Miracle-dz/UniFAR-FTUs huggingface dataset:
Escherichia coli Thioredoxin-like Protein YbbN Contains an Atypical Tetratricopeptide Repeat Motif and Is a Negative Regulator of GroEL*

Many proteins contain a thioredoxin (Trx)-like domain fused with one or more partner domains that diversify protein function by the modular construction of new molecules. The Escherichia coli protein YbbN is a Trx-like protein that contains a C-terminal domain with low homology to tetratricopeptide repeat motifs. YbbN has been proposed to act as a chaperone or co-chaperone that aids in heat stress response and DNA synthesis. We report the crystal structure of YbbN, which is an elongated molecule with a mobile Trx domain and four atypical tetratricopeptide repeat motifs. The Trx domain lacks a canonical CXXC active site architecture and is not a functional oxidoreductase. A variety of proteins in E. coli interact with YbbN, including multiple ribosomal protein subunits and a strong interaction with GroEL. YbbN acts as a mild inhibitor of GroESL chaperonin function and ATPase activity, suggesting that it is a negative regulator of the GroESL system. Combined with previous observations that YbbN enhances the DnaK-DnaJ-GrpE chaperone system, we propose that YbbN coordinately regulates the activities of these two prokaryotic chaperones, thereby helping to direct client protein traffic initially to DnaK. Therefore, YbbN may play a role in integrating the activities of different chaperone pathways in E. coli and related bacteria.
A Phase I Trial of Vorinostat and Alvocidib in Patients with Relapsed, Refractory, or Poor Prognosis Acute Leukemia, or Refractory Anemia with Excess Blasts-2

Purpose: This phase I study was conducted to identify the maximum-tolerated dose (MTD) of alvocidib when combined with vorinostat in patients with relapsed, refractory, or poor prognosis acute leukemia, or refractory anemia with excess blasts-2. Secondary objectives included investigating the pharmacokinetic and pharmacodynamic effects of the combination. Experimental Design: Patients received vorinostat (200 mg orally, three times a day, for 14 days) on a 21-day cycle, combined with 2 different alvocidib administration schedules: a 1-hour intravenous infusion, daily × 5; or a 30-minute loading infusion followed by a 4-hour maintenance infusion, weekly × 2. The alvocidib dose was escalated using a standard 3+3 design. Results: Twenty-eight patients were enrolled and treated. The alvocidib MTD was 20 mg/m2 (30-minute loading infusion) followed by 20 mg/m2 (4-hour maintenance infusion) on days one and eight, in combination with vorinostat. The most frequently encountered toxicities were cytopenias, fatigue, hyperglycemia, hypokalemia, hypophosphatemia, and QT prolongation. Dose-limiting toxicities (DLT) were cardiac arrhythmia-atrial fibrillation and QT prolongation. No objective responses were achieved although 13 of 26 evaluable patients exhibited stable disease. Alvocidib seemed to alter vorinostat pharmacokinetics, whereas alvocidib pharmacokinetics were unaffected by vorinostat. Ex vivo exposure of leukemia cells to plasma obtained from patients after alvocidib treatment blocked vorinostat-mediated p21CIP1 induction and downregulated Mcl-1 and p-RNA Pol II for some specimens, although parallel in vivo bone marrow responses were infrequent. Conclusions: Alvocidib combined with vorinostat is well tolerated. Although disease stabilization occurred in some heavily pretreated patients, objective responses were not obtained with these schedules. Clin Cancer Res; 19(7); 1873–83. ©2013 AACR.
The merits of measuring challenge and hindrance appraisals

Background and Objectives: The challenge–hindrance framework has shown that challenge stressors (work characteristics associated with potential personal gain) tend to have positive outcomes, whereas hindrance stressors (those which obstruct goals) have negative outcomes. However, typical research methods assume that stressors allocated to these categories are appraised consistently by different people and across different situations. We validate new measures of challenge and hindrance appraisals and demonstrate their utility in stress research. Design and Methods: We used a cross-sectional survey of American employees (Study 1, n = 333), a diary survey of Australian employees (Study 2, n = 241), and a survey of Australian college students whose performance was evaluated independently (Study 3, n = 350). Results: Even after accounting for the effects of stressors, challenge and hindrance appraisals consistently explained unique variance in affective states, with indications that stressors have indirect effects via appraisals. Such effects were seen within- as well as between-participants (Study 2). Appraisals also had expected associations with specific coping behaviors (Study 1), while challenge appraisal was associated with task performance (Study 3). Conclusions: The scales of challenge and hindrance appraisals were psychometrically sound across multiple contexts. Results highlight the merit of considering appraisal in stress research.
Review of tick-borne encephalitis and vaccines: clinical and economical aspects

