Miracle-dz/UniFAR-FTUs huggingface dataset:
Discriminant Kernel Learning Discriminant Kernel Learning via Convex Programming

Regularized Kernel Discriminant Analysis (RKDA) performs linear discriminant analysis in the feature space via the kernel trick. Its performance depends on the selection of kernels. We show that this kernel learning problem can be formulated as a semidefinite program (SDP). Based on the equivalence relationship between RKDA and least square problems in the binary-class case, we propose an efficient Quadratically Constrained Quadratic Programming (QCQP) formulation for the kernel learning problem. We extend these formulations to the multi-class case based on a key result established in this paper. That is, the multi-class RKDA kernel learning problem can be decomposed into a set of binaryclass kernel learning problems which are constrained to share a common kernel. From this decomposition property, a compact SDP formulation is proposed for the multi-class case. Furthermore, it leads naturally to an efficient QCQP formulation for the multi-class case. As the performance of RKDA depends on the value of the regularization parameter, we show that its value can also be optimized in a joint framework with the kernel. Extensive experiments have been conducted and analyzed, and connections to other algorithms are discussed.
Ginkgo-Spezialextrakt EGb 761® in der Behandlung der Demenz: Evidenz für Wirksamkeit und Verträglichkeit

The Ginkgo biloba extract EGb 761 interferes with pathomechanisms relevant to dementia, such as Abeta aggregation, mitochondrial dysfunction, insulin resistance, and hypoperfusion. The efficacy of EGb 761 in the treatment of dementia (Alzheimer's disease and vascular dementia) has been studied in 10 randomised, controlled, double-blind clinical trials. In three of the four large trials conducted in accordance with recent recommendations EGb 761 was significantly superior to placebo with respect to cognitive performance and one or more further (global, functional or behavioural) outcomes demonstrating the clinical relevance of the findings. The findings from the six smaller trials are in line with those of the large trials. One trial was inconclusive, but of questionable external validity due to uncommonly rigorous patient selection. Subgroup analyses of this study together with the findings from the most recent clinical trial suggest that EGb 761 may be most beneficial to patients with neuropsychiatric symptoms, who actually constitute the majority of dementia patients. Delay in symptom progression, rates of clinically significant treatment response and numbers needed to treat (NNT) found for EGb 761 are in the same range as those reported for cholinesterase inhibitors. In an exploratory trial comparing EGb 761 and donepezil, no statistically significant or clinically relevant differences were seen. Hence, EGb 761 has its place in the treatment of dementia.
Prevalence and risk factors of hepatitis B and C viruses among hemodialysis patients in Isfahan, Iran

Background: The aim of this study was to assess the prevalence of hepatitis B virus (HBV) and hepatitis C virus (HCV) and their associated risk factors among hemodialysis patients in Isfahan, Iran in 2011. Materials and Methods : In this cross-sectional study, a total of 499 chronic hemodialysis patients from eight governmental hemodialysis centers were tested. Demographic information, time duration on hemodialysis, history of blood transfusion, and the number of transfused blood units as risk factors to HBV and HCV infections were calculated. The status of HBsAg and anti-HCV was assessed by serological testing. Results: The overall prevalence of HBV-positive and HCV-positive among study population was 1.2% and 5.2%, respectively. Age, sex, and time duration on hemodialysis were not statistically significant in HBV- and HCV-patients compared with other hemodialysis patients (P0 > 0.05). History of blood transfusion and the number of transfused blood units in HBV infected patients were similar to other patients (P > 0.05). The main risk factors in hemodialysis patients infected by HCV were history of blood transfusion and the number of transfused blood units (P < 0.0001). Conclusion: In conclusion, the prevalence of HBV and HCV infections in hemodialysis centers in Isfahan is lower than in some other cities of Iran. History of blood transfusion and the number of blood units transfused might be a risk factor for HCV gaining. However, further studies are needed to assess the role of other demographic and clinical risk factors in these patients.
Story Cloze Ending Selection Baselines and Data Examination

