that \emph{worst-case} update time $\tilde{O}(n^{2+3/4})$ can be achieved. In this article, we make substantial progress on the problem. We present the following new results: (1) We present the first deterministic data structure that breaks the $\tilde{O}(n^{2+3/4})$ worst-case update time bound by Thorup which has been standing for almost 15 years. We improve the worst-case update time to $\tilde{O}(n^{2+5/7}) = \tilde{O}(n^{2.71.})$ and to $\tilde{O}(n^{2+3/5}) = \tilde{O}(n^{2.6})$ for unweighted graphs. (2) We present a simple deterministic algorithm with $\tilde{O}(n^{2+3/4})$ worst-case update time ($\tilde{O}(n^{2+2/3})$ for unweighted graphs), and a simple Las-Vegas algorithm with worst-case update time $\tilde{O}(n^{2+2/3})$ ($\tilde{O}(n^{2 + 1/2})$ for unweighted graphs) that works against a non-oblivious adversary. Both data structures require space $\tilde{O}(n^2)$. These are the first exact dynamic algorithms with truly-subcubic update time \emph{and} space usage. This makes significant progress on an open question posed in multiple articles [COCOON'01, STOC '03, ICALP'04, Encyclopedia of Algorithms '08] and is critical to algorithms in practice [TALG '06] where large space usage is prohibitive. Moreover, they match the worst-case update time of the best previous algorithms and the second algorithm improves upon a Monte-Carlo algorithm in a weaker adversary model with the same running time [SODA '17].
An Improved Quadrature Voltage-Controlled Oscillator with Through-Silicon-Via Inductor in Three-dimensional Integrated Circuits

Low-power quadrature voltage-controlled oscillator (QVCO) design utilizing transformer-feedback and current-reuse techniques with increased frequency range is proposed in this paper. With increasing demand for QVCOs in on-chip applications, the conventional spiral inductor based approaches for QVCOs has become a major bottleneck due to their large size. To address this concern, we propose to replace the conventional spiral inductor based approaches with through-silicon-via (TSV) inductor based approach in three-dimensional integrated circuits (3D ICs). In addition, the proposed QVCO circuit can provide higher frequency range of operation compared with conventional designs. Experimental results show by replacing conventional spiral transformers with TSV transformers, up to 3.9x reduction in metal resource consumption. The proposed QVCOs achieves a phase noise of -114 $dBc/Hz$@1 $MHz$ and -111.2 $dBc/Hz$@1 $MHz$ at the carrier of 2.5 $GHz$ for toroidal TSV transformed based-QVCO and vertical spiral transformer based-QVCO respectively. The power consumption is only 1.5 $mW$ and 1.7 $mW$ for toroidal TSV transformed based-QVCO and vertical spiral transformer based-QVCO respectively, under the supply voltage of 0.7 $V$.
Stochastic approximation for optimization in shape spaces

In this work, we present a novel approach for solving stochastic shape optimization problems. Our method is the extension of the classical stochastic gradient method to infinite-dimensional shape manifolds. We prove convergence of the method on Riemannian manifolds and then make the connection to shape spaces. The method is demonstrated on a model shape optimization problem from interface identification. Uncertainty arises in the form of a random partial differential equation, where underlying probability distributions of the random coefficients and inputs are assumed to be known. We verify some conditions for convergence for the model problem and demonstrate the method numerically.
Stochastic analysis of an adaptive cubic regularization method under inexact gradient evaluations and dynamic Hessian accuracy

We here adapt an extended version of the adaptive cubic regularization method with dynamic inexact Hessian information for nonconvex optimization in Bellavia et al. [Adaptive cubic regularization methods with dynamic inexact hessian information and applications to finite-sum minimization. IMA Journal of Numerical Analysis. 2021;41(1):764–799] to the stochastic optimization setting. While exact function evaluations are still considered, this novel variant inherits the innovative use of adaptive accuracy requirements for Hessian approximations introduced in the just quoted paper and additionally employs inexact computations of the gradient. Without restrictions on the variance of the errors, we assume that these approximations are available within a sufficiently large, but fixed, probability and we extend, in the spirit of Cartis and Scheinberg [Global convergence rate analysis of unconstrained optimization methods based on probabilistic models. Math Program Ser A. 2018;159(2):337–375], the deterministic analysis of the framework to its stochastic counterpart, showing that the expected number of iterations to reach a first-order stationary point matches the well-known worst-case optimal complexity. This is, in fact, still given by , with respect to the first-order ϵ tolerance. Finally, numerical tests on nonconvex finite-sum minimization confirm that using inexact first- and second-order derivatives can be beneficial in terms of the computational savings.
Examining the Benefits of Capsule Neural Networks

