Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcription of [FeFe]-Hydrogenase Genes during H2 Production in Clostridium and Desulfovibrio spp. Isolated from a Paddy Field Soil

Changes in the relative abundances of the transcripts of hydA gene paralogs for [FeFe]-hydrogenase in Clostridium sp. strain H2 and Desulfovibrio sp. strain A1 isolated from paddy field soil were analyzed during H2 production. Strains H2 and A1 had at least five and two phylogenetically different hydA genes, respectively. The relative abundances of their hydA transcripts differed among the paralogs and H2 production activity changed in a manner that depended on the growth phase and conditions. Increases or decreases in the relative abundances of the transcripts of two out of five hydA genes in strain H2 correlated with changes in H2 production rates, whereas those of the others remained unchanged or decreased. In strain A1, the relative abundances of the transcripts of two hydA genes differed between monoculture, sulfate-reducing, and syntrophic, methanogenic conditions. The relative abundance of the transcripts of one hydA gene, predicted to encode a cytosolic [FeFe]-hydrogenase, was higher under syntrophic, methanogenic conditions than sulfate-reducing conditions, while that of the transcripts of the other hydA gene decreased with time under both conditions. This study showed that the transcription of the hydA gene during growth with active H2 production was differently regulated among the paralogs in H2 producers isolated from paddy field soil.
Performance comparison of forecasting models applied to LAN/MAN traffic prediction

The literature of network traffic analysis has successfully investigated several sophisticated models to be used in computer network traffic forecasting. Although these models have shown very good results in many controlled studies, the complexity of their implementation may be an important factor for preventing their large adoption in real production environment. We advocate that simpler forecasting models can also show very good accuracy — similar to the complex ones — for real scenarios of LAN/MAN network traffic, and being less intricate to implement and deploy in practical network management applications. In this paper we investigate the goodness of fit of nine classic forecast models applied to IP traffic samples drawn from real networks. The obtained results support our hypothesis given that the simpler investigated models demonstrate prediction accuracy very close to the advanced models for the studied scenarios.
Assessment of Erythropoietin Levels and Some Iron Indices in Chronic Renal Failure and Liver Cirrhosis Patients

This study was constructed to investigate the relationship between renal anaemia and erythropoietin (EPO) concentrations in chronic renal failure (CRF) patients and to evaluate the possible role of the liver. Serum EPO levels were measured in blood samples from 20 CRF patients on hemodialysis (HD), 20 liver cirrhosis (LC) patients, 20 patients having both CRF and LC and undergoing HD, and 20 normal control subjects. Blood cell counts, iron indices (iron, total iron-binding capacity (TIBC) and ferritin), renal function (blood urea nitrogen (BUN) and creatinine), hepatic function (ALT, AST, ALP and bilirubin) investigations were carried out for all the subjects enrolled in this study. CRF patients without LC had serum EPO concentration of 6.21 ± 0.53 mU/ml (mean ± SE), which was significantly higher than that in patients having both CRF and LC (4.32 ± 0.52) (p < 0.01). Both groups showed significantly lower values than the controls (12.75 ± 0.70) (p < 0.001). LC patients with intact kidneys had significantly higher EPO level (22.70 ± 1.70) (p < 0.001). No correlation was found between EPO level and any of the hematologic or iron indices.
CIS‐diamminedichloroplatinum(II) inhibits p34cdc2 protein kinase in human lung‐cancer cells