This paper describes two supervised baseline systems for the Story Cloze Test Shared Task (Mostafazadeh et al., 2016a). We first build a classifier using features based on word embeddings and semantic similarity computation. We further implement a neural LSTM system with different encoding strategies that try to model the relation between the story and the provided endings. Our experiments show that a model using representation features based on average word embedding vectors over the given story words and the candidate ending sentences words, joint with similarity features between the story and candidate ending representations performed better than the neural models. Our best model based on achieves an accuracy of 72.42, ranking 3rd in the official evaluation.
Comparison of ribotyping, arbitrarily primed PCR, and pulsed-field gel electrophoresis for molecular typing of Listeria monocytogenes

Fifty-one clinical isolates of Listeria monocytogenes (15 isolates from two outbreaks and 36 epidemiologically unrelated isolates) were typed by conventional serotyping, ribotyping (RT), pulsed-field gel electrophoresis (PFGE), and arbitrarily primed PCR (AP-PCR). Serotyping was unable to distinguish between related and unrelated strains of L. monocytogenes. Each of the three molecular methods showed excellent typeability and reproducibility. Restriction with EcoRI and PvuII gave 16 and 23 RT patterns, respectively. Restriction with ApaI or SmaI generated 22 and 26 PFGE profiles, respectively. ApaI profiles were easier to interpret, with 10 to 15 bands each, while SmaI profiles had 15 to 20 bands each. AP-PCR with two different primers yielded 29 and 31 randomly amplified polymorphic DNA patterns, respectively. Strains from the same outbreak shared concordant patterns by each of the three methods. Of the three techniques evaluated, RT was the least discriminating and could not distinguish between strains from the two outbreaks. The abilities of AP-PCR and PFGE to differentiate between strains were comparable. However, AP-PCR was more rapid and easier to perform. We conclude that the DNA profiles generated by either AP-PCR or PFGE can be used to differentiate outbreak strains from epidemiologically unrelated strains and to clearly identify unrelated strains as being distinct from one another. We recommend that at least two independent primers be used for AP-PCR typing in order to improve its discriminatory power.
The Oligosaccharyltransferase Complex from Saccharomyces cerevisiae

The key step of N-glycosylation of proteins, an essential and highly conserved protein modification, is catalyzed by the hetero-oligomeric protein complex oligosaccharyltransferase (OST). So far, eight genes have been identified in Saccharomyces cerevisiae that are involved in this process. Enzymatically active OST preparations from yeast were shown to be composed of four (Ost1p, Wbp1p, Ost3p, Swp1p) or six subunits (Ost2p and Ost5p in addition to the four listed). Genetic studies have disclosed Stt3p and Ost4p as additional proteins needed for N-glycosylation. In this study we report the identification and functional characterization of a new OST gene, designated OST6, that has homology to OST3 and in particular a strikingly similar membrane topology. Neither gene is essential for growth of yeast. Disruption of OST6 orOST3 causes only a minor defect inN-glycosylation, but an Δost3Δost6double mutant displays a synthetic phenotype, leading to a severe underglycosylation of soluble and membrane-bound glycoproteinsin vivo and to a reduced OST activity in vitro. Moreover, each of the two genes has also a specific function, since agents affecting cell wall biogenesis reveal different growth phenotypes in the respective null mutants. By blue native electrophoresis and immunodetection, a ∼240-kDa complex was identified consisting of Ost1p, Stt3p, Wbp1p, Ost3p, Ost6p, Swp1p, Ost2p, and Ost5p, indicating that probably all so far identified OST proteins are constituents of the OST complex. It is also shown that disruption of OST3 and OST6 leads to a defect in the assembly of the complex. Hence, the function of these genes seems to be essential for recruiting a fully active complex necessary for efficient N-glycosylation.
Charge separation kinetics in intact photosystem II core particles is trap-limited. A picosecond fluorescence study.

