Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of interventions and optimal strategies in the stochastic system approach to causality.

We consider the problem of defining the effect of an intervention on a time-varying risk factor or treatment for a disease or a physiological marker; we develop here the latter case. So, the system considered is $(Y,A,C)$, where $Y=(Y_t)$, is the marker process of interest, $A=A_t$ the treatment. A realistic case is that the treatment can be changed only at discrete times. In an observational study the treatment attribution law is unknown; however, the physical law can be estimated without knowing the treatment attribution law, provided a well-specified model is available. An intervention is specified by the treatment attribution law, which is thus known. Simple interventions will simply randomize the attribution of the treatment; interventions that take into account the past history will be called "strategies". The effect of interventions can be defined by a risk function $R^{\intr}=\Ee_{\intr}[L(\bar Y_{t_J}, \bar A_{t_{J}},C)]$, where $L(\bar Y_{t_J}, \bar A_{t_{J}},C)$ is a loss function, and contrasts between risk functions for different strategies can be formed. Once we can compute effects for any strategy, we can search for optimal or sub-optimal strategies; in particular we can find optimal parametric strategies. We present several ways for designing strategies. As an illustration, we consider the choice of a strategy for containing the HIV load below a certain level while limiting the treatment burden. A simulation study demonstrates the possibility of finding optimal parametric strategies.
Moisture Effects on Properties of Polymeric Composite Laminates with Different Void Content

Composite materials, especially carbon fiber reinforced polymers (CFRPs), have been broadly used due to their high specific strength and stiffness ratio compared to metallic materials in the past few decades. CFRPs are widely utilized in aerospace, civil infrastructure and marine sectors under harsh environments. As a result, there exists a strong demand to observe the mechanical behavior of composite materials in the presence of moisture in order to avoid unpredictable effects. Composite structures are often cured in an autoclave to achieve the required aerospace grade quality. However, curing large structures requires access to large autoclaves which is limited and expensive. As a result, fabrication of large structures using out-of-autoclave prepreg materials will lead to a great amount of savings in manufacturing costs. In the out-of-autoclave processing method, the presence of voids inside the laminate has been an issue due to the lack of high pressure during manufacturing. This study aims primarily to observe the moisture absorption response of composite samples containing different levels of void. By changing the vacuum level inside the bag during the manufacturing process, three different unidirectional laminates at three levels of void have been manufactured. After immersing the samples in warm water at 60˚C for about one year, the maximum moisture absorption level and rate of absorption were monitored through experiments and diffusion coefficients were calculated for all the samples using Fick’s law. Results show that the moisture absorption coefficient, its rate and the maximum level of moisture can be correlated to the void volume fraction. Moreover, the sensibility of the CFRPs under moisturized environment has been investigated. The mechanical behavior of these laminates has been studied at four different moisture levels by performing dynamic mechanical analysis (DMA) and interlaminar shear strength (ILSS) tests. Empirical results indicate that in most of the cases, interlaminar shear strength, glass transition temperature, and storage modulus decrease during the exposure of the samples with different void contents to the moisture environment. Finally, a finite element analysis has been done to study the change of moisture concentration through the thickness of the material.
Numerical Modeling of 3-D Separated Flows at Reynolds Numbers Appropriate for Turbine Blades and Unmanned Aero Vehicles

