Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimization With Parity Constraints: From Binary Codes to Discrete Integration

Many probabilistic inference tasks involve summations over exponentially large sets. Recently, it has been shown that these problems can be reduced to solving a polynomial number of MAP inference queries for a model augmented with randomly generated parity constraints. By exploiting a connection with max-likelihood decoding of binary codes, we show that these optimizations are computationally hard. Inspired by iterative message passing decoding algorithms, we propose an Integer Linear Programming (ILP) formulation for the problem, enhanced with new sparsification techniques to improve decoding performance. By solving the ILP through a sequence of LP relaxations, we get both lower and upper bounds on the partition function, which hold with high probability and are much tighter than those obtained with variational methods.
Meta-analysis of the health effects of using the glycaemic index in meal-planning

Diabetes mellitus and CVD are some of the leading causes of mortality and morbidity. Accumulating data indicate that a diet characterised by low-glycaemic index (GI) foods may improve the management of diabetes or lipid profiles. The objective of the present meta-analysis was to critically analyse the scientific evidence that low-GI diets have beneficial effects on carbohydrate and lipid metabolism compared with high-GI diets. We searched for randomised controlled trials with a crossover or parallel design published in English between 1981 and 2003, investigating the effect of low-GI v. high-GI diets on markers for carbohydrate and lipid metabolism. Unstandardised differences in mean values were examined using the random effects model. The main outcomes were fructosamine, glycated Hb (HbA1c), HDL-cholesterol, LDL-cholesterol, total cholesterol and triacylglycerol. Literature searches identified sixteen studies that met the strict inclusion criteria. Low-GI diets significantly reduced fructosamine by –0·1 (95 % CI –0·20, 0·00) mmol/l (P=0·05), HbA1c by 0·27 (95 % CI –0·5, –0·03) % (P=0·03), total cholesterol by –0·33 (95 % CI –0·47, –0·18) mmol/l (P>0·0001) and tended to reduce LDL-cholesterol in type 2 diabetic subjects by –0·15 (95 % CI –0·31, –0·00) mmol/l (P=0·06) compared with high-GI diets. No changes were observed in HDL-cholesterol and triacylglycerol concentrations. No substantial heterogeneity was detected, suggesting that the effects of low-GI diets in these studies were uniform. Results of the present meta-analysis support the use of the GI as a scientifically based tool to enable selection of carbohydrate-containing foods to reduce total cholesterol and to improve overall metabolic control of diabetes.
Down-Regulated miR-125a-5p Promotes the Reprogramming of Glucose Metabolism and Cell Malignancy by Increasing Levels of CD147 in Thyroid Cancer.

BACKGROUND CD147 contributes to increased aerobic glycolysis through which it promotes tumor growth. Accumulating evidence suggests that CD147 exerts a variety of functions in thyroid cancer (TC) progression but the molecular mechanisms and therapeutic value of CD147 remain unclear. METHODS CD147 levels in TC tissues were analyzed to assess its relationship with prognosis and disease progression. A microRNA (miRNA) microarray and bioinformatics approach were used to identify microRNA regulators of CD147 through measurement of the expression and functions of these miRNAs in TC tissues and cell lines. Precursor miRNA-transfected cells were used to assess regulation of CD147 by miRNA. The effect of miRNA on TC cells via inhibition of glycolysis through CD147 targeting was also evaluated. RESULTS We found that miR-125a-5p regulates CD147 and is negatively correlated with its expression and function. Moreover, CD147 knockdown or increased miR-125a-5p expression significantly reduced the viability, migration, and invasion of TC cells. Our mechanistic studies demonstrate that, through directly repressing the expression of the CD147 protein, miR-125a-5p suppresses aerobic glycolysis and lactate production and subsequently reduces TC cell viability, migration, and invasion, thereby exerting tumor suppressor functions. CONCLUSIONS The novel connection identified between miR-125a-5p and CD147 suggests a new diagnostic and prognostic role for miR-125a-5p and that CD147 inhibition may be a candidate therapeutic target in the therapy of for TC.
Responses to Sedimentation in Ramet Populations of the Clonal Plant Carex brevicuspis

