Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutagenic Analysis of Functional Residues in Putative Substrate-binding Site and Acidic Domains of Vacuolar H+-Pyrophosphatase*

Vacuolar H+-translocating inorganic pyrophosphatase (V-PPase) uses PPi as an energy donor and requires free Mg2+ for enzyme activity and stability. To determine the catalytic domain, we analyzed charged residues (Asp253, Lys261, Glu263, Asp279, Asp283, Asp287, Asp723, Asp727, and Asp731) in the putative PPi-binding site and two conserved acidic regions of mung bean V-PPase by site-directed mutagenesis and heterologous expression in yeast. Amino acid substitution of the residues with alanine and conservative residues resulted in a marked decrease in PPi hydrolysis activity and a complete loss of H+ transport activity. The conformational change of V-PPase induced by the binding of the substrate was reflected in the susceptibility to trypsin. Wild-type V-PPase was completely digested by trypsin but not in the presence of Mg-PPi, while two V-PPase mutants, K261A and E263A, became sensitive to trypsin even in the presence of the substrate. These results suggest that the second acidic region is also implicated in the substrate hydrolysis and that at least two residues, Lys261and Glu263, are essential for the substrate-binding function. From the observation that the conservative mutants K261R and E263D showed partial activity of PPi hydrolysis but no proton pump activity, we estimated that two residues, Lys261 and Glu263, might be related to the energy conversion from PPi hydrolysis to H+transport. The importance of two residues, Asp253 and Glu263, in the Mg2+-binding function was also suggested from the trypsin susceptibility in the presence of Mg2+. Furthermore, it was found that the two acidic regions include essential common motifs shared among the P-type ATPases.
Numerical modelling of an air-helium buoyant jet in a two vented enclosure

Nous cherchons a modeliser numeriquement un jet flottant air-helium dans une cavite avec deux ouvertures a partir de simulations aux grandes echelles (LES) et de simulations numeriques directes (DNS). La configuration consideree est basee sur une etude experimentale menee au CEA de Saclay reproduisant une fuite d'hydrogene en environnement confine. La dimension de la cavite a ete choisie pour permettre une transition laminaire-turbulent intervenant environ a la mi-hauteur de la cavite. Cette etude porte principalement sur trois points majeurs : l'influence des conditions aux limites sur le developpement du jet et son interaction avec l'environnement exterieur, la validite du modele numerique qui est analysee en comparant la distribution de vitesse obtenue numeriquement aux mesures experimentales (PIV) et, enfin, la comprehension de la distribution air-helium et le phenomene de stratification qui s'etablit a l'interieur de la cavite. Nous observons dans un premier temps que des conditions limites de pression constante appliquees directement au ras des events conduisent a une sous-estimation du debit volumique d'air entrant dans la cavite et donc a une surestimation de la masse de l'helium a l'interieur de la cavite, ce qui n'est pas acceptable dans un contexte d'evaluation du risque hydrogene. En revanche, la prise en compte, dans le domaine de calcul, d'une region exterieure a la cavite predit correctement le flux d'air entrant. Les resultats numeriques sont alors en bon accord avec les donnees PIV. Il a ete montre que les predictions de la DNS, par rapport a la LES, concordent mieux avec les mesures de vitesse par PIV. Le champ de concentration predit numeriquement presente une couche homogene en haut de la cavite, dont la concentration est en accord avec le modele theorique de Linden et al. 1990. Cependant, sa position et son epaisseur ne correspondent pas au modele. Ceci est principalement du aux interactions directes entre le jet flottant et, d'une part, avec les limites solides de la cavite et d'autre part, avec l'environnement exterieur. L'analyse statistique concernant la production de la flottabilite de l'energie cinetique turbulente (TKE) a permis d'identifier les limites du jet flottant.
Introduction of Jumping Fragments in Combination with QSARs for the Assessment of Classification in Ecotoxicology

