Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting and Validating Protein Interactions Using Network Structure

Protein interactions play a vital part in the function of a cell. As experimental techniques for detection and validation of protein interactions are time consuming, there is a need for computational methods for this task. Protein interactions appear to form a network with a relatively high degree of local clustering. In this paper we exploit this clustering by suggesting a score based on triplets of observed protein interactions. The score utilises both protein characteristics and network properties. Our score based on triplets is shown to complement existing techniques for predicting protein interactions, outperforming them on data sets which display a high degree of clustering. The predicted interactions score highly against test measures for accuracy. Compared to a similar score derived from pairwise interactions only, the triplet score displays higher sensitivity and specificity. By looking at specific examples, we show how an experimental set of interactions can be enriched and validated. As part of this work we also examine the effect of different prior databases upon the accuracy of prediction and find that the interactions from the same kingdom give better results than from across kingdoms, suggesting that there may be fundamental differences between the networks. These results all emphasize that network structure is important and helps in the accurate prediction of protein interactions. The protein interaction data set and the program used in our analysis, and a list of predictions and validations, are available at http://www.stats. ox.ac. uk/bioinfo/resources/PredictingInteractions.
A Large Video Database for Computational Models of Induced Emotion

To contribute to the need for emotional databases and affective tagging, the LIRIS-ACCEDE is proposed in this paper. LIRIS-ACCEDE is an Annotated Creative Commons Emotional DatabasE composed of 9800 video clips extracted from 160 movies shared under Creative Commons licenses. It allows to make this database publicly available without copyright issues. The 9800 video clips (each 8-12 seconds long) are sorted along the induced valence axis, from the video perceived the most negatively to the video perceived the most positively. The annotation was carried out by 1518 annotators from 89 different countries using crowd sourcing. A baseline late fusion scheme using ground truth from annotations is computed to predict emotion categories in video clips.
Understanding patterns of genetic diversity in the oak gallwasp Biorhiza pallida: demographic history or a Wolbachia selective sweep?

The endosymbiont Wolbachia can be responsible for selective sweeps on mitochondrial DNA variability within species. Similar signals can also result from demographic processes, although crucially the latter affect nuclear as well as mitochondrial loci. Here we present data on Wolbachia infection status and phylogeographic patterning for a widely distributed insect host, the oak gallwasp Biorhiza pallida (Hymenoptera: Cynipidae). Two hundred and eighteen females from eight European countries were screened for Wolbachia. All individuals from Hungary, Italy, France, U.K., Ireland, Switzerland, Sweden, and northern and southern Spain were infected with a single group A strain of Wolbachia, while populations in central Spain were not infected. A mitochondrial marker (cytochrome b) shows low variation and departure from neutrality in infected populations, but greater variation and no deviation from neutrality in Wolbachia-free populations. This pattern is compatible with a Wolbachia-induced selective sweep. However, we also find parallel differences between infected and uninfected populations for nuclear markers (sequence data for ITS1 and ITS2). All markers support the existence of a deep split between populations in Spain (some free of Wolbachia), and those in the rest of Europe (all infected). Allelic variation for five allozyme loci is also consistent with the Spain–rest of Europe split. Concordant patterns for nuclear and mitochondrial markers suggest that differences in the nature and extent of genetic diversity between these two regions are best explained by differing demographic histories (perhaps associated with range expansion from Pleistocene glacial refugia), rather than a Wolbachia-associated selective sweep.
Fucoidan as a Potential Therapeutic for Major Blinding Diseases—A Hypothesis

Fucoidan is a heterogeneous group of sulfated polysaccharide with a high content of l-fucose, which can be extracted from brown algae and marine invertebrates. It has many beneficial biological activities that make fucoidan an interesting candidate for therapeutic application in a variety of diseases. Age-related macular degeneration and diabetic retinopathy are major causes for vision loss and blindness in the industrialized countries and increasingly in the developing world. Some of the characteristics found in certain fucoidans, such as its anti-oxidant activity, complement inhibition or interaction with the Vascular Endothelial Growth factor, which would be of high interest for a potential application of fucoidan in age-related macular degeneration or diabetic retinopathy. However, the possible usage of fucoidan in ophthalmological diseases has received little attention so far. In this review, biological activities of fucoidan that could be of interest regarding these diseases will be discussed.
Food intake and energy expenditure of male and female farmers from Upper-Volta

