Miracle-dz/UniFAR-FTUs huggingface dataset:
Notes on Linearity ( Group Homomorphism ) Testing

Let G and H be two groups. For simplicity, we denote by + the group operation in each of these groups. A function f : G → H is called a (group) homomorphism if for every x, y ∈ G it holds that f(x + y) = f(x) + f(y). One important special case of interest is when H is a finite field and G is a vector space over this field; that is, G = H for some natural number m. In this case, a homomorphism f from G to H can be presented as f(x1, ., xm) = ∑m i=1 cixi, where x1, . , xm, c1, . , cm ∈ H. In this case, f is a linear function over H, which explains why testing group homomorphism is often referred to as linearity testing. Group homomorphisms are among the simplest and most basic classes of finite functions. They may indeed claim the title of the most natural algebraic functions. This chapter addresses the problem of testing whether a given function is a group homomorphism or is far from any group homomorphism.
Why Is MPI So Slow? Analyzing the Fundamental Limits in Implementing MPI-3.1

This paper provides an in-depth analysis of the software overheads in the MPI performance-critical path and exposes mandatory performance overheads that are unavoidable based on the MPI-3.1 specification. We first present a highly optimized implementation of the MPI-3.1 standard in which the communication stack-all the way from the application to the low-level network communication API-takes only a few tens of instructions. We carefully study these instructions and analyze the root cause of the overheads based on specific requirements from the MPI standard that are unavoidable under the current MPI standard. We recommend potential changes to the MPI standard that can minimize these overheads. Our experimental results on a variety of network architectures and applications demonstrate significant benefits from our proposed changes. CCS CONCEPTS • Computing methodologies $\rightarrow$ Concurrent algorithms; Massively parallel algorithms;
Amino Acid Deprivation Induces the Transcription Rate of the Human Asparagine Synthetase Gene through a Timed Program of Expression and Promoter Binding of Nutrient-responsive Basic Region/Leucine Zipper Transcription Factors as Well as Localized Histone Acetylation*

Expression of human asparagine synthetase (ASNS), which catalyzes asparagine and glutamate biosynthesis, is transcriptionally induced following amino acid deprivation. Previous overexpression and electrophoresis mobility shift analysis showed the involvement of the transcription factors ATF4, C/EBPβ, and ATF3-FL through the nutrient-sensing response element-1 (NSRE-1) within the ASNS promoter. Amino acid deprivation caused an elevated mRNA level for ATF4, C/EBPβ, and ATF3-FL, and the present study established that the nuclear protein content for ATF4 and ATF3-FL were increased during amino acid limitation, whereas C/EBPβ-LIP declined slightly. The total amount of C/EBPβ-LAP protein was unchanged, but changes in the distribution among multiple C/EBPβ-LAP forms were observed. Overexpression studies established that ATF4, ATF3-FL, and C/EBPβ-LAP could coordinately modulate the transcription from the human ASNS promoter. Chromatin immunoprecipitation demonstrated that amino acid deprivation increased ATF3-FL, ATF4, and C/EBPβ binding to the ASNS promoter and enhanced promoter association of RNA polymerase II, TATA-binding protein, and TFIIB of the general transcription machinery. A time course revealed a markedly different temporal order of interaction between these transcription factors and the ASNS promoter. During the initial 2 h, there was a 20-fold increase in ATF4 binding and a rapid increase in histone H3 and H4 acetylation, which closely paralleled the increased transcription rate of the ASNS gene, whereas the increase in ATF3-FL and C/EBPβ binding was considerably slower and more closely correlated with the decline in transcription rate between 2 and 6 h. The data suggest that ATF3-FL and C/EBPβ act as transcriptional suppressors for the ASNS gene to counterbalance the transcription rate activated by ATF4 following amino acid deprivation.
Association of hemoglobin and survival in peritoneal dialysis patients.