In aquatic ecosystems, sedimentation is an important factor that affects plant growth, mainly due to sediment depth. Clonal morphological plasticity is an effective strategy in clonal plants for acclimatization to sediment burial. To date, few studies have examined growth responses to sedimentation on the clonal plants at the ramet population level. This study aimed to explore the interactive effects of population size and burial depth on growth and clonal morphology of Carex brevicuspis. Three population sizes (2, 8, and 32 ramets) and 3 burial depths (0 cm, 5 cm, and 10 cm) were used in this experiment. Under shallow (5 cm) and deep (10 cm) burial conditions, biomass accumulation and relative growth rate (RGR) were lower than in the no burial treatment (P < 0.05). RGR of the small and medium populations was especially high compared to the large populations (P < 0.05). Biomass allocation was higher to belowground parts than aboveground parts, except for the small populations in the 5 cm burial treatments. Both shallow burial and smaller populations led to more biomass being allocated to aboveground parts. Deep burial elongated the first order spacer more than shallow burial, and sedimentation had negative effects on the second order spacer length. The number of new ramets did not decrease in the 5 or 10 cm burial treatments compared to the unburial treatment, and larger populations usually had more ramets than smaller ones; the proportion of clumping ramets was higher than the proportion of spreading ramets, and deeper burial and smaller populations led to higher proportions of spreading ramets. These results indicated that the growth of C. brevicuspis was limited by sediment burial at the ramet population level. Smaller populations enable C. brevicuspis to adjust its escape response to burial stress, may allow this species to effectively survive and widely distribute in Dongting Lake wetland.
Long-Term Restoration of Thymidine Phosphorylase Function and Nucleoside Homeostasis Using Hematopoietic Gene Therapy in a Murine Model of Mitochondrial Neurogastrointestinal

Javier Torres-Torronteras, Raquel Cabrera-Pérez, Ignasi Barba, Carme Costa, Noemı́ de Luna, Antoni L. Andreu, Jordi Barquinero, Michio Hirano, Yolanda Cámara, and Ramon Martı́* Research Group on Neuromuscular and Mitochondrial Diseases; Research Group on Cardiocirculatory Pathology; Servei de Neurologia-Neuroimmunologia, Centre d’Esclerosi Múltiple de Catalunya; and Gene and Cell Therapy Laboratory, Vall d’Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Department of Neurology, H. Houston Merritt Center, Columbia University Medical Center, New York, New York.
Image-based Deformable 3D Reconstruction using Differential Geometry and Cartan's Connections. (Reconstruction 3D déformable basée sur l'image utilisant la géométrie différentielle et les connexions de Cartan)

Reconstructing the 3D shape of objects from multiple images is an important goal in computer vision and has been extensively studied for both rigid and non-rigid (or deformable) objects. Structure-from-Motion (SfM) is an algorithm that performs the 3D reconstruction of rigid objects using the inter-image visual motion from multiple images obtained from a moving camera. SfM is a very accurate and stable solution. Deformable 3D reconstruction, however, has been widely studied for monocular images (obtained from a single camera) and still emains an open research problem. The current methods exploit visual cues such as the inter-image visual motion and shading in order to formalise a reconstruction algorithm. This thesis focuses on the use of the inter-image visual motion for solving this problem. Two types of scenarios exist in the literature: 1) Non-Rigid Structure-from-Motion (NRSfM) and 2) Shape-from-Template (SfT). The goal of NRSfM is to reconstruct multiple shapes of a deformable object as viewed in multiple images while SfT (also referred to as template-based reconstruction) uses a single image of a deformed object and its 3D template (a textured 3D shape of the object in one configuration) to recover the deformed shape of the object. We propose an NRSfM method to reconstruct the deformable surfaces undergoing isometric deformations (the objects do not stretch or shrink under an isometric deformation) using Riemannian geometry. This allows NRSfM to be expressed in terms of Partial Differential Equations (PDE) and to be solved algebraically. We show that the problem has linear complexity and the reconstruction algorithm has a very low computational cost compared to existing NRSfM methods. This work motivated us to use differential geometry and Cartan’s theory of connections to model NRSfM, which led to the possibility of extending the solution to deformations other than isometry. In fact, this led to a unified theoretical framework for modelling and solving both NRSfM and SfT for various types of deformations. In addition, it also makes it possible to have a solution to SfT which does not require an explicit modelling of deformation. An important point is that most of the NRSfM and SfT methods reconstruct the thin-shell surface of the object. The reconstruction of the entire volume (the thin-shell surface and the interior) has not been explored yet. We propose the first SfT method that reconstructs the entire volume of a deformable object.
Coordinated Regulation of the EIIMan and fruRKI Operons of Streptococcus mutans by Global and Fructose-Specific Pathways