1. The energy balance of eleven male and fourteen female adult farmers was measured for 6 d after the harvest, in December-January. Their energy intake was recorded by weighing their food consumption and their energy expenditure was determined using indirect calorimetry. 2. Body-weight, expressed as percentage of expected weight-for-height was 91 and 86% of the Inter-departmental Committee on Nutrition for National Development (1963) standard for women and men respectively. 3. The staple foods were sorghum (Sorghum vulgare) and millet (Pennisetum typhoïdes); carbohydrates, fat and protein supplied approximately 80, 13 and 12% of the total energy of the diet respectively. 4. In the male group, the mean energy intake (9.0 MJ (2148 kcal)) was in good agreement with the average energy output (8.91 MJ (2130 kcal)). By contrast, in the female group, the mean energy expenditure (8.11 MJ (1941 kcal)) exceeded the mean energy intake (6.3 MJ (1515 kcal)) and the deficit was statistically significant. 5. This study allows an evaluation of the adequacy of food intake for subjects living in a particular hostile environment, by using their actual energy output instead of current standard values. The energy deficit found for female farmers whose energy intake was similar to that reported in other developing countries emphasizes the need for a better understanding of the regulation of energy balance in such conditions.
A Team-Based Methodology of Memory Hierarchy-Aware Runtime Support in Coarray Fortran

We describe how 2-level memory hierarchies can be exploited to optimize the implementation of teams in the parallel facet of the upcoming Fortran 2015 standard. We focus on reducing the cost associated with moving data within a computing node and between nodes, finding that this distinction is of key importance when looking at performance issues. We introduce a new hardware-aware approach for PGAS, to be used within a runtime system, to optimize the communications in the virtual topologies and clusters that are binding different teams together. We have applied, and implemented into the CAF OpenUH compiler, this methodology to three important collective operations, namely barrier, all-to-all reduction and one-to-all broadcast, this is the first Fortran compiler that both provides teams and handles such a memory hierarchy methodology within teams.
L1 analysis of sampled-data systems via fast-lifting and piecewise linear approximation

This paper revisits the L<sub>1</sub> analysis of sampled-data systems, by which we mean the computation of the L<sub>∞</sub>-induced norm of sampled-data systems. More precisely, we apply fast-lifting by which the sampling interval [0, h) is divided into M subintervals with an equal width, and provide a method for computing the L<sub>∞</sub>-induced norm by using an idea of piecewise linear approximation. Through this method, we show that we can compute upper bound and lower bounds of the L<sub>∞</sub>-induced norm and that the computation error associated with this method converges to 0 at the rate of 1/M<sup>2</sup>. This is in sharp contrast with a conventional method via fast-sample/fast-hold approximation, which only shows that the computation error converges to 0 in the rate of 1/M, without providing any explicit upper and lower bounds of the L<sub>∞</sub>-induced norm.
Regulation of conductance by the number of fixed positive charges in the intracellular vestibule of the CFTR chloride channel pore