BACKGROUND AND OBJECTIVES Interventional trials and some observational studies show target hemoglobin >13 g/dl to be associated with higher mortality in erythropoiesis-stimulating agent-treated (ESA-treated) hemodialysis patients; data for peritoneal dialysis (PD) patients are limited. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We tested our hypothesis that higher and lower achieved hemoglobin levels are associated with increased mortality in 9269 ESA-treated PD patients from all DaVita dialysis clinics during the time period July 2001 through June 2006 followed through June 2007 using a time-dependent analysis. RESULTS Lower hemoglobin was associated with significantly higher all-cause mortality in ESA-treated PD patients: with hemoglobin of 11.0 to <12.0 g/dl as reference, the time-dependent adjusted death hazard ratios for hemoglobin levels of 10.0 to <11.0, 9.0 to <10.0, and ≤9.0 g/dl were 1.12 (1.00 to 1.24), 1.30 (1.12 to 1.50), and 1.38 (1.14 to 1.67), respectively. The time-dependent adjusted hazard ratios for cardiovascular death with hemoglobin levels of 10.0 to <11.0, 9.0 to <10.0, and ≤9.0 g/dl were 1.11 (0.93 to 1.32), 1.37 (1.09 to 1.72), and 1.12 (0.79 to 1.57), respectively. The same trend for association of lower hemoglobin level with higher mortality was seen in African-American and non-African American men and women. In contrast, there was no association between higher achieved hemoglobin and all-cause or cardiovascular mortality in ESA-treated PD patients. CONCLUSIONS Lower, but not higher, achieved hemoglobin is associated with higher mortality in ESA-treated PD patients. Randomized controlled trials are needed to examine the target hemoglobin level with lowest mortality in PD patients.
Factors Affecting Preconditioned Calf Price Differentials: How much do Market and Sale Conditions Matter?

Feeder calf prices are determined by the interaction of many factors. This study uses transactions data from Iowa preconditioned and regular feeder calf auction sales to investigate the impact of a wide variety of factors, many of which have not been used in previous studies on feeder calf prices. Unlike previous studies, this analysis explicitly incorporates changes in feeder cattle market fundamentals during the data collection period. Notably, market premiums for preconditioned sales versus regular sales, feedlot capacity utilization, and seller reputation are significant factors affecting feeder calf prices.
Missense mutations in transmembrane domains of proteins: Phenotypic propensity of polar residues for human disease

Previous experiments on the cystic fibrosis transmembrane conductance regulator suggested that non‐native polar residues within membrane domains can compromise protein structure/function. However, depending on context, replacement of a native residue by a non‐native residue can result either in genetic disease or in benign effects (e.g., polymorphisms). Knowledge of missense mutations that frequently cause protein malfunction and subsequent disease can accordingly reveal information as to the impact of these residues in local protein environments. We exploited this concept by performing a statistical comparison of disease‐causing mutations in protein membrane‐spanning domains versus soluble domains. Using the Human Gene Mutation Database of 240 proteins (including 80 membrane proteins) associated with human disease, we compared the relative phenotypic propensity to cause disease of the 20 naturally occurring amino acids when removed from—or inserted into—native protein sequences. We found that in transmembrane domains (TMDs), mutations involving polar residues, and ionizable residues in particular (notably arginine), are more often associated with protein malfunction than soluble proteins. To further test the hypothesis that interhelical cross‐links formed by membrane‐embedded polar residues stabilize TMDs, we compared the occurrence of such residues in the TMDs of mesophilic and thermophilic prokaryotes. Results showed a significantly higher proportion of ionizable residues in thermophilic organisms, reinforcing the notion that membrane‐embedded electrostatic interactions play critical roles in TMD stability. Proteins 2004;54:000.000. © 2004 Wiley‐Liss, Inc.
Therapeutic applications of aptamers

Aptamers constitute a new class of oligonucleotides that have gained therapeutic importance. With the approval of the first aptamer drug, pegaptanib, interest in this class of oligonucleotides, often referred to as ‘chemical antibodies’, has increased. This article discusses aptamers in relation to other oligonucleotide molecules such as antisense nucleotides, short inhibitory sequences, ribozymes and so on. The development of pegaptanib is looked at from the point of view of the challenges faced in converting aptamers into therapeutic molecules. Cases of other aptamers, which show promise as drugs, are discussed in slightly greater detail. Comparison with antibodies and small molecules, which have hitherto held monopoly in this area, is also made.
Kinetic parameters of monoclonal antibodies ESH2, ESH4, ESH5, and ESH8 on coagulation factor VIII and their influence on factor VIII activity

