Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning Compact Representations of Neural Networks using DiscriminAtive Masking (DAM)

Let f denote the continuous function expressed by our neural network with learnable parameters Θ. The loss function for training the neural network for the target task can then be denoted as L = L(f(x,Θ, βi)) (e.g., cross-entropy loss for supervised structured pruning problems and reconstruction error for representation learning problems), where x denotes the input features to the neural network. Using gradient descent methods with a learning rate of η, the expected update formula of βi in DAM is given by:
A Practical Security Framework for Cloud Storage and Computation

: Cloud computing is a fast growing technology that transforms the way IT services is used in businesses. Collaborative cloud or federated cloud extends this potential even more by offering true unlimited capacity. Despite its potential to provide millions of organizations with storage and computational power at low costs and great speed, many organizations are still skeptical to use these services due to security concerns. This is because “privacy” in cloud has not been well defined and involves trust on the Cloud Service Provider. The objective of this paper is to propose a novel method, which provides a secure way of storing data in the cloud, and at the same time, allows the user to perform some computation on the stored data without compromising the security of the data. This method combines the ideas of searchable encryption with partial homomorphism. The applicability of this idea and its strengths has been tested with appropriate experiments.
Clustering time series gene expression data with TMixClust

A large number of longitudinal studies measuring gene expression aim to stratify the genes according to their diﬀerential temporal behaviors. Genes with similar expression patterns may reﬂect functional responses of biological relevance. However, these measurements come with intrinsic noise which makes their time series clustering a diﬃcult task. Here, we show how to cluster such data with the package TMixClust. TMixClust is a soft-clustering method which employs mixed-eﬀects models with nonparametric smoothing spline ﬁtting and is able to robustly stratify genes by their complex time series patterns. The package has, besides the main clustering method, a set of functionalities assisting the user to visualise and assess the clustering results, and to choose the optimal clustering solution. In this manual, we present the general workﬂow of using TMixClust for analysing time series gene expression data and explain the theoretical background of the clustering method used in the package implementation.
Software Compliance in Different Industries: A Systematic Literature Review

With the emergence of new software development paradigms (e.g., distributed teams and crowd-sourcing), the software supply chain became more complicated than ever. This, in turn, raises concerns in software compliance in many industries, as ensuring adherence beyond functional requirements is very critical. This paper uses a systematic literature review, to investigate the frameworks used for managing compliance of software and software services and their applications across different industries. The review also looked into industry-specific software compliance requirements. A total of 156 primary studies have been collected, of which 63 studies match the criteria indicated in the review protocol. The study develops a classification of these frameworks based on industry-specific needs, business requirements, and the context of compliance. Findings of this research help researchers and practitioners to identify important aspects of software compliance and set directions for future research and development.
Original Contribution Interactive Effect of Cigarette Smoking With Human 8-Oxoguanine DNA N-Glycosylase 1 (hOGG1) Polymorphisms on the Risk of Lung Cancer: A Case-Control Study in Taiwan

Human 8-oxoguanine DNAN-glycosylase 1 (hOGG1) plays an important role in repairing oxidative DNA damage induced by tobacco carcinogens. In this case-control study, the authors examined the interactive effect of hOGG1 gene polymorphisms and cigarette smoking on the risk of lung cancer in Taiwan. A total of 1,096 cases and 1,007 controls were enrolled from 6 medical centers in Taiwan during 2002–2004. hOGG1 Ser326Cys genetic polymorphisms were determined using the MassARRAY system (SEQUENOM, Inc., San Diego, California). Tobacco smoking history was obtained through personal interview according to a structured questionnaire. Logistic regression analysis was used to estimate multivariate-adjusted odds ratios and 95% confidence intervals. The odds of developing lung cancer for persons with the Cys/Cys genotype versus the Ser/Ser genotype were 1.11 (95% confidence interval (CI): 0.74, 1.65) for never smokers, 1.45 (95% CI: 0.74, 2.83) for moderate smokers, and 3.52 (95% CI: 1.54, 8.06) for heavy smokers. The P value for interaction in the logistic model was 0.01. The increased risk associated with the Cys/Cys genotype among heavy smokers remained statistically significant for various histologic types of lung cancer, including adenocarcinoma, squamous cell carcinoma, and small cell carcinoma. The authors conclude that there was a noticeable modifying effect on the association between hOGG1 genotype and lung cancer risk by cigarette smoking status.
Towards Porting Hardware-Oblivious Vectorized Query Operators to GPUs