The fluorescence kinetics in intact photosystem II core particles from the cyanobacterium Thermosynechococcus elongatus have been measured with picosecond resolution at room temperature in open reaction centers. At least two new lifetime components of approximately 2 and 9 ps have been resolved in the kinetics by global analysis in addition to several known longer-lived components (from 42 ps to approximately 2 ns). Kinetic compartment modeling yields a kinetic description in full agreement with the one found recently by femtosecond transient absorption spectroscopy [Holzwarth et al. (2005) submitted to Proc. Natl. Acad. Sci. U.S.A. ]. We have for the first time resolved directly the fluorescence spectrum and the kinetics of the equilibrated excited reaction center in intact photosystem II and have found two early radical pairs before the electron is transferred to the quinone Q(A). The apparent lifetime for primary charge separation is 7 ps, that is, by a factor of 8-12 faster than assumed on the basis of earlier analyses. The main component of excited-state decay is 42 ps. The effective primary charge separation rate constant is 170 ns(-)(1), and the secondary electron-transfer rate constant is 112 ns(-)(1). Both electron-transfer steps are reversible. Electron transfer from pheophytin to Q(A) occurs with an apparent overall lifetime of 350 ps. The energy equilibration between the CP43/CP47 antenna and the reaction center occurs with a main apparent lifetime of approximately 1.5 ps and a minor 10 ps lifetime component. Analysis of the overall trapping kinetics based on the theory of energy migration and trapping on lattices shows that the charge separation kinetics in photosystem II is extremely trap-limited and not diffusion-to-the-trap-limited as claimed in several recent papers. These findings support the validity of the assumptions made in deriving the earlier exciton radical pair equilibrium model [Schatz, G. H. , Brock, H. , and Holzwarth, A. R. (1988) Biophys. J. 54, 397-405].
High Variability of Mitochondrial Gene Order among Fungi

From their origin as an early alpha proteobacterial endosymbiont to their current state as cellular organelles, large-scale genomic reorganization has taken place in the mitochondria of all main eukaryotic lineages. So far, most studies have focused on plant and animal mitochondrial (mt) genomes (mtDNA), but fungi provide new opportunities to study highly differentiated mtDNAs. Here, we analyzed 38 complete fungal mt genomes to investigate the evolution of mtDNA gene order among fungi. In particular, we looked for evidence of nonhomologous intrachromosomal recombination and investigated the dynamics of gene rearrangements. We investigated the effect that introns, intronic open reading frames (ORFs), and repeats may have on gene order. Additionally, we asked whether the distribution of transfer RNAs (tRNAs) evolves independently to that of mt protein-coding genes. We found that fungal mt genomes display remarkable variation between and within the major fungal phyla in terms of gene order, genome size, composition of intergenic regions, and presence of repeats, introns, and associated ORFs. Our results support previous evidence for the presence of mt recombination in all fungal phyla, a process conspicuously lacking in most Metazoa. Overall, the patterns of rearrangements may be explained by the combined influences of recombination (i.e., most likely nonhomologous and intrachromosomal), accumulated repeats, especially at intergenic regions, and to a lesser extent, mobile element dynamics.
Contraction-induced muscle damage is unaffected by vitamin E supplementation.

PURPOSE Vitamin E supplementation may confer a protective effect against eccentrically biased exercise-induced muscle damage through stabilization of the cell membrane and possibly via inhibition of free radical formation. Evidence supporting a protective role of vitamin E after contraction-induced muscle injury in humans is, however, inconsistent. The present study sought to determine the effect of vitamin E supplementation on indices of exercise-induced muscle damage and the postexercise inflammatory response after performance of repeated eccentric muscle contractions. METHODS Young healthy men performed a bout of 240 maximal isokinetic eccentric muscle contractions (0.52 rad.s-1) after being supplemented for 30 d with either vitamin E (N = 9; 1200 IU.d-1) or placebo (N = 7; safflower oil). RESULTS Measurements of torque (isometric and concentric) decreased (P < 0.05) below preexercise values immediately post- and at 48 h post-exercise. Biopsies taken 24 h postexercise showed a significant increase in the amount of extensive Z-band disruption (P < 0.01); however, neither the torque deficit nor the extent of Z-band disruption were affected by vitamin E. Exercise resulted in increased macrophage cell infiltration (P = 0.05) into muscle, which was also unaffected by vitamin E. Serum CK also increased as a result of the exercise (P < 0.05) with no effect of vitamin E. CONCLUSION We conclude that vitamin E supplementation (30 d at 1200 IU.d-1), which resulted in a 2.8-fold higher serum vitamin E concentration (P < 0.01), had no affect on indices of contraction-induced muscle damage nor inflammation (macrophage infiltration) as a result of eccentrically biased muscle contractions.
Analysis of Aflatoxin B1 in Iranian Foods Using HPLC and a Monolithic Column and Estimation of its Dietary Intake