Tick-borne encephalitis (TBE) disease is an increasing burden not only locally but also globally. In most endemic countries, vaccination coverage is too low to reduce the TBE burden significantly; however, vaccination is the most effective protection against TBE, with various vaccines currently available. In spite of rising awareness of TBE, little attention is directed toward the health economics of the disease. The purpose of the present review is to compile information on TBE and its explicit clinical and economical aspects. Given the scarcity of studies, the authors conclude that more attention is needed for health economics of TBE. Notably, this would help establish guidance on efficient policies for TBE prevention, reduce disease burden and achieve population health benefits.
Learning and managerial horizons : Beyond career concerns

This paper presents a unified moral hazard framework with renegotiation and anticipated managerial turnover for examining incentive dynamics given correlated performance measures and long-term actions which is applicable to CEO turnover studies and related work on the “horizon problem”. The main contribution is an explicit solution for the dynamic agency with short-term contracts and a proof of its equivalence to the renegotiation-proof contract. The results present an alternative to performancerelated turnover explanations of incentive dynamics and extend the work done with career concerns models by considering general performance measures and long-term actions. The main effects identified in the optimal contracts are: a learning effect, and a horizon effect consisting of risk and incentive externalities. Both an inverted U shape of managerial performance over a manager’s tenure and V shaped performance around managerial turnover are consistent with negatively correlated accounting-based performance measures and long-term actions.
Power-efficient calibration and reconfiguration for on-chip optical communication

On-chip optical communication infrastructure has been proposed to provide higher bandwidth and lower power consumption for the next-generation high performance multicore systems. Online calibration of these optical components is essential to building a robust optical communication system, which is highly sensitive to process and thermal variation. However, the power consumption of existing tuning methods to properly calibrate the optical devices would be prohibitively high. We propose two calibration and reconfiguration techniques that can significantly reduce the worst case tuning power of a ring-resonator-based optical modulator: 1) a channel re-mapping scheme, with sub-channel redundant resonators, which results in significant reduction in the amount of required tuning, typically within the capability of voltage based tuning, and 2) a dynamic feedback calibration mechanism used to compensate for both process and thermal variations of the resonators. Simulation results demonstrate that these techniques can achieve a 48X reduction in tuning power - less than 10W for a network with 1-million ring resonators.
Low Myocardial Protein Kinase G Activity in Heart Failure With Preserved Ejection Fraction

Background— Prominent features of myocardial remodeling in heart failure with preserved ejection fraction (HFPEF) are high cardiomyocyte resting tension (Fpassive) and cardiomyocyte hypertrophy. In experimental models, both reacted favorably to raised protein kinase G (PKG) activity. The present study assessed myocardial PKG activity, its downstream effects on cardiomyocyte Fpassive and cardiomyocyte diameter, and its upstream control by cyclic guanosine monophosphate (cGMP), nitrosative/oxidative stress, and brain natriuretic peptide (BNP). To discern altered control of myocardial remodeling by PKG, HFPEF was compared with aortic stenosis and HF with reduced EF (HFREF). Methods and Results— Patients with HFPEF (n=36), AS (n=67), and HFREF (n=43) were free of coronary artery disease. More HFPEF patients were obese (P<0.05) or had diabetes mellitus (P<0.05). Left ventricular myocardial biopsies were procured transvascularly in HFPEF and HFREF and perioperatively in aortic stenosis. Fpassive was measured in cardiomyocytes before and after PKG administration. Myocardial homogenates were used for assessment of PKG activity, cGMP concentration, proBNP-108 expression, and nitrotyrosine expression, a measure of nitrosative/oxidative stress. Additional quantitative immunohistochemical analysis was performed for PKG activity and nitrotyrosine expression. Lower PKG activity in HFPEF than in aortic stenosis (P<0.01) or HFREF (P<0.001) was associated with higher cardiomyocyte Fpassive (P<0.001) and related to lower cGMP concentration (P<0.001) and higher nitrosative/oxidative stress (P<0.05). Higher Fpassive in HFPEF was corrected by in vitro PKG administration. Conclusions— Low myocardial PKG activity in HFPEF was associated with raised cardiomyocyte Fpassive and was related to increased myocardial nitrosative/oxidative stress. The latter was probably induced by the high prevalence in HFPEF of metabolic comorbidities. Correction of myocardial PKG activity could be a target for specific HFPEF treatment.
Characterization of a fungal protein kinase from Cryphonectria parasitica and its transcriptional upregulation by hypovirus

