Miracle-dz/UniFAR-FTUs huggingface dataset:
Different Genes Interact with Particulate Matter and Tobacco Smoke Exposure in Affecting Lung Function Decline in the General Population

Background Oxidative stress related genes modify the effects of ambient air pollution or tobacco smoking on lung function decline. The impact of interactions might be substantial, but previous studies mostly focused on main effects of single genes. Objectives We studied the interaction of both exposures with a broad set of oxidative-stress related candidate genes and pathways on lung function decline and contrasted interactions between exposures. Methods For 12679 single nucleotide polymorphisms (SNPs), change in forced expiratory volume in one second (FEV1), FEV1 over forced vital capacity (FEV1/FVC), and mean forced expiratory flow between 25 and 75% of the FVC (FEF25-75) was regressed on interval exposure to particulate matter <10 µm in diameter (PM10) or packyears smoked (a), additive SNP effects (b), and interaction terms between (a) and (b) in 669 adults with GWAS data. Interaction p-values for 152 genes and 14 pathways were calculated by the adaptive rank truncation product (ARTP) method, and compared between exposures. Interaction effect sizes were contrasted for the strongest SNPs of nominally significant genes (pinteraction<0.05). Replication was attempted for SNPs with MAF>10% in 3320 SAPALDIA participants without GWAS. Results On the SNP-level, rs2035268 in gene SNCA accelerated FEV1/FVC decline by 3.8% (pinteraction = 2.5×10−6), and rs12190800 in PARK2 attenuated FEV1 decline by 95.1 ml pinteraction = 9.7×10−8) over 11 years, while interacting with PM10. Genes and pathways nominally interacting with PM10 and packyears exposure differed substantially. Gene CRISP2 presented a significant interaction with PM10 (pinteraction = 3.0×10−4) on FEV1/FVC decline. Pathway interactions were weak. Replications for the strongest SNPs in PARK2 and CRISP2 were not successful. Conclusions Consistent with a stratified response to increasing oxidative stress, different genes and pathways potentially mediate PM10 and tobacco smoke effects on lung function decline. Ignoring environmental exposures would miss these patterns, but achieving sufficient sample size and comparability across study samples is challenging.
A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants1[OPEN]

Programmed cell death occurring as an integral part of plant development is characterized by the transcriptional activation of a distinct core of conserved cell death-associated genes. A plethora of diverse programmed cell death (PCD) processes has been described in living organisms. In animals and plants, different forms of PCD play crucial roles in development, immunity, and responses to the environment. While the molecular control of some animal PCD forms such as apoptosis is known in great detail, we still know comparatively little about the regulation of the diverse types of plant PCD. In part, this deficiency in molecular understanding is caused by the lack of reliable reporters to detect PCD processes. Here, we addressed this issue by using a combination of bioinformatics approaches to identify commonly regulated genes during diverse plant PCD processes in Arabidopsis (Arabidopsis thaliana). Our results indicate that the transcriptional signatures of developmentally controlled cell death are largely distinct from the ones associated with environmentally induced cell death. Moreover, different cases of developmental PCD share a set of cell death-associated genes. Most of these genes are evolutionary conserved within the green plant lineage, arguing for an evolutionary conserved core machinery of developmental PCD. Based on this information, we established an array of specific promoter-reporter lines for developmental PCD in Arabidopsis. These PCD indicators represent a powerful resource that can be used in addition to established morphological and biochemical methods to detect and analyze PCD processes in vivo and in planta.
Robust Output Voltage Regulation for DC–DC Buck Converters Under Load Variations via Sampled-Data Sensorless Control

The global robust output voltage regulation problem for dc–dc buck converter systems is investigated by means of designing a sampled-data almost disturbance decoupling (ADD) control methodology. Aiming to effectively restrain the output fluctuation caused by load variations, a physically realizable robust controller is proposed by employing a linear discrete-time observer to generate reliable state-reconstructed information under the conception of sensorless control. By virtue of output feedback domination approach, the proposed control strategy is able to achieve ADD, i.e., the output voltage interference can be arbitrarily attenuated in the $L_{2}$ gain sense. To ensure the theoretical rationality of the proposed approach, rigorous stability analysis for the hybrid closed-loop system is provided. Moreover, both simulation and experimental results demonstrate the effectiveness of the proposed controller, and the regulating principle and robustness analysis of involved parameter selection are studied. The direct-designed digital compensator will facilitate the practical implementation in power electronic systems.
Seroprevalence of Toxoplasma Gondii Infection among Pregnant Women in River Nile State, Sudan, from April to June 2017

