Miracle-dz/UniFAR-FTUs huggingface dataset:
Positive Regulation of Sugar Catabolic Pathways in the Cyanobacterium Synechocystis sp. PCC 6803 by the Group 2 σ Factor SigE*

The sigE gene of Synechocystis sp. PCC 6803 encodes a group 2 σ factor for RNA polymerase and has been proposed to function in transcriptional regulation of nitrogen metabolism. By using microarray and Northern analyses, we demonstrated that the abundance of transcripts derived from genes important for glycolysis, the oxidative pentose phosphate pathway, and glycogen catabolism is reduced in a sigE mutant of Synechocystis maintained under the normal growth condition. Furthermore, the activities of the two key enzymes of the oxidative pentose phosphate pathway, glucose-6-phosphate dehydrogenase and 6-phophogluconate dehydrogenase, encoded by the zwf and gnd genes were also reduced in the sigE mutant. The dark enhancements in both enzyme activity and transcript abundance apparent in the wild type were eliminated by the mutation. In addition, the sigE mutant showed a reduced rate of glucose uptake and an increased intracellular level of glycogen. Moreover, it was unable to proliferate under the light-activated heterotrophic growth conditions. These results indicate that SigE functions in the transcriptional activation of sugar catabolic pathways in Synechocystis sp. PCC 6803.
Automated structure discovery and parameter tuning of neural network language model based on evolution strategy

Long short-term memory (LSTM) recurrent neural network based language models are known to improve speech recognition performance. However, significant effort is required to optimize network structures and training configurations. In this study, we automate the development process using evolutionary algorithms. In particular, we apply the covariance matrix adaptation-evolution strategy (CMA-ES), which has demonstrated robustness in other black box hyper-parameter optimization problems. By flexibly allowing optimization of various meta-parameters including layer wise unit types, our method automatically finds a configuration that gives improved recognition performance. Further, by using a Pareto based multi-objective CMA-ES, both WER and computational time were reduced jointly: after 10 generations, relative WER and computational time reductions for decoding were 4.1% and 22.7% respectively, compared to an initial baseline system whose WER was 8.7%.
Different growth patterns of a cancer cell population as a function of its starting growth characteristics: analysis by mathematical modelling

The growth kinetics of a cancer cell population as a function of the total number of cells and the proportion of proliferating and resting cells at the beginning of the growth has been analysed by a mathematical model. The model takes into account the processes of cell division, death and transition from proliferation to rest and backwards. It is shown that a single cell population growing under the same environmental conditions has an extremely broad spectrum of growth patterns. The whole multiplicity of possible growth patterns has been determined by the inherent cellular growth characteristics of the population, while the growth pattern actually realized of the variety of growth curves depends on the total number of cells and the proportion of proliferating and resting cells at the initial moment of growth. The model is shown to provide a good prediction of experimentally measured kinetics of regrowth of tumour cells subcultured after various times of the growth in unfed cultures, and the kinetics of tumour cell growth after severe hypoxia. The role of cell transitions between proliferating and resting stages in the problem of growth control is discussed.
Solanum nigrum produces nitric oxide via nuclear factor-&kgr;B activation in mouse peritoneal macrophages

Nitric oxide (NO) is an antitumour molecule produced in activated macrophages and Solanum nigrum is a plant used in oriental medicine to treat tumours. In this study using mouse peritoneal macrophages, we have examined the mechanism by which Solanum nigrum regulates NO production. When Solanum nigrum was used in combination with 20 U/ml of recombinant interferon-&ggr; (rIFN-&ggr;), there was a marked cooperative induction of NO production. The increase in NO synthesis was reflected as an increased amount of inducible NO synthase (iNOS) protein. The production of NO from rIFN-&ggr; plus Solanum nigrum-stimulated peritoneal macrophages was decreased by treatment with NG-monomethyl-L-arginine or N&agr;-tosyl-Phe chloromethyl ketone, an iNOS inhibitor. Additionally, the increased production of NO from rIFN-&ggr; plus Solanum nigrum-stimulated cells was almost completely inhibited by pretreatment with 100 μmol/l of pyrrolidine dithiocarbamate, an inhibitor of nuclear factor κB (NF-κB). Furthermore, Solanum nigrum increased activation of NF-κB. These findings suggest that Solanum nigrum increases the production of NO by rIFN-&ggr;-primed macrophages and NF-κB plays a critical role in mediating these effects.
The Relative Cost of Internal vs. External Equity in South Africa: The Impact of Capital Gains and Dividend Taxes