The chestnut blight fungus Cryphonectria parasitica and its hypovirus comprise useful model system to study the mechanisms of hypoviral infection. We used degenerate primers based on fungal protein kinases to isolate a gene, cppk1, which encodes a novel Ser/Thr protein kinase of C. parasitica. The gene showed highest homology to ptk1, a Ser/Thr protein kinase from Trichoderma reesei. The encoded protein had a predicted mass of 70.5 kDa and a pI of 7.45. Northern blot analyses revealed that the cppk1 transcript was expressed from the beginning of culture, with a slight increase by 5 days of culture. However, its expression was specifically affected by the presence of virus, and it was transcriptionally upregulated in the fungal strain infected with the hypovirus. A kinase assay using Escherichia coli‐derived CpPK1 revealed CpPK1‐specific phosphorylated proteins with estimated masses of 50 kDa and 44 kDa. In addition, the phosphorylation of both proteins was higher in a cell‐free extract from the hypovirulent strain. The increased expression of cppk1 by the introduction of an additional copy results in a subset of viral symptoms of reduced pigmentation and conidiation in a virus‐free isolate. cppk1 overexpression also causes the downregulation of mating factor genes Mf2/1 and Mf2/2, resulting in female sterility. The present study suggests that the hypovirus disturbs fungal signalling by transcriptional upregulation of cppk1, which results in reduced pigmentation and conidiation and female sterility.
Variance Shifts, Structural Breaks, and Stationarity Tests

This article considers the problem of testing the null hypothesis of stochastic stationarity in time series characterized by variance shifts at some (known or unknown) point in the sample. It is shown that existing stationarity tests can be severely biased in the presence of such shifts, either oversized or undersized, with associated spurious power gains or losses, depending on the values of the breakpoint parameter and on the ratio of the prebreak to postbreak variance. Under the assumption of a serially independent Gaussian error term with known break date and known variance ratio, a locally best invariant (LBI) test of the null hypothesis of stationarity in the presence of variance shifts is then derived. Both the test statistic and its asymptotic null distribution depend on the breakpoint parameter and also, in general, on the variance ratio. Modifications of the LBI test statistic are proposed for which the limiting distribution is independent of such nuisance parameters and belongs to the family of Cramér–von Mises distributions. One such modification is particularly appealing in that it is simultaneously exact invariant to variance shifts and to structural breaks in the slope and/or level of the series. Monte Carlo simulations demonstrate that the power loss from using our modified statistics in place of the LBI statistic is not large, even in the neighborhood of the null hypothesis, and particularly for series with shifts in the slope and/or level. The tests are extended to cover the cases of weakly dependent error processes and unknown breakpoints. The implementation of the tests are illustrated using output, inflation, and exchange rate data series.
Cyclic Cumulative Damaging of Reinforced Concrete in Post-Peak Regions

Repetition of higher stresses apparently causes progressive damage, which is also strain/stress rate-dependent. This paper aims to separate time-dependent cumulative nolinearity and the effect of repetition of strain path on the overall damage evolution of concrete in compression. Cyclic uniaxial compression tests of concrete were conducted and time-dependent plasticity and stiffness degradation were subtracted from total stress-strain relations to purely extract the effect of repeated stress cycle. Coupling of time dependency and authentic cyclic accumulation of damage was examined by both material and structural experiments especially in post-peak regions, and its applicability was experimentally verified mainly under low cyclic (N 100) fatigue life predicted by the proposed constitutive law was also verified in terms of the S-N curve.
A Genome-Wide Investigation of MicroRNA Expression Identifies Biologically-Meaningful MicroRNAs That Distinguish between High-Risk and Low-Risk Intraductal Papillary Mucinous Neoplasms of the Pancreas