Flow separation strongly affects flows for unmanned aerial vehicles (UAV), micro air vehicles (MAV) and turbomachinery. The unsteady effects of flow separation greatly influence blade/wing lift and drag thus performance of UAV’s, and efficiency and robustness of turbomachinery because of its impact on high cycle fatigue (HCF). The Reynolds numbers for the aforementioned devices are usually low to moderate. Low Reynolds number separated flows have been successfully simulated using direct numerical simulations (DNS). However, the large computational cost of DNS makes this technique not practical for industrial applications. Reynolds averaged Navier-Stokes (RANS) techniques have been only partially able to predict some features of low Reynolds number separated flows so far, leaving Large Eddy Simulation (LES) as a primary candidate for fast and accurate prediction tool for such flows. In this report we investigate the ability of LES techniques to accurately predict the behavior of such flows at a computational cost reduced significantly from the cost of DNS. We have performed 2-D and 3-D simulations of a laminar separation bubble on a NACA-0012 airfoil at Rec = 5 × 10 at 5 degree of incidence with resolution reduced from that used in DNS. For the 2-D simulations the results to date show good predictions for the pressure coefficient Cp and the friction coefficient Cf but only when using dissipative numerical schemes. For the 3-D simulations the results show a good prediction of the separation point, but inaccurate predictions of the reattachment point.
SNP-set Tests for Sequencing and Genome-Wide Association Studies

In this dissertation we propose methodology for testing SNP-sets for genetic associations, both for sequencing and genome-wide association studies. Due to the large scale of this kind of data, there is an emphasis on producing methodology that is not only accurate and powerful, but also computationally efficient. In the Chapter 1, we aim at using extreme phenotype sampling to increase the power to identify rare variants associated with complex traits. We confirm both analytically and numerically that sampling individuals with extreme phenotypes can enrich the presence of causal rare variants and can therefore lead to an increase in power compared to random sampling. While application of traditional rare variant association tests to these extreme phenotype samples requires dichotomizing the continuous phenotypes before analysis, the dichotomization procedure can decrease the power by reducing the information in the phenotypes. To avoid this, we propose a novel statistical method based on optimal SKAT (SKAT-O) that allows us to test for rare variant effects using continuous phenotypes in the analysis of extreme phenotype samples. The increase in power of this method is demonstrated through simulation of a wide range of scenarios as well as in the triglyceride data of the Dallas Heart Study. In Chapter 2, we present the higher criticism, a signal detection method that is effective for testing the joint null hypothesis against a sparse alternative, in the context of SNP-set testing. This test is useful for testing the effect of a gene or a genetic pathway that consists of d genetic markers. Accurate p-value calculations for the higher criticism based on the asymptotic distribution require a very large d, which is not the case for the number of genetic variants in a gene or a pathway. We propose an analytic method that
Reducing risk in Deaf mental health

Summary of general considerations for the development of Deaf mental health services: Staffing and bed numbers for the New Zealand context are given in table 7 below. 1. Where there are poor community support services Deaf inpatient admissions will be as high as 30 -40/1000 Deaf/year [20]. The minimum formula suggested for adult inpatient beds is 1/1000 and 4/1000 for residential beds. Staffing levels for signing staff should be basically the same as for hearing – 2/bed for inpatient and 1/bed for residential. 2. Deaf needs for community mental health services will be 2-3 times higher than for hearing [14, 20]. This means we should be planning for 6 – 9% of the Deaf population (60-90/1000). Survey data indicates the use of mental health services is at least 9%. In addition there is an extensive use of counselling services and a large unmet need. Social support, counselling and employment services will be needed by perhaps 40% of the Deaf population. Using the Irish model, 7/1000 Deaf is the suggested staffing level for such services. 3. Assessments and therapeutic interventions take at least twice as long to do with Deaf as they do with hearing [20]. Gold standard models such as PACT (Programme for Assertive Community Treatment) advocate a 1:10 staff/client ratio for CMH clients. New Zealand services operate on 1:20. Bristol services operate at 1:11 for Deaf, assuming 7.5% of the Deaf population use the services. This seems reasonable.
Genetic Diversity of Fusarium oxysporum f. sp. cubense Causing Panama Wilt of Banana in the Philippines

