Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Domains of the ClpA and ClpX Molecular Chaperones Identified by Limited Proteolysis and Deletion Analysis*

Escherichia coli ClpA and ClpX are ATP-dependent protein unfoldases that each interact with the protease, ClpP, to promote specific protein degradation. We have used limited proteolysis and deletion analysis to probe the conformations of ClpA and ClpX and their interactions with ClpP and substrates. ATPγS binding stabilized ClpA and ClpX such that that cleavage by lysylendopeptidase C occurred at only two sites. Both proteins were cleaved within in a loop preceding an α-helix-rich C-terminal domain. Although the loop varies in size and composition in Clp ATPases, cleavage occurred within and around a conserved triad, IG(F/L). Binding of ClpP blocked this cleavage, and prior cleavage at this site rendered both ClpA and ClpX defective in binding and activating ClpP, suggesting that this site is involved in interactions with ClpP. ClpA was also cut at a site near the junction of the two ATPase domains, whereas the second cleavage site in ClpX lay between its N-terminal and ATPase domains. ClpP did not block cleavage at these other sites. The N-terminal domain of ClpX dissociated upon cleavage, and the remaining ClpXΔN remained as a hexamer, associated with ClpP, and expressed ATPase, chaperone, and proteolytic activity. A truncated mutant of ClpA lacking its N-terminal 153 amino acids also formed a hexamer, associated with ClpP, and expressed these activities. We propose that the N-terminal domains of ClpX and ClpA lie on the outside ring surface of the holoenzyme complexes where they contribute to substrate binding or perform a gating function affecting substrate access to other binding sites and that a loop on the opposite face of the ATPase rings stabilizes interactions with ClpP and is involved in promoting ClpP proteolytic activity.
Pathways of Relevance: Exploring Inflows of Knowledge into Subunits of Multinational Corporations

To understand what determines knowledge flows into organizational subunits, the study reported here examines the relevance of the knowledge to the operations performed at the receiving subunit. This study analyzes inflows of knowledge from peers and supervising units into subunits of multinational corporations. It examines factors that affect the relevance of extra-unit knowledge to receiving subunits and explores empirically how these factors affect knowledge flows. The results show that knowledge travels along established ties from large knowledge bases into unspecialized, codified, locally responsive knowledge bases. The results are consistent with the view that relevance provides pathways through which new knowledge connects to prior knowledge.
Serological evidence of flaviviruses infection among acute febrile illness patients in Afghanistan.

INTRODUCTION Current published reports on the causative agents of acute febrile illness (AFI) in Afghanistan are scarce, and the burden of disease due to flaviviruses is unknown. METHODOLOGY A hospital-based surveillance study for AFI was established in 2008 through 2010 to determine the seroepidemiology of West Nile virus (WNV), tick-borne encephalitis virus (TBEV) and dengue viruses (DENV) using commercial ELISA kits. Due to major logistical challenges, only acute sera were collected. RESULTS Serological analysis for IgG were as follows: WNV 30.4% (277/913); TBEV 23.4% (214/913); DENV 19.7% (180/913). Single positive IgG reactions for WNV, TBEV and DENV were noted in 11% (100/913), 7.2% (66/913), and 5% (47/913), respectively. Reactivity for all three screened flaviviruses was detected in 44.5% (406/913) of sera. IgM positivity was uncommon, with only 0.5% (5/913), 2.2% (20/913) and 2.6% (8/312) of samples positive for WNV, TBEV, and DENV, respectively. Serological findings were confirmed in random positive samples by neutralization assay. CONCLUSIONS These serological results suggest circulation of WNV, TBEV, and DENV within Afghanistan, with evidence of current or prior infection noted in a significant proportion of patients seeking care for AFI. Obtaining additional information on the prevalence of these and other causes of AFI is paramount for improving the distribution of available limited syndromic treatment and improving the existing health protection policy in Afghanistan.
Incidence of awareness with recall during general anaesthesia