Nowadays, query processing in column-store database systems is highly tuned to the underlying (co-)processors. This approach works very well from a performance perspective, but has several shortcomings from a conceptual perspective. For example, this tuning introduces high implementation as well as maintenance cost and one implementation cannot be ported to other (co-)processors. To overcome that, we developed a column-store speciﬁc abstraction layer for hardware-driven vectorization based on the Single Instruction Multiple Data (SIMD) parallel paradigm. Thus, we are able to implement vectorized query operators in a hardware-oblivious manner, which can be specialized to diﬀerent SIMD instruction set extensions of modern x86-processors. To soften the limitation to x86-processors, we describe our vision to integrate GPUs in our abstraction layer by interpreting GPUs as virtual vector engines in this paper. Moreover, we present some initial evaluation results to determine a reasonable virtual vector size. We conclude the paper with an outlook on our ongoing research in that direction.
Suppression of Cytosolic NADPH Pool by Thionicotinamide Increases Oxidative Stress and Synergizes with Chemotherapy

NAD+ kinase (NADK) is the only known cytosolic enzyme that converts NAD+ to NADP+, which is subsequently reduced to NADPH. The demand for NADPH in cancer cells is elevated as reducing equivalents are required for the high levels of nucleotide, protein and fatty acid synthesis found in proliferating cells, as well as for neutralizing high levels of reactive oxygen species (ROS). The aim of this study was to determine whether inhibition of NADK activity is a valid anti-cancer strategy alone and in combination with chemotherapeutic drugs known to induce ROS. In vitro and in vivo inhibition of NADK with either shRNA or thionicotinamide inhibited proliferation. Thionicotinamide enhanced ROS produced by several chemotherapeutic drugs and produced synergistic cell kill. NADK inhibitors alone or in combination with drugs that increase ROS-mediated stress may represent an efficacious antitumor combination and should be explored further.
Interferon regulatory factor-1 (IRF-1) shapes both innate and CD8â†o T cell immune responses against West Nile virus infection

Interferon regulatory factor (IRF)-1 is an immunomodulatory transcription factor that functions downstream of pathogen recognition receptor signaling and has been implicated as a regulator of type I interferon (IFN)-ab expression and the immune response to virus infections. However, this role for IRF-1 remains controversial because altered type I IFN responses have not been systemically observed in IRF-1 mice. To evaluate the relationship of IRF-1 and immune regulation, we assessed West Nile virus (WNV) infectivity and the host response in IRF-1 cells and mice. IRF-1 mice were highly vulnerable to WNV infection with enhanced viral replication in peripheral tissues and rapid dissemination into the central nervous system. Ex vivo analysis revealed a cell-type specific antiviral role as IRF-1 macrophages supported enhanced WNV replication but infection was unaltered in IRF-1 fibroblasts. IRF-1 also had an independent and paradoxical effect on CD8 T cell expansion. Although markedly fewer CD8 T cells were observed in naı̈ve animals as described previously, remarkably, IRF-1 mice rapidly expanded their pool of WNV-specific cytolytic CD8 T cells. Adoptive transfer and in vitro proliferation experiments established both cell-intrinsic and cell-extrinsic effects of IRF-1 on the expansion of CD8 T cells. Thus, IRF-1 restricts WNV infection by modulating the expression of innate antiviral effector molecules while shaping the antigenspecific CD8 T cell response. Citation: Brien JD, Daffis S, Lazear HM, Cho H, Suthar MS, et al. (2011) Interferon Regulatory Factor-1 (IRF-1) Shapes Both Innate and CD8 T Cell Immune Responses against West Nile Virus Infection. PLoS Pathog 7(9): e1002230. doi:10.1371/journal.ppat. 1002230 Editor: Jean K. Lim, Mount Sinai School of Medicine, United States of America Received January 3, 2011; Accepted July 14, 2011; Published September 1, 2011 Copyright: 2011 Brien et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: NIH grants U54 AI081680 (Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research), U19 AI083019 (M.G. and M.S.D), and R01 AI074973 (M.G. and M.S.D.) supported this work. J.D. B. , H.M. L, and M.S. were supported by NIH Training grants (T32-AI07163-30, T32AI007172, and T32-AI0074-11, respectively). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: diamond@borcim.wustl. edu
Nutritional Epidemiology Decreased Consumption of Dried Mature Beans Is Positively Associated with Urbanization and Nonfatal Acute Myocardial Infarction