Panama wilt, caused by Fusarium oxysporum f. sp. cubense (Foc) is considered one of the most devastating banana diseases in recorded history. The disease threatens the banana industry due to Tropical Race 4 (TR4) infecting the Cavendish cultivar. Forty-two of the 45 representative isolates from Luzon were pathogenic, based on leaf symptom index and vascular discoloration rating. Accurate, fast and reliable identification are pre-requisites for effective management considering there are yet no proven effective chemicals to control the disease, thus the confirmation by a PCR-based diagnostic tool is essential. Using race-specific primers, FocTr4-F/FocTr4-R and Foc-1/Foc-2, the absence of TR4 in Luzon has been confirmed, however, the occurrence of Race 4 has been reported, which should also be taken in consideration as the latter can also cause severe damage under favorable conditions. Furthermore, to examine genetic diversity of Foc in bananas, 55 of the 164 isolates collected from Regions I, II, III, IV and Cordillera Administrative Region (CAR) were analyzed by fingerprinting techniques using M13, ERIC and REP primers. Twenty-two reference isolates from Mindanao were also analyzed using the same primers. Foc isolates were differentiated into two clades at 25% similarity level, classifying all Mindanao isolates to clade A. Consistently high genetic variation was obtained from Luzon isolates using M13, an arbitrarily primed fingerprinting technique and repetitive elements, REP and ERIC-PCR, while low genetic variation was obtained from Mindanao isolates. ERIC-PCR was the most informative and predictive fingerprinting method as the TR4 isolates from Mindanao were grouped together. No grouping of Foc isolates was observed with respect to geographical origin, except isolates from Mindanao. In addition, grouping of Foc4 is also regardless of host variety in all analyses conducted. Overall, high genetic variability was recorded in Foc Philippine population for the three primers used, which might render host resistance vulnerable.
Physical performance characteristics of university male tennis players in division I and II

Purpose: The purposes of this study were to examine the physical performance characteristics of Division-I (D-I) and Division-II (D-II) university male tennis players and to evaluate whether these characteristics could be determinative on the divisional differentiation. Material: Twenty athletes who compete in D=I (n=10) and D-II (n=10) of Turkey university tennis league (n=10) and also ranked in top-ten in their division voluntarily participated in this study. Results: Measurement of agility, upper and lower body explosive powers, fatigue index, aerobic and anaerobic powers was conducted on two non-consecutive days. Significant differences were observed in physical performance characteristics powers between the groups (p<0.05). D-I players had significantly greater anaerobic power, agility, vertical jump height, upper and lower body explosive powers, and lower fatigue index level than D-II players. However, aerobic power did not differ between groups. Conclusions: It may be possible that these results allow us to suggest that physical performance characteristics should be regarded as one of the important discriminative factors in determining the competitive level of university male tennis players.
Non-linear simulations of disruption mitigation using massive gas injection on Tore Supra

Disruptions are identified as a major threat to ITER and reactor-size tokamaks. They produce excessive heat loads on plasma facing components, induce electromagnetic (EM) forces in the vessel structures and generate multi-MeV runaway electrons. Therefore, disruption mitigation will be needed for next-generation devices. Massive Gas Injection (MGI) is one of the methods proposed to be installed on future machines [1]. Most of the tokamaks in the world have carried out MGI experiments and showed the method was efficient at reducing EM forces, heat loads and more marginally runaway generation. However, the magnitude of this efficiency still varies between machines, and results are not directly scalable to larger devices. The plasma energy density for such tokamaks is likely to be several orders of magnitude higher than in current ones, and it is unclear how the physical mechanisms involved in gas jet penetration scale with the machine size. Therefore, simulations are needed to assess the efficiency of the method on next generation devices. In this paper 3D MHD simulations of the pre-disruptive phase of massive gas injections on Tore Supra-like plasmas using the JOREK code are reported. First validation of the simulations with experimental observations are made, with the long term goal being to predict the plasma response to a massive gas injection in a larger tokamak like ITER.
Lyssavirus Spp. – Rabies Viruses As A Still-Present Problem

