Miracle-dz/UniFAR-FTUs huggingface dataset:
Two Adjacent Protein Binding Motifs in the cbh2(Cellobiohydrolase II-encoding) Promoter of the Fungus Hypocrea jecorina (Trichoderma reesei) Cooperate in the Induction by Cellulose*

The cellulase system of the filamentous fungusHypocrea jecorina (Trichoderma reesei) consists of several cellobiohydrolases, endoglucanases, and β-glucosidases, encoded by separate genes, which are coordinately expressed in the presence of cellulose or the disaccharide sophorose. Using cell-free extracts from sophorose-induced and noninduced mycelia and various fragments of the cbh2 promoter of H. jecorinain electrophoretic mobility shift assay (EMSA) analysis and performingin vitro and in vivo footprinting analysis, we detected the nucleotide sequence 5′-ATTGGGTAATA-3′ (consequently namedcbh2-activating element (CAE)) to bind a protein complex with different migration in EMSA of induced and noninduced cell-free extracts. EMSA analysis, employing oligonucleotide fragments containing specifically mutated versions of CAE, revealed that protein binding requires the presence of an intact copy of either one of two adjacent motifs: a CCAAT (=ATTGG) box on the template strand and a GTAATA box on the coding strand, whereas a simultaneous mutation in both completely abolished binding. H. jecorina transformants, containing correspondingly mutated versions of the cbh2 promoter fused to the Escherichia coli hph gene as a reporter, expressed hph in a manner paralleling the efficacy of CAE-protein complex formation in EMSA, suggesting that the presence of either of both motifs is required for induction of cbh2gene transcription. Antibody supershift experiments with anti-HapC antiserum as well as EMSA competition experiments with CCAAT binding promoter fragments of the Aspergillus nidulans amdSpromoter suggest that the H. jecorina CCAAT box binding complex contains a homologue of HapC. The nature of the adjacent, GTAATA-binding protein(s) and its cooperation with the HapC homologue in cbh2 gene induction is discussed.
Calcium binding and allosteric signaling mechanisms for the sarcoplasmic reticulum Ca2+ ATPase

The sarcoplasmic reticulum Ca2+ ATPase (SERCA) is a membrane‐bound pump that utilizes ATP to drive calcium ions from the myocyte cytosol against the higher calcium concentration in the sarcoplasmic reticulum. Conformational transitions associated with Ca2+‐binding are important to its catalytic function. We have identified collective motions that partition SERCA crystallographic structures into multiple catalytically‐distinct states using principal component analysis. Using Brownian dynamics simulations, we demonstrate the important contribution of surface‐exposed, polar residues in the diffusional encounter of Ca2+. Molecular dynamics simulations indicate the role of Glu309 gating in binding Ca2+, as well as subsequent changes in the dynamics of SERCA's cytosolic domains. Together these data provide structural and dynamical insights into a multistep process involving Ca2+ binding and catalytic transitions.
Membrane ionic mechanisms activated by noradrenaline in cells isolated from the rabbit portal vein.

1. Membrane currents were recorded in cells freshly dispersed from the rabbit portal vein with patch pipette techniques in the whole‐cell configuration of recording. In potassium‐containing solutions at a holding potential of ‐50 mV noradrenaline usually evoked an inward current and enhanced greatly the outward current evoked by depolarizing voltage steps. 2. The ionic mechanism of the inward current was investigated in potassium‐free solutions in which the inward current elicited by noradrenaline was produced by an increase in membrane conductance. 3. In the first series of experiments NaCl was the main salt in the patch pipette solution (representing the intracellular milieu) and the ionic composition of the bathing solution was altered. In these conditions the reversal potential of the noradrenaline‐induced current was close to the chloride equilibrium potential (ECl). 4. When sodium glutamate was the major salt in the pipette solution the reversal potential of the noradrenaline‐evoked current was influenced by the cation rather than the anion gradient. 5. With 89 mM‐BaCl2 in the external solution (and sodium glutamate in the pipette) noradrenaline produced a membrane current with a reversal potential which was much more positive than ECl or ENa. These results indicate that noradrenaline opens a chloride‐selective channel and a cation channel which is permeable to monovalent and divalent cations. 6. Bath application of 10 mM‐caffeine evoked a membrane current with a reversal potential close to ECl with either NaCl or sodium glutamate in the pipette. This is interpreted to mean that the increase in membrane chloride conductance can occur as a consequence of a rise in intracellular calcium concentration. It is less evident that the cation channel is calcium activated.
Thermorudis pharmacophila sp. nov., a novel member of the class Thermomicrobia isolated from geothermal soil, and emended descriptions of Thermomicrobium roseum, Thermomicrobium carboxidum, Thermorudis peleae and Sphaerobacter thermophilus.