cis‐Diamminedichloroplatinum(II) (CDDP) induced G2‐phase arrest in PC‐9 human cancer cells. To elucidate how CDDP acts on cell‐cycle regulation, we analyzed the effect of CDDP on cell‐cycle regulators such as p34cdc2 protein kinase. p34cdc2 protein kinase activity was maximum in G2 phase and decreased after G2/M transition in synchronized PC‐9 human lung cancer cells. Evidence for a phosphorylated p34cdc2 protein kinase complexed with cyclin B was obtained from cells in G2 phase and the p34cdc2 protein kinase appeared to be dephosphorylated at M phase. After exposure to CDDP in G, phase, PC‐9 cells were arrested in G2 phase. The activation of p34cdc2 protein kinase was inhibited by CDDP. Cyclin A and wee‐1 kinase were not affected by the exposure to CDDP. Cyclin B was degraded in M phase in PC‐9 cells. Exposure to CDDP did not affect the degradation of cyclin B. Our data suggest that the effect of CDDP on cell‐cycle phase might be regulated by the dephosphorylation of p34cdc2 protein kinase. To determine whether the p34cdc2 protein kinase is a primary target for CDDP, we examined the direct effect of CDDP on tyrosine dephosphorylation of p34cdc2 protein kinase in cellular extracts. Cell lysates from synchronized PC‐9 in G2 phase were immunoprecipitated with p 13‐Sepharose beads. In vitro dephosphorylation of phosphotyrosine of p34cdc2 protein kinase was observed after exposure to okadaic acid in a concentration‐dependent manner. The dephosphorylation of p34cdc2 protein kinase by okadaic acid was inhibited by CDDP. We hypothesize that inhibition of p34cdc2 dephorphorylation by CDDP is important for its growth‐inhibiting properties.
Low Turn-On Voltage and High-Current $\hbox{InP}/ \hbox{In}_{0.37}\hbox{Ga}_{0.63}\hbox{As}_{0.89}\hbox{Sb}_{0.11}/\hbox{In}_{0.53}\hbox{Ga}_{0.47}\hbox{As}$  Double Heterojunction Bipolar Transistors

We report on the dc and microwave characteristics of an InP/In<sub>0.37</sub>Ga<sub>0.63</sub>As<sub>0.89</sub>Sb<sub>0.11</sub>/In<sub>0.53</sub>Ga<sub>0.47</sub>As double heterojunction bipolar transistor grown by solid-source molecular beam epitaxy. The pseudomorphic In<sub>0.37</sub>Ga<sub>0.63</sub>As<sub>0.89</sub>Sb<sub>0.11</sub> base reduces the conduction band offset DeltaE<sub>C</sub> at the emitter/base junction and the base band gap, which leads to a very low V<sub>BE</sub> turn-on voltage of 0.35 V at 1 A/cm<sup>2</sup>. A current gain of 125 and a peak f<sub>T</sub> of 238 GHz have been obtained on the devices with an emitter size of 1times10 mum<sup>2</sup>, suggesting that a high collector average velocity and a high current capability are achieved due to the type-II lineup at the InGaAsSb/InGaAs base/collector junction.
Identification of a New Chloroplast Carbonic Anhydrase in Chlamydomonas reinhardtii1

Carbonic anhydrases (CA) are zinc-containing metalloenzymes that catalyze the reversible hydration of CO2. The three evolutionarily unrelated families of CAs are designated α-, β-, and γ-CA. Aquatic photosynthetic organisms have evolved different forms of CO2 concentrating mechanisms (CCMs) to aid Rubisco in capturing CO2 from the surrounding environment. One aspect of all CCMs is the critical roles played by various specially localized extracellular and intracellular CAs. Five CAs have previously been identified in Chlamydomonas reinhardtii, a green alga with a well-studied CCM. Here we identify a sixth gene encoding a β-type CA. This new β-CA, designated Cah6, is distinct from the two mitochondrial β-CAs in C. reinhardtii. Nucleotide sequence data show that the Cah6 cDNA contains an open reading frame encoding a polypeptide of 264 amino acids with a leader sequence likely targeting the protein to the chloroplast stroma. We have fused the Cah6 open reading frame to the coding sequence of maltose-binding protein in a pMal expression vector. The purified recombinant fusion protein is active and was used to partially characterize the Cah6 protein. The purified recombinant fusion protein was cleaved with protease Factor Xa to separate Cah6 from the maltose-binding protein and the purified Cah6 protein was used to raise an antibody. Western blots, immunolocalization studies, and northern blots collectively indicated that Cah6 is constitutively expressed in the stroma of chloroplasts. A possible role for Cah6 in the CCM of C. reinhardtii is proposed.
Single-photon imaging in complementary metal oxide semiconductor processes