Rapid chloride permeation through the cystic fibrosis transmembrane conductance regulator (CFTR) Cl− channel is dependent on the presence of fixed positive charges in the permeation pathway. Here, we use site-directed mutagenesis and patch clamp recording to show that the functional role played by one such positive charge (K95) in the inner vestibule of the pore can be “transplanted” to a residue in a different transmembrane (TM) region (S1141). Thus, the mutant channel K95S/S1141K showed Cl− conductance and open-channel blocker interactions similar to those of wild-type CFTR, thereby “rescuing” the effects of the charge-neutralizing K95S mutation. Furthermore, the function of K95C/S1141C, but not K95C or S1141C, was inhibited by the oxidizing agent copper(II)-o-phenanthroline, and this inhibition was reversed by the reducing agent dithiothreitol, suggesting disulfide bond formation between these two introduced cysteine side chains. These results suggest that the amino acid side chains of K95 (in TM1) and S1141 (in TM12) are functionally interchangeable and located closely together in the inner vestibule of the pore. This allowed us to investigate the functional effects of increasing the number of fixed positive charges in this vestibule from one (in wild type) to two (in the S1141K mutant). The S1141K mutant had similar Cl− conductance as wild type, but increased susceptibility to channel block by cytoplasmic anions including adenosine triphosphate, pyrophosphate, 5-nitro-2-(3-phenylpropylamino)benzoic acid, and Pt(NO2)42− in inside-out membrane patches. Furthermore, in cell-attached patch recordings, apparent voltage-dependent channel block by cytosolic anions was strengthened by the S1141K mutation. Thus, the Cl− channel function of CFTR is maximal with a single fixed positive charge in this part of the inner vestibule of the pore, and increasing the number of such charges to two causes a net decrease in overall Cl− transport through a combination of failure to increase Cl− conductance and increased susceptibility to channel block by cytosolic substances.
Glucocorticoids Suppress Mitochondrial Oxidant Production via Upregulation of Uncoupling Protein 2 in Hyperglycemic Endothelial Cells

Diabetic complications are the leading cause of morbidity and mortality in diabetic patients. Elevated blood glucose contributes to the development of endothelial and vascular dysfunction, and, consequently, to diabetic micro- and macrovascular complications, because it increases the mitochondrial proton gradient and mitochondrial oxidant production. Therapeutic approaches designed to counteract glucose-induced mitochondrial reactive oxygen species (ROS) production in the vasculature are expected to show efficacy against all diabetic complications, but direct pharmacological targeting (scavenging) of mitochondrial oxidants remains challenging due to the high reactivity of some of these oxidant species. In a recent study, we have conducted a medium-throughput cell-based screening of a focused library of well-annotated pharmacologically active compounds and identified glucocorticoids as inhibitors of mitochondrial superoxide production in microvascular endothelial cells exposed to elevated extracellular glucose. The goal of the current study was to investigate the mechanism of glucocorticoids' action. Our findings show that glucocorticoids induce the expression of the mitochondrial UCP2 protein and decrease the mitochondrial potential. UCP2 silencing prevents the protective effect of the glucocorticoids on ROS production. UCP2 induction also increases the oxygen consumption and the “proton leak” in microvascular endothelial cells. Furthermore, glutamine supplementation augments the effect of glucocorticoids via further enhancing the expression of UCP2 at the translational level. We conclude that UCP2 induction represents a novel experimental therapeutic intervention in diabetic vascular complications. While direct repurposing of glucocorticoids may not be possible for the therapy of diabetic complications due to their significant side effects that develop during chronic administration, the UCP2 pathway may be therapeutically targetable by other, glucocorticoid-independent pharmacological means.
Orphans of the AIDS epidemic? The extent, nature and circumstances of child-headed households in South Africa

Abstract There is widespread concern that the number of children living in “child-headed households” is rapidly increasing as a result of AIDS-related adult mortality in much of sub-Saharan Africa. Based on analyses of data from several representative national surveys over the period 2000–2007, this paper examines the extent to which this is the case in South Africa. It explores trends in the number of children living in child-only households and characterises these children relative to children living in households with adults (mixed-generation households). The findings indicate that the proportion of child-only households is relatively small (0.47% in 2006) and does not appear to be increasing. In addition, the vast majority (92.1%) of children resident in child-only households have a living parent. The findings raise critical questions about the circumstances leading to the formation of child-only households and highlight that they cannot for the main part be ascribed to HIV orphaning. Nonetheless, the number of children living in this household form is not insignificant, and their circumstances, when compared with children in mixed-generation households, indicate a range of challenges, including greater economic vulnerability and inadequate service access. We argue that a solitary focus on the HIV epidemic and its related orphaning as the cause of child-only households masks other important issues for consideration in addressing their needs, and risks the development of inappropriate policies, programmes and interventions.
Surrogate-model based method and software for practical design optimization problems

