Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation of an acetyl‐CoA synthetase gene (ZbACS2) from Zygosaccharomyces bailii

A gene homologous to Saccharomyces cerevisiae ACS genes, coding for acetyl‐CoA synthetase, has been cloned from the yeast Zygosaccharomyces bailii ISA 1307, by using reverse genetic approaches. A probe obtained by PCR amplification from Z. bailii DNA, using primers derived from two conserved regions of yeast ACS proteins, RIGAIHSVVF (ScAcs1p; 210–219) and RVDDVVNVSG (ScAcs1p; 574–583), was used for screening a Z. bailii genomic library. Nine clones with partially overlapping inserts were isolated. The sequenced DNA fragment contains a complete ORF of 2027 bp (ZbACS2) and the deduced polypeptide shares significant homologies with the products of ACS2 genes from S. cerevisiae and Kluyveromyces lactis (81% and 82% identity and 84% and 89% similarity, respectively). Phylogenetic analysis shows that the sequence of Zbacs2 is more closely related to the sequences from Acs2 than to those from Acs1 proteins. Moreover, this analysis revealed that the gene duplication producing Acs1 and Acs2 proteins has occurred in the common ancestor of S. cerevisiae, K. lactis, Candida albicans, C. glabrata and Debaryomyces hansenii lineages. Additionally, the cloned gene allowed growth of S. cerevisiae Scacs2 null mutant, in medium containing glucose as the only carbon and energy source, indicating that it encodes a functional acetyl‐CoA synthetase. Also, S. cerevisiae cells expressing ZbACS2 have a shorter lag time, in medium containing glucose (2%, w/v) plus acetic acid (0.1–0.35%, v/v). No differences in cell response to acetic acid stress were detected both by specific growth and death rates. The mode of regulation of ZbACS2 appears to be different from ScACS2 and KlACS2, being subject to repression by a glucose pulse in acetic acid‐grown cells. The nucleotide sequence of a common 5269 bp fragment has been deposited in the EMBL Data Library under Accession No. AJ314837. Copyright © 2004 John Wiley & Sons, Ltd.
Software defect prediction based on class-association rules

Although there have lots of studies on using static code attributes to identify defective software modules, there still have many challenges. For instance, it is difficult to implement the Apriori-type algorithm to predict defects by learning from an imbalanced dataset. For more accurate and understandable defect prediction, a novel approach based on class-association rules algorithm is proposed. Class-association rules are looked as a separate class label, which is a specific type of association rules that explores the relationship between attributes and categories. In an empirical comparison with four datasets, the novel approach is superior to other four classification techniques and accordingly, proved it's valuable for defect prediction.
Efficient Data-Driven Task Allocation for Future Many-Cluster On-chip Systems

Continuous demand for higher performance is adding more pressure on hardware designers to provide faster machines with low energy consumption. Recent technological advancements allow placing a group of silicon dies on top of a conventional interposer (silicon layer), which provides space to integrate logic and interconnection resources to manage active processing cores. However, such large resource availability requires an adequate Program eXecution Model (PXM) as well as an efficient mechanism to allocate resources in the system. From this perspective, fine-grain data-driven PXMs represent an attractive solution to reduce the cost of synchronising concurrent activities. The contribution of this work is twofold. First, a hardware architecture called TALHES - a Task ALlocator for HEterogeneous System is proposed to support scheduling of multi-threaded applications (adhering to an explicit data-driven PXM). TALHES introduces a Network-on-Chip (NoC) extension: i) while on-chip 2D-mesh NoCs are used to support locality of computations in the execution of a single task; ii) a global task scheduler integrated into the silicon interposer orchestrates application tasks among different clusters of cores (eventually with different computing capabilities). The second contribution of the paper is a simulation framework that is tailored to support the analysis of such fine-grain data-driven applications. In this work, Linux Containers are used to abstract and efficiently simulate clusters of cores (i.e., a single die), as well as the behaviour of the global scheduling unit.
Establishment and Validation of Computational Model for MT1-MMP Dependent ECM Degradation and Intervention Strategies