Background: Toxoplasmosis is worldwide distribution disease, about 20% to 90% of the adult population in the world are reported with toxoplasmosis. Objectives: To know the prevalence of toxoplasmosis among selected group of pregnant women from Atbara and Aldamer towns, River Nile State ,Sudan by applying Latex agglutination and ELISA serological methods and to compare between these two serological methods Methodology: Blood specimen were collected from 50 pregnant women participated in this studies and then specimens were processed and examined by Latex agglutination and ELISA. Result: 24% were seropositive and 76% were seronegative, 24% positive with latex agglutination and 18% positive with ELISA. Discussion, conclusion and recommendations: ELISA is more specific than latex agglutination method, further studies are required with large sample size and more diagnostic methods. GJMR-C Classification: NLMC Code: QX 140 Seroprevalence of Toxoplasma Gondii Infection among Pregnant Women in River Nile State, Sudan, from April to June 2017 Mosab NM Hamad , Alaa M M Mustafa , Mona M Alkheir , Abd Alnasir Suliman , Tagwa Tarig , Basil Morsi , Anwer Mohialdeen , Mohammed Ismail ν & Abdallah Atayib Ѳ AbstractBackground: Toxoplasmosis is worldwide distribution disease, about 20% to 90% of the adult population in the world are reported with toxoplasmosis. Background: Toxoplasmosis is worldwide distribution disease, about 20% to 90% of the adult population in the world are reported with toxoplasmosis. Objectives: To know the prevalence of toxoplasmosis among selected group of pregnant women from Atbara and ALdamer towns, River Nile State ,Sudan by applying Latex agglutination and ELISA serological methods and to compare between these two serological methods Methodology: Blood specimen were collected from 50 pregnant women participated in this studies and then specimens were processed and examined by Latex agglutination and ELISA. Result: 24% were seropositive and 76% were seronegative, 24% positive with latex agglutination and 18% positive with ELISA. Discussion, conclusion and recommendations: ELISA is more specific than latex agglutination method, further studies are required with large sample size and more diagnostic methods.
Magnetoresistive Properties of Tb/Ti and Tb/Si Multilayers

Magnetic, magnetoresistive and structural properties of Tb/Ti and Tb/Si nanoscale multilayers prepared by alternative deposition of Tb layers and Ti or Si spacers are comparatively studied. It was concluded that spin disorder scattering is responsible for the negative longitudinal magnetoresistance observed in multilayers of both types.
The Use of Rice Husk Ash as Partial Replacement for Cement in Concrete

The study examines the use of rice husk ash as partial replacement for cement in concrete by determining various properties of rice husk ash through laboratory experiments. The objective of the study includes, determining the specific gravity of RHA, the effect of RHA on compressive strength of concrete and on properties of concrete such as density and workability. The results of the study revealed specific gravity of 2.36 for the RHA used. The use of RHA in the mix caused a significant decrease in the slump compared with concrete produced with only OPC. The water absorbing quality of RHA is a major physical property which affects the workability of OPC/RHA concrete. Compressive strength tests carried out on OPC/RHA concrete at varying ages up to 28 days and at varying water cement ratios appear to indicate that the material is adequate for concrete making. In addition, OPC/RHA concrete gain strength faster as a result of reduction in porosity caused by RHA. At 28 days, specimens with 0.6 watercement ratios gave strength greater than 20N/mm2. Thus, concrete mix of OPC/RHA at water-cement ratios of 0.7 and above may not produce concrete of 20N/mm2 (min.) required for structural purposes as recommended by CP 110. Rice husk is a local raw material for construction industry which is produced daily as waste and it can be obtained at a much lower cost than the cement which it replaces. Also, its usage should minimize the disposal problems faced by the producing companies and enhance environmental protection.
Doping assessment in GaAs nanowires

Semiconductor nanowires (NWs) are a candidate technology for future optoelectronic devices. One of the critical issues in NWs is the control of impurity doping for the formation of p–n junctions. In this study, beryllium (p-type dopant) and tellurium (n-type dopant) in self-assisted GaAs NWs was studied. The GaAs NWs were grown on (111) Si by molecular beam epitaxy using the self-assisted method. The dopant incorporation in the self-assisted GaAs NWs was investigated using Raman spectroscopy, photoluminescence, secondary ion mass spectrometry and electron holography. Be-doped NWs showed similar carrier concentration as compared to thin film (TF) standards. However, Te-doped NWs showed at least a one order of magnitude lower carrier concentration as compared to TF standards. Dopant incorporation mechanisms in NWs are discussed.
Collision risk assessment for possible collision vehicle in occluded area based on precise map