One thousand patients who were anaesthetised between February and April 1990 at University Hospital, Nottingham were interviewed between 20 and 36 hours after their operation. Patients under 16 years of age, those who had undergone obstetric or intracranial surgery, those who were unable to communicate and patients who were discharged from hospital before the postoperative visit were not interviewed. A standard set of questions was used to determine the incidences of recall of events and dreams during the operation. These incidences were 0.2% and 0.9% respectively, considerably lower than reported in previous comparable studies.
Improved Modulation Scheme for Loss Balancing of Three-Level Active NPC Converters

The three-level neutral point-clamped (NPC) converter has attracted much attention in high-power medium-voltage applications, but it is well-known that the NPC topology suffers from unequal power loss distribution among its semiconductor devices. The power loss unbalance problem becomes especially severe when the converter is operating at low fundamental frequencies. To overcome the loss unbalance problem of the NPC converter, the active NPC (ANPC) technique was introduced. However, it is demonstrated in this paper that in many cases, the conventional modulation method for the ANPC converter only marginally relieves the loss unbalance problem. This paper proposes a new modulation scheme (named the adaptive doubled frequency modulation) for the three-level ANPC converter, which significantly improves the power loss and thermal sharing among the semiconductor devices. The basic idea of the proposed scheme is adaptively adjusting the duty cycles of the switching states for every switching cycle, so as to optimize the power loss distribution. Simulation and experimental results verify this new method.
Global Feedback Stabilization for a Class of Nonlocal Transport Equations: The Continuous and Discrete Case

In this paper, we prove the global output feedback stabilization for a class of nonlinear transport equations with nonlocal velocity. It models a highly re-entrant system which is widely encountered in semiconductor manufacturing. The exponential stability of the solution to a constant equilibrium is proved by a Lyapunov function method under a natural feedback law. The smallness restriction on the initial data in [J.-M. Coron and Z. Wang, SIAM J. Math. Anal. , 45 (2013), pp. 2646--2665] is removed by using the special feature of the velocity function. The exponential stabilization results for the related discretized system with an upwind scheme are obtained by the eigenvalue decomposition method and by a Lyapunov function method. Numerical simulations are provided to supplement the theoretical results.
Insulin-Like Growth Factor Binding Protein-I; a Rapid Detection of Amniotic Fluid Leakage after Amniocentesis

The aim of this study was to assess the diagnostic value of vaginal insulin-like growth factor binding protein-1 (IGFBP-I) in the detection of amniotic fluid leakage after amniocentesis. It includes 58 healthy pregnant women who successfully underwent amniocentesis at 15-20 weeks of gestation. After amniocentesis patients were evaluated for amniotic fluid leakage at 60 min, 48 h, and 6 weeks after the procedure with speculum examination, nitrazine paper test and microscopic evidence of ferning, and were grouped into Group I (at least 2 positive tests) and Group II (others) according to the first evaluation. All patients tested for vaginal IGFBP-I. A total of 1.1% (7/58) of patients met the Group I criteria. Vaginal bleeding and contraction occurrence was nonsignificantly higher in Group I. One false positive and one false negative result were obtained from IGFBP-I testing. The sensitivity of this test was 85%, specificity was 98%, positive predictive value (PPV) was 85% and negative predictive value (NPV) was 98%. After 48 h the sensitivity of this test was 75%, specificity was 98%, PPV was 75% and NPV was 98%. Results at the 6th week were similar to those at 48 h.
Characterization of nitrated sugar alcohols by atmospheric-pressure chemical-ionization mass spectrometry.

