Miracle-dz/UniFAR-FTUs huggingface dataset:
Introduction to the mass transportation theory ; Applications ( Pre-ultimate draft )

The Monge-Kantorovich mass transportation theory finds its roots in three influential papers. The first one is written by a great geometer, G. Monge [35]. The second and third one are due to Kantorovich [31] [30], who received a Nobel prize for related work in economics [36]. The Monge-Kantorovich theory is having a growing number of applications in various areas of sciences including Economics, optic (e.g. the reflector problem), meteorology, oceanography, kinetic theory, partial differential equations and functional analysis (e.g. geometric inequalities). The purpose of these fives hour lectures is to develop basic tools for the Monge-Kantorovich theory. We will briefly mention its impact in kinetic theory and meteorology. These applications are fully developed in the following preprints, [11] [13] [16] [26], which you can download from my webpage at www.math.gatech.edu/ gangbo/publications/. The contribution on the mass of transportation theory by the author and its collaborators, to geometric inequalities as well as computer vision and the reflector problem, can be found at the same webpage. These notes have been written as a set of lectures for the 2004 Summer Institute at Carnegie Mellon University. It is a pleasure to thanks the organizers of that Summer Institute for their support and hospitality.
Enhanced synaptic plasticity in mice with phosphomimetic mutation of the GluA1 AMPA receptor

Phosphorylation of the GluA1 subunit of AMPA receptors has been proposed to regulate receptor trafficking and synaptic transmission and plasticity. However, it remains unclear whether GluA1 phosphorylation is permissive or sufficient for enacting these functional changes. Here we investigate the role of GluA1 phosphorylation at S831 and S845 residues in the hippocampus through the analyses of GluA1 S831D/S845D phosphomimetic knock-in mice. S831D/S845D mice showed normal total and surface expression and subcellular localization of GluA1 as well as intact basal synaptic transmission. In addition, theta-burst stimulation, a protocol that was sufficient to induce robust long-term potentiation (LTP) in WT mice, resulted in LTP of similar magnitude in S831D/S845D mice. However, S831D/S845D mice showed LTP induced with 10-Hz stimulation, a protocol that is weaker than theta-burst stimulation and was not sufficient to induce LTP in WT mice. Moreover, S831D/S845D mice exhibited LTP induced with spike-timing–dependent plasticity (STDP) protocol at a long pre-post interval that was subthreshold for WT mice, although a suprathreshold STDP protocol at a short pre-post interval resulted in similarly robust LTP for WT and S831D/S845D mice. These results indicate that phosphorylation of GluA1 at S831 and S845 is sufficient to lower the threshold for LTP induction, increasing the probability of synaptic plasticity.
Peroxisomal and Mitochondrial Fatty Acid β-Oxidation in Mice Nullizygous for Both Peroxisome Proliferator-activated Receptor α and Peroxisomal Fatty Acyl-CoA Oxidase

Fatty acid β-oxidation occurs in both mitochondria and peroxisomes. Long chain fatty acids are also metabolized by the cytochrome P450 CYP4A ω-oxidation enzymes to toxic dicarboxylic acids (DCAs) that serve as substrates for peroxisomal β-oxidation. Synthetic peroxisome proliferators interact with peroxisome proliferator activated receptor α (PPARα) to transcriptionally activate genes that participate in peroxisomal, microsomal, and mitochondrial fatty acid oxidation. Mice lacking PPARα (PPARα−/−) fail to respond to the inductive effects of peroxisome proliferators, whereas those lacking fatty acyl-CoA oxidase (AOX−/−), the first enzyme of the peroxisomal β-oxidation system, exhibit extensive microvesicular steatohepatitis, leading to hepatocellular regeneration and massive peroxisome proliferation, implying sustained activation of PPARα by natural ligands. We now report that mice nullizygous for both PPARα and AOX (PPARα−/− AOX−/−) failed to exhibit spontaneous peroxisome proliferation and induction of PPARα-regulated genes by biological ligands unmetabolized in the absence of AOX. In AOX−/− mice, the hyperactivity of PPARα enhances the severity of steatosis by inducing CYP4A family proteins that generate DCAs and since they are not metabolized in the absence of peroxisomal β-oxidation, they damage mitochondria leading to steatosis. Blunting of microvesicular steatosis, which is restricted to few liver cells in periportal regions in PPARα−/−AOX−/− mice, suggests a role for PPARα-induced genes, especially members of CYP4A family, in determining the severity of steatosis in livers with defective peroxisomal β-oxidation. In age-matched PPARα−/− mice, a decrease in constitutive mitochondrial β-oxidation with intact constitutive peroxisomal β-oxidation system contributes to large droplet fatty change that is restricted to centrilobular hepatocytes. These data define a critical role for both PPARα and AOX in hepatic lipid metabolism and in the pathogenesis of specific fatty liver phenotype.
Active and Passive Side-Channel Attacks on Delay Based PUF Designs