The murine monoclonal antibodies ESH2, ESH4, ESH5, and ESH8 specifically bind and inhibit the procoagulant activity of human coagulation factor VIII (FVIII). They are frequently used as a model of inhibitors which are raised against injected FVIII in about 25% of hemophiliacs as a serious side effect of substitution therapy. However, binding kinetics of the interaction of these antibodies with FVIII and their influence on FVIII activity (inhibition) have not yet been examined systematically. For this, we examined association and dissociation of protein:antibody interaction using surface plasmon resonance (SPR) and determined their ability to inhibit the FVIII activity in a one‐stage and a two‐stage assay. SPR‐analysis revealed that the equilibrium dissociation constants (KD) of ESH8 and ESH4 are low and in a similar range (ESH8: KD(ESH8) = 0.542 nM; ESH4: KD(ESH4) = 0.761 nM). A 5.7 times higher KD than for ESH4 was observed for ESH2 (4.33 nM), whereas ESH5 showed the highest KD of 28.8 nM. In accordance with the lowest KD, ESH8, and ESH4 reduced FVIII activity of normal human plasma almost completely in a one‐stage clot inhibition assay (ESH8: 91.9%; ESH4: 90.1%). However, ESH8 inhibited FVIII activity more efficiently as only 1.0 µg/ml ESH8 was sufficient to obtain maximum inhibition compared to up to 600 µg/ml of ESH4. Despite its attenuated KD, ESH2 inhibits FVIII:C still efficiently, reducing 61.3% of FVIII activity at a concentration of 9 µg/ml in the one‐stage clotting assay. However, a discrepancy of inhibitory efficiency was found depending on the method used to measure FVIII activity. These effects seem to be mainly caused by differences of activation time of FVIII during both FVIII activity assays. The systematic assessment of these results should support FVIII interaction studies, and can provide data to rationally test peptides/mimotopes to remove or neutralize inhibitors of FVIII activity. Copyright © 2009 John Wiley & Sons, Ltd.
Effect of Albumin on the in Vitro Conjugation of Bilirubin by Rat Liver Microsomes

Abstract These studies were carried out to determine whether bovine serum albumin (BSA), which is usually included in the incubation mixture for the in vitro determination of bilirubin-UDP-glucuronyl transferase (GT) activity, affects GT activity. Using bilirubin as substrate, addition of BSA to the enzyme reaction mixture at concentrations varying from 2 to 30 mg/ml resulted in a dose-related inhibition of “native” GT activity of rat liver microsomes. When detergent-activated enzyme was employed, increasing concentrations of BSA also required higher concentrations of deoxycholate, digitonin, or Triton X-100 to produce maximal bilirubin conjugation. Low BSA concentrations (2 mg/ml) prevented enzyme activation by both detergents and UDP-N-acetyl glucosamine. When BSA was omitted and bilirubin dissolved in dimethyl sulfoxide, UDP-N-acetyl glucosamine failed to enhance GT activity, and activation by detergents was only 15-25% of that observed in the presence of optimal concentrations of BSA. When rat albumin was substituted for BSA, a similar dose-related inhibition of in vitro bilirubin conjugation by untreated microsomes was observed, although at any given albumin concentration, GT activity was lower with rat than with bovine albumin. Additionally, both detergents and UDP-N-acetyl glucosamine produced similar GT activation regardless of the rat albumin concentration. Finally, these effects of BSA and rat albumin could not be reproduced when β-lactoglobulin was employed and/or when p-nitrophenol was the acceptor substrate of GT. These findings indicate that albumin, in particular BSA, profoundly and selectively influences the in vitro activity of microsomal GT toward bilirubin as the acceptor substrate.
Blind source separation based on independent low-rank matrix analysis with sparse regularization for time-series activity