RATIONALE The nitrated sugar alcohols mannitol hexanitrate (MHN), sorbitol hexanitrate (SHN) and xylitol pentanitrate (XPN) are in the same class of compounds as the powerful military-grade explosive pentaerythritol tetranitrate (PETN) and the homemade explosive erythritol tetranitrate (ETN) but, unlike for PETN and ETN, ways to detect MHN, SHN and XPN by mass spectrometry (MS) have not been fully investigated. METHODS Atmospheric-pressure chemical-ionization mass spectrometry (APCI-MS) was used to detect ions characteristic of nitrated sugar alcohols. APCI time-of-flight mass spectrometry (APCI-TOF MS) and collision-induced dissociation tandem mass spectrometry (CID MS/MS) were used for confirmation of each ion assignment. In addition, the use of the chemical ionization reagent dichloromethane was investigated to improve sensitivity and selectivity for detection of MHN, SHN and XPN. RESULTS All the nitrated sugar alcohols studied followed similar fragmentation pathways in the APCI source. MHN, SHN and XPN were detectable as fragment ions formed by the loss of NO2 , HNO2 , NO3 , and CH2 NO2 groups, and in the presence of dichloromethane chlorinated adduct ions were observed. It was determined that in MS/MS mode, chlorinated adducts of MHN and SHN had the lowest limits of detection (LODs), while for XPN the lowest LOD was for the [XPN-NO2 ]- fragment ion. Partially nitrated analogs of each of the three compounds were also present in the starting materials, and ions attributable to these compounds versus those formed from in-source fragmentation of MHN, SHN, and XPN were distinguished and assigned using liquid chromatography APCI-MS and ESI-MS. CONCLUSIONS The APCI-MS technique provides a selective and sensitive method for the detection of nitrated sugar alcohols. The methods disclosed here will benefit the area of explosives trace detection for counterterrorism and forensics. Copyright © 2016 John Wiley & Sons, Ltd.
“Target” cells, cellular phenotypes, and lineage fidelity in human leukaemia

A detailed analysis of lymphoid leukaemia cells with a panel of monoclonal antibodies plus other markers indicates a striking conservation of phenotype that closely mimics that of normal lymphoid precursor or progenitor cells and reflects the imposition of maturation arrest. The composite phenotypes detected show some minimal deviations or asynchronies (with respect to maturation “stages”) but are faithful with respect to cell lineage. These observations are suggested to shed light on the available “target” populations for lymphoid malignancy in humans and challenge the view that de‐differentiation or qualitatively aberrant gene expression is common and important in malignancy. They are further taken to support the view that normal gene products that regulate or couple proliferation and maturation are critically involved in the successive clonal selection events underlying the evolution of leukaemia. No qualitatively unique and consistent leukaemia “markers” may exist or be required. The only exception to this rule are the nonrandom chromosome changes, which, it is suggested, involve genetic loci critical to the regulation of growth and maturation in particular normal cell types.
Purine nucleoside phosphorylase and fludarabine phosphate gene‐directed enzyme prodrug therapy suppresses primary tumour growth and pseudo‐metastases in a mouse model of prostate cancer

Gene‐directed enzyme prodrug therapy based on the E. coli purine nucleoside phosphorylase (PNP) gene produces efficient tumour cell killing. PNP converts adenosine analogs into toxic metabolites that diffuse across cell membranes to kill neighbouring untransduced cells (PNP‐GDEPT). Interference with DNA, RNA and protein synthesis kills dividing and non‐dividing cells, an important consideration for slow‐growing prostate tumours. This study examined the impact of administering PNP‐GDEPT into orthotopically grown RM1 prostate cancers (PCas) on the growth of lung pseudo‐metastases of immunocompetent mice. C57BL/6 mice bearing orthotopic RM1 PCas received a single intraprostatic injection of OAdV220 (1010 particles), a recombinant ovine atadenovirus containing the PNP gene controlled by the Rous Sarcoma virus promoter, followed by fludarabine phosphate (∼600 mg/m2/day) administered intraperitoneally (ip) once daily for 5 days. Pseudo‐metastases were induced 2 days after intraprostatic vector administration by tail‐vein injection of untransduced RM1 cells. Mice given PNP‐GDEPT showed a significant reduction both in prostate volume (∼50%) and in lung colony counts (∼60%). Apoptosis was increased two‐fold in GDEPT‐treated prostates compared with controls (P < 0.01), but was absent in the lungs. Staining for proliferating cell nuclear antigen (PCNA) indicated that proliferation of both RM1 prostate tumours (P < 0.01) and lung colonies (P < 0.01) was significantly suppressed after GDEPT. Although prostate tumour immune cell infiltration did not differ significantly between treatments, immunostaining for Thy‐1.2 (CD90) showed that GDEPT promoted Thy‐1.2+ cell infiltration into the prostate tumour site. This study showed that a single course of PNP‐GDEPT significantly suppressed local PCa growth and reduced lung colony formation in the aggressive RM1 tumour model. Copyright © 2004 John Wiley & Sons, Ltd.
The Cdc6 Protein Is Ubiquitinated in Vivo for Proteolysis in Saccharomyces cerevisiae *