Capsule networks are a recently developed class of neural networks that potentially address some of the deficiencies with traditional convolutional neural networks. By replacing the standard scalar activations with vectors, and by connecting the artificial neurons in a new way, capsule networks aim to be the next great development for computer vision applications. However, in order to determine whether these networks truly operate differently than traditional networks, one must look at the differences in the capsule features. To this end, we perform several analyses with the purpose of elucidating capsule features and determining whether they perform as described in the initial publication. First, we perform a deep visualization analysis to visually compare capsule features and convolutional neural network features. Then, we look at the ability for capsule features to encode information across the vector components and address what changes in the capsule architecture provides the most benefit. Finally, we look at how well the capsule features are able to encode instantiation parameters of class objects via visual transformations.
Searching for Quasiperiodic Modulations in γ-Ray Active Galactic Nuclei

We perform a systematic search of quasiperiodic variabilities in γ-ray active galactic nuclei in the third Fermi Large Area Telescope source catalog (3FGL). We employ two techniques, Lomb–Scargle Periodogram and Weighted Wavelet Z-transform, to obtain power spectra of γ-ray light curves covering from 2008 August to 2016 December. The results show that besides several objects that have been reported in previous works, an additional source, the flat spectrum radio quasars PKS 0601-70 has a possible quasiperiodic variability of 450 days in its γ-ray light curves with the significance of >3σ. The physical implications of our findings are discussed.
SECURITY PROBLEM ON THE INTERNET OF THINGS NETWORKS

Background. The number of IoT devices is increasing every year. At the same time, the number of data transmitted by these systems over networks is growing. Smart devices do not need a powerful processor, and the amount of memory is usually measured in kilobytes, so antivirus software and firewalls are not installed on such devices. Cybercriminals are increasingly exploiting the vulnerabilities of such home networks for the purpose of extortion or simply hooliganism. There is a security problem in the Internet of things networks that needs to be solved. Objective. The aim of the article is to identify the main causes of vulnerabilities in smart home systems and networks and to offer protection. Methods. As methods, we consider the most common attacks on smart home systems Results. The main security features on the Internet of things are timely software updates, changing default settings, multifactor authentication, encrypting traffic on your home network, installing a firewall on your home router and filtering traffic. When managing devices through a browser and remotely connecting to your home network via the Internet, you must use a VPN. Conclusions. The proposed methods for ensuring security in the networks of the Internet of things can protect smart devices and the network from attack by intruders.
Variability of vegetation index NDVI during periods of drought in the Tomsk Region

Current climate changes are characterized by an increase in the frequency of occurrence of extreme natural phenomena, which include droughts and over moistening periods of the territory. The main indicator of drought / over moistening periods is the state of vegetation. Estimation of the interannual and intraseasonal variability of drought can be carried out using vegetation indicators obtained from satellite image data. In article statistical characteristics of NDVI for seven basic types of land cover, identified at the territory of the Tomsk region were studied. NDVI is most stable during the summer in wetlands, changing on average during the study period from 0.58 in May to 0.71 in July, then decreasing to September to 0.64. The variability of NDVI in dark coniferous forests is slightly greater (0.64–0.81). The greatest variability of NDVI was obtained for floodplain meadows (0.46-0.81) and croplands (0.51-0.79). VCI is used to identify drought situations and determine the onset, especially in areas where drought episodes are localized and ill defined. According to the analysis of the VCI index, in May the greatest frequency of dry periods was observed in the Tomsk region. Analysis of changes in frequency of extreme events occurrence have shown that the number of droughts decreases, and number of excessive moisture periods increases since 2000 till 2017.
Heterosis for number of fruits and seed yields in jatropha (Jatrophacurcas L.)