Abstract In order to investigate the impact of South Africa’s unique historical secondary tax on companies (STC) on optimal capital structure, we adapt the US methodology developed by Lewellen and Lewellen (2006) to cater for STC. Using our derived STC-models, we examine the combined effect of South Africa’s capital gains tax and, respectively, its historical and current dividend tax regimes, on the relative costs of internal and external equity, and thus the theoretical optimal South African capital structure both historically and currently. We examine the expected position of each of these areas in light of South Africa’s transition from STC to the new shareholder dividend tax (SDT) regime that replaced it on 1 April 2012. We conclude that there is a net tax benefit to utilising internal equity under certain conditions and that firm financing and payout decisions that ignore this benefit are fundamentally incomplete.
Bilateral cochlear implantation in Friedreich's ataxia: A case study

Abstract With an incidence of 1:29 000 among Caucasians, Friedreich's ataxia (FRDA) is the most common inherited ataxia, leading to both sensory and motor degeneration. Despite many FRDA patients exhibiting normal or near normal sound detection thresholds, many individuals show abnormal neural conduction along their central auditory pathways. Electrophysiological testing can show abnormal or absent cochlear nerve and auditory brainstem recordings in the presence of normal pre-neural cochlear function (otoacoustic emissions or cochlear microphonics). This pattern of normal pre-neural cochlear function and disrupted neural conduction has been termed auditory neuropathy spectrum disorder (ANSD). Studies of FRDA patients with ANSD have shown that they exhibit severe deficits in temporal processing, impaired frequency discrimination, and deficits in speech perception. Rehabilitation of these auditory percept deficits remains difficult, as hearing aids may amplify sounds without adding clarity to the temporally disrupted or distorted signal that FRDA patients with ANSD may receive. There is limited data on the best intervention for patients with FRDA with ANSD, although personal radio aids (FM systems) have been shown to be beneficial. We report a case, where cochlear implantation has led to a dramatic improvement in speech perception in an individual with FRDA and ANSD. The majority of the literature on ANSD treatment has focused on paediatric patients with the ‘dyssynchrony’ type of ANSD, rather than the true neuropathy type underlying the hearing loss in FRDA patients.
Comparative analysis of the safety and tolerability of fixed-dose artesunate/amodiaquine versus artemether/lumefantrine combinations for uncomplicated falciparum malaria in pregnancy: a randomized open label study

A comparative clinical study was conducted to evaluate the safety and tolerability of two commonly used fixed dose artemisinin-based combinations for the treatment of uncomplicated Plasmodium falciparum malaria in the second and third trimester of pregnancy. To achieve this, a total of 155 participants were recruited for the study. Eighty of these were drawn from pregnant women who came for routine antenatal care while 40 nonpregnant participants were recruited from apparently healthy females in the community. Eighty pregnant participants with uncomplicated P. falciparum malaria were randomized into artesunate/amodiaquine (AA) and artemether/lumefantrine (AL) treatment arms while 40 nonpregnant and 35 nonmalarious pregnant women were used as control. The interventional groups received standard fixed dose combinations of AA (100/270 mg) daily or AL (20/120 mg) twice daily for 3 days. Blood samples were collected on day 4 and patients were followed-up closely to ascertain the safety of the drugs. The study showed a significant (p<0.0001) elevation of alkaline phosphatase in the AA and AL group compared to the nonpregnant control and a significant (p<0.05) elevation of alanine transaminase and aspartate transaminase level in the AL combination group when compared with the AA group. The elevated hepatic enzymes were within the normal range for pregnancy and were not clinically significant. Adverse event rate was higher in the AA group (n=28 [70%]) when compared to the AL group (n=4 [10%]) although the drugs were well-tolerated in both treatment arms. In conclusion, the use of these combinations is safe in the second and third trimester of pregnancy. However, we recommend active pharmacovigilance and spontaneous drug reporting of the agents in order to continuously monitor safety in the vastly heterogeneous population.
Human lactoferrin efficiently targeted into caprine beta-lactoglobulin locus with transcription activator-like effector nucleases