MT1-MMP is a potent invasion-promoting membrane protease employed by aggressive cancer cells. MT1-MMP localizes preferentially at membrane protrusions called invadopodia where it plays a central role in degradation of the surrounding extracellular matrix (ECM). Previous reports suggested a role for a continuous supply of MT1-MMP in ECM degradation. However, the turnover rate of MT1-MMP and the extent to which the turnover contributes to the ECM degradation at invadopodia have not been clarified. To approach this problem, we first performed FRAP (Fluorescence Recovery after Photobleaching) experiments with fluorescence-tagged MT1-MMP focusing on a single invadopodium and found very rapid recovery in FRAP signals, approximated by double-exponential plots with time constants of 26 s and 259 s. The recovery depended primarily on vesicle transport, but negligibly on lateral diffusion. Next we constructed a computational model employing the observed kinetics of the FRAP experiments. The simulations successfully reproduced our FRAP experiments. Next we inhibited the vesicle transport both experimentally, and in simulation. Addition of drugs inhibiting vesicle transport blocked ECM degradation experimentally, and the simulation showed no appreciable ECM degradation under conditions inhibiting vesicle transport. In addition, the degree of the reduction in ECM degradation depended on the degree of the reduction in the MT1-MMP turnover. Thus, our experiments and simulations have established the role of the rapid turnover of MT1-MMP in ECM degradation at invadopodia. Furthermore, our simulations suggested synergetic contributions of proteolytic activity and the MT1-MMP turnover to ECM degradation because there was a nonlinear and marked reduction in ECM degradation if both factors were reduced simultaneously. Thus our computational model provides a new in silico tool to design and evaluate intervention strategies in cancer cell invasion.
Is university education an investment or a consumption good in a small open economy

Traditionally, university education (UE) has been considered as an investment in human capital. In the last two decades, however, there is a transitional refocusing that people, by holding a university degree, enjoy certain intangible benefits, such as a lasting feeling of self-fulfilment and self-esteem, i.e., they simply treat UE as a consumption good. In this empirical study we take a broader view of UE by distinguishing and quantifying three kinds of benefits arising from UE: a) monetary benefits; b) social status benefits; c) psychic benefits, using a sample of 832 graduates of three Greek universities. We find that graduates of all three universities enjoy significant psychic benefits which are not influenced by family educational background, while monetary motivations are strong substitutes to psychic motivations, thus a deterioration of monetary incentives, e.g., during a period of economic crisis, will propel psychic benefits to a key motivational issue for undertaking UE.
Celiac disease markers in patients with liver diseases: a single center large scale screening study.

AIM To study the coincidence of celiac disease, we tested its serological markers in patients with various liver diseases. METHODS Large-scale screening of serum antibodies against tissue transglutaminase (tTG), and deamidated gliadin using enzyme-linked immunosorbent assay and serum antibodies against endomysium using immunohistochemistry, in patients with various liver diseases (n = 962) and patients who underwent liver transplantation (OLTx, n = 523) was performed. The expression of tTG in liver tissue samples of patients simultaneously suffering from celiac disease and from various liver diseases using immunohistochemistry was carried out. The final diagnosis of celiac disease was confirmed by histological analysis of small-intestinal biopsy. RESULTS We found that 29 of 962 patients (3%) with liver diseases and 5 of 523 patients (0.8%) who underwent OLTx were seropositive for IgA and IgG anti-tTG antibodies. However, celiac disease was biopsy-diagnosed in 16 patients: 4 with autoimmune hepatitis type I, 3 with Wilson's disease, 3 with celiac hepatitis, 2 with primary sclerosing cholangitis, 1 with primary biliary cirrhosis, 1 with Budd-Chiari syndrome, 1 with toxic hepatitis, and 1 with non-alcoholic steatohepatitis. Unexpectedly, the highest prevalence of celiac disease was found in patients with Wilson's disease (9.7%), with which it is only rarely associated. On the other hand, no OLTx patients were diagnosed with celiac disease in our study. A pilot study of the expression of tTG in liver tissue using immunohistochemistry documented the overexpression of this molecule in endothelial cells and periportal hepatocytes of patients simultaneously suffering from celiac disease and toxic hepatitis, primary sclerosing cholangitis or autoimmune hepatitis type I. CONCLUSION We suggest that screening for celiac disease may be beneficial not only in patients with associated liver diseases, but also in patients with Wilson's disease.
Interpersonal violence among women seeking welfare: unraveling lives.