Jatropha production is still low, thereforedevelopment of high-yielding varieties by hybridization is needed This study aimed to determine heterosis and heterobeltiosis in jatropha and estimate the mode of gene action. The hybridizations were carried out between two improved population and one provenance, well known as high yield genotypes as female parents, and 18 provenances indicating high oil content as male parentsat Karangploso Experimental Station, Malang, East Java in 2010. In 2011, F1 seeds were planted in Asembagus Experimental Station, Situbondo, East Java and then were selected with criteria high fruit number and seed yield. The selected F1, were clonally multiplied using stem cutting and were planted in 2012 for evaluation purposes. The results showed that theheterosis and heterobeltiosis values from hybrid jatrophawere varied. The crossing between HS49 X SP65, HS49 X SP54, HS49 X SP103, IP3P X SP7, IP3A X SP65 and IP3A X Sp 89 demonstrated high significant positive heterosis and heterobeltiosis values. These hybrids could be used as materials for developinghigh-yielding varieties. The potence ratio of jatrophahybridwas found positively overdominance gene action which could be useful information for future jatropha breeding program.
FORSCHUNGSZENTRUM On the limit load of a square plate with an elliptical hole

SUMMARY The mathematical theory of plasticity is applied to the problem of a thin square plate, with an elliptical hole, yielding under loads applied at its outside edges. Lower and upper bounds to the external loads are determined for all parameters of the elliptical hole compared to the length of the side of the plate. The analytical bounds are compared to Finite Element calculations.
Signal Transduction for TNFα-Induced Type II SOCS Expression and Its Functional Implication in Growth Hormone Resistance in Carp Hepatocytes

In mammals, local production of tumor necrosis factor α (TNFα) inhibits growth hormone (GH)-induced IGF-I expression at tissue level and contributes to GH resistance caused by sepsis/endotoxemia and inflammation. Although the loss of GH responsiveness can be mediated by a parallel rise in SOCS expression, the signaling mechanisms for TNFα-induced SOCS expression at the hepatic level have not been characterized and the comparative aspects of the phenomenon, especially in lower vertebrates, are still unknown. Recently, type II SOCS, including SOCS1-3 and CISH, have been cloned in grass carp and shown to act as the feedback repressors for GH signaling via JAK2/STAT5 pathway. To shed light on the mechanisms for TNFα-induced GH resistance in fish model, grass carp TNFα was cloned and confirmed to be a single-copy gene expressed in various tissues including the liver. In carp hepatocytes, incubation with the endotoxin LPS induced TNFα expression with parallel rises in SOCS1-3 and CISH mRNA levels. Similar to LPS, TNFα treatment could block GH-induced IGF-I/-II mRNA expression and elevate SOCS1, SOCS3, and CISH transcript levels. However, TNFα was not effective in altering SOCS2 expression. In parallel experiment, LPS blockade of IGF-I/-II signals caused by GH could be partially reverted by TNFα receptor antagonism. At hepatocyte level, TNFα induction also triggered rapid phosphorylation of IκBα, MEK1/2, ERK1/2, MKK3/6, P38MAPK, Akt, JAK2, and STAT1,3,5, and TNFα-induced SOCS1, SOCS3, and CISH mRNA expression could be negated by inhibiting the IKK/NFκB, MAPK, PI3K/Akt, and JAK/STAT cascades. Our findings, as a whole, suggest that local production of TNFα may interfere with IGF-I/-II induction by GH in the carp liver by up-regulation of SOCS1, SOCS3, and CISH via IKK/NFκB, MAPK, PI3K/Akt, and JAK/STAT-dependent mechanisms, which may contribute to GH resistance induced by endotoxin in carp species.
Optimization of ATP Synthase c–Rings for Oxygenic Photosynthesis