An aerobic, thermophilic and cellulolytic bacterium, designated strain WKT50.2T, was isolated from geothermal soil at Waikite, New Zealand. Strain WKT50.2T grew at 53-76 °C and at pH 5.9-8.2. The DNA G+C content was 58.4 mol%. The major fatty acids were 12-methyl C18 : 0 and C18 : 0. Polar lipids were all linked to long-chain 1,2-diols, and comprised 2-acylalkyldiol-1-O-phosphoinositol (diolPI), 2-acylalkyldiol-1-O-phosphoacylmannoside (diolP-acylMan), 2-acylalkyldiol-1-O-phosphoinositol acylmannoside (diolPI-acylMan) and 2-acylalkyldiol-1-O-phosphoinositol mannoside (diolPI-Man). Strain WKT50.2T utilized a range of cellulosic substrates, alcohols and organic acids for growth, but was unable to utilize monosaccharides. Robust growth of WKT50.2T was observed on protein derivatives. WKT50.2T was sensitive to ampicillin, chloramphenicol, kanamycin, neomycin, polymyxin B, streptomycin and vancomycin. Metronidazole, lasalocid A and trimethoprim stimulated growth. Phylogenetic analysis of 16S rRNA gene sequences showed that WKT50.2T belonged to the class Thermomicrobia within the phylum Chloroflexi, and was most closely related to Thermorudis peleae KI4T (99.6% similarity). DNA-DNA hybridization between WKT50.2T and Thermorudis peleae DSM 27169T was 18.0%. Physiological and biochemical tests confirmed the phenotypic and genotypic differentiation of strain WKT50.2T from Thermorudis peleae KI4T and other members of the Thermomicrobia. On the basis of its phylogenetic position and phenotypic characteristics, we propose that strain WKT50.2T represents a novel species, for which the name Thermorudis pharmacophila sp. nov. is proposed, with the type strain WKT50.2T ( = DSM 26011T = ICMP 20042T). Emended descriptions of Thermomicrobium roseum, Thermomicrobium carboxidum, Thermorudis peleae and Sphaerobacter thermophilus are also proposed, and include the description of a novel respiratory quinone, MK-8 2,3-epoxide (23%), in Thermomicrobium roseum.
Complexes of Nitric Oxide with Nucleophiles as Agents for the Controlled Biological Release of Nitric Oxide: Hemodynamic Effect in the Rabbit

Summary: Nitric oxide (NO) and drugs that generate NO are potent vasodilators. We investigated the in vivo vasodilator potential of a unique group of compounds that release NO spontaneously in solution, the NO/ nucleophile complexes. The hemodynamic effects of di-ethylamine/NO complex (DEA/NO) (half-life <3 min) and the spermine/NO complex (SPER/NO) (half-life <30 min) administered intravenously were compared with those of sodium nitroprusside in anesthetized New Zealand white rabbits. Arterial pressure and systemic vascular resistance decreased, but central venous pressure, pulmonary arterial pressure, heart rate, and thermodilution cardiac output did not change in association with any of the three drugs in the doses administered. The hemodynamic effects were dose dependent. As predicted from their rates of spontaneous NO release, DEA/NO is a short-acting vasodilator with a duration similar to that of sodium nitroprusside, whereas SPER/NO is a longer-acting agent with a significant hypotensive effect 30 min after bolus injection. DEA/NO was equipotent to sodium nitroprusside, causing significant reductions in blood pressure and systemic vascular resistance at the lowest dose tested (1.5 nmol/kg). The data indicate that the NO/nucleophile complexes have predictable vasorelaxant effects in vivo as well as in vitro and suggest that their amenability to facile structure-reactivity and structure-activity modification should allow the design of NO donor drugs for a variety of applications in cardiovascular pharmacology.
Metrological Characterization of a Method for Blood Pressure Estimation Based on Arterial Lumen Area Model