OBJECTIVES Exposure to violence is a widespread problem among women who receive welfare benefits. Research has focused on partner violence among women with children on Temporary Assistance for Needy Families (TANF), ignoring low-income women without dependent children who are eligible for General Assistance (GA). METHODS We report findings from a survey of 1235 women seeking TANF (N=1095) and GA (N=140) throughout a California county. RESULTS Estimates of recent physical, sexual, and severe violence were high in both populations. However, the highest rates occurred among women without children seeking GA, suggesting that they are at higher risk for sexual violence and more severe forms of physical violence, especially from intimate partners. This increased risk is partly accounted for by the co-occurrence of other serious health and social problems. In multivariate analyses, past-year violence was associated with substance use (adjusted odds ratio [AOR]=2.0, 95% confidence interval [CI] = 1.5, 2.9), recent homelessness (AOR = 1.9, 95% CI = 1.4, 2.6), family fragmentation including divorce or separation (AOR=3.1, 95% CI 1.8, 5.2), or foster care involvement (AOR=2.2, 95% CI=1.1, 4.5) CONCLUSIONS Welfare reform created TANF programs to address domestic violence. Women seeking GA may need similar services because of the high prevalence of violence.
Evaluation of a Multiplex Real-Time PCR Assay for Detecting Major Bacterial Enteric Pathogens in Fecal Specimens: Intestinal Inflammation and Bacterial Load Are Correlated in Campylobacter Infections

ABSTRACT A total of 1,056 native or Cary-Blair-preserved stool specimens were simultaneously tested by conventional stool culturing and by enteric bacterial panel (EBP) multiplex real-time PCR for Campylobacter jejuni, Campylobacter coli, Salmonella spp. , and shigellosis disease-causing agents (Shigella spp. and enteroinvasive Escherichia coli [EIEC]). Overall, 143 (13.5%) specimens tested positive by PCR for the targets named above; 3 coinfections and 109 (10.4%) Campylobacter spp. , 17 (1.6%) Salmonella spp. , and 20 (1.9%) Shigella spp. /EIEC infections were detected. The respective positive stool culture rates were 75 (7.1%), 14 (1.3%), and 7 (0.7%). The median threshold cycle (CT ) values of culture-positive specimens were significantly lower than those of culture-negative ones (CT values, 24.3 versus 28.7; P < 0.001), indicating that the relative bacterial load per fecal specimen was significantly associated with the culture results. In Campylobacter infections, the respective median fecal calprotectin concentrations in PCR-negative/culture-negative (n = 40), PCR-positive/culture-negative (n = 14), and PCR-positive/culture-positive (n = 15) specimens were 134 mg/kg (interquartile range [IQR], 30 to 1,374 mg/kg), 1,913 mg/kg (IQR, 165 to 3,813 mg/kg), and 5,327 mg/kg (IQR, 1,836 to 18,213 mg/kg). Significant differences were observed among the three groups (P < 0.001), and a significant linear trend was identified (P < 0.001). Furthermore, the fecal calprotectin concentrations and CT values were found to be correlated (r = −0.658). Our results demonstrate that molecular screening of Campylobacter spp. , Salmonella spp. , and Shigella spp. /EIEC using the BD Max EBP assay will result in timely diagnosis and improved sensitivity. The determination of inflammatory markers, such as calprotectin, in fecal specimens may aid in the interpretation of PCR results, particularly for enteric pathogens associated with mucosal damage and colonic inflammation.
Rous sarcoma virus direct repeat cis elements exert effects at several points in the virus life cycle