The conversion of sunlight into useable cellular energy occurs via the proton–coupled electron transfer reactions of photosynthesis. Light is absorbed by photosynthetic pigments and transferred to photochemical reaction centers to initiate electron and proton transfer reactions to store energy in a redox gradient and an electrochemical proton gradient (proton motive force, pmf), composed of a concentration gradient (ΔpH) and an electric field (Δψ), which drives the synthesis of ATP through the thylakoid FoF1-ATP synthase. Although ATP synthase structure and function are conserved across biological kingdoms, the number of membrane–embedded ion–binding c subunits varies between organisms, ranging from 8 to 17, theoretically altering the H+/ATP ratio for different ATP synthase complexes, with profound implications for the bioenergetic processes of cellular metabolism. Of the known c–ring stoichiometries, photosynthetic c–rings are among the largest identified stoichiometries, and it has been proposed that decreasing the c-stoichiometry could increase the energy conversion efficiency of photosynthesis. Indeed, there is strong evidence that the high H+/ATP of the chloroplast ATP synthase results in a low ATP/nicotinamide adenine dinucleotide phosphate (NADPH) ratio produced by photosynthetic linear electron flow, requiring secondary processes such as cyclic electron flow to support downstream metabolism. We hypothesize that the larger c subunit stoichiometry observed in photosynthetic ATP synthases was selected for because it allows the thylakoid to maintain pmf in a range where ATP synthesis is supported, but avoids excess Δψ and ΔpH, both of which can lead to production of reactive oxygen species and subsequent photodamage. Numerical kinetic simulations of the energetics of chloroplast photosynthetic reactions with altered c–ring size predicts the energy storage of pmf and its effects on the photochemical reaction centers strongly support this hypothesis, suggesting that, despite the low efficiency and suboptimal ATP/NADPH ratio, a high H+/ATP is favored to avoid photodamage. This has important implications for the evolution and regulation of photosynthesis as well as for synthetic biology efforts to alter photosynthetic efficiency by engineering the ATP synthase.
Low-Density Lipoprotein Cholesterol and Alzheimer's Disease: A Systematic Review and Meta-Analysis

Objective: To assess the association between low-density lipoprotein cholesterol (LDL-c) and risk of Alzheimer's disease (AD). Methods: Embase, Pubmed, and Web of Science were searched until June 2019. Standard mean difference (SMD) with 95% confidence intervals (CI) was estimated using random-effects models. Results: Our meta-analysis of 26 studies revealed higher levels of LDL-c in AD than that of non-dementia controls (SMD = 0.35, 95% CI 0.12–0.58, p < 0.01). The meta-regression analysis on confounders showed that age (p < 0.01, Adj R-squared = 92.41%) and cardiovascular disease (p = 0.01, Adj R-squared = 85.21%), but not the body mass index, education, smoking, hypertension and diabetes mellitus, exerted an impact on the relationship between LDL-c and risk of ICH. Further subgroup analysis of age showed LDL-c levels in AD patients aged 60–70 were higher than that of non-dementia (60 ≤ age < 70: SMD = 0.80, 95% CI 0.23–1.37, p < 0.01); but no association between the SMD of AD in LDL-c and age over 70 was noted across the studies (70 ≤ age < 77: SMD = −0.02, 95% CI −0.39~0.34, p = 9.0; 77 ≤ age < 80: SMD = 0.15, 95% CI −0.17~0.47, p = 0.35; ≥80: SMD = 0.53, 95% CI −0.04~1.11, p = 0.07). The concentrations of LDL-c during the quintile interval of 3~4 were positively associated with AD (121 ≤ concentration < 137: SMD = 0.98, 95% CI 0.13~1.82, p = 0.02; ≥137: SMD = 0.62, 95% CI 0.18~1.06, p < 0.01); whereas there was no correlation between AD and LDL-c within the quintile interval of 1~2 (103.9 ≤ concentration < 112: SMD = 0.08, 95% CI −0.20~0.35, p = 0.59; 112 ≤ concentration < 121: SMD = −0.26, 95% CI −0.58~0.06, p = 0.11). Conclusions: Elevated concentration of LDL-c (>121 mg/dl) may be a potential risk factor for AD. This association is strong in patients aged 60–70 years, but vanishes with advancing age.
Human Pathogen Colonization of Lettuce Dependent Upon Plant Genotype and Defense Response Activation