Objective To create genetically modified goat as a biopharming source of recombinant human lacotoferrin (hLF) with transcription activator-like effector nucleases. Methods TALENs and targeting vector were transferred into cultured fibroblasts to insert hLF cDNA in the goat beta-lactoglobulin (BLG) locus with homology-directed repair. The gene targeted efficiency was checked using sequencing and TE7I assay. The bi-allelic gene targeted colonies were isolated and confirmed with polymerase chain reaction, and used as donor cells for somatic cell nuclear transfer (SCNT). Results The targeted efficiency for BLG gene was approximately 10%. Among 12 Bi-allelic gene targeted colonies, five were used in first round SCNT and 4 recipients (23%) were confirmed pregnant at 30 d. In second round SCNT, 7 (53%), 4 (31%), and 3 (23%) recipients were confirmed to be pregnant by ultrasound on 30 d, 60 d, and 90 d. Conclusion This finding signifies the combined use of TALENs and SCNT can generate bi-allelic knock-in fibroblasts that can be cloned in a fetus. Therefore, it might lay the foundation for transgenic hLF goat generation and possible use of their mammary gland as a bioreactor for large-scale production of recombinant hLF.
FAKTOR-FAKTOR YANG BERPENGARUH TERHADAP PRODUKTVITAS PEKERJA SEKTOR PERTANIAN DAN INDUSTRI PENGOLAHAN

In the Province of East Java, the agricultural sector contributes the largest in employment, while its contribution to GDP is the lowest. On the other hand, the processing industry sector contributes the lowest in employment but its contribution to GDP is higher than the agricultural sector. Thereby it is important to study the productivity of both sectors. This study aims to examine the effect of sectoral attractiveness, individual characteristics and suitability ofjob options on the productivity of workers in the agricultural sector and manufacturing industry in East Java. Analysis of the data using a structural equation model (Structural Equation Modeling/SEM) and AMOS (Structural Analysis of Moment) application program. The study shows that the sectoral attractiveness and individual characteristics significantly influence the productivity of workers in both agriculture and manufacturing industry. But as an intermediate variable, the suitability ofjob options has no significant effect on workers' productivity. Thus, the effects of- sectoral attractiveness and individual characteristics on - workers productivity are direct. Keywords: the sectoral attractiveness, individual characteristics, suitability of job options, and labor productivity.
Concepts of capacity and performance in assessment of functioning amongst stroke survivors: A comparison of the Functional Independence Measure and the International Classification of Functioning, Disability and Health.

OBJECTIVE To investigate the use of concepts of capacity and performance when assessing functioning of stroke survivors, measured with the Functional Independence Measure (FIM) and the International Classification of Functioning, Disability and Health (ICF). METHODS During an inpatient interdisciplinary rehabilitation programme for 62 subacute stroke survivors, limitations in speaking, walking, toileting and eating were assessed at admission and discharge with both the FIM and a scale based on the ICF Brief Core Set for stroke. Correlation between the results obtained with these 2 scales was assessed using Spearman's correlation coefficient. RESULTS The level of restriction of functioning, defined as capacity or performance in terms of the ICF, correlated well with the results obtained with the FIM (0.47-0.87) . The only statistically significant difference was found in assessing limitations in eating, where assessment with the FIM had a higher correlation with the concept of capacity than performance (0.75 vs 0.55). The observed correlations were not associated with stroke severity. CONCLUSION Even though the FIM and an ICF-based scale may describe limitation of functioning of stroke survivors similarly, ICF is probably more comprehensive in describing both capacity and performance.
Beyond the Hype: On Using Blockchains in Trust Management for Authentication