In this paper, we propose a new blind source separation (BSS) method based on independent low-rank matrix analysis (ILRMA) with novel sparse regularization. ILRMA is a recently proposed BSS algorithm that simultaneously estimates a demixing matrix and source spectrogram models based on nonnegative matrix factorization (NMF). To improve the separation accuracy and stability, an additional constraint such as sparseness is needed but there have been no studies on this so far. In this study, we introduce an a priori statistical model for time-series amplitudes of source spectrograms, employing a new frequency-wise sparse regularization using estimates from the Bayesian postfilter to enhance the modeling accuracy. This regularization results in a bilevel optimization problem that consists of the estimation of a sparsity-emphasized source model using NMF and the separation of sources by ILRMA. In this paper, we present two approximated optimization schemes and their combination for performing regularized ILRMA. The efficacy of the proposed method is confirmed in a BSS experiment.
Maternal factors relating to breast-feeding duration in areas around Guadalajara, Mexico

To investigate breast-feeding pafferns and factors encouraging early weaning, a survey was conducted in Tonald and Tlaquepaque, two suburbs within Guadalajara’s metropolitan area, in 1991. For this purpose a multiphase probabilistic sample of infants born in these areas from May 1990 through April 1991 was selected. This was done by choosing at random primary health care units in the study areas, kealfk posts associated with these units, and all infants meeting the above criteria at each selected post. A total of 166 homes was visited and interviews were conducted with 141 mothers (91% of the 155 predicted) in June and July 1991. These interviews made use of a 33-item questionnaire developed for the purpose; the interviewers were social workers previously trained in suck activities. Logistic regression models were used to calculate the relative risk (RR) and probability of early weaning being associated with certain variables. To kelp ensure the validity of the results, several regression models were constructed for the purpose of selecting the one best fitting the data. In addition, the attributable population risk (APR) was calculated. The results indicate that failure to breast-feed and early weaning were prevalent in the study population, 34.8% of the study infants being breast-fed less than 1 month. Three risk factors were associated statistically (P < 0.05) with early weaning, these being maternal age ~20 years (RR = 3.75; 95% Cl = 1.53-9.19), maternal marital status single (RR = 2.88; 95% Cl = l.OS--7.69), and social status of fhe main family provider other than “worker”-i.e., employee, professional (RR = 2.72; 95% Cl = 1.17-6.28). The likelihood that a study infant would have been breast-fed less than a month was 0.84 if fke infant was exposed to all three of these identified risk factors and 0.15 if he or she was exposed to none of them. The high percentages of study mothers less then 20 years old and with a social status other than “worker” were reflected in high attributable population risks found for these variables. In general, the findings point up a need to reduce the influence of these risk factors and to prolong maternal breast-feeding in the study population.
Performance evaluation of full-duplex AF relaying with direct link under residual self-interference

This paper investigates the error performance of a full-duplex (FD) amplify-and-forward (AF) single-relay system under the effect of residual self-interference whose variance is proportional to the λ-th power of the transmitted power (0≤λ ≤1). Our focus is on the cooperative FD linear relaying (LR) protocol that makes use of direct source-destination link. At first, a closed-form expression of the pairwise error probability (PEP) is derived for the considered system. This expression allows us to analyze the diversity behavior in high transmission power regions. Thanks to the use of the direct link, it is shown that the FD LR system can attain the same diversity function as its half-duplex (HD) counterpart as long as a suitable precoder is applied. Different from previous works that either ignore the direct link or treat it as a source of interference, a non-zero diversity order is thus achieved and the error floor behavior can be eliminated despite the existence of self-interference in FD. More interestingly, it is then demonstrated that transmitting a superposition of all symbols in HD mode maximizes the asymptotic coding gain. Although HD relaying is hence asymptotically optimal, simulations results reveal that FD is advantageous at practical bit error rate (BER) levels when λ is sufficiently small.
Visibility Graph For Path Planning In The Presence Of Moving Obstacles