Legumes may protect against myocardial infarction (MI). The objective of this study was to determine whether consumption of dried mature beans (referred to as beans), the main legume in Latin America, is associated with MI. The cases (n 2119) were survivors of a first acute MI and were matched by age, sex, and area of residence to randomly selected population controls (n 2119) in Costa Rica. Dietary intake was assessed with a validated FFQ. Of the population, 69% consumed 1 serving of beans/d (1 serving one-third cup of cooked beans, 86 g). Consumption of 1 serving/d was significantly higher (P 0.001) in rural (81%) than in urban (65%) areas. Individuals who never eat dried beans or whose consumption was 1 time/mo were classified as nonconsumers. Compared with nonconsumers, intake of 1 serving of beans/d was inversely associated with MI in analyses adjusted for smoking, history of diabetes, history of hypertension, abdominal obesity, physical activity, income, intake of alcohol, total energy, saturated fat, trans fat, polyunsaturated fat, and cholesterol [odds ratio (OR) 0.62; 95% CI: 0.45–0.88]. No further protection was observed with increased number of servings/d (OR 0.73; 95% CI: 0.52–1.03 for 1 serving/d). In summary, we found that consumption of 1 serving of beans/d is associated with a 38% lower risk of MI. No additional protection was observed at intakes 1 serving/d. These findings are timely given the trend toward increased obesity, cardiovascular disease, and a reduction in the intake of beans in Latin American countries. J. Nutr. 135: 1770–1775, 2005.
Hacking supply chain 2.0 with smart machines: Supply chain 2.0 might be at risk, if not train enough against the hacking ML algorithms.

: When we talk about the use of expert and intelligent supply chain in supply chain 2.0, we should know that any intelligent system can be affected by wrong data and information. Since in supply chain 2.0, decision-making takes place according to system decision-making scenarios, it is certainly possible for these systems to be hacked. Especially as supply chains develop in competition with each other, and sometimes non-commercial motives are involved. There are different systems that generate basic information for other systems. For example, systems that provide traffic information as a service or systems that provide weather information to others. Many supply chain smart systems which are based on ML algorithm, usually do not semantically verify information received from other systems and may not be smart enough to do so. Therefore, machine learning algorithms in supply chain intelligence must be generated with a continuous look at the verification of data received from other systems or gathered from the environment. In this article, we examine how to extract meaningful data from machine learning classifiers so that is possible to infer unexpected but useful information from ML classifiers. In particular, we build a novel meta-classifier and train it to hack other classifiers, obtaining meaningful information about their training sets.
Genome-wide association analysis of coffee drinking suggests association with CYP1A1CYP1A2 and NRCAM

Citation for published version (APA): Amin, N. , Byrne, E. , Johnson, J., Chenevix-Trench, G. , Walter, S. , Nolte, I. M. , Vink, J. M. , Rawal, R. , Mangino, M. , Teumer, A. , Keers, J. C. , Verwoert, G. , Baumeister, S. , Biffar, R. , Petersmann, A. , Dahmen, N. , Doering, A. , Isaacs, A. , Broer, L. , . kConFab Investigators (2012). Genome-wide association analysis of coffee drinking suggests association with CYP1A1/CYP1A2 and NRCAM. Molecular Psychiatry, 17(11), 1116-1129. https://doi.org/10.1038/mp.2011. 101
Logic & Philosophy of Science Second Order Properties: Why Kim’s Reduction Does Not Work