Starting from a random set of structures taken from the European Chemical Bureau (ECB) Web site, an estimation of the classification by acute category in ecotoxicology was carried out. This estimation was based on two approaches. One approach consists in starting with global quantitative structure-activity relationship (QSAR) equations, analyzing the results and defining an interpretation in terms of overall results and mode of action. The other starts with the notion of emerging fragments and more specifically with the introduction of a particular concept: the jumping fragments. This publication studies the scopes and limitations of each approach for the classification of the derivatives. A promising combination of the two methods is proposed for the classification and also for bringing new information about the importance, for the ecotoxicity, of specific chemical fragments considered alone or in association with others.
d-Mannitol Utilization in Salmonella typhimurium

A biochemical and genetic analysis of d-mannitol metabolism in Salmonella typhimurium indicates that d-mannitol is phosphorylated by the phosphoenolpyruvate-dependent phosphotransferase system. d-Mannitol-1-phosphate is converted to d-fructose-6-phosphate by mannitol-1-phosphate dehydrogenase. Two classes of mannitol mutants are described. Both map at about 115 min on the Salmonella chromosome. Mutants missing mannitol-1-phosphate dehydrogenase activity are mannitol sensitive; i.e., either growth is inhibited or the cells are lysed in the presence of mannitol. In a strain missing adenyl cyclase activity, the mannitol genes require exogenous cyclic adenosine-3′,5′-monophosphate for expression.
Reservation based optimal parking lot recommendation model in Internet of Vehicle environment

In order to solve the problem that the drivers can't find the optimal parking lot timely, a reservation based optimal parking lot recommendation model in Internet of Vehicle (IoV) environment is designed. Based on the users oriented parking information recommendation system, the model considers subjective demands of drivers comprehensively, makes a deeply analysis of the evaluation indicators. This recommendation model uses a phased selection method to calculate the optimal objective parking lot. The first stage is screening which based on the users' subjective parking demands; the second stage is processing the candidate parking lots through multiple attribute decision making. Simulation experiments show that this model can effectively solve the problems encountered in the process of finding optimal parking lot, save the driver's parking time and parking costs and also improve the overall utilization of parking facilities to ease the traffic congestion caused by vehicles parked patrol.
A Mathematical Derivation of a Resource Allocation Matrix for an OFDMA System

In this paper, a resource allocation matrix (RAM) for an orthogonal frequency division multiple access (OFDMA) system is derived to maximize overall data throughput under a strict condition for user fairness. The RAM identifies the most preferable allocation state of OFDMA sub-bands. It is subject to a user fairness condition such that one sub-band is allocated per user during an OFDMA time-slot, allowing each user an equal opportunity to use the sub-bands. The proposed resource allocation scheme using the RAM is evaluated in terms of throughput and user fairness by comparison with the Proportional Fairness (PF) scheme and the Max C/I scheme. Numerical results show that the proposed scheme has much higher throughput under the strict user fairness condition. Even though the PF and Max C/I are given an advantage of ignoring the user fairness condition, the throughput performance of the proposed scheme is quite comparable to that of the PF and Max C/I.
Fisher's fundamental theorem of natural selection revisited.

W. J. Ewens, following G. R. Price, has stressed that Fisher's fundamental theorem of natural selection about the increase in mean fitness is of general validity without any restrictive assumptions on the mating system, the fitness parameters, or the numbers of loci and alleles involved, but that it concerns only a partial change in mean fitness. This partial change is obtained by replacing the actual genotypic fitnesses by the corresponding additive genetic values and by keeping these values fixed in the change of the mean with respect to changes in genotype frequencies. We propose an alternate interpretation for this partial change which uses partial changes in genotype frequencies directly consequent on changes in gene frequencies, the fitness parameters being kept constant. We argue that this interpretation agrees more closely with Fisher's own explanations. Moreover, this approach leads to a decomposition for the total change in mean fitness which explains, unifies, and extends previous decompositions. We consider a wide range of models, from discrete-time selection models with nonoverlapping generations to continuous-time models with overlapping generations and age effects on viability and fecundity, which is the original framework for Fisher's fundamental theorem.
A novel contextual classification of hyperspectral data using probabilistic label relaxation process