Two approximately 135-nucleotide (nt) direct repeats flank the Rous sarcoma virus (RSV) oncogene src and are composed of two smaller repeats, dr1 (approximately 100 nt) and dr2 (approximately 36 nt). These sequences have been reported to contain cis-acting signals necessary for RNA packaging and elements that allow cytoplasmic accumulation of unspliced RNA (cytoplasmic transport elements). In this report, we show that avian fibroblasts infected with the Prague A strain of RSV with precise deletions of both dr1 elements express src and are transformed by this mutant virus but production of virus particles is very low and virus spread throughout the culture requires several weeks. We show that the replication defect is due to complex effects on viral RNA transport, viral RNA half-life, and virus particle assembly. The dr1 elements may contain binding sites for a permissive cell-specific factor(s) that facilitates efficient nuclear-cytoplasmic transport, RNA stability, and cytoplasmic utilization of unspliced viral RNA. The implications of these results for understanding the defects of nonpermissive virus infections in mammalian cells are discussed.
Sizing of the Drone Delivery Fleet Considering Energy Autonomy

One of the most innovative solutions treated in the literature in order to reduce the environmental impact of urban parcel delivery logistics is the use of drones for delivery on the last kilometer. Consequently, nowadays, the primary challenge is essentially related to the drones’ fleet sizing according to its means of support for the urban delivery of parcels. In this paper, we will discuss the issue of dimensioning from a forecast of deliveries of an urban perimeter, the size of the fleet, the stock of battery to dispose of and the strategy of battery charging. We will present an analytical model expressing the proposed problem of the optimal drones’ delivery mission taking into account the issues of autonomy and energy consumption related to the drone’s technical specification. According to the developed analytical model, two optimization policies will be proposed. The first policy consists of planning missions under reducing distance. The second policy tries to make a compromise between the distance and the number of drones. A case study will be presented in order to compare the two policies based on the overall cost of a plan. The main objective of the study is to create a decision-making tool for the design of a drone fleet in the case of forecast deliveries over a time horizon under operational constraints.
Oxidative stress in chronic venous leg ulcers

Venous leg ulcers are common and cause considerable morbidity in the population. As healing may be slow or may never be achieved, ulcers create persistent and substantial demands on clinical resources. Great efforts have been made to accelerate tissue repair in chronic venous leg ulcers with limited success. This may at least be partly due to the limited knowledge on the microenvironment of chronic wounds. In fact, the tremendous impact of the microenvironmental conditions on the outcome of wound healing has increasingly become apparent. Oxidative stress as a consequence of an imbalance in the prooxidant‐antioxidant homeostasis in chronic wounds is thought to drive a deleterious sequence of events finally resulting in the nonhealing state. The majority of reactive oxygen species are most likely released by neutrophils and macrophages and to an unknown extent from resident fibroblasts and endothelial cells. As the inflammatory phase does not resolve in chronic wounds, the load of reactive oxygen species persists over a long period of time with subsequent continuous damage and perpetuation of the inflammation. In this article, we will critically discuss recent findings that support the role of oxidative stress in the pathophysiology of nonhealing chronic venous leg ulcers.
A new computationally efficient dynamic scheduling for multiple resource constrained procedures

Scheduling of multiple resource systems with resource constraints is a computationally expensive task especially when one is dealing with a large number of procedures. Scheduling through assessing the specific order of tasks for each procedure not only minimizes the makespan of a schedule but also maximizes the utilization of resources. This paper develops a new scheduling formulation that is computationally efficient and enforces constraints of multiple resource procedures. We showed that by applying genetic algorithm to this method we can schedule 100 of multiple resource procedures in less than 2 minutes on a personal computer. We also developed a dynamic scheduling technique that is capable of re-scheduling as new procedures arrive in a system. The scheduling performance is consistent with different numbers of procedures.
Frequency of urination and its effects on metabolism, pharmacokinetics, blood hemoglobin adduct formation, and liver and urinary bladder DNA adduct levels in beagle dogs given the carcinogen 4-aminobiphenyl.