Trust Management (TM) systems for authentication are vital to the security of online interactions, which are ubiquitous in our everyday lives. Various systems, like the Web PKI (X.509) and PGP's Web of Trust are used to manage trust in this setting. In recent years, blockchain technology has been introduced as a panacea to our security problems, including that of authentication, without sufficient reasoning, as to its merits.In this work, we investigate the merits of using open distributed ledgers (ODLs), such as the one implemented by blockchain technology, for securing TM systems for authentication. We formally model such systems, and explore how blockchain can help mitigate attacks against them. After formal argumentation, we conclude that in the context of Trust Management for authentication, blockchain technology, and ODLs in general, can offer considerable advantages compared to previous approaches. Our analysis is, to the best of our knowledge, the first to formally model and argue about the security of TM systems for authentication, based on blockchain technology. To achieve this result, we first provide an abstract model for TM systems for authentication. Then, we show how this model can be conceptually encoded in a blockchain, by expressing it as a series of state transitions. As a next step, we examine five prevalent attacks on TM systems, and provide evidence that blockchain-based solutions can be beneficial to the security of such systems, by mitigating, or completely negating such attacks.
Investigating the effect of carbon leakage on the environmental Kuznets curve using luminosity data

Abstract This paper studies the effect of carbon leakage on the environmental Kuznets curve (EKC) using satellite nighttime light data. It shows that nighttime lighting is an important variable for estimating carbon dioxide emissions that is superior to other existing indicators and covers all countries in the world, finding evidence of an inverted-U shaped relationship between light and, thus, greenhouse gas emissions and income, with a turning point at approximately US$50,000. However, the relationship is primarily driven by changes in the structure of international trade, implying strong carbon leakage effects. Consequently, environmental regulations that become operative in only one part of the world may fail without global coordination.
Transcription factors NFI and NFIII/oct-1 function independently, employing different mechanisms to enhance adenovirus DNA replication

Initiation of adenovirus DNA replication is strongly enhanced by two transcription factors, nuclear factor I (NFI) and nuclear factor III (NFIII/oct-1). These proteins bind to two closely spaced recognition sequences in the origin. We produced NFI and NFIII/oct-1, as well as their biologically active, replication-competent DNA-binding domains (NFI-BD and the POU domain), in a vaccinia virus expression system and purified these polypeptides to apparent homogeneity. By DNase I footprinting and gel retardation, we show that the two proteins, as well as their purified DNA-binding domains, bind independently and without cooperative effects to their recognition sequences. By using a reconstituted system consisting of the purified viral proteins (precursor terminal protein-DNA polymerase complex (pTP-pol) and DNA-binding protein, we show that NFIII/oct-1 or the POU domain stimulates DNA replication in the absence of NFI or NFI-BD and vice versa. When added together, the enhancing effect of the two transcription factors was independent and nonsynergistic. Interestingly, stimulation by NFI or NFI-BD was strongly dependent on the concentration of the pTP-pol complex. At low pTP-pol concentrations, NFI or NFI-BD stimulated up to 50-fold, while at high concentrations, the stimulation was less than twofold, indicating that the need for NFI can be overcome by high pTP-pol concentrations. In contrast, stimulation by NFIII/oct-1 or the POU domain was much less dependent on the pTP-pol concentration. These data support a model in which NFI enhances initiation through an interaction with pTP-pol. Glutaraldehyde cross-linking experiments indicate contacts between pTP-pol and NFI but not NFIII/oct-1. The site of interaction is located in the NFI-BD domain.
New Genotype of Avian Influenza H5N1 Viruses Isolated from Tree Sparrows in China

ABSTRACT The 2004 outbreaks of highly pathogenic avian influenza H5N1 disease in China led to a great poultry loss and society attention. A survey of avian influenza viruses was conducted on tree sparrows (Passer montanus) collected in China in 2004. Four viruses were isolated from free-living tree sparrows. The results of the whole-genome analysis indicated that an H5N1 virus with a new genotype is circulating among tree sparrows. The hemagglutinin and neuraminidase genes of the new genotype were derived from Gs/Gd/96-like viruses and the nuclear protein gene descended from the 2001 genotype A H5N1 viruses, while the other inner genes originated from an unknown influenza virus. In experimental infection, all four viruses were highly pathogenic to chickens but not pathogenic to ducks or mice. The four tree sparrow viruses were different from the 2003 tree sparrow strain (genotype Z) in Hong Kong. The results suggested that H5N1 viruses might be distributed widely in tree sparrows.
Metabolic syndrome, testosterone deficiency and erectile dysfunction never come alone