Abstract The genus Lyssavirus spp. currently includes 14 species that are responsible for causing rabies, rabies-like and rabies-related diseases. The first symptoms of infection are similar to a cold and mainly include fever, headache and general fatigue. Then comes brain dysfunction and acute neurological symptoms, and ultimately – in most cases – death. Lyssaviruses are spread mainly through direct contact with the carrier that contains the viral reservoir. The gold standard in diagnostics is the method of direct immunofluorescence, through which viral antigens are detected – mainly in the saliva of a patient. Currently, rabies treatment is an experimental form of therapy according to the Milwaukee protocol. 1. Introduction. 2. Systematics. 2.1. Lagos bat virus. 2.2. Mokola virus. 2.3 Duvenhage virus. 2.4. European bat 1 lyssavirus. 2.5. European bat 2 lyssavirus. 2.6. Australian bat lyssavirus. 3. Characteristics. 3.1. Molecular structure. 3.2. Genome and gene expression. 3.3. Life cycle. 4. Pathogenicity. 4.1. Pathogenesis. 4.2. Rabies symptoms. 5. Prevention, prophylaxis, diagnostics, treatment. 5.1. Vaccinations. 5.2. Postexposure prophylaxis. 5.3. Diagnostics. 5.4. Experimental treatment. 6. Summary
A Modeling Framework for Reliability of Erasure Codes in SSD Arrays

Emergence of Solid-State Drives (SSDs) have evolved the data storage industry where they are rapidly replacing Hard Disk Drives (HDDs) due to their superiority in performance and power. Meanwhile, SSDs have reliability issues due to bit errors, bad blocks, and bad chips. To help reliability, Redundant Array of Independent Disks (RAID) configurations, originally proposed to increase both performance and reliability of HDDs, are also applied to SSD arrays. However, the conventional reliability models of HDD RAID cannot be intactly applied to SSD arrays, as the nature of failures in SSDs are totally different from HDDs. Previous studies on the reliability of SSD arrays are based on the deprecated SSD failure data, and only focus on limited failure types, device failures, and page failures caused by the bit errors, while recent field studies have reported other failure types including bad blocks and bad chips, and a high correlation between failures. In this paper, we investigate the reliability of SSD arrays using field storage traces and real-system implementation of conventional and emerging erasure codes. The reliability is evaluated by statistical fault injection experiments that post-process the usage logs obtained from the real-system implementation, while the fault/failure attributes are obtained from the state-of-the-art field data by previous works. As a case study, we examine conventional RAID5 and RAID6 and emerging Partial-MDS (PMDS) codes, Sector-Disk (SD) codes, and STAIR codes in terms of both reliability and performance using an open-source software RAID controller, MD (in Linux kernel version 3.10.0-327), and arrays of Samsung 850 Pro SSDs. Our detailed analysis on the data loss breakdown shows that a) emerging erasure codes fail to replace RAID6 in terms of reliability, b) row-wise erasure codes are the most efficient choices for contemporary SSD devices, and c) previous models overestimate the SSD array reliability by up to six orders of magnitude, as they just focus on the coincidence of bad pages (bit errors) and bad chips within a data stripe that holds the minority of root cause of data loss in SSD arrays. Our experiments show that the combination of bad chips with bad blocks is recognized as the major source of data loss in RAID5 and emerging codes (contributing more than 54 and 90 percent of data loss in RAID5 and emerging codes, respectively), while RAID6 remains robust under these failure combinations. Finally, the fault injection results reveal that SSD array reliability, as well as the failure breakdown is significantly correlated with SSD type.
Regional Drought Assessment over India using SPEI under Climate Change