Path planning and navigation are two important areas in the control of autonomous mobile robots. In both cases, the resolution of the problem is to move the mobile robot while taking into account internal and external constraints. In this paper, we present an approach that operates in three steps. First, a construction of the visibility tree is performed. The following treatments are not performed on the original image but the result tree whose elements are specific points of the environment linked by the relationship of visibility. We construct thereafter a visibility graph which one seeks the shortest path. This approach has a great interest because of its fast execution speed. The path search is performed also in the presence of moving obstacles in their turn may be other mobile robots whose trajectories and speeds are known initially. At the end, an application is provided on solving a problem that aviation is the guiding plane avoiding collisions. Keywords-component; path planning, navigation, robotics, visibility graph, obstacles contours, moving obstacles, space-time representation
Multi-Channel late reverberation power spectral density estimation based on nuclear norm minimization

Multi-channel methods for estimating the late reverberation power spectral density (PSD) generally assume that the reverberant PSD matrix can be decomposed as the sum of a rank-1 matrix and a scaled diffuse coherence matrix. To account for modeling or estimation errors in the estimated reverberant PSD matrix, in this paper we propose to decompose this matrix as the sum of a low rank (not necessarily rank-1) matrix and a scaled diffuse coherence matrix. Among all pairs of scalars and matrices that yield feasible decompositions, the late reverberation PSD can then be estimated as the scalar associated with the matrix of minimum rank. Since rank minimization is an intractable non-convex optimization problem, we propose to use a convex relaxation approach and estimate the late reverberation PSD based on nuclear norm minimization (NNM). Experimental results show the advantages of using the proposed NNM-based late reverberation PSD estimator in a multichannel Wiener filter for speech dereverberation, significantly outperforming a state-of-the-art maximum likelihood-based PSD estimator and yielding a similar or better performance than a recently proposed eigenvalue decomposition-based PSD estimator.
Oligotyping analysis of the human oral microbiome

Significance The human body, including the mouth, is home to a diverse assemblage of microbial organisms. Although high-throughput sequencing of 16S rRNA genes provides enormous amounts of census data, accurate identification of taxa in these large datasets remains problematic because widely used computational approaches do not resolve closely related but distinct organisms. We used a computational approach that relies on information theory to reanalyze the human oral microbiome. This analysis revealed organisms differing by as little as a single rRNA nucleotide, with dramatically different distributions across habitats or individuals. Our information theory-based approach in combination with habitat analysis demonstrates the potential to deconstruct entire microbiomes, detect previously unrecognized diversity, and provide deep insight into microbial communities in health and disease. The Human Microbiome Project provided a census of bacterial populations in healthy individuals, but an understanding of the biomedical significance of this census has been hindered by limited taxonomic resolution. A high-resolution method termed oligotyping overcomes this limitation by evaluating individual nucleotide positions using Shannon entropy to identify the most information-rich nucleotide positions, which then define oligotypes. We have applied this method to comprehensively analyze the oral microbiome. Using Human Microbiome Project 16S rRNA gene sequence data for the nine sites in the oral cavity, we identified 493 oligotypes from the V1-V3 data and 360 oligotypes from the V3-V5 data. We associated these oligotypes with species-level taxon names by comparison with the Human Oral Microbiome Database. We discovered closely related oligotypes, differing sometimes by as little as a single nucleotide, that showed dramatically different distributions among oral sites and among individuals. We also detected potentially pathogenic taxa in high abundance in individual samples. Numerous oligotypes were preferentially located in plaque, others in keratinized gingiva or buccal mucosa, and some oligotypes were characteristic of habitat groupings such as throat, tonsils, tongue dorsum, hard palate, and saliva. The differing habitat distributions of closely related oligotypes suggest a level of ecological and functional biodiversity not previously recognized. We conclude that the Shannon entropy approach of oligotyping has the capacity to analyze entire microbiomes, discriminate between closely related but distinct taxa and, in combination with habitat analysis, provide deep insight into the microbial communities in health and disease.