A high performance liquid chromatographic method was developed for determination of aflatoxin B1 (AFB1) in foods using a monolithic column with sample clean up on an immunoaffinity column. The method was validated for analysis of AFB1 in rice, bread, puffed corn snack, wheat flour and peanut samples. The average recoveries for AFB1 in different foods ranged from 94.4 to 102.5% with the coefficient of variation lower than 10% for all foods. Limit of detection was 0.01 ng/g. A survey of AFB1 was performed on 90 samples collected from Tehran retail market in June 2005. The results showed that none of the bread and wheat flour samples were contaminated with AFB1. The mean AFB1 levels in rice, puffed corn snack and peanut samples were 4.17, 0.11, and 1.97 ng/g, respectively. The level of contamination of 3 samples (one rice sample and two peanuts samples) to AFB1 was found to be higher than 5 ng/g. Although all food samples had mean concentration of AFB1 below the maximum tolerated level in Iran, the mean intake of AFB1 from rice was estimated 3.49 times higher than the guidance value of 1 ng AFB1/Kg body weight/day. Therefore, it is strongly recommended to monitor AFB1 in foods, especially in rice, in Iran. This is the first study on exposure assessment of Iranian population to AFB1.
Sticky Prices and Monetary Policy Shocks

Models with sticky prices predict that monetary policy changes will affect relative prices and relative quantities in the short run because some prices are more flexible than others. In U.S. micro data, the degree of price stickiness differs dramatically across consumption categories. This study exploits that diversity to ask whether popular measures of monetary shocks (for example, innovations in the federal funds rate) have the predicted effects. The study finds that they do not. Short-run responses of relative prices have the wrong sign. And monetary policy shocks seem to have persistent effects on both relative prices and relative quantities, rather than the transitory effects one would expect from differences in price flexibility across goods. The findings reject the joint hypothesis that the sticky-price models typically employed in policy analysis capture the U.S. economy and that commonly used monetary policy shocks represent exogenous shifts.
Entropic Forces in Geophysical Fluid Dynamics

Theories and numerical models of atmospheres and oceans are based on classical mechanics with added parameterizations to represent subgrid variability. Reformulated in terms of derivatives of information entropy with respect to large scale configurations, we find systematic forces very different from those usually assumed. Two examples are given. We see that entropic forcing by ocean eddies systematically drives, rather than retards, large scale circulation. Additionally we find that small scale turbulence systematically drives up gradient (“un-mixing”) fluxes. Such results confront usual understanding and modeling practice.
Reduced kidney function in acute coronary syndrome patients with undiagnosed diabetes or pre‐diabetes

Chronic kidney disease is highly prevalent in the diabetic population and it is also associated with adverse outcomes in patients with acute coronary syndrome (ACS). However, the risk of reduced kidney function (RKF) in ACS patients with undiagnosed diabetes or pre‐diabetes is yet to be clear. Herein, the present study attempts to investigate the risk for RKF in ACS patients with special reference to undiagnosed diabetes and pre‐diabetes, generating possible recommendations for early intervention and management in ACS patients.
Relationship of post‐transfusion viability to deformability of stored red cells

Summary. During storage in the liquid state, red cells progressively lose their ability to survive in vivo and they become less deformable. An opportunity to test the hypothesis that these two changes are directly related arose when a donor was encountered whose red cells survived particularly badly after storage. It was found that red cells from this donor lost deformability abnormally rapidly during storage. Measurement of red cell deformability after storage may be of value in predicting the viability of the cells.
Site-specific Glycoforms of Haptoglobin in Liver Cirrhosis and Hepatocellular Carcinoma*