In this paper I argue that recent reductionist’s arguments marshaled by Jaegwon Kim on the causal status of mental properties do not get the point they are aimed at. In particular, in the first part, tackling epistemological issues, I show that Kim’s arguments concerning the heterogeneity of disjunctive properties if accepted would undermine most scientific practice; in the second part, devoted to metaphysical issues, I argue that Kim’s reductive functionalism, if taken as a metaphysical thesis, cannot be applied neither to qualitative states nor to intentional ones. In particular, qualitative states cannot be reduced by Kim’s admissions, while intentional states cannot be reduced given Kripke’s argument concerning the nature of theoretical identifications. Being mental states either qualitative or intentional, Kim’s strategy fails to make his point. Finally, I argue that the mental properties can be interpreted as micro-based properties, so showing that the so-called ‘generalization argument’ either holds or licenses us in crediting mental properties with causal powers. Riassunto In questo articolo sostengo che gli argomenti recentemente avanzati da Kim a favore di un riduzionismo circa lo statuto causale delle proprietà mentali non colgono il segno. In particolare, nella prima parte, dedicata a trattare questioni epistemologiche, mostro che se gli argomenti di Kim circa l’eterogeneicità delle proprietà disgiuntive venissero accettati porterebbero a mettere in crisi molta pratica scientifica; nella seconda parte, destinata a questioni metafisiche, sostengo che il funzionalismo riduttivo di Kim, visto come tesi metafisica, non può essere applicato né agli stati qualitativi né a quelli intenzionali. Nello specifico, gli stati qualitativi non possono essere ritoddi per ammissione dello stesso Kim mentre quelli intenzionali non possono esserlo in virtù degli argomenti di Kripke relativi alla natura delle identificazioni teoriche. Poiché gli statimentali sono o qualitativi o intenzionali, la strategia di Kim fallisce nei propri obiettivi. Infine, sostengo che le proprietà mentali possono essere interpretate come proprietà micro-basate evidenziando così che il cosiddetto “argomento della generalizzazione” è o valido o ci autorizza ad attribuire poteri causali alle proprietà mentali.
Orientation Estimation of Abdominal Ultrasound Images with Multi-Hypotheses Networks

Ultrasound imaging can provide valuable information to clinicians during interventions, in particular when fused with other modalities. Multi-modal image registration algorithms however require a somewhat accurate initialization, which is particularly difficult to estimate for ultrasound images as their orientation is arbitrary and their content ambiguous (limited field of view, artifacts, etc.). In this work, we not only train neural networks to predict the absolute orientation of ultrasound frames, but also to produce a confidence for each prediction. This allows us to select only the most confident frames in the clip. Our networks are trained to produce multiple hypotheses using a simple yet overlooked meta-loss that is specifically designed to capture the ambiguity of the input data. We show on several abdominal ultrasound datasets that multi-hypotheses networks provide better uncertainty estimates than Monte-Carlo dropout while being more efficient than network ensembling. Generic, easy to implement and able to quantify both data ambiguity and out-of-distribution samples, they represent a preferable alternative to traditional baselines for uncertainty estimation. On a clinical test our method produces estimates within 20 ◦ of the true orientation, which we can use to improve the accuracy of a subsequent registration algorithm down to less than 10 ◦ .
Secure System for Remote Telemonitoring of Patients with Chronic Forms of Heart Disease

This paper considers modern technologies of home telemonitoring related to CPC patients. It presents a new secure intellectual telemedicine service based on remote monitoring of patients’ health status, which can be used for CPS patients for their health screenings in remote and hard-to-reach locations, as well as in-house hospitals. It also discusses technologies, problems and prospects of remote telemonitoring systems’ development and implementation.
Parallel Electron Heating through Landau Resonance with Lower Hybrid Waves at the Edge of Reconnection Ion Jets