Physical Unclonable Functions (PUFs) have emerged as a lightweight alternative to traditional cryptography. The fact that no secret key needs to be stored in non-volatile memory makes PUFs especially well suited for embedded systems in which securely generating and storing secret keys is difficult and expensive. Compared to traditional cryptography, PUFs are often believed to be more resistant to implementation attacks. In this paper we will take a closer look at this assumption. Using a controlled Arbiter PUF as an example, we show that just like traditional cryptography strong PUFs are susceptible to implementation attacks. By combining machine learning with with sidechannel analysis we are able to attack designed based on Arbiter PUFs that on are resistant to normal machine learning attacks. We use two different side-channels for our attacks: a passive power side-channel and an active fault attack based on altering the supply voltage of the controlled PUF. Even in the presence of considerable noise both attacks can accurately model the Controlled Arbiter PUF. Hence, the assumption that PUFs are generally more resistant against side-channel attacks is not necessarily true and side-channel resistance needs to be considered when PUF designs are evaluated.
Automating Efficient RAM-Model Secure Computation

RAM-model secure computation addresses the inherent limitations of circuit-model secure computation considered in almost all previous work. Here, we describe the first automated approach for RAM-model secure computation in the semi-honest model. We define an intermediate representation called SCVM and a corresponding type system suited for RAM-model secure computation. Leveraging compile-time optimizations, our approach achieves order-of-magnitude speedups compared to both circuit-model secure computation and the state-of-art RAM-model secure computation.
Lifecourse Activity Participation From Early, Mid, and Later Adulthood as Determinants of Cognitive Aging: The Lothian Birth Cohort 1921

Objectives: To examine potential sensitive periods for activity participation across adulthood to reduce cognitive decline and to determine whether associations persist after accounting for the lifetime stability of cognitive ability. Method: The Lothian Birth Cohort 1921 is a longitudinal study of cognitive aging. Participants were born in 1921 and most completed a mental ability test at the age of 11 years. Cognitive assessments were completed at mean ages 79 (N = 550), 83 (N = 321), 87 (N = 235), and 90 years (N = 129). Participants provided retrospective details of their activity participation for young (20–35 years), mid (40–55 years), and later adulthood (60–75 years), and contemporaneously at age 79. Results: Associations between activity and the level of, and change in, cognitive ability in old age were examined with latent growth curve models. Accounting for demographics and childhood cognitive ability, engagement in leisure activities in midlife was positively associated with cognitive ability level (path coefficient = .32), whereas higher physical activity in later adulthood was associated with less cognitive decline (.27). Discussion: The findings support a lifecourse approach in identifying determinants of cognitive aging; leisure and physical activity during different periods of adulthood may enhance cognitive abilities or reduce decline.
Down-regulating HIF-1α by lentivirus-mediated shRNA for therapy of triple negative breast cancer