ABSTRACT The glucose/mannose-phosphotransferase system (PTS) permease EIIMan encoded by manLMN in the dental caries pathogen Streptococcus mutans has a dominant influence on sugar-specific, CcpA-independent catabolite repression (CR). Mutations in manL affect energy metabolism and virulence-associated traits, including biofilm formation, acid tolerance, and competence. Using promoter::reporter fusions, expression of the manLMN and the fruRKI operons, encoding a transcriptional regulator, a fructose-1-phosphate kinase and a fructose-PTS permease EIIFru, respectively, was monitored in response to carbohydrate source and in mutants lacking CcpA, FruR, and components of EIIMan. Expression of genes for EIIMan and EIIFru was directly regulated by CcpA and CR, as evinced by in vivo and in vitro methods. Unexpectedly, not only was the fruRKI operon negatively regulated by FruR, but also so was manLMN. Carbohydrate transport by EIIMan had a negative influence on expression of manLMN but not fruRKI. In agreement with the proposed role of FruR in regulating these PTS operons, loss of fruR or fruK substantially altered growth on a number of carbohydrates, including fructose. RNA deep sequencing revealed profound changes in gene regulation caused by deletion of fruK or fruR. Collectively, these findings demonstrate intimate interconnection of the regulation of two major PTS permeases in S. mutans and reveal novel and important contributions of fructose metabolism to global regulation of gene expression. IMPORTANCE The ability of Streptococcus mutans and other streptococcal pathogens to survive and cause human diseases is directly dependent upon their capacity to metabolize a variety of carbohydrates, including glucose and fructose. Our research reveals that metabolism of fructose has broad influences on the regulation of utilization of glucose and other sugars, and mutants with changes in certain genes involved in fructose metabolism display profoundly different abilities to grow and express virulence-related traits. Mutants lacking the FruR regulator or a particular phosphofructokinase, FruK, display changes in expression of a large number of genes encoding transcriptional regulators, enzymes required for energy metabolism, biofilm development, biosynthetic and degradative processes, and tolerance of a spectrum of environmental stressors. Since fructose is a major component of the modern human diet, the results have substantial significance in the context of oral health and the development of dental caries.
A Pilot Test of Group Based Cognitive Behavioral Therapy to Augment Vocational Services for Persons With Serious Mental Illness: Feasibility and Competitive Work Outcomes

Abstract Persons with serious mental illness (SMI) struggle with work functioning even with the assistance of vocational services. The current study sought to address this problem by examining a cognitive-behavioral therapy to augment vocational services. Fifty-two adults with SMI receiving vocational services participated in a pre-post feasibility trial of the Cognitive Behavior Therapy for Work Success (CBTw) intervention. CBTw is a 12-week manualized intervention that addresses cognitive and behavioral factors that impact work functioning. Competitive work outcomes were assessed in the 12 weeks preceding baseline and after the intervention. The results demonstrate strong session attendance and a low attrition rate. There were also significant improvements in work outcomes. Specifically, among participants unemployed at baseline, 50.0% attained work during follow-up. These findings provide preliminary evidence that CBTw may be a feasible intervention to augment vocational services; further controlled research should examine its benefit to work outcomes in people with SMI.
[Bone mineral density in overweight and obese adolescents].