Due to blockage by large obstacles, perception of detection sensors such as lidar, radar, and stereo vision can have visibility restrictions. The assessment of collision risk against moving vehicles in the occluded area is difficult because vehicle motion information for perception is not available. In order to overcome this difficulty, this paper presents a probabilistic approach of collision risk assessment for the potential collision of vehicles in the occluded area. The probabilistic assessment consists of three steps: a field of view (FoV) modeling of perception, a motion prediction of potential collision, and a probabilistic collision risk assessment. The first step is a FoV modeling of perception to classify the occluded region of perception visibility. The second step is motion predictions of the potential collision vehicles by applying the modeled FoV to the roadway geometry in the precise map. The final step is a probabilistic assessment of the collision risk for the occluded vehicles based on the motion predictions and probabilistic modeling of vehicle speed on the road. The proposed collision risk assessment was evaluated using various occlusion scenarios in real traffic situations, such as an alleyway.
A Domain is only as Good as its Buddies: Detecting Stealthy Malicious Domains via Graph Inference

Inference based techniques are one of the major approaches to analyze DNS data and detect malicious domains. The key idea of inference techniques is to first define associations between domains based on features extracted from DNS data. Then, an inference algorithm is deployed to infer potential malicious domains based on their direct/indirect associations with known malicious ones. The way associations are defined is key to the effectiveness of an inference technique. It is desirable to be both accurate (i.e., avoid falsely associating domains with no meaningful connections) and with good coverage (i.e., identify all associations between domains with meaningful connections). Due to the limited scope of information provided by DNS data, it becomes a challenge to design an association scheme that achieves both high accuracy and good coverage. In this paper, we propose a new approach to identify domains controlled by the same entity. Our key idea is an in-depth analysis of active DNS data to accurately separate public IPs from dedicated ones, which enables us to build high-quality associations between domains. Our scheme avoids the pitfall of naive approaches that rely on weak "co-IP" relationship of domains (i.e., two domains are resolved to the same IP) that results in low detection accuracy, and, meanwhile, identifies many meaningful connections between domains that are discarded by existing state-of-the-art approaches. Our experimental results show that the proposed approach not only significantly improves the domain coverage compared to existing approaches but also achieves better detection accuracy. Existing path-based inference algorithms are specifically designed for DNS data analysis. They are effective but computationally expensive. To further demonstrate the strength of our domain association scheme as well as improve the inference efficiency, we construct a new domain-IP graph that can work well with the generic belief propagation algorithm. Through comprehensive experiments, we show that this approach offers significant efficiency and scalability improvement with only a minor impact to detection accuracy, which suggests that such a combination could offer a good tradeoff for malicious domain detection in practice.
Towards Property Driven Hardware Security

Secure hardware design is a challenging task due to the fact that security properties are difficult or impossible to model and subsequently verify using traditional hardware design tools. The "state of the art" for hardware design security relies heavily on functional verification, manual inspection, and code review to identify security vulnerabilities. This labor intensive process significantly reduces productivity while proving no guarantee that a security flaw will be identified. In this paper, we describe a property driven approach to hardware security, which allows automatic synthesis and verification of both qualitative and quantitative security properties. We address hardware security by enforcing information flow and statistical security properties. By incorporating a new security property specification language, such security properties can be specified, translated and verified using hardware design tools. We present design examples to demonstrate our property driven hardware security solution for proving isolation, detecting timing channel, eliminating hardware Trojan, and enforcing security related statistical properties.
ERMP1, a novel potential oncogene involved in UPR and oxidative stress defense, is highly expressed in human cancer

Endoplasmic reticulum (ER) stress and unfolded protein response (UPR) are highly activated in cancer and involved in tumorigenesis and resistance to anti-cancer therapy. UPR is becoming a promising target of anti-cancer therapies. Thus, the identification of UPR components that are highly expressed in cancer could offer new therapeutic opportunity. In this study, we demonstrate that Endoplasmic Reticulum Metallo Protease 1 (ERMP1) is broadly expressed in a high percentage of breast, colo-rectal, lung, and ovary cancers, regardless of their stage and grade. Moreover, we show that loss of ERMP1 expression significantly hampers proliferation, migration and invasiveness of cancer cells. Furthermore, we show that this protein is an important player in the UPR and defense against oxidative stress. ERMP1 expression is strongly affected by reticular stress induced by thapsigargin and other oxidative stresses. ERMP1 silencing during reticular stress impairs the activation of PERK, a key sensor of the UPR activation. Loss of ERMP1 also prevents the expression of GRP78/BiP, a UPR stress marker involved in the activation of the survival pathway. Finally, ERMP1 silencing in cells exposed to hypoxia leads to inhibition of the Nrf2-mediated anti-oxidant response and to reduction of accumulation of HIF-1, the master transcription factor instructing cells to respond to hypoxic stress. Our results suggest that ERMP1 could act as a molecular starter to the survival response induced by extracellular stresses. Moreover, they provide the rationale for the design of ERMP1-targeting drugs that could act by inhibiting the UPR initial adaptive response of cancer cells and impair cell survival.
Bayesian adaptive bandit-based designs using the Gittins index for multi-armed trials with normally distributed endpoints