In this paper, we propose a novel contextual classification of hyperspectral data. We use probabilistic label relaxation (PLR) process to incorporate context information into the spectral pixelwise classification procedure. In conventional PLR procedure, first a maximum likelihood classification is performed and class probabilities are computed by using multivariate normal models. However this method is not efficient for hyperspectral data with limited training samples. In this paper we suggest to use support vector machine (SVM) in order to initial classification and also use class probability estimates which are obtained from SVM classification for PLR postprocess. Experimental results are presented for an agricultural hyperspectral data. The proposed method improve dramatically classification accuracies, when compare to spectral pixelwise classification. Moreover our proposed method can improve performance of conventional PLR postprocess for hyperspectral data.
Sol–gel derived lithium-releasing glass for cartilage regeneration

Wnt-signalling cascade is one of the crucial pathways involved in the development and homeostasis of cartilage. Influencing this pathway can potentially contribute to improved cartilage repair or regeneration. One key molecular regulator of the Wnt pathway is the glycogen synthase kinase-3 enzyme, the inhibition of which allows initiation of the signalling pathway. This study aims to utilise a binary SiO2–Li2O sol–gel derived glass for controlled delivery of lithium, a known glycogen synthase kinase-3 antagonist. The effect of the dissolution products of the glass on chondrogenic differentiation in an in vitro 3D pellet culture model is reported. Dissolution products that contained 5 mM lithium and 3.5 mM silicon were capable of inducing chondrogenic differentiation and hyaline cartilaginous matrix formation without the presence of growth factors such as TGF-β3. The results suggest that sol–gel derived glass has the potential to be used as a delivery vehicle for therapeutic lithium ions in cartilage regeneration applications.
Polymorphisms in the MAOA, MAOB, and COMT genes and aggressive behavior in schizophrenia

Some studies have reported associations between COMT and MAO genotypes and aggression, though results have been inconsistent. We examined the relationship between Overt aggression scale (OAS) scores, and both MAOA and MAOB polymorphisms in a well‐powered sample of 346 subjects with schizophrenia. We also examined COMT in a Stage II replication sample of 150 individuals, and combined these results with our previously reported (Stage I) findings for COMT. We found no evidence of any associations between OAS ratings and any of the polymorphisms investigated under different genetic models. There was no evidence of epistatic interaction between MAOA and COMT on OAS scores. These results fail to support the theory that functional polymorphisms within the MAOA, MAOB, or COMT genes, as determinants of catecholamine enzymatic activity, are risk factors for aggressive behavior. © 2004 Wiley‐Liss, Inc.
Assessment of changes in psychomotor performance of elderly subjects.

1. The repeatability of a computerised psychomotor test battery on a day-to-day and week-to-week basis was assessed by determining its test-retest reliability and variations in group-means and intraindividual psychomotor performance scores of elderly people. 2. Psychomotor performance was assessed in 50 well-screened elderly subjects (21 males, 29 females; mean age 70.4 +/- 5.0 (s.d.) years) on 5 consecutive days and over 4 weeks in standardised test conditions. 3. The psychomotor test battery consisted of computerised versions of symbol digit substitution test (SDST), continuous attention test (CAT), choice reaction time (CRT), critical flicker fusion test (CFFT), cognitive flexibility test (FLEX), paired word association test (PWAT) and inspection time (INSP). 4. Main outcome measures were test-retest reliability, group variability and intraindividual variability. 5. There was no significant variation in group-means for all components of the test battery over 5 days or 4 weeks on two way analysis of variance. The intraindividual coefficient of variation was low for SDST, CRT, CFFT, FLEX, PWAT and INSP during the period of assessment. Test retest reliability was greater than 0.8 for SDST, CAT, CRT and PWAT. 6. Tests in the Automated Psychomotor Test Battery are reliable and repeatable measures of psychomotor performance on a day-to-day and week-to-week basis.
The trauma symptom inventory: Italian validation of an instrument for the assessment of post-traumatic symptoms