The human urinary bladder carcinogen, 4-aminobiphenyl (ABP), is known to undergo hepatic metabolism to an N-hydroxy arylamine and its corresponding N-glucuronide. It has been proposed that these metabolites are both transported through the blood via renal filtration to the urinary bladder lumen where acidic pH can facilitate the hydrolysis of the N-glucuronide and enhance the conversion of N-hydroxy-4-aminobiphenyl (N-OH-ABP) to a reactive electrophile that will form covalent adducts with urothelial DNA. Blood ABP-hemoglobin adducts, which have been used to monitor human exposure to ABP, are believed to be formed by reactions within the erythrocyte involving N-OH-ABP that has entered the circulation from the liver or from reabsorption across the urothelium. To test these hypotheses directly, experimental data were obtained from female beagles given [3H]ABP (p.o., i.v., or intraurethrally). [3H]N-OH-ABP (i.v. or intraurethrally), or [3H]N-OH-ABP N-glucuronide (i.v.). Analyses included determinations of total ABP in whole blood and plasma, ABP-hemoglobin adducts in blood erythrocytes, ABP and N-OH-ABP levels (free and N-glucuronide) in urine, urine pH, frequency of urination (controlled by urethral catheter), rates of reabsorption of ABP and N-OH-ABP across the urothelium, and apparent volumes of distribution in the blood/tissue compartment. The major ABP-DNA adduct, N-(guan-8-yl)-4-aminobiphenyl, was also measured in urothelial and liver DNA using a sensitive immunochemical method. An analog/digital hybrid computer was then utilized to construct a multicompartmental pharmacokinetic model for ABP and its metabolites that separates: (a) absorption; (b) hepatic metabolism and distribution in blood and tissues; (c) ABP-hemoglobin adduct formation; (d) hydrolysis and reabsorption in the urinary bladder lumen; and (e) excretion. Using this model, cumulative exposure of the urothelium to free N-OH-ABP was simulated from the experimental data and used to predict ABP-DNA adduct formation in the urothelium. The results indicated that exposure to N-OH-ABP and subsequent ABP-DNA adduct formation are directly dependent on voiding frequency and to a lesser extent on urine pH. This was primarily due to the finding that, after p.o. dosing of ABP to dogs, the major portion of the total N-OH-ABP entering the bladder lumen was free N-OH-ABP (0.7% of the dose), with much lower amounts as the acid-labile N-glucuronide (0.3% of the dose). (ABSTRACT TRUNCATED AT 400 WORDS)
The effect of on-site experience and place attachment on loyalty: Evidence from Chinese tourists in a hot-spring resort

ABSTRACT As an antecedent of place attachment, on-site experience plays a key role in obtaining customer loyalty in the context of a hot-spring resort operation. However, few studies have addressed the consequences of on-site experience in terms of its components and examined empirically the relationship between on-site experience and place attachment. This study was focused on ascertaining the dimensions of on-site experience and examining the relationship between on-site experience and loyalty through place attachment. A conceptualization of on-site experience is proposed, with three dimensions: environmental experience, on-site self-related experience, and on-site social interaction. The results revealed interesting relationships between components of on-site experience and place attachment. Finally, managerial implications of the results are discussed for managers of hot-spring resorts.
The Parameterized Phoneme Identity Feature as a Continuous Real-Valued Vector for Neural Network Based Speech Synthesis

In the speech synthesis systems, the phoneme identity feature indicated as the pronunciation unit is influenced by external contexts like the neighboring words and phonemes. This paper proposes to encode such relatedness and parameterize the pronunciation of the phoneme identity feature as a continuous real-valued vector. The vector, composed by a phoneme embedded vector (PEV) and a word embedded vector (WEV), is applied to substitute the binary vector whose representation is one-hot. It is realized in the word embedding model with the joint training structure where the PEV and WEV are learned together. The effectiveness of the proposed technique was evaluated by comparing it with the binary vector in the bidirectional long short term memory recurrent neural network (BLSTM-RNN) based speech synthesis systems. Improvement on the quality of the synthesized speech has been achieved from the proposed system, which proves the effectiveness of replacing the binary vector with the continuous real-valued vector in describing the phoneme identity feature.