Fresh produce contaminated with human pathogens may result in foodborne disease outbreaks that cause a significant number of illnesses, hospitalizations, and death episodes affecting both public health and the agribusiness every year. The ability of these pathogens to survive throughout the food production chain is remarkable. Using a genetic approach, we observed that leaf colonization by Salmonella enterica serovar Typhimurium 14028s (S. Typhimurium 14028s) and Escherichia coli O157:H7 was significantly affected by genetic diversity of lettuce (Lactuca sativa L. and L. serriola L.). In particular, there was a significant variation among 11 lettuce genotypes in bacterial attachment, internalization, and apoplastic persistence after surface- and syringe-inoculation methods. We observed a significant correlation of the bacterial leaf internalization rate with stomatal pore traits (width and area). Moreover, bacterial apoplastic populations significantly decreased in 9 out of 11 lettuce genotypes after 10 days of surface inoculation. However, after syringe infiltration, populations of E. coli O157:H7 and S. Typhimurium 14028s showed positive, neutral, or negative net growth in a 10-day experimental period among seedlings of different lettuce types. The relative ability of the bacteria to persist in the apoplast of lettuce genotypes after syringe inoculation was minimally altered when assessed during a longer period (20 days) using 3.5- to 4-week-old plants. Interestingly, contrasting bacterial persistence in the lettuce genotypes Red Tide and Lollo Rossa was positively correlated with significant differences in the level of reactive oxygen species burst and callose deposition against S. Typhimurium 14028s and E. coli O157:H7 which are related to plant defense responses. Overall, we characterized the genetic diversity in the interaction between lettuce genotypes and enterobacteria S. Typhimurium 14028s and E. coli O157:H7 and discovered that this genetic diversity is linked to variations in plant immune responses towards these bacteria. These results provide opportunities to capitalize on plant genetics to reduce pathogen contamination of leaves.
Phosphoinositides and the Fate of Legionella in Phagocytes

Legionella pneumophila is the causative agent of a severe pneumonia called Legionnaires' disease. The environmental bacterium replicates in free-living amoebae as well as in lung macrophages in a distinct compartment, the Legionella-containing vacuole (LCV). The LCV communicates with a number of cellular vesicle trafficking pathways and is formed by a plethora of secreted bacterial effector proteins, which target host cell proteins and lipids. Phosphoinositide (PI) lipids are pivotal determinants of organelle identity, membrane dynamics and vesicle trafficking. Accordingly, eukaryotic cells tightly regulate the production, turnover, interconversion, and localization of PI lipids. L. pneumophila modulates the PI pattern in infected cells for its own benefit by (i) recruiting PI-decorated vesicles, (ii) producing effectors acting as PI interactors, phosphatases, kinases or phospholipases, and (iii) subverting host PI metabolizing enzymes. The PI conversion from PtdIns(3)P to PtdIns(4)P represents a decisive step during LCV maturation. In this review, we summarize recent progress on elucidating the strategies, by which L. pneumophila subverts host PI lipids to promote LCV formation and intracellular replication.
Organic acids and 2,4-Di-tert-butylphenol: major compounds of Weissella confusa WM36 cell-free supernatant against growth, survival and virulence of Salmonella Typhi

Background Salmonella Typhi (S. Typhi), the causative agent of typhoid fever, causes serious systemic disease in humans. Antibiotic treatment is required for the S. Typhi infection, while the inappropriate use of antibiotics causes increased drug-resistant S. Typhi. Hence, alternative therapies through non-antibiotic approaches are urgently needed. The use of beneficial lactic acid bacterium and/or its metabolites to control typhoid fever represent a promising approach, as it may exert protective actions through various mechanisms. Method In this study, the cell-free culture supernatant (CFCS) of Weissella confusa WM36 was evaluated via the antibacterial activity, and its metabolites were identified. In addition, the effects of CFCS on Salmonella virulence behaviors were also investigated. Result Based on strong inhibition the growth of S. Typhi DMST 22842, organic acids (lactic acid and acetic acid) and 2,4-Di-tert-butylphenol (2,4 DTBP), were the main antibacterial metabolites presented in CFCS of strain WM36. Minimum inhibitory concentration (MIC) at 40% WM36–CFCS dramatically reduced the S. Typhi population to more than 99.99% at 4 h and completely inhibited biofilm formation, while sub-MIC at 20% (v/v) and MIC could reduce 100% of motility. Additionally, sub-MIC at only 10% (v/v) WM36–CFCS did down-regulate the expression of virulence genes which are responsible for the type-III secretion system, effector proteins, and quorum sensing system in this pathogen. Conclusion W. confusa WM36 and its metabolites are shown to be a promising candidates, and an effective approach against typhoid Salmonella burden.