Hypoxia is associated with poor response to treatment in various cancers. Hypoxia inducible factor 1 (HIF-1) is a major transcription factor that mediates adaptation of cancer cells to a hypoxic environment and regulates many genes that are involved in key cellular functions, including cell immortalization, stem cell maintenance, autocrine growth/survival, angiogenesis, invasion/metastasis, and resistance to chemotherapy. HIF-1α has been considered as an attractive therapeutic target for cancer treatment, but there is limited success in this research field. In the present study, we designed a recombinant lentivirus containing HIF-1α siRNA, developed stably transfected cell lines, and tested the anticancer effects of the siRNA on cancer cells in vitro and in vivo. Our results indicated that the stable downregulation of HIF-1α reversed chemoresistance, inhibited proliferation, migration and invasion of cancer cells, and slowed down the tumor growth in breast cancer xenograft models. In conclusion, the recombinant lentivirus containing HIF-1α siRNA provides a new avenue for developing novel therapy for triple negative breast cancer.
Overarching Training Needs on Farm Infrastructures and Participation: A Case Study of Irrigation Scheme Beneficiaries in Zanyokwe, Eastern Cape South Africa

ABSRACT The paper examined the role of smallholder irrigation scheme beneficiaries in training decision making and the relationship between farm characteristics and participation in training on the use of farm infrastructures. The study adopted purposive sampling techniques with a total of 44 male and 16 female farmers sampled from the population. The data collected were subjected to screening for analysis. In other to determine the statistical relationship between farm characteristics and participation in training, logistic regression analysis was used. Findings shows that there is a very strong relationship between the sizes of allocated plots to farmers in the irrigation scheme and participation in training. The result of the study revealed that Farm Experience (p-value =.001) and size of allocated plots (p-value = 0.002) has significant relationship to farmers’ participation in training. The study concluded that the training of farmers has the potentials of increasing the efficient use and maintenance of farm infrastructures for effective optimal production.
Volatilized N-NH3, N, and C stocks in soil after green manuring of coffee crops

Volatilization of nitrogen ammonia (N-NH3) and rapid incorporation of mineralized nitrogen (N) into soil organic matter fractions can reduce the efficiency of green manuring. The objective of this study was to characterize N-NH3 loss through volatilization and the changes in carbon (C) and N stocks in soil fertilized with Crotalaria juncea and ammonium sulfate during coffee plant cultivation. The N-NH3 collectors were installed and evaluated at 1, 2, 3, 4, 5, 6, 9, 12, 15, 18, 25, 32, 67 and 123 days after their installation. Total organic carbon (TOC) and total nitrogen (TN) in the 0–5and 5–10-cm soil layers were evaluated at 0, 60, 120, 180, 240, and 300 days after fertilization. After 9 days, 20.83 kg ha-1 (N-NH3) had volatilized from the 41.88 kg ha-1 observed at the end of the evaluation period. The TOC stock in both soil layers was 5.81 Mg ha-1, and after 300 days, the stocks were 8.84 and 8.36 Mg ha-1 for the 0–5 and 5–10 cm layers, respectively. The TN stock in the 0–5 cm layer increased from 1.74 to 1.98 Mg ha-1 over 60 days, and then decreased. There was no time dependency in the TN stock in the 5–10 cm layer. Volatilization of N-NH3 was rapid but low. The increase in TOC stocks was not followed by an increase in TN stocks.
Improved Use of Continuous Attributes in C4.5

A reported weakness of C4.5 in domains with continuous attributes is addressed by modifying the formation and evaluation of tests on continuous attributes. An MDL-inspired penalty is applied to such tests, eliminating some of them from consideration and altering the relative desirability of all tests. Empirical trials show that the modifications lead to smaller decision trees with higher predictive accuracies. Results also confirm that a new version of C4.5 incorporating these changes is superior to recent approaches that use global discretization and that construct small trees with multi-interval splits.
Food and the gut microbiota in inflammatory bowel diseases: a critical connection