Until a decade ago the ailments of elderly men, such as atherosclerosis, hypertension, diabetes mellitus, lower urinary tract symptoms and erectile dysfunction (ED), were regarded as distinct diagnostic/therapeutic entities but there is a growing awareness that these entities are not disparate and, to improve the health of the ageing male, require an integral approach. There is an inter‐dependence between the metabolic syndrome, ED and patterns of testosterone in ageing men. The main features of the metabolic syndrome are abdominal obesity, insulin resistance, hypertension and dyslipidaemia, significant factors in the aetiology of erectile function. The metabolic syndrome is associated with lower‐than‐normal testosterone levels. A new concept of the role of testosterone in male physiology suggests that testosterone plays also a significant role in the development and maintenance of bone and muscle mass and is a determinant of glucose homeostasis and lipid metabolism. Testosterone is not only a factor in libido but exerts also essential effects on the anatomical and physiological substrate of penile erection. With these recent insights, the health problems of elderly men must be placed in a context that allows an integral approach. Treatment of testosterone deficiency is to become part and parcel of this approach.
GATA-3 significantly downregulates IFN-gamma production from developing Th1 cells in addition to inducing IL-4 and IL-5 levels.

IL-12 and IL-4 are dominant factors driving the development of Th1 and Th2 cells, respectively, by their activation of Stat-4 and Stat-6 signaling molecules. Activation of Stat factors, although specific, is a rapid event; however, differentiation of Th cells takes place over several days. Thus, it is unlikely that the expression of effector cytokines is mediated solely by Stat factors. Recently there have been indications that link other molecular factors to Th subset development. The transcription factor GATA-3 is selectively expressed in Th2 cells and has been shown to induce the expression of Th2 cytokines in developing Th1 cells. Using retroviral infection of naive T cells to introduce GATA-3 cDNA, we measured its direct effects on the development of Th1 cytokine production. We now show that ectopic expression of GATA-3 in developing Th1 cells significantly inhibits IFN-gamma, as well as enhancing IL-4 and IL-5 production. Furthermore, GATA-3 inhibits production of IFN-gamma by developing Th1 cells in the complete absence of IL-4. Thus, antagonism of Th1 development by GATA-3 may facilitate rapid divergence of Th subsets toward a Th2 phenotype in concert with other factors.
Arabidopsis CYP98A3 Mediating Aromatic 3-Hydroxylation. Developmental Regulation of the Gene, and Expression in Yeast1

The general phenylpropanoid pathways generate a wide array of aromatic secondary metabolites that range from monolignols, which are ubiquitous in all plants, to sinapine, which is confined to crucifer seeds. The biosynthesis of these compounds involves hydroxylated and methoxylated cinnamyl acid, aldehyde, or alcohol intermediates. Of the three enzymes originally proposed to hydroxylate the 4-, 3-, and 5-positions of the aromatic ring, cinnamate 4-hydroxylase (C4H), which converts trans-cinnamic acid top-coumaric acid, is the best characterized and is also the archetypal plant P450 monooxygenase. Ferulic acid 5-hydroxylase (F5H), a P450 that catalyzes 5-hydroxylation, has also been studied, but the presumptive 3-hydroxylase converting p-coumarate to caffeate has been elusive. We have found that Arabidopsis CYP98A3, also a P450, could hydroxylate p-coumaric acid to caffeic acid in vivo when expressed in yeast (Saccharomyces cerevisiae) cells, albeit very slowly.CYP98A3 transcript was found in Arabidopsis stem and silique, resembling both C4H and F5Hin this respect. CYP98A3 showed further resemblance toC4H in being highly active in root, but differed fromF5H in this regard. In transgenic Arabidopsis, the promoters of CYP98A3 and C4H showed wound inducibility and a comparable developmental regulation throughout the life cycle, except in seeds, where the CYP98A3 promoter construct was inactive while remaining active in silique walls. Within stem and root tissue, the gene product and the promoter activity ofCYP98A3 were most abundant in lignifying cells. Collectively, these studies show involvement of CYP98A3 in the general phenylpropanoid metabolism, and suggest a downstream function for CYP98A3 relative to the broader and upstream role of C4H.