Summary. In a practical simulation-based design process most of the required simulations are carried out by using commercial software producing simulation responses but no gradient data. When applying mathematical optimization routines to such design process all the function evaluators must be considered as black-box solvers and the optimization can be integrated to design process efficiently using e.g. surrogate modeling techniques or heuristic optimization algorithms. In this paper we present a design optimization method that can be integrated very easily to any simulation-based design process. Special attention is paid on software implementation issues of the proposed method.
Microdecompression and Uninstrumented Single‐level Fusion for Spinal Canal Stenosis With Degenerative Spondylolisthesis

Study Design. A retrospective review was completed on 21 patients who had a "least invasive" (one or two level) microdecompression and uninstrumented single‐segment lumbar fusion for spinal canal stenosis with degenerative spondylolisthesis. Objective. To determine whether a "least invasive" approach to lumbar spinal canal stenosis and degenerative spondylolisthesis would yield acceptable results. Summary of Background Data. The prevailing surgical technique for symptomatic spinal canal stenosis with degenerative spondylolisthesis is a wide midline decompression and instrumented fusion. Methods. On an average of 38 months postoperatively, 21 patients were personally assessed on four scores: 1) their overall satisfaction with the outcome of surgery, 2) an analog back and leg pain scale, 3) a functional evaluation scale, and 4) Ferguson (upshot) anterior‐posterior lumbosacral and lateral flexion‐extension radiographs. Results. The overall satisfactory outcome on all four scales was 16 (76%) of 21. Twenty of twenty‐one patients had relief of their claudicant leg pain; the overall fusion rate was 18 (86%) of 21. Two of three patients with a pseudarthrosis had a successful outcome on the patient‐oriented outcome (1, 2, and 3) scales (excluding the radiograph scale), and one was a failure. One patient with a solid fusion was a failure because of continuing back pain. One patient with a solid fusion was a failure because of continuing leg pain. The overall satisfactory outcome on the nonradiographic scales was 18 of 21, for an 86% patient satisfaction rate. Conclusions. In this retrospective study, a "least invasive" surgical approach to lumbar degenerative spondylolisthesis with spinal canal stenosis causing claudicant leg pain produced acceptable results.
Dietary lycopene, angiogenesis, and prostate cancer: a prospective study in the prostate-specific antigen era.

BACKGROUND The role of lycopene in prostate cancer prevention remains controversial. We examined the associations between dietary lycopene intake and prostate cancer, paying particular attention to the influence of prostate-specific antigen screening, and evaluated tissue biomarkers in prostate cancers in relation to lycopene intake. METHODS Among 49898 male health professionals, we obtained dietary information through questionnaires and ascertained total and lethal prostate cancer cases from 1986 through January 31, 2010. Cox regression was used to estimate multivariable hazard ratios (HRs) and 95% confidence intervals (CIs). Tissue microarrays and immunohistochemistry were used to assess tumor biomarker expression in a subset of men. Two-sided χ(2) tests were used to calculate the P values. RESULTS Higher lycopene intake was inversely associated with total prostate cancer and more strongly with lethal prostate cancer (top vs bottom quintile: HR = 0.72; 95% CI = 0.56 to 0.94; P(trend) = . 04). In a restricted population of screened participants, the inverse associations became markedly stronger (for lethal prostate cancer: HR = 0.47; 95% CI = 0.29 to 0.75; P trend = .009). Comparing different measures of dietary lycopene, early intake, but not recent intake, was inversely associated with prostate cancer. Higher lycopene intake was associated with biomarkers in the cancer indicative of less angiogenic potential. CONCLUSIONS Dietary intake of lycopene was associated with reduced risk of lethal prostate cancer and with a lesser degree of angiogenesis in the tumor. Because angiogenesis is a strong progression factor, an endpoint of lethal prostate cancer may be more relevant than an endpoint of indolent prostate cancer for lycopene in the era of highly prevalent prostate-specific antigen screening.
Threshold implementations : as countermeasure against higher-order differential power analysis