Aim. The trauma symptom inventory (TSI; Briere, 1995) is a useful instrument for the assessment of post-traumatic and common trauma-related mental health symptoms. The purpose of the study was to validate the Italian version of the original TSI. Methods. Participants from non-clinical (n = 285), clinical (n = 110) and post-traumatic (n = 30) samples completed the TSI as part of a battery that included self-report measures of trauma exposure [MMPI-2 PK scale and Impact of Event Scale-Revised (IES-R)] and of psychological symptoms [brief symptom inventory (BSI) and symptom questionnaire (SQ)]. TSI validity scales were compared with MMPI-2 validity scales in order to assess convergent validity. Results. The TSI Italian version showed adequate internal consistency reliability and a good convergent validity. Discriminant function analysis indicates a classification accuracy of TSI scales of 90% for true-positive and 91.4% for true-negative post-traumatic stress disorder (PTSD) cases. A revised three-factor structural model, which demonstrated an adequate and the best fit for the data, was proposed. Conclusions. The study extended the generalization and validity of TSI and provided some suggestions for eventually revisiting factorial structure of the questionnaire.
Novel link adaptation algorithm for multichannel wireless systems with datastream repetition

The paper derives a novel link adaptation algorithm of modulation and coding schemes (MCS) and parameters of multichannel transmission choosing. The developed algorithm is based on a special type of MCS switching table and a new performance metric of system payload and is intended for wireless data transmission systems with capability of datastream repetition through different simultaneously active wireless channels. The presented scheme provides the best choice of MCS and datastream repetition parameters in terms of wireless system resources minimization with respect to maximum transmission speed and fixed uPER level (unrecoverable packet error rate for repetitive datastream).
Reduced Permeability to Rifampicin by Capsular Thickening as a Mechanism of Antibiotic Persistence in Mycobacterium tuberculosis

Persisters constitute a subpopulation of bacteria that can tolerate lethal concentrations of antibiotics. Multiple mechanisms have been suggested for bacterial persistence against antibiotics. With mycobacteria being no exception to this behaviour, we had reported the de novo emergence of genetically antibiotic-resistant Mycobacterium tuberculosis from persister cells upon prolonged exposure to microbicidal concentrations of the anti-tuberculosis drugs, rifampicin and moxifloxacin. Here, we present evidence for reduced permeability to rifampicin as a mechanism for persistence of Mycobacterium tuberculosis in vitro. We observed that rifampicin persistent M. tuberculosis cells developed a thick outer layer (TOL) capsule. The TOL restricted the entry of fluorochrome-conjugated rifampicin, 5-carboxyfluorescein-rifampicin (5-FAM-rifampicin), which retained only 2.5% of its original bactericidal activity, but high levels of permeability, on actively growing mid-log phase cells. Gentle mechanical removal of TOL significantly enhanced 5-FAM-rifampicin entry into the persister cells. The level of 5-FAM-rifampicin in the persister cells was not affected by the pre-incubation of the cells with verapamil, a drug efflux pump inhibitor, ruling out the involvement of efflux pumps in the reduced intracellular concentration of 5-FAM-rifampicin. GC-MS analysis of TOL showed the presence of ∼7-fold, ∼5-fold and ∼2- fold higher levels of α-D-glucopyranoside, 1,2,5-linked-mannitol, and 3,4-linked mannose, respectively, among ∼2-fold higher levels of derivatives of several other types of sugars such as arabinose and galactose. Taken together, the present study reveals that rifampicin-persistent M. tuberculosis cells develop TOL that enables the bacilli to restrict entry of rifampicin and thereby remain tolerant to the antibiotic in vitro.
Bioactive extracts from Senecio samnitum Huet

The antimicrobial and cytotoxic activities of extracts from Senecio samnitum Huet are reported. Extracts from S. samnitum were able to inhibit the in vitro proliferation of four human tumor cell lines. The dichloromethane extract demonstrated effective cytotoxic activity with IC50 of 22.89 µg mL−1 on the Caco-2 cell line and the EtOAc extract had IC50 value of 11.91 µg mL−1 against the COR-L23 cell line. The n-hexane extract displayed the best antibacterial activity against Gram positive bacteria, particularly Staphylococcus aureus. The antifungal activity of all extracts was also seen, particularly against the dermatophytes Trichophyton tonsurans and Microsporum gypseum for the methanol and n-hexane extracts.
A distributed energy-efficient algorithm in green Content-Centric Networks