Accuracy of blood pressure (BP) measurement is a challenging issue in oscillometry. Most of the automated noninvasive BP monitors estimate BP from envelope of the measured oscillometric pulses. The peak and the trough of the oscillometric pulses are very sensitive to noise caused by breathing, heart-rate variability, motion artifacts, muscle contraction, and environmental noise. Therefore, accuracy of the estimated BP based on the oscillometric waveform envelopes is not reliable in some cases. Recently, employing a modeling approach to estimate BP, we obtained the accurate results for a set of healthy subjects. The method is based on the lumen area oscillations model and estimates BP by comparing the actual and corresponding simulated waveforms. The method’s accuracy worsened when we tested it on a broader range of healthy subjects, while a significant drop was observed when the method was used for patients with chronic cardiovascular diseases. The work presented in this paper represents an improved version of our previous approach. We tested the proposed method on both healthy subjects and patients with chronic cardiovascular diseases, and compared the results to two popular BP estimation algorithms: maximum amplitude algorithm and maximum/minimum slope algorithm. We observed up to 56.7% and 57.3% improvements in mean absolute error, 98.9% and 64.4% improvements in mean error, 50% and 59% improvements in standard deviation of errors, and up to 57.6% and 55.8% in measurement uncertainty for the estimated systolic and diastolic pressures, respectively.
Quality evaluation of pansharpening techniques on different land cover types

Nowadays, high spatial resolution remote sensing systems collect simultaneously a low resolution multispectral image plus a high resolution panchromatic image. The objective of pixel level fusion methods is to combine this information in order to obtain a new multispectral image that exhibits the spectral characteristics of the multispectral image and the spatial resolution of the panchromatic image. There are many image pansharpening methods that have been proposed in the literature however, in general, none of them exhibits the best performance for all type of images. Thus, in this paper we present a comparative analysis of different fusion methods applied over a database of Geoeye-1 images having different types of land covers. We have analyzed qualitatively and quantitatively the pansharpened images in order to select those methods providing the best performance to each particular type of cover.
An evaluation system based on concepts and components of end-user computing competency

In a computing environment, the computing capability of an end-user mostly influences the performance of individual business tasks. It needs the evaluation and management of end-user computing capability. This study presents an evaluation system that comprises an evaluation model, evaluation method and process. The evaluation model has four evaluation domains and evaluation items. The model construct was verified by factor analysis and reliability analysis through a pilot test. The application of the developed system was confirmed by applying it to evaluating the end-users in a computing environment and presenting its results. This system will contribute to developing a practical evaluation system and improving the end-user computing capability.
Ground deformation measurement with radar interferometry in Exupéry

The Exupery project funded by the German Federal Ministry of Education and Research is a multidisciplinary project aiming at setting-up an Early Response System (VFRS) for Volcanic Activity. The core of the system builds on established volcanic monitoring techniques such as seismicity, ground deformation, and remote sensing tools for gas measurements. A major novelty of this mobile system is the attempt of a direct inclusion of satellite based observations to deduce ground deformation, to detect hazardous gas emissions and to monitor thermal activity. Within the project, the study group at the Technical University of Munich and at the German Aerospace Center DLR is responsible for ground deformation measurements with satellite observations. Millimetric subsidence or uplift can be retrieved from SAR images by using interferometric techniques. The multi-frequency SAR data-set used for the test sites include three different sorts of band data, X-, C- and L-Band, respectively. Azores (Portugal) and Stromboli (Italy) were chosen for the test sites. The volcanic movements were measured with the differential phases and the measurement accuracy will be compared with on site measurements including GPS and ground based DInSAR measurements later for field campaign in Azores. The estimated deformation will be then incorporated into geophysical stress models to initialize, calibrate and, ultimately, improve the models. Our presentation gives a short overview of the Exupery project and presents first results from multi-wavelength InSAR data and different processing techniques such as PSI.
δ- and γ-Tocopherols, but not α-Tocopherol, Inhibit Colon Carcinogenesis in Azoxymethane-Treated F344 Rats