OBJECTIVE To study bone density as a concomitant factor for obesity in post-pubertal adolescents, controlling for other variables that may interfere in such a relation. METHODS Study comprising 83 overweight and obese adolescents (BMI > or = P85) and 89 non obese ones (P5 < or = BMI < or = P85). Cases and controls were selected out of 1,420 students (aged 14-19) from a public school in the city of São Paulo. The bone mineral density of the lumbar spine (L2-L4 in g/cm2) was assessed by dual-energy x-ray absorptiometry (LUNARtrade mark DPX-L). The variable bone density was dichotomized using 1.194 g/cm2 as cutoff point. Bivariate analyses were conducted considering the prevalence of overweight and obesity followed by multivariate analysis (logistic regression) according to a hierarchical conceptual model. RESULTS The prevalence of bone density above the median was twice more frequent among cases (69.3%) than among controls (32.1%). In the bivariate analysis such prevalence resulted in an odds ratio (OR) of 4.78. The logistic regression model showed that the association between obesity and mineral density is yet more intense with an OR of 6.65 after the control of variables related to sedentary lifestyle and intake of milk and dairy products. CONCLUSION Obese and overweight adolescents in the final stages of sexual maturity presented higher bone mineral density in relation to their normal-weight counterparts; however, cohort studies will be necessary to evaluate the influence of such characteristic on bone resistance in adulthood and, consequently, on the incidence of osteopenia and osteoporosis at older ages.
Labeled Graph Clustering via Projected Gradient Descent

Advances in recovering low-rank matrices from noisy observations have led to tractable algorithms for clustering from general pairwise labels with provable performance guarantees. Based on convex relaxation, it has been shown that the ground truth clusters can be recovered with high probability under a generalized stochastic block model by solving a semidefinite program. Although tractable, the algorithm is typically too slow for sufficiently large problems in practice. Inspired by recent advances in non-convex approaches to low-rank recovery problems, we propose an algorithm based on projected gradient descent that enjoys similar provable guarantees as the convex counterpart, but can be orders of magnitude faster. Our theoretical results are further supported by encouraging empirical results.
Blood Safety Status in WHO African Region Countries: Lessons Learnt from Mauritius

In 2001, the WHO Office for Africa adopted a strategy for blood safety defining four targets. This paper describes the progress made by Mauritius in the implementation of this strategy. The blood safety indicators were collected and compared with the norms recommended by WHO. The country has formulated its blood policy and developed a strategic plan for its implementation since 2004. The total number of blood donations increased from 31,228 in 2002 to 43,742 in 2016, giving an annual blood collection rate evolving from 26.3 per 1000 inhabitants in 2002 to 34.2 per 1000 inhabitants in 2016. The percentage of voluntary donations rose from 60% to 82.5%. Since 2002, all the blood units collected have been tested for the mandatory infectious markers. The Blood Transfusion Service has been certified ISO2008-9001 and nucleic acid testing has been introduced. The preparation of blood components increased from 60% to 98.2%. The most transfused blood components were red cell concentrates, platelet concentrates, and fresh frozen plasma. In addition to transfusion activities, there were other departments performing antenatal serology, tissue typing, special investigations, and reagent preparation. Despite the progress made, some challenges remain, namely, legal framework and haemovigilance system. A regulatory system for blood needs to be established.
EphA2 receptor is a key player in the metastatic onset of Ewing sarcoma