Purpose of review The inflammatory bowel diseases (IBD) are chronic inflammatory diseases of the gastrointestinal tract apparently due to an abnormal immune response to environmental factors in genetically susceptible hosts. The composition of the gut microbiota is thought to be a critical environmental factor in IBD, and recent evidence suggests a connection between diet and the intestinal bacteria. In this review, we describe the current evidence regarding the impact of diet on the gut microbiome and how this may be relevant to the pathogenesis of IBD. Recent findings Novel culture-independent DNA sequencing technology has revolutionized the approach to the characterization of intestinal bacterial communities. Recent studies have demonstrated an association between the diet and the human microbiome. Because the development of a ‘dysbiotic’ microbiota is thought to be involved in the pathogenesis of IBD, diet is being investigated as an important etiologic factor. Summary The recent studies highlighting the impact of diet on the gut microbiome provide a strong rationale for further investigation of the link between diet, the gut microbiome, and the development of IBD. Such studies may provide novel information about disease pathogenesis as well as identify new therapeutic alternatives for patients suffering from IBD.
Association between body height and chronic low back pain: a follow-up in the Nord-Trøndelag Health Study

Objective To study potential associations between body height and subsequent occurrence of chronic low back pain (LBP). Design Prospective cohort study. Setting The North-Trøndelag Health Study (HUNT). Data were obtained from a whole Norwegian county in the HUNT2 (1995–1997) and HUNT3 (2006–2008) surveys. Participants Altogether, 3883 women and 2662 men with LBP, and 10 059 women and 8725 men without LBP, aged 30–69 years, were included at baseline and reported after 11 years whether they suffered from LBP. Main outcome measure Chronic LBP, defined as pain persisting for 3 months during the previous year. Results Associations between body height and risk and recurrence of LBP were evaluated by generalised linear modelling. Potential confounders, such as BMI, age, education, employment, physical activity, smoking, blood pressure and lipid levels were adjusted for. In women with no LBP at baseline and body height ≥170 cm, a higher risk of LBP was demonstrated after adjustment for other risk factors (relative risk 1.19, 95% CI 1.03 to 1.37; compared with height <160 cm). No relationship was established among men or among women with LBP at baseline. Conclusions In women without LBP, a body height ≥170 cm may predispose to chronic LBP 11 years later. This may reflect mechanical issues or indicate a hormonal influence.
The Arginine/ADMA Ratio Is Related to the Prevention of Atherosclerotic Plaques in Hypercholesterolemic Rabbits When Giving a Combined Therapy with Atorvastatine and Arginine

Supplementation with arginine in combination with atorvastatin is more efficient in reducing the size of an atherosclerotic plaque than treatment with a statin or arginine alone in homozygous Watanabe heritable hyperlipidemic (WHHL) rabbits. We evaluated the mechanism behind this feature by exploring the role of the arginine/asymmetric dimethylarginine (ADMA) ratio, which is the substrate and inhibitor of nitric oxide synthase (NOS) and thereby nitric oxide (NO), respectively. Methods: Rabbits were fed either an arginine diet (group A, n = 9), standard rabbit chow plus atorvastatin (group S, n = 8), standard rabbit chow plus an arginine diet with atorvastatin (group SA, n = 8) or standard rabbit chow (group C, n = 9) as control. Blood was sampled and the aorta was harvested for topographic and histological analysis. Plasma levels of arginine, ADMA, cholesterol and nitric oxide were determined and the arginine/ADMA ratio was calculated. Results: The decrease in ADMA levels over time was significantly correlated to fewer aortic lesions in the distal aorta and total aorta. The arginine/ADMA ratio was correlated to cholesterol levels and decrease in cholesterol levels over time in the SA group. A lower arginine/ADMA ratio was significantly correlated to lower NO levels in the S and C group. Discussion: A balance between arginine and ADMA is an important indicator in the prevention of the development of atherosclerotic plaques.
Leader selection in directed networks