Haptoglobin is a liver-secreted glycoprotein with four N-glycosylation sites. Its glycosylation was reported to change in several cancer diseases, which prompted us to examine site-specific glycoforms of haptoglobin in liver cirrhosis and hepatocellular carcinoma. To this end, we have used two-dimensional separation composed of hydrophilic interaction and nano-reverse phase chromatography coupled to QTOF mass spectrometry of the enriched glycopeptides. Our results show increased fucosylation of haptoglobin in liver disease with up to six fucoses associated with specific glycoforms of one glycopeptide. Structural analysis using exoglycosidase treatment and MALDI-MS/MS of detached permethylated glycans led to the identification of Lewis Y-type structures observed particularly in the pooled hepatocellular carcinoma sample. To confirm the increase of the Lewis Y structures observed by LC-MS, we have used immunoaffinity detection with Lewis Y-specific antibodies. The presence of multiply fucosylated Lewis Y glycoforms of haptoglobin in the disease context could have important functional implications.
Easily manageable prognostic factors in 152 Chinese elderly acute myeloid leukemia patients: a single-center retrospective study

Abstract We retrospectively investigated the prognostic factors of acute myeloid leukemia (AML) in 152 Chinese patients with de novo AML who were older than 60 years of age and who received treatment at our hospital. Log-rank test showed that 6 parameters including older age, higher white blood cell (WBC) counts, lactate dehydrogenase (LDH) and bone marrow (BM) blasts at diagnosis, unfavorable risk cytogenetics, and non-mutated CEBPα were significant adverse prognostic factors of overall survival (OS) for elderly AML patients (P = 0.0013, 0.0358, 0.0132, 0.0242, 0.0236 and 0.0130, respectively). Moreover, older age and higher LDH were significant adverse predictors for relapse-free survival (RFS) (P = 0.0447 and 0.0470, respectively). Univariate analysis revealed similar results for OS to those of the log-rank test and only higher LDH at diagnosis was a significant adverse predictor for RFS (P = 0.028, HR: 1.979, 95%CI: 1.075–3.644). In multivariate analysis, we identified 2 trends towards independent prognostic factors for OS, including BM blasts at diagnosis (P = 0.057, HR: 1.676, 95%CI: 0.984–2.854) and mutation status of CEBPα (P = 0.064, HR: 4.173, 95%CI: 0.918–18.966). Our data indicated that older age, gender and a previous history of hematologic diseases resulted in lower complete remission rate (P = 0.012, 0.051 and 0.086, respectively). We further developed an easy scoring system for predicting prognosis and response to induction therapy in older AML patients. Patients who had lower scores showed significantly longer OS and RFS (P = 0.0006 and 0.1001, respectively) and higher CR rate (P = 0.014). Our research is limited by its retrospective nature and the results from our study need to be further validated by prospective randomized clinical trials.
The Cure Rate after Placebo or No Therapy in American Cutaneous Leishmaniasis: A Systematic Review and Meta-Analysis

Introduction There are few drugs with proven efficacy in cutaneous leishmaniasis (CL), and pentavalent antimonial derivatives are still the main first-line therapeutic agents worldwide, despite their recognized high toxicities. Randomized controlled clinical trials assessing the efficacy and safety of new therapeutic modalities are of high priority, and the definition of the design of such trials raises debate about the use of placebo as a comparator. To support the use of placebo as a comparator, two main points need to be addressed: 1- the cure rate without any therapeutic intervention and 2- the damage caused by CL and its impact on patients. Objective The aim of this study was to systematically assess the spontaneous cure rate for American CL and to broaden the discussion about placebo use in CL trials. Methods The PRISMA guidelines for systematic reviews and the Cochrane manual were followed. The sources used were the PubMed and LILACS databases. Studies were included if they reported cure rates using placebo or no treatment in American CL. Results Thirteen studies of a total of 352 patients were ultimately included in this review. The summarized global cure rates for all Leishmania species according to the intention-to-treat analyses performed at approximately three (“initial cure”) and nine (“definitive cure”) months after “no treatment” or placebo use were 26% (CI95%: 16 to 40%) and 26% (CI95%:16 to 38%), respectively. Notably, a significantly lower cure rate was observed for L. braziliensis infection (6.4%, CI95%:0.2 to 20%) than for L. mexicana infection (44%, CI95%:19 to 72%), p = 0.002. Of note, relapse occurred in 20% of patients with initial healing (CI95%:9.2 to 38.9%). Conclusion These results clearly demonstrate a low spontaneous cure rate following no-treatment or placebo use, confirming that this strategy for the control group in CL studies expose patients to greater morbidity, especially for CL caused by L. braziliensis. Therefore, from this point, the crucial questionto consider regarding placebo use isthe seriousness of the suffering caused by this disease.