Ewing sarcoma (ES) is the second most common bone malignancy affecting children and young adults with poor prognosis due to high metastasis incidence. Our group previously described that EphA2, a tyrosine kinase receptor, promotes angiogenesis in Ewing sarcoma (ES) cells via ligand‐dependent signaling. Now we wanted to explore EphA2 ligand‐independent activity, controlled upon phosphorylation at S897 (p‐EphA2S897), as it has been linked to metastasis in several malignancies. By reverse genetic engineering we explored the phenotypic changes after EphA2 removal or reintroduction. Gene expression microarray was used to identify key players in EphA2 signaling. Mice were employed to reproduce metastatic processes from orthotopically implanted engineered cells. We established a correlation between ES cells aggressiveness and p‐EphA2S897. Moreover, stable overexpression of EphA2 in low EphA2 expression ES cells enhanced proliferation and migration, but not a non‐phosphorylable mutant (S987A). Consistently, silencing of EphA2 reduced tumorigenicity, migration and invasion in vitro, and lung metastasis incidence in experimental and spontaneous metastasis assays in vivo. A gene expression microarray revealed the implication of EphA2 in cell signaling, cellular movement and survival. ADAM19 knockdown by siRNA technology strongly reproduced the negative effects on cell migration observed after EphA2 silencing. Altogether, our results suggest that p‐EphA2S897 correlates with aggressiveness in ES, so blocking its function may be a promising treatment.
Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms

Significance Clustered genomic polymorphisms in DNA, such as microindels and stretches of nucleotide changes, play an important role in genome evolution. Here, we report a mutation mechanism responsible for such genomic polymorphisms where short, single-stranded DNA molecules invade double-stranded DNA and replace short genomic segments. We show, in a bacterial model organism, that the genomic replacements occur with very low levels of sequence identity (microhomologies). The invading DNA can be of intagenomic or foreign origin. Genotoxic stress, horizontally taken-up DNA, or lack of genome maintenance functions increase the mutation frequency up to 7,000-fold. Bioinformatic approaches suggest that this class of mutations is widespread in prokaryotes and eukaryotes and may have a role in tumorigenesis. In a screen for unexplained mutation events we identified a previously unrecognized mechanism generating clustered DNA polymorphisms such as microindels and cumulative SNPs. The mechanism, short-patch double illegitimate recombination (SPDIR), facilitates short single-stranded DNA molecules to invade and replace genomic DNA through two joint illegitimate recombination events. SPDIR is controlled by key components of the cellular genome maintenance machinery in the gram-negative bacterium Acinetobacter baylyi. The source DNA is primarily intragenomic but can also be acquired through horizontal gene transfer. The DNA replacements are nonreciprocal and locus independent. Bioinformatic approaches reveal occurrence of SPDIR events in the gram-positive human pathogen Streptococcus pneumoniae and in the human genome.
Serum bilirubin levels in acute stroke in Chinese population : a meta-analysis

Studies on serum bilirubin levels in acute stroke have yielded conflicting results. The objective of this meta-analysis was to investigate the correlation between serum bilirubin levels and acute stroke. We searched for relevant studies in PubMed, EMBASE, China BioMedicine, CKNI, Wanfang and VIP database until October 15, 2015. Studies reporting the serum bilirubin levels in acute cerebral infarction or hemorrhage were included. Pooled results were expressed as weighted mean difference (WMD) with 95% confidence intervals (CI). A total of 24 case-control studies were identified and analyzed. Overall meta-analysis indicated that serum bilirubin levels were significantly lower (WMD=-1.77 μmol/L; 95% CI=-3.08 to -0.47) in acute cerebral infarction patients than those in healthy controls. Subgroup analysis showed that the difference of serum bilirubin levels was insignificant within 24 hours after stroke. In cerebral hemorrhage patients, pooled data from 5 studies revealed that serum bilirubin levels were significantly higher (WMD=4.79 μmol/L; 95% CI=1.97 to 7.62) than those in healthy controls. This meta-analysis suggests that decreased serum bilirubin levels are correlated with acute cerebral infarction and elevated serum bilirubin levels may be correlated with acute cerebral hemorrhage.