In Content-Centric Networking (CCN), most existing works do not consider energy savings by turning off network devices in CCN. In this paper, we systematically analyze the energy efficiency problem in CCN by turning off the content routers and network links. We formulate the energy consumption issue as a Mixed Integer Linear Programming (MILP) model, and propose a centralized solution via spanning tree heuristic and a fully distributed consensus optimization algorithm via the alternating direction method of multipliers (ADMM) to solve the problem for CCN. By duplicating flow variables, the energy consumption problem decomposes into node specific subproblems with local variables. These variables are iteratively driven into consensus via the ADMM. Simulation results reveal that the proposed distributed algorithm is amenable to energy-efficient implementation, due to smaller amount of local information exchange at each iteration. Moreover, the proposed algorithm can converge to final status in a significantly smaller number of iterations compared to the method based on dual decomposition. In addition, our algorithm scales better to large networks and it does not require intensive finetuning of the step size.
Effects of infiltration of the incision site with bupivacaine on postoperative pain and incisional healing in dogs undergoing ovariohysterectomy.

OBJECTIVE To determine the effects of infiltration of the incision site with bupivacaine hydrochloride as part of a multimodal analgesia protocol (incisional block) on postoperative analgesia and incisional healing. DESIGN Randomized controlled clinical trial. ANIMALS 92 shelter-owned female dogs undergoing routine ovariohysterectomy. PROCEDURES As part of a multimodal analgesic protocol for ovariohysterectomy, dogs received 1 of the following treatments at the incision site: no injection (26 dogs), preincisional infiltration with saline (0.9% NaCl) solution (12 dogs) or bupivacaine (21 dogs), or postincisional infiltration with bupivacaine (33 dogs). Postoperative pain was assessed with the Glasgow pain scale and response to mechanical stimulation with von Frey filaments. Incisions were monitored for signs of inflammation (edema, erythema, and discharge) and complications in wound healing. RESULTS There was no difference in pain scores or response to mechanical stimulation over time among treatments. There were no significant differences in incisional edema or discharge among treatments. There was significantly more erythema in dogs that received preincisional infiltration with saline solution at 4 hours after surgery and less erythema in dogs that received postincisional infiltration with bupivacaine at 24 hours after surgery, compared with other treatments. The number of complications for dogs that had preincisional infiltration of bupivacaine was higher than for dogs that had other treatments; complications included excessive inflammation, splenic laceration, and herniation. CONCLUSIONS AND CLINICAL RELEVANCE No additional analgesic benefit was found in dogs that underwent local bupivacaine infiltration as part of a multimodal analgesic protocol for ovariohysterectomy.
Latent fingerprints segmentation based on Rearranged Fourier Subbands

In this work, we present a latent fingerprint segmentation algorithm based on spatial-frequency domain analysis. The algorithm arranges the overlapped block-based Fourier coefficients into groups of frequency and orientation subbands, called Rearranged Fourier Subband (RFS). The RFS reveals latent fingerprint spectra in only a limited number of subbands. The algorithm then boosts, sorts, and extracts, from complex background and noise, the latent fingerprint spectra in the RFS subbands. Several experiments are evaluated based on ground truth comparison, feature extraction, and latent matching on the NIST SD27 latent database. Our experimental results show that the proposed algorithm achieves better accuracy compared to those of the published automatic segmentation algorithms.
An Efficient Hybrid Beamforming Scheme for Sparse Millimeter Wave Channel

Millimeter wave (mmWave) experiences a high path-loss in free space. To overcome this weakness, antenna array is used to obtain a high beamforming gain. However, due to high complexity of digital beamforming systems, the hybrid structure consisting of baseband and analog precoder has been proposed. We consider the well known block diagonalization (BD) precoding for transmission technique. Because of the practical constraints such as channel estimation error, the limited number of radio frequency (RF) chains and the quantized analog phase shifters, the BD precoder cannot provide accurate interference-free effective channel. In this paper, we propose the extended BD precoding method which extends the null space of interference channels to reduce the effect of practical constraints. Simulation results show that the proposed method provides much improved sum rate and error performances than original BD precoder.