Background Intraductal papillary mucinous neoplasms (IPMNs) are pancreatic ductal adenocarcinoma (PDAC) precursors. Differentiating between high-risk IPMNs that warrant surgical resection and low-risk IPMNs that can be monitored is a significant clinical problem, and we sought to discover a panel of mi(cro)RNAs that accurately classify IPMN risk status. Methodology/Principal Findings In a discovery phase, genome-wide miRNA expression profiling was performed on 28 surgically-resected, pathologically-confirmed IPMNs (19 high-risk, 9 low-risk) using Taqman MicroRNA Arrays. A validation phase was performed in 21 independent IPMNs (13 high-risk, 8 low-risk). We also explored associations between miRNA expression level and various clinical and pathological factors and examined genes and pathways regulated by the identified miRNAs by integrating data from bioinformatic analyses and microarray analysis of miRNA gene targets. Six miRNAs (miR-100, miR-99b, miR-99a, miR-342-3p, miR-126, miR-130a) were down-regulated in high-risk versus low-risk IPMNs and distinguished between groups (P<10−3, area underneath the curve (AUC) = 87%). The same trend was observed in the validation phase (AUC = 74%). Low miR-99b expression was associated with main pancreatic duct involvement (P = 0.021), and serum albumin levels were positively correlated with miR-99a (r = 0.52, P = 0.004) and miR-100 expression (r = 0.49, P = 0.008). Literature, validated miRNA:target gene interactions, and pathway enrichment analysis supported the candidate miRNAs as tumor suppressors and regulators of PDAC development. Microarray analysis revealed that oncogenic targets of miR-130a (ATG2B, MEOX2), miR-342-3p (DNMT1), and miR-126 (IRS-1) were up-regulated in high- versus low-risk IPMNs (P<0.10). Conclusions This pilot study highlights miRNAs that may aid in preoperative risk stratification of IPMNs and provides novel insights into miRNA-mediated progression to pancreatic malignancy. The miRNAs identified here and in other recent investigations warrant evaluation in biofluids in a well-powered prospective cohort of individuals newly-diagnosed with IPMNs and other pancreatic cysts and those at increased genetic risk for these lesions.
Efficient Parallel Path Checking for Linear-Time Temporal Logic With Past and Bounds

Path checking, the special case of the model checking problem where the model under consideration is a single path, plays an important role in monitoring, testing, and verification. We prove that for linear-time temporal logic (LTL), path checking can be efficiently parallelized. In addition to the core logic, we consider the extensions of LTL with bounded-future (BLTL) and past-time (LTL+Past) operators. Even though both extensions improve the succinctness of the logic exponentially, path checking remains efficiently parallelizable: Our algorithm for LTL, LTL+Past, and BLTL+Past is in AC^1(logDCFL) \subseteq NC.
A Multispecies Fungal Biofilm Approach to Enhance the Celluloyltic Efficiency of Membrane Reactors for Consolidated Bioprocessing of Plant Biomass

The constraints and advantages in cellulolytic enzymes production by fungal biofilms for a consolidated bioconversion process were investigated during this study. The biofilm cultivations were carried out in reactors designed for consolidated bioprocessing Multispecies Biofilm Membrane reactors, (MBM) where an aerobic fungal biofilm produces the lignocellulolytic enzymes while a fermenting microorganism forms the fermentation product at anaerobic conditions. It was shown that although mycelial growth was limited in the MBM reactors compared to submerged cultivations, the secretion of cellulolytic enzymes per cell dry weight was higher. When Trichoderma reesei was used as the sole enzyme producer, cellobiose accumulated in the liquid medium as the result of the deficiency of β-glucosidase in the fungal secretome. To enhance β-glucosidase activity, T. reesei was co-cultivated with A. phoenicis which is a β-glucosidase overproducer. The two fungi formed a multispecies biofilm which produced a balanced cellulolytic cocktail for the saccharification of plant biomass. The mixed biofilm reached a 2.5 fold increase in β-glucosidase production, compared to the single T. reesei biofilm. The enzymatic systems of single and mixed biofilms were evaluated regarding their efficiency on cellulosic substrates degradation. Washed solids from steam pretreated beechwood, as well as microcrystalline cellulose were used as the substrates. The enzymatic system of the multispecies biofilm released four times more glucose than the enzymatic system of T. reesei alone from both substrates and hydrolyzed 78 and 60% of the cellulose content of washed solids from beechwood and microcrystalline cellulose, respectively.
64 x 64 Bit Multiplier Using Pass Logic