The Saccharomyces cerevisiae Cdc6 protein is necessary for the formation of pre-replicative complexes that are required for firing DNA replication at origins at the beginning of S phase. Cdc6p protein levels oscillate during the cell cycle. In a normal cell cycle the presence of this protein is restricted to G1, partly because the CDC6 gene is transcribed only during G1 and partly because the Cdc6p protein is rapidly degraded at late G1/early S phase. We report here that the Cdc6p protein is degraded in a Cdc4-dependent manner, suggesting that phosphorylated Cdc6 is specifically recognized by the ubiquitin-mediated proteolysis machinery. Indeed, we have found that Cdc6 is ubiquitinated in vivo and degraded by a Cdc4-dependent mechanism. Our data, together with previous observations regarding Cdc6 stability, suggest that under physiological conditions budding yeast cells degrade ubiquitinated Cdc6 every cell cycle at the beginning of S phase.
High impedance fault detection based on wavelet transform and statistical pattern recognition

A novel method for high impedance fault (HIF) detection based on pattern recognition systems is presented in this paper. Using this method, HIFs can be discriminated from insulator leakage current (ILC) and transients such as capacitor switching, load switching (high/low voltage), ground fault, inrush current and no load line switching. Wavelet transform is used for the decomposition of signals and feature extraction, feature selection is done by principal component analysis and Bayes classifier is used for classification. HIF and ILC data was acquired from experimental tests and the data for transients was obtained by simulation using EMTP program. Results show that the proposed procedure is efficient in identifying HIFs from other events.
Detection of adventitious presence of genetically modified seeds in lots of non transgenic soybean 1

The difficulty on identifying, lack of segregation systems and absence of suitable standards for coexistence of non trangenic and transgenic soybean are contributing for contaminations that occur during productive system. The objective of this study was to evaluate the efficiency of two methods for detecting mixtures of seeds genetically modified (GM) into samples of non-GM soybean, in a way that seed lots can be assessed within the standards established by seed legislation. Two sizes of soybean samples (200 and 400 seeds), cv. BRSMG 810C (non-GM) and BRSMG 850GRR (GM), were assessed with four contamination levels (addition of GM seeds, for obtaining 0.0%, 0.5%, 1.0%, and 1.5% contamination), and two detection methods: immunoassay of lateral flux (ILF) and bioassay (pre-imbibition into 0.6% herbicide solution; 25 oC; 16 h). The bioassay is efficient in detecting presence of GM seeds in seed samples of non-GM soybean, even for contamination lower than 1.0%, provided that seeds have high physiological quality. The ILF was positive, detecting the presence of target protein in contaminated samples, indicating test effectiveness. There was significant correlation between the two detection methods (r = 0.82; p ≤ 0.0001). Sample size did not influence efficiency of the two methods in detecting presence of GM seeds.
Distinct roles for PI3K in proliferation and survival of oligodendrocyte progenitor cells

Phosphoinositol 3‐kinase (PI3K) is a downstream effector for multiple ligand‐activated receptors and modulates cell responses through activation of its target protein kinase B (Akt). We examined the roles of PI3K‐Akt signaling in a primary glial (oligodendrocyte) progenitor cell culture system that is ligand‐dependent for cell proliferation, survival, and prevention of differentiation. We demonstrate that PI3K and Akt (Ser‐473 phosphorylation) are activated in response to platelet‐derived growth factor but not basic fibroblast growth factor‐2 (FGF2) and that distinct forms of PI3K are activated in early progenitors and later‐maturation pro‐oligodendroblasts as identified by their sensitivity to wortmannin. By establishing conditions to examine effects on cell proliferation and survival independently, we demonstrate that PI3K is necessary for a full mitogenic response and that PI3K is also necessary for early progenitor survival. Our results therefore demonstrate that PI3K‐Akt signaling independently regulates proliferation and survival, that the form of PI3K is distinct in early progenitors and pro‐oligodendroblasts, and that FGF2 does not activate this pathway in either primary glial cell population. J. Neurosci. Res. 62:336–345, 2000. © 2000 Wiley‐Liss, Inc.
Uracil-DNA glycosylase causes 5-bromodeoxyuridine photosensitization in Escherichia coli K-12