ABSTRACT Adaptive designs for multi-armed clinical trials have become increasingly popular recently because of their potential to shorten development times and to increase patient response. However, developing response-adaptive designs that offer patient-benefit while ensuring the resulting trial provides a statistically rigorous and unbiased comparison of the different treatments included is highly challenging. In this paper, the theory of Multi-Armed Bandit Problems is used to define near optimal adaptive designs in the context of a clinical trial with a normally distributed endpoint with known variance. We report the operating characteristics (type I error, power, bias) and patient-benefit of these approaches and alternative designs using simulation studies based on an ongoing trial. These results are then compared to those recently published in the context of Bernoulli endpoints. Many limitations and advantages are similar in both cases but there are also important differences, specially with respect to type I error control. This paper proposes a simulation-based testing procedure to correct for the observed type I error inflation that bandit-based and adaptive rules can induce.
Cytosolic proteins can exploit membrane localization to trigger functional assembly

Cell division, endocytosis, and viral budding would not function without the localization and assembly of protein complexes on membranes. What is poorly appreciated, however, is that by localizing to membranes, proteins search in a reduced space that effectively drives up concentration. Here we derive an accurate and practical analytical theory to quantify the significance of this dimensionality reduction in regulating protein assembly on membranes. We define a simple metric, an effective equilibrium constant, that allows for quantitative comparison of protein-protein interactions with and without membrane present. To test the importance of membrane localization for driving protein assembly, we collected the protein-protein and protein-lipid affinities, protein and lipid concentrations, and volume-to-surface-area ratios for 46 interactions between 37 membrane-targeting proteins in human and yeast cells. We find that many of the protein-protein interactions between pairs of proteins involved in clathrin-mediated endocytosis in human and yeast cells can experience enormous increases in effective protein-protein affinity (10-1000 fold) due to membrane localization. Localization of binding partners thus triggers robust protein complexation, suggesting that it can play an important role in controlling the timing of endocytic protein coat formation. Our analysis shows that several other proteins involved in membrane remodeling at various organelles have similar potential to exploit localization. The theory highlights the master role of phosphoinositide lipid concentration, the volume-to-surface-area ratio, and the ratio of 3D to 2D equilibrium constants in triggering (or preventing) constitutive assembly on membranes. Our simple model provides a novel quantitative framework for interpreting or designing in vitro experiments of protein complexation influenced by membrane binding.
Generalized selection of complementary matrices in the inclusion principle

This paper presents a strategy for choosing complementary matrices in the framework of the inclusion principle with state LQ optimal control of LTI systems, it is based on translating the basic restrictions given by the inclusion principle into explicit block structures for these matrices, the degree of freedom given by these structures is illustrated by means of an example of overlapping decentralized control design.
Correlation With Iron Overload And Thyroid Dysfunction In Children With Thalassemia On Regular Transfusion Therapy

BMI (Body Mass Index) Body Fat %, Obesity PFT (FEV1, FVC, FEV1/FVC %) Skin fold thickness WHR (Waist-Hip Ratio) BACKGROUND: Thalassemia majoris a hereditary anemia which is caused by defective synthesis of hemoglobin, ineffective erythropoiesis and rapid erythrocyte breakdown.Transfusions in beta thalassemia major are necessary for survival of these patients.Frequent blood transfusions and inadequate iron chelation therapy can result in iron overload which may lead to various endocrine complication such as Thyroid dysfunction, Cardiomyopathy, Daibetes Mellitus, Hypogonadism. OBJECTIVES:To study the frequency of hypothyroidism in thalassemia and To study the correlation between iron overload as measured by serum ferritin levels and incidence of thyroid dysfunction, in children with thalassemia major on regular transfusion therapy. METHODS:This is asingle center cross sectional study including 91 children attending thalassemia day care center and on regular blood transfusion therapy for a minimum of 2 years. Detailed history and examination were recorded in the proforma. Blood was drawn for serum ferritin levels and thyroid function tests in these children. RESULTS: Subclinical hypothyroidism was found in 21% of children in our study. 17 children had subclinical hypothyroidism and 2 had compensated hypothyroidism. There was no correlation between serum ferritin levels and thyroid dysfunction. CONCLUSION: Hypothyroidism was found to be a complication of thalassemia in around 21% children in our study. Detection of hypothyroidism is important as effective replacement therapy is available. Therefore, thyroid function should be followed periodically, particularly when other iron overload-associated complications occur. Early recognition and hence prevention of these complications might help improve the quality of life of these patients.