by SHIBI P.THANKACHAN Under the Direction of A. P. Preethy ABSTRACT Due to the rapid progress in the field of VLSI, improvements in speed, power and area are quite evident. Research and development in this field are motivated by growing markets of portable mobile devices such as personal multimedia players, cellular phones, digital camcorders and digital cameras. Among the recently popular logic families, pass transistor logic is promising for low power applications as compared to conventional static CMOS because of lower transistor count. This thesis proposes four novel designs for Booth encoder and selector logic using pass logic principles. These new designs are implemented and used to build a 64 x 64-bit multiplier. The proposed Booth encoder and selector logic are competitive with the existing and shows substantial reduction in transistor count. It also shows improvements in delay when compared to two of the three published works.
Site-Specific Role of Catechol-O-Methyltransferase in Dopamine Overflow within Prefrontal Cortex and Dorsal Striatum

Accumulating evidence from clinical and preclinical studies shows that catechol-O-methyltransferase (COMT) plays a significant role in dopamine metabolism in the prefrontal cortex, but not in the striatum. However, to what extent dopamine overflow in the prefrontal cortex and striatum is controlled by enzymatic degradation versus reuptake is unknown. We used COMT deficient mice to investigate the role of COMT in these two brain regions with in vivo voltammetry. A real-time analysis of evoked dopamine overflow showed that removal of dopamine was twofold slower in the prefrontal cortex of mice lacking COMT than in wild-type mice, indicating that half of the dopamine decline in this brain region results from COMT-mediated enzymatic degradation. Lack of COMT did not influence dopamine overflow/decline in the dorsal striatum. COMT-deficient mice demonstrated a small (20–25%) but consistent increase in evoked dopamine release in the prefrontal cortex, but not in the dorsal striatum. Cocaine affected equally dopaminergic neurotransmission in the prefrontal cortex in both genotypes by prolonging 3–4 times dopamine elimination from extracellular space. Paradoxically, this happened without increase of the peak levels of evoked dopamine release. The present findings represent the first demonstration of the significant contribution of COMT in modulating the dynamics of dopamine overflow in the prefrontal cortex and underscore the therapeutic potential of manipulating COMT activity to alter dopaminergic neurotransmission in the prefrontal cortex.
Snapshot of Moving and Expanding Clones of Mycobacterium tuberculosis and Their Global Distribution Assessed by Spoligotyping in an International Study

ABSTRACT The present update on the global distribution of Mycobacterium tuberculosis complex spoligotypes provides both the octal and binary descriptions of the spoligotypes for M. tuberculosis complex, including Mycobacterium bovis, from >90 countries (13,008 patterns grouped into 813 shared types containing 11,708 isolates and 1,300 orphan patterns). A number of potential indices were developed to summarize the information on the biogeographical specificity of a given shared type, as well as its geographical spreading (matching code and spreading index, respectively). To facilitate the analysis of hundreds of spoligotypes each made up of a binary succession of 43 bits of information, a number of major and minor visual rules were also defined. A total of six major rules (A to F) with the precise description of the extra missing spacers (minor rules) were used to define 36 major clades (or families) of M. tuberculosis. Some major clades identified were the East African-Indian (EAI) clade, the Beijing clade, the Haarlem clade, the Latin American and Mediterranean (LAM) clade, the Central Asian (CAS) clade, a European clade of IS6110 low banders (X; highly prevalent in the United States and United Kingdom), and a widespread yet poorly defined clade (T). When the visual rules defined above were used for an automated labeling of the 813 shared types to define nine superfamilies of strains (Mycobacterium africanum, Beijing, M. bovis, EAI, CAS, T, Haarlem, X, and LAM), 96.9% of the shared types received a label, showing the potential for automated labeling of M. tuberculosis families in well-defined phylogeographical families. Intercontinental matches of shared types among eight continents and subcontinents (Africa, North America, Central America, South America, Europe, the Middle East and Central Asia, and the Far East) are analyzed and discussed.