This paper describes the basics of single-photon counting in complementary metal oxide semiconductors, through single-photon avalanche diodes (SPADs), and the making of miniaturized pixels with photon-counting capability based on SPADs. Some applications, which may take advantage of SPAD image sensors, are outlined, such as fluorescence-based microscopy, three-dimensional time-of-flight imaging and biomedical imaging, to name just a few. The paper focuses on architectures that are best suited to those applications and the trade-offs they generate. In this context, architectures are described that efficiently collect the output of single pixels when designed in large arrays. Off-chip readout circuit requirements are described for a variety of applications in physics, medicine and the life sciences. Owing to the dynamic nature of SPADs, designs featuring a large number of SPADs require careful analysis of the target application for an optimal use of silicon real estate and of limited readout bandwidth. The paper also describes the main trade-offs involved in architecting such chips and the solutions adopted with focus on scalability and miniaturization.
Multi-Level Linear Location Tree for Efficient Sequential Pattern Mining

Discovering sequential patterns from a large database of sequences is an important problem in the field of knowledge discovery and data mining. Most of the previously used sequential pattern mining data structure follows a complex hash-tree structure which has poor locality. Since the hash-tree uses the repetition of a simple search instead of a consecutive search, the hash-based sequential pattern mining, though it reduces search time, may exhibit low performance. In this paper, we propose a novel multi-level linear location tree (or MLLT in short) with an excellent locality structure and develop an efficient MLLT-tree based sequential pattern mining algorithm for mining the complete set of frequent sequence by linear copy of nodes. Our performance study shows that MLLT runs considerably faster than the hash-tree based GSP algorithm.
Frequency scalable video coding using the MDCT

Efficient video coding incorporating motion compensation and overlapped transforms requires different coding architectures and methods of motion estimation to those used in traditional DCT block based coding schemes. In this paper a transform domain motion estimation procedure is proposed for the MDCT. This method of motion estimation, while performed in the spatial domain, is equivalent to minimising the sum square error of transform coefficients. The application of the MDCT to frequency scalable video coding is investigated. A performance advantage is achieved over an equivalent DCT based coder for both the reconstructed low resolution and high resolution sequences of an open loop frequency scalable video coder. <<ETX>>
Proceedings of International Conference on Microwave-08 Design and Simulation of Dielectric Tapered Rod as Feed for Dielectric Lens Antenna at 140 GHz

2 Abstract The paper discusses the design of dielectric rod antenna at D band which can be used as a feed for dielectric lens antennas. This feed replaces the metallic corrugated I dual mode horns which are difficult to fabricate at these frequencies. Tapering of dielectric rod has been done to achieve low side lobe level. The designed antenna has been simulated on 3D EM software HFSS (High Frequency Structure Simulator). The designed antenna has symmetrical azimuth and elevation beam width and having very low cross polarization. The simulated results show very good agreement with the designed parameters. Index Terms Corrugated horn, dielectric lens, dielectric constant, dual mode horn, Side lobes.
Analysis of interactive image technologies

Interactive images can increase the popularity of some existing technologies. Although the most popular way to create interactive images is using the already popular maps engines, there is a large number of available options. In this paper, we analyze several Maps APIs and evaluate the most suitable API for interactive images regarding its usability, accessibility and performance. The result is that the Google Maps API, Leaflet, and Open Layers are solutions that can be easily fit for use in interactive images. Nevertheless, if the users tend to have a full control of these APIs they should stick to the open source solutions since their opponents require API keys and are free of charge for a limited time only.
Nimodipine in Animal Model Experiments of Focal Cerebral Ischemia: A Systematic Review

Background and Purpose— Based on the results of animal experiments, clinical trials were performed with nimodipine, which did not demonstrate a beneficial effect on outcome after stroke. The aim of this study was to determine whether the evidence from animal experiments with nimodipine supported the use of nimodipine in clinical trials. Methods— We performed a systematic review of animal experiments with nimodipine in focal cerebral ischemia. Studies were identified by searching Medline and Embase. We assessed whether these studies showed a beneficial effect of active treatment. In-depth analyses were performed on infarct size and amount of edema, and subgroup analyses were performed on the length of the time window to the initiation of treatment and the methodological quality of the studies. Results— Of 225 identified articles, 20 studies were included. The methodological quality of the studies was poor. Of the included studies, 50% were in favor of nimodipine. In-depth analyses showed statistically significant effects in favor of treatment (10 studies). No influence of the length of time to the initiation of treatment or of the methodological quality on the results was found. Conclusions— We conclude that the results of this review did not show convincing evidence to substantiate the decision to perform trials with nimodipine in large numbers of patients. There were no differences between the results of the animal experiments and clinical studies. Surprisingly, we found that animal experiments and clinical studies ran simultaneously.
Data Quality in Genome Databases