Among the extreme climate events, droughts are the most widespread and slowly developing atmospheric hazards which remain for a long duration affecting natural resources, environment, and people. Drought is a temporary deviation from normal weather conditions. It corresponds to the failure of spatial and temporal precipitation and water availability and therefore consequent impact on agriculture, ecosystem and socioeconomic activities of human being. Understanding the drought characteristics in the context of climate change is critical for water resources management in water stressed countries such as India. The frequency of severe and widespread multi-year droughts has increased in India during the recent decades due to the erratic summer monsoon and increase in air temperature and thereby creating a huge damage to crops and society. India has experienced 23 large-scale droughts starting from 1891 to 2009 and the frequency of droughts is increasing. In this context, several drought indices have been developed, which evaluate the deviation of climate variables in a given year from the normal conditions. These drought indices serve as monitoring tools and operational indicators for regional water resources management. The Standardized Precipitation and Evapotranspiration Index (SPEI) became one of the popular drought indices in the context of increasing temperatures under global warming conditions in recent periods. The SPEI is estimated by fitting a probability distribution to the difference between Precipitation (P) and Potential Evapotranspiration (PET) (P-PET), which represents the climatic water balance. SPEI has been widely used in the drought characterization for the Indian context but none of the drought studies analyzed the applicability of SPEI in the Indian context. So, in this study, the applicability of the SPEI over India has been evaluated and modified to account for the spatio-temporal heterogeneity of rainfall and seasonality present due to the monsoon rainfall variability. The choice of an inappropriate probability distribution may lead to bias in the index values leading to distorted drought severity. Further, application of SPEI with a single probability distribution all over India may not be a meaningful index due to the large spatial heterogeneity in the rainfall patterns at various temporal scales of Indian monsoon rainfall. So, the ability of a group of candidate probability distributions over seven meteorological homogeneous zones of India has been evaluated. The results suggested that the Log-Logistic distribution which was used in the original formulation of SPEI was not the best distribution to fit the water balance series for the Indian context. Pearson type III distribution for shorter time scales (3 and 6 months) and GEV distribution for longer time scales (12 and 24 months) have been identified as the best distributions for fitting SPEI for Indian case study. India being a country associated with strong seasonal rainfall (80% rain in June-September) it is important
Characterisation of the PQ-loop repeat membrane protein family in arabidopsis thaliana

This thesis describes the characterisation of the PQ-loop repeat family, a novel family of membrane proteins from Arabidopsis thaliana. The family consists of six members (AtPQL1-6) all predicted to contain seven transmembrane segments and two copies of the PQ-loop domain. The repeated PQ-loop domain is a well conserved feature present in several eukaryotic proteins. However, the functional significance of the domain remains to be determined. Although most PQ-loop repeat proteins are of unknown function some have been characterised from non-plant species. Those studied include CTNS - a lysosomal cystine transporter from humans, STM1 - a putative G-protein coupled receptor from Schizosaccharomyces pombe, ERS1 - a Saccharomyces cerevisiae protein isolated as a suppressor of a trafficking mutant and LEC35/MPDU1 - an endoplasmic reticulum protein from mammals involved in the utilisation of dolichol monosaccharides during glycosylation. The AtPQL family can be divided into three groups based on similarity with their non-plant homologues. Detailed sequence analysis was carried out to investigate conserved motifs, topology, domain organisation and genome distribution of the six genes. The implications of these findings for putative functions are discussed. AtPQL gene expression was investigated using promoter::GUS fusions and quantitative PCR. Whereas AtPQL4 and AtPQL6 appear to be expressed ubiquitously, AtPQL1, AtPQL2 and AtPQL5 are all preferentially expressed in floral tissues and AtPQL3 is expressed primarily in roots. Several family members showed rhythmic expression over the course of a day and induction by both viral infection and wounding. Localisation at the sub-cellular level was investigated using green fluorescent protein fusions and confocal microscopy. At least four AtPQL proteins are targeted to intracellular compartments. AtPQL1 and AtPQL5-GFP fusions both highlight the tonoplast whereas AtPQL4 and AtPQL6-GFP appear to highlight the ER. A number of knockout and over-expresser mutants were isolated for each gene. Although no physiological phenotype could be found, mutants with altered expression of AtPQL4 and AtPQL6, the two closest A. thaliana homologues of MPDU1/LEC35, showed a clear molecular phenotype. These mutants displayed differential regulation of a number of genes encoding N-glycoproteins as well as defence, cell-surface, lipid biosynthesis and ER stress associated proteins. Finally, the functional importance of the AtPQL family is discussed and a role for AtPQL4 and AtPQL6 in glycosylation proposed.