We study the problem of leader selection in directed consensus networks. In this problem, certain `leader' nodes in a consensus network are equipped with absolute information about their state. This corresponds to diagonally strengthening a dynamical generator given by the negative of a directed graph Laplacian. We provide a necessary and sufficient condition for the stabilization of directed consensus networks via leader selection and form regularized H2 and H∞ optimal problem leader selection problems. We draw on recent results that establish the convexity of the H2 and H∞ norms for structured decentralized control of positive systems and identify sparse sets of leaders by imposing an ℓ1 penalty on the vector of leader weights. This allows us to develop a method that simultaneously assigns leader weights and selects a limited number of leaders. We use proximal gradient and subgradient method to solve the optimization problems and provide examples to illustrate our developments.
Do anxious boys and girls differ in emotion recognition accuracy?

INTRODUCTION Difficulty recognizing emotions may contribute to childhood anxiety and anxiety-related social difficulties. METHODS We examined the relationship between gender and emotion recognition accuracy in children with and without anxiety disorders. RESULTS Gender did not predict emotion recognition accuracy except for disgust. DISCUSSION Disgust recognition was significantly less accurate in clinically anxious girls than in clinically anxious boys. There was also a trend towards anxious girls being less accurate than non-anxious girls in recognizing disgust.
Simplified representation of vector fields

Vector field visualization remains a difficult task. Many local and global visualization methods for vector fields such as flow data exist, but they usually require extensive user experience on setting the visualization parameters in order to produce images communicating the desired insight. We present a visualization method that produces simplified but suggestive images of the vector field automatically, based on a hierarchical clustering of the input data. The resulting clusters are then visualized with straight or curved arrow icons. The presented method has a few parameters with which users can produce various simplified vector field visualizations that communicate different insights on the vector data.
Fully parallel associative memory with human memory type learning model

In this paper, fully parallel associative memory architecture with learning model is proposed. It uses a mixed digital-analog associative memory for reference pattern recognition and a learning model based on a short and long-term memory similar to that in human brain. In addition a ranking mechanism is used to manage the transition of reference vectors between two memories and an optimization algorithm is used to adjust the reference vectors components as well as their distribution continuously. The main advantage of the proposed model is no need to pre-training phase as well as its hardware-friendly structure which makes it implementable by an efficient LSI architecture without requiring a large amount of resources. The system was implemented on an FPGA platform and tested with real data of handwritten and printed English characters and the classification results found satisfactory.
A comparative study of different feature sets for recognition of handwritten Arabic numerals using a Multi Layer Perceptron

The work presents a comparative assessment of seven different feature sets for recognition of handwritten Arabic numerals using a Multi Layer Perceptron (MLP) based classifier. The seven feature sets employed here consist of shadow features, octant centroids, longest runs, angular distances, effective spans, dynamic centers of gravity, and some of their combinations. On experimentation with a database of 3000 samples, the maximum recognition rate of 95.80% is observed with both of two separate combinations of features. One of these combinations consists of shadow and centriod features, i. e. 88 features in all, and the other shadow, centroid and longest run features, i. e. 124 features in all. Out of these two, the former combination having a smaller number of features is finally considered effective for applications related to Optical Character Recognition (OCR) of handwritten Arabic numerals. The work can also be extended to include OCR of handwritten characters of Arabic alphabet.
Accelerated Profile HMM Searches

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the “multiple segment Viterbi” (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call “sparse rescaling”. These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches.
On the Complexity of Linear Authorization Logics

Linear authorization logics (LAL) are logics based on linear logic that can be used for modeling effect-based authentication policies. LAL has been used in the context of the Proof-Carrying Authorization framework, where formal proofs are constructed in order for a principal to gain access to some resource elsewhere. This paper investigates the complexity of the provability problem, that is, determining whether a linear authorization logic formula is provable or not. We show that the multiplicative propositional fragment of LAL is already undecidable in the presence of two principals. On the other hand, we also identify a first-order fragment of LAL for which provability is PSPACE-complete. Finally, we argue by example that the latter fragment is natural and can be used in practice.