Embedded devices are used pervasively in a wide range of applications some of which require cryptographic algorithms in order to provide security. Sensitive information, such as the secret key used in the algorithm, can be derived from the physical leakage of these devices. The most common attack based on the physical leakages is differential power analysis (DPA) which exploits the correlation between the instantaneous power consumption of a device and the intermediate results of a cryptographic algorithm. Different countermeasures have been proposed to prevent DPA. Here, we focus on a powerful approach called threshold implementation (TI) which is based on secret sharing and multi-party computation and is proven secure even in the presence of glitches by Nikova et al. in ICICS’06. TI relies on four properties, namely correctness, non- completeness, uniformity of the shared variables and uniformity of the shared functions. Achieving all four properties for linear functions is straight-forward. However, it can be challenging when nonlinear functions, such as the S-boxes of symmetric-key algorithms, are considered. Satisfying all the properties can impose using extra randomness or increasing the number of shares both of which imply an increase of resources. The contribution of this thesis is two-fold. In the first part of the thesis, we introduce the theory for generating higher-order TI which can counteract higher-order DPA. The early works of TI provide security against first-order DPA attacks. However, it has been shown that second-order attacks are also feasible even though the amount of traces required for a successful attack increases exponentially in the noise standard deviation. Therefore, increasing the security using higher-order TI is valuable. In the second part of the thesis, we examine area- randomness-security trade-offs during a TI. In order to do that, we first investigate all 3 × 3 and 4 × 4, and some cryptographically significant classes of 5 × 5 and 6 × 6 invertible S-boxes. Then, we extend our research to the TIs of standardized symmetric-key algorithms AES and SHA-3 with detailed investigation on the trade-offs.
Type-Specific Cervico-Vaginal Human Papillomavirus Infection Increases Risk of HIV Acquisition Independent of Other Sexually Transmitted Infections

Background Sexually transmitted infections (STIs) such as herpes simplex virus (HSV)-2 are associated with an increased risk of HIV infection. Human papillomavirus (HPV) is a common STI, but little is know about its role in HIV transmission. The objective of this study was to determine whether cervico-vaginal HPV infection increases the risk of HIV acquisition in women independent of other common STIs. Methods and Findings This prospective cohort study followed 2040 HIV-negative Zimbabwean women (average age 27 years, range 18–49 years) for a median of 21 months. Participants were tested quarterly for 29 HPV types (with L1 PCR primers) and HIV (antibody testing on blood samples with DNA or RNA PCR confirmation). HIV incidence was 2.7 per 100 woman-years. Baseline HPV prevalence was 24.5%, and the most prevalent HPV types were 58 (5.0%), 16 (4.7%), 70 (2.4%), and 18 (2.3%). In separate regression models adjusting for baseline variables (including age, high risk partner, positive test for STIs, positive HSV-2 serology and condom use), HIV acquisition was associated with having baseline prevalent infection with HPV 58 (aHR 2.13; 95% CI 1.09–4.15) or HPV 70 (aHR 2.68; 95% CI 1.08–6.66). In separate regression models adjusting for both baseline variables and time-dependent variables (including HSV-2 status, incident STIs, new sexual partner and condom use), HIV acquisition was associated with concurrent infection with any non-oncogenic HPV type (aHR 1.70; 95% CI 1.02–2.85), any oncogenic HPV type (aHR 1.96; 95% CI 1.16–3.30), HPV 31 (aHR 4.25; 95% CI 1.81–9.97) or HPV 70 (aHR 3.30; 95% CI 1.50–7.20). Detection of any oncogenic HPV type within the previous 6 months was an independent predictor of HIV acquisition, regardless of whether HPV status at the HIV acquisition visit was included (aHR 1.95; 95% CI 1.19–3.21) or excluded (aHR 1.96; 95% CI 1.02–2.85) from the analysis. Conclusions/Significance Cervico-vaginal HPV infection was associated with an increased risk of HIV acquisition in women, and specific HPV types were implicated in this association. The observational nature of our study precludes establishment of causation between HPV infection and HIV acquisition. However, given the high prevalence of HPV infection in women, further investigation of the role of HPV in HIV transmission is warranted.