The cancer preventive activity of vitamin E has been extensively discussed, but the activities of specific forms of tocopherols have not received sufficient attention. Herein, we compared the activities of δ-tocopherol (δ-T), γ-T, and α-T in a colon carcinogenesis model. Male F344 rats, seven weeks old, were given two weekly subcutaneous injections of azoxymethane (AOM) each at a dose of 15 mg/kg body weight. Starting 1 week before the AOM injection, the animals were maintained on a modified AIN76A diet, or the same diet containing 0.2% of δ-T, γ-T, α-T, or a γ-T-rich mixture of tocopherols (γ-TmT), until the termination of the experiment at 8 weeks after the second AOM injection. δ-T treatment showed the strongest inhibitory effect, decreasing the numbers of aberrant crypt foci by 62%. γ-T and γ-TmT were also effective, but α-T was not. Immunohistochemical analysis showed that δ-T and γ-T treatments reduced the levels of 4-hydroxynonenal and nitrotyrosine and the expression of cyclin D1 in the colon, preserved the expression of PPAR-γ, and decreased the serum levels of prostaglandin E2 and 8-isoprostane. Supplementation with 0.2% δ-T, γ-T, or α-T increased the respective levels of tocopherols and their side-chain degradation metabolites in the serum and colon tissues. Rather high concentrations of δ-T and γ-T and their metabolites were found in colon tissues. Our study provides the first evidence for the much higher cancer preventive activity of δ-T and γ-T than α-T in a chemically induced colon carcinogenesis model. It further suggests that δ-T is more effective than γ-T. Cancer Prev Res; 5(4); 644–54. ©2012 AACR.
Genetic analysis of the attenuator of the Rhizobium meliloti trpE(G) gene

It was previously reported that transcription of the Rhizobium meliloti trpE(G) gene starts at the adenine residue of the AUG codon of the leader peptide coding sequence (trpL), suggesting that translation of the trpL sequence starts without the Shine-Dalgarno sequence. We constructed mutations replacing the AUG codon of the trpL sequence with AAG or ACG. These mutations reduced the expression of a trpL'-'lacZ fusion gene to 0.1 and 0.2% of the wild-type level, respectively, indicating that the AUG codon is the translation initiation codon for the trpL coding sequence. In addition, these mutations, as well as a mutation converting the eighth codon (UCG) of the trpL sequence to UGA, abolished regulation by attenuation when introduced upstream of the tandem tryptophan codons in a trpE'-'lacZ fusion. Mutations affecting the stability of the probable antiterminator and terminator secondary structures in trpL mRNA were also constructed. Studies using these mutations indicate that the attenuator of R. meliloti functions in a way analogous to that of the Escherichia coli trp attenuator.
Membrane Processes

This review, for literature published in 2017, contains information related to membrane processes for municipal and industrial applications. This review is a subsection of the Treatment Systems section of the annual Water Environment Federation literature review and covers the following topics: membrane bioreactor (MBR) configuration, design, nutrient removal, operation, industrial treatment, anaerobic membrane systems, reuse, microconstituents removal, membrane technology advances, membrane fouling, and modeling. Other sub‐sections of the Treatment Systems section that might relate to this literature review include: Biological Fixed‐Film Systems, Activated Sludge and Other Aerobic Suspended Culture Processes, Anaerobic Processes, and Water Reclamation and Reuse. The following sections might also have related information on membrane processes: Industrial Wastes, Hazardous Wastes, and Fate and Effects of Pollutants.
Prenatal Diagnosis for β-Thalassemia Major in the Iranian Province of Hormozgan

β-Thalassemias are a group of heterogenous recessive disorders common in many parts of the world. Despite the great advances in the treatment of thalassemia, there is so far no cure, but perhaps bone marrow transplantation (BMT) is a possibility. Prevention, using prenatal diagnosis and selective abortion in the cases where the fetus is found to be affected, should be considered as a sensible alternative. During the past 5 years, 112 couples have been referred to our Center for detection of their β-thalassemia (β-thal) carrier status. In this group, common and rare mutations were detected. Of these, 106 couples (94.6%) came for counseling during pregancy and six (5.4%) came before becoming pregnant. Prenatal diagnosis was performed for the 106 couples at risk. Fetal DNA was obtained from both chorionic villus sampling (CVS) (99) and amniotic fluid (7). Using reverse hybridization, 64 (60.4%) were found to be heterozygous for a β-thal mutation and 24 (22.6%) were normal. Eighteen (17.0%) were found to carry an affected fetus and these pregnancies were terminated.
Rice FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (OsFKF1) promotes flowering independent of photoperiod.