An Escherichia coli uracil-DNA glycosylase-defective mutant (ung-1 thyA) was more resistant than its wild-type counterpart (ung+ thyA) to the killing effect of UV light when cultured in medium containing 5-bromouracil or 5-bromo-2'-deoxyuridine (BrdUrd). The phenotype of resistance to BrdUrd photosensitization and the uracil-DNA glycosylase deficiency appeared to be 100% cotransduced by P1 phage. During growth with BrdUrd, both strains exhibited similar growth rates and 5-bromouracil incorporation into DNA. The resistant phenotype of the ung-1 mutant was observed primarily during the stationary phase. In cells carrying 5-bromouracil-substituted DNA, mutations causing resistance to rifampin and valine were induced by UV irradiation at a higher frequency in the wild type than in the ung-1 mutant. This Ung-dependent UV mutagenesis required UmuC function. These results suggest that the action of the uracil-DNA glycosylase on UV-irradiated 5-bromouracil-substituted DNA produces lethal and mutagenic lesions. The BrdUrd photosensitization-resistant phenotype allowed us to develop a new, efficient method for enriching and screening ung mutants.
Rank-Based Network Coding for Content Distribution in Vehicular Networks

We propose a rank-based network coding scheme for distributing content in vehicular ad-hoc networks, in which vehicles adaptively broadcast packets based on the content reception status of their neighbors. In contrast to the previous work, CodeOn, vehicles in the proposed method only exchange content reception information in the service channel. The packet injection probability in the proposed method is proportional to the estimated innovation that a vehicle can provide to its neighbors. We also give an analytical model to analyze the system throughput when vehicles apply rank-based network coding to broadcast data. Simulation results demonstrate that the proposed method improves the throughput by more than 32% while maintaining lower end-to-end delay and protocol overhead than the previous work.
An approximate generalized linear model with random effects for informative missing data.

This paper develops a class of models to deal with missing data from longitudinal studies. We assume that separate models for the primary response and missingness (e.g., number of missed visits) are linked by a common random parameter. Such models have been developed in the econometrics (Heckman, 1979, Econometrica 47, 153-161) and biostatistics (Wu and Carroll, 1988, Biometrics 44, 175-188) literature for a Gaussian primary response. We allow the primary response, conditional on the random parameter, to follow a generalized linear model and approximate the generalized linear model by conditioning on the data that describes missingness. The resultant approximation is a mixed generalized linear model with possibly heterogeneous random effects. An example is given to illustrate the approximate approach, and simulations are performed to critique the adequacy of the approximation for repeated binary data.
When accuracy hurts: Reactions of anxious–ambivalent dating partners to a relationship-threatening situation.

Why are anxious-ambivalent individuals especially likely to have turbulent and unstable relationships'. ' To help answer this question, the authors use 3 theoretical perspectives to examine how heightened empathic accuracy in a relationship-threatening situation is associated with personal and relational distress. Dating couples inferred their partners' thoughts and feelings from a videotaped interaction m which they each rated slides of opposite-sex individuals. Highly anxious—ambivalent individuals were more empathically accurate in this relationship-threatening situation: however, their self-reported thoughts and feelings indicated greater distress and less confidence in their partners and relationships. The more anxious-ambivalent women reported a slight decrease in the perceived closeness of their relationships. Four months later, more anxious-ambivalent men's relationships were more likely to have ended. These findings are discussed in terms of their theoretical and applied implications.