: Genome databases store data about molecular biological entities such as genes, proteins, diseases, etc. The main purpose of creating and maintaining such databases in commercial organizations is their importance in the process of drug discovery. Genome data is analyzed and interpreted to gain so-called leads , i.e., promising structures for new drugs. Following a lead through the process of drug development, testing, and finally several stages of clinical trials is extremely expensive. Thus, an underlying high quality data-base is of utmost importance. Due to the exploratory nature of genome databases, commercial and public, they are inaccurate, incomplete, outdated and in an overall poor state. This paper highlights the important challenges of determining and improving data quality for databases storing molecular biological data. We examine the production process for genome data in detail and show that producing incorrect data is intrinsic to the process at the same time highlight common types of data errors. We compare these error classes with existing solutions for data cleansing and come to the conclusion that traditional and proven data cleansing techniques of other application domains do not suffice for the particular needs and problem types of genomic databases.
Differences in the Bioenergetic Response of the Isolated Perfused Rat Heart to Selective &bgr;1- and &bgr;2-Adrenergic Receptor Stimulation

Background—In the heart, striking functional differences exist after stimulation of the &bgr;1- and &bgr;2-adrenergic receptor (AR) subtypes. These may be linked to differences in metabolic response during &bgr;1- and &bgr;2-AR stimulation. Methods and Results—The relation between work and metabolism was examined during selective &bgr;1- and &bgr;2-AR stimulation (&bgr;1 and &bgr;2 groups, respectively) in the isolated perfused rat heart. Measurements were made of rate-pressure product (RPP=LV developed pressure × heart rate), phosphorus-containing metabolites, and pH by 31P nuclear magnetic resonance spectroscopy and of O2 consumption by fiber-optic oximetry. Experiments were performed under high constant flow (HCF) and under flow-limiting conditions (constant pressure, CP). Despite substantially greater RPP increases relative to baseline during &bgr;1-AR (HCF, 475%; CP, 150%) than &bgr;2-AR (HCF, 90%; CP, 72%) stimulation, the relative decrease in the intracellular energy charge relative to baseline was similar for the &bgr;1 (HCF, 49%; CP, 64%) and &bgr;2 (HCF, 59%; CP, 55%) groups. For each group, an increase in oxygen consumption (M&OV0312;o2) occurred commensurate with workload during HCF (&bgr;1, 141%; &bgr;2, 30%). During CP, however, the M&OV0312;o2 increase was similar (&bgr;1, 39%; &bgr;2, 34%), despite the large RPP difference between the groups. During both protocols, there was greater acidosis during &bgr;1-AR than during &bgr;2-AR stimulation. Thus, at a given workload, intracellular energy charge decreased, and M&OV0312;o2 (CP) increased to a greater extent during &bgr;2 than &bgr;1-AR stimulation. Conclusions—The bioenergetic differences are consistent with access to an additional substrate pool during &bgr;1-AR stimulation. This may occur via increased glycogenolysis during &bgr;1-AR stimulation, facilitating increased energy production by oxidative phosphorylation, and under flow-limiting conditions, anaerobic glycolysis.
TB±tree: Index structure for Information Retrieval Systems

Information Retrieval Systems (IR) is using different indexing techniques to retrieve information such as, Inverted files, and Signature files. However, Signature files are suitable for small IR systems due to its slow response, while inverted file have better response time but its space overhead is high. Moreover, inverted files use B±trees for single-word queries. In this paper, a new indexing structure called TB±tree to be used in the design of inverted files for large information retrieval systems. The TB±tree is a variant of the B±tree that supports single key-word queries and phrase queries efficiently. In TB±tree algorithms which represent each key-word stored in the index by a numeric value, and this numeric value can be used as encryption and inforce security. The numeric value for each keyword is stored in binary format, which may reduce the size of the index file by 19%. The records in TB±tree may be of variable length.
Can we avoid treatment interruption studies in the search for an HIV cure?