In the facultative long-day (LD) plant Arabidopsis thaliana, FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) is activated by blue light and promotes flowering through the transcriptional and post-translational regulation of CONSTANS under inductive LD conditions. By contrast, the facultative short day (SD) plant rice (Oryza sativa) flowers early under inductive SD and late under non-inductive LD conditions; the regulatory function of OsFKF1 remains elusive. Here we show that osfkf1 mutants flower late under SD, LD and natural LD conditions. Transcriptional analysis revealed that OsFKF1 up-regulates the expression of the floral activator Ehd2 and down-regulates the expression of the floral repressor Ghd7; these regulators up- and down-regulate Ehd1 expression, respectively. Moreover, OsFKF1 can up-regulate Ehd1 expression under blue light treatment, without affecting the expression of Ehd2 and Ghd7. In contrast to the LD-specific floral activator Arabidopsis FKF1, OsFKF1 likely acts as an autonomous floral activator because it promotes flowering independent of photoperiod, probably via its distinct roles in controlling the expression of rice-specific genes including Ehd2, Ghd7 and Ehd1. Like Arabidopsis FKF1, which interacts with GI and CDF1, OsFKF1 also interacts with OsGI and OsCDF1 (also termed OsDOF12). Thus, we have identified similar and distinct roles of FKF1 in Arabidopsis and rice.
An optimized electroporation protocol applicable to a wide range of cell lines.

A number of transfection methods for mammalian cells are available; however, many cell lines may appear resistant to efficient transfection, or at best, necessitate lengthy optimization procedures in recommended protocols. We describe here an electroporation protocol that yields highly efficient gene transfer (20%-100% of surviving cells) in all 19 cell lines tested so far, including lymphoid, myeloid, glial, fibroblast and COS cells. Unlike earlier electroporation protocols, adaptation of this protocol to a cell line of interest only requires the optimization of a single parameter, i.e., the voltage, and can be performed within a day. Furthermore, it is also superior to transfection protocols for other methods (calcium phosphate precipitation, lipofection, DEAE-dextran transfection and transferrinfection) in terms of reproducibility, economy and average transfection efficiency for a wide variety of cell lines.
The influence of personality factors on disease progression and health‐related quality of life in people with ALS

We aimed to perform a prospective long‐term follow‐up of health‐related quality of life (QOL) in ALS and to investigate the relationship of personality factors with changes in QOL and disease progression. Data on QOL were collected prospectively for 12 months from 31 ALS patients. Personality factors were studied using the NEO‐FFI (NEO Five Factor Inventory). Monthly self‐ratings of global QOL, and seven health‐related QOL functions, as well as ALSFRS (ALS Functional Rating Scale) scores were analyzed using a linear mixed model approach. QOL and ALSFRS scores decreased during follow‐up. Patients who scored higher on the agreeableness personality dimension, despite similar total duration of disease, had higher QOL at the beginning of the follow‐up period but the reduction of QOL over time was significantly steeper than in patients who scored lower on agreeableness, associated with faster disease progression. These findings suggest that being less agreeable might serve as a protective factor with respect to QOL and disease progression in ALS.
Miniaturized Gysel Power Divider Based on Composite Right/Left-Handed Transmission Lines

A miniaturized Gysel power divider (PD) is developed by using composite right-/left-handed (CRLH) transmission lines (TLs) consisting of microstrip lines and lumped elements. The theoretical closed-form design equations are presented to calculate the element values of the CRLH TLs. For verification purpose, a miniaturized Gysel PD based on CRLH TLs for GSM frequency of 900 MHz is designed, simulated, fabricated, and measured. The proposed Gysel CRLH TL PD is extremely compact, occupying only 18.2% of the conventional microstrip line-based Gysel PD. Less than 1 dB insertion loss has been achieved at the center frequency. Also, the simulated results agree well with the measured results.