We investigate lower hybrid waves in magnetic reconnection at the flank magnetopause using Magnetospheric Multiscale data. Intense emissions of lower hybrid waves are observed at the density boundary of the reconnection ion jet. Associated with the lower hybrid waves, electrons exhibit signatures of heating in the direction parallel to the magnetic field. Near the Landau resonance energy, the electron fluxes parallel to the magnetic field show oscillations at the same frequency as the lower hybrid waves. The electron flux oscillations are in phase or antiphase with the wave parallel electric field. These observations provide direct evidence for Landau resonance. Our analysis indicates that the density gradient at the edge of the ion jets provides free energy for the lower hybrid waves that further contribute to electron heating through Landau damping. These results shed light on the role of wave−particle interactions in the energy conversion chain of reconnection ion jets.
Research of the Optical Fibers Structure Influence on the Acousto-Optic Interaction Characteristics and the Brillouin Scattering Spectrum Profile

The research results of the structure influence of single-mode optical fibers of various types on the interaction characteristics of the optic and acoustical modes of lower orders are presented in this work. A method for obtaining of optic and acoustical modes distribution in single-mode optic fibers is considered. The structures of the radial distribution of refractive index profiles for some varieties of single-mode optical fibers with dispersion shift (ITU–T recommendation G.653 and G.653) are presented. The obtained graphs for varieties of optical fibers are presented.
Determination of the thrust of an ion thruster by the aerodynamic method of double angle (AMαβ-method)

This paper presents the results of an experimental study of the jet thrust of a mixed jet of neutral and ionized nitrogen flowing from the working chamber of an experimental sample of an accelerator ion thruster into a vacuum space. The main method of the study was the aerodynamic double angle method (AMαβ-method). The method of determining low thrust and the design of the stand for the implementation of the AMαβ-method are proposed. The object of research is a prototype of an accelerator two-phase ion thruster with a solid-state microwave plasma generator and a toroidal resonator. The study showed that a 2.5 W microwave generator together with a 2.5 W accelerating potential difference voltage source with a nitrogen consumption of 0.05 -1 mg/s can increase the speed of the working gas by 2.3 times. The jet thrust, according to the test results, was 1-3.6 μN. It is shown that the thrust components (the gas-dynamic component, the ion component of a high-frequency discharge, the ion component of a glow discharge) have different levels depending on the mass flow rate of the gas.
Mapping the Three-dimensional Lyα Forest Large-scale Structure in Real and Redshift Space

This work presents a new physically motivated supervised machine-learning method, hydro-bam, to reproduce the three-dimensional Lyα forest field in real and redshift space, which learns from a reference hydrodynamic simulation and thereby saves about seven orders of magnitude in computing time. We show that our method is accurate up to k ∼ 1 h Mpc−1 in the one- (probability distribution function), two- (power spectra), and three-point (bispectra) statistics of the reconstructed fields. When compared to the reference simulation including redshift-space distortions, our method achieves deviations of ≲2% up to k = 0.6 h Mpc−1 in the monopole and ≲5% up to k = 0.9 h Mpc−1 in the quadrupole. The bispectrum is well reproduced for triangle configurations with sides up to k = 0.8 h Mpc−1. In contrast, the commonly adopted Fluctuating Gunn–Peterson approximation shows significant deviations, already when peculiar motions are not included (real space) at configurations with sides of k = 0.2–0.4 h Mpc−1 in the bispectrum and is also significantly less accurate in the power spectrum (within 5% up to k = 0.7 h Mpc−1). We conclude that an accurate analysis of the Lyα forest requires considering the complex baryonic thermodynamical large-scale structure relations. Our hierarchical domain-specific machine-learning method can efficiently exploit this and is ready to generate accurate Lyα forest mock catalogs covering the large volumes required by surveys such as DESI and WEAVE.