Although combined antiretroviral therapy (cART) is able to achieve sustained control of viral replication in blood plasma and to significantly reduce HIV-associated mortality and morbidity, it cannot, to date, yield viral eradication. Indeed, during the earliest phases of primary HIV infection (PHI), HIV establishes a reservoir in its target cells, particularly in the CD4þ memory T-cell subsets [1,2]. The half-life of these latent cells can reach up to several years and supplies to the persistence of the infection. cART has small or no impact on this cellassociated HIV-DNA (CA-HIV-DNA) even after several years of sustained viral suppression [3,4]. In addition, anatomical sites, such as the male genital tract [5,6] and the central nervous system [7], may also act as viral sanctuaries, contributing to HIV persistence despite cART, partly because of the poor penetration of antiretroviral drugs in these anatomical compartments [8]. Thus, cART is a life-long treatment for people living with HIV (PLHIV). Although new generation antiretroviral drugs are more potent, better tolerated, and with a lower pill burden, concerns still remain about long-term toxicity of these drugs, the need for long-term adherence to cART to avoid the emergence of HIV resistance, and cost issues, especially in low-income countries with a high prevalence of PLHIV. Thus, one of the major goals of researchers in the field of HIV infection is the evaluation of new strategies to achieve a cART-free remission of HIV infection. In this issue, Li et al. [9]
Cardiovascular disease and type 2 diabetes in evolutionary perspective: A critical role for helminths?

Heart disease and type 2 diabetes are commonly believed to be rare among contemporary subsistence-level human populations, and by extension prehistoric populations. Although some caveats remain, evidence shows these diseases to be unusual among well-studied hunter-gatherers and other subsistence populations with minimal access to healthcare. Here we expand on a relatively new proposal for why these and other populations may not show major signs of these diseases. Chronic infections, especially helminths, may offer protection against heart disease and diabetes through direct and indirect pathways. As part of a strategy to insure their own survival and reproduction, helminths exert multiple cardio-protective effects on their host through their effects on immune function and blood lipid metabolism. Helminths consume blood lipids and glucose, alter lipid metabolism, and modulate immune function towards Th-2 polarization—which combined can lower blood cholesterol, reduce obesity, increase insulin sensitivity, decrease atheroma progression, and reduce likelihood of atherosclerotic plaque rupture. Traditional cardiometabolic risk factors, coupled with the mismatch between our evolved immune systems and modern, hygienic environments may interact in complex ways. In this review, we survey existing studies in the non-human animal and human literature, highlight unresolved questions and suggest future directions to explore the role of helminths in the etiology of cardio-metabolic disease.
Congenital idiopathic hypogonadotropic hypogonadism: evidence of defects in the hypothalamus, pituitary, and testes.

CONTEXT Idiopathic hypogonadotropic hypogonadism (IHH) with normal smell (normosmic IHH) or anosmia (Kallmann syndrome) is associated with defects in the production or action of GnRH. Accordingly, most IHH patients respond to physiological pulsatile GnRH replacement by normalizing serum LH, FSH, and testosterone (T) levels and achieving gametogenesis; some patients, however, show atypical responses. Interestingly, several IHH-associated genes are expressed in multiple compartments of the hypothalamic-pituitary-gonadal axis. OBJECTIVE The aim of the study was to investigate whether the clinical, biochemical, or genetic characteristics of IHH men with atypical responses to GnRH indicate alternative or additional defects in the hypothalamic-pituitary-gonadal axis. SUBJECTS We studied 90 IHH men undergoing long-term pulsatile GnRH treatment over 30 yr. DESIGN AND SETTING We conducted a retrospective study of response to GnRH at a Clinical Research Center. INTERVENTIONS Physiological regimens of pulsatile s.c. GnRH were administered for at least 12 months. Dose-response studies using i.v. GnRH pulses assessed the pituitary LH response. MAIN OUTCOME MEASURES We measured serum T, LH, FSH, and inhibin B levels, sperm in ejaculate, and determined the sequence of IHH-associated genes. RESULTS Twenty-six percent of subjects displayed atypical responses to GnRH: 1) 10 remained hypogonadotropic and hypogonadal, demonstrating pituitary and testicular defects; 2) eight achieved spermatogenesis and normal T but only with hypergonadotropism, indicating impaired testicular responsiveness to gonadotropins; and 3) five remained azoospermic despite achieving adult testicular volumes and normal hormonal profiles, suggesting primary defects in spermatogenesis. Mutations were identified only in KAL1 across groups. CONCLUSION In addition to hypothalamic GnRH deficiency, IHH men can have primary pituitary and/or testicular defects, which are unmasked by GnRH replacement.