Miracle-dz/UniFAR-FTUs huggingface dataset:
The Mechanism of Velocity Modulated Allosteric Regulation in −3-Phosphoglycerate Dehydrogenase SITE-DIRECTED MUTAGENESIS OF EFFECTOR BINDING SITE RESIDUES*

-3-Phosphoglycerate dehydrogenase (EC) from Escherichia coli catalyzes the first committed step in serine biosynthesis and is allosterically regulated by -serine, the end product of the pathway. Each subunit of the homotetramer is made up of three distinct domains with one of the intersubunit contacts being between adjacent regulatory domains. Each regulatory domain interface contains two symmetrical serine binding sites such that serine forms hydrogen bonds to both domains across the interface. Previous work (Al-Rabiee, R., Lee, E. J., and Grant, G. A. (1996) J. Biol. Chem. 271, 13013-13017) demonstrated that when adjacent regulatory domains are covalently linked to one another by engineered disulfide bonds, the enzyme was inactivated. Breaking the disulfide bonds by reduction restored enzymatic activity. This study demonstrates that the complementary situation is also true. Site-directed mutagenesis of three residues at the effector binding site, His344, Asn346, and Asn364′, render the enzyme increasingly less susceptible to inhibition by the effector. When mutations result in a situation where it is no longer possible to establish a stable hydrogen bonding network across the regulatory domain interface, the inhibitory capacity of the effector is lost. Furthermore, mutations that produce as much as 5 orders of magnitude decrease in the ability of -serine to inhibit the enzyme have no appreciable effect on the Km or kcat of the enzyme. These observations support the model that predicts that catalytic activity in −3-phosphoglycerate dehydrogenase is regulated by the movement of adjacent regulatory domains about a flexible hinge and that effector binding tethers the regulatory domains together producing a state that results in a stable, open active site cleft that is no longer able to promote catalysis.
Effect of head-only sub-chronic and chronic exposure to 900-MHz GSM electromagnetic fields on spatial memory in rats

Primary objective: This study was carried out to investigate the behavioural effects of sub-chronic and chronic head-only exposure to 900 MHz GSM (Global System for Mobile communications) in male rats. Methods: Rats were exposed for 45 minutes per day, at a brain-averaged specific absorption rate (SAR) = 1.5 W Kg−1or 15 minutes per day at a SAR = 6 W Kg−1, during 8 or 24 weeks. Then, their spatial memory was tested using the radial-arm maze. In the first phase (10 days), rats were trained to visit the eight arms of the maze without returning to an arm already visited. In the second phase (8 days), a 45-minute intra-trial delay was introduced after four visited arms. Results: Performance of exposed rats (1.5 or 6 W Kg−1) was compared with that of sham, negative control and positive control rats. Scopolamine treatment in the positive control rats induced deficit in spatial memory task in the second phase of the test. However, spatial memory task was unaffected in exposed rats. Conclusion: Sub-chronic and chronic head-only exposure of rats to GSM 900 MHz signal (45-minutes, SAR = 1.5 or 15-minutes, SAR = 6 W Kg−1) did not induce spatial memory deficit in the radial-arm maze.
A New Type Nonlinear Antenna Array Design

Applications of millimeter-wave radar, imaging and communication technology requires cost effective implementation of intelligent scanning antenna systems. This paper presents the design and measurement results of a new type nonlinear antenna array based on injection-locking theory. The required phase relation for each array element is obtained by electronic tuning through injection-locking technique, and the beam-scanning capability is demonstrated, so a shifterless beam scanning method is proposed, and an 1 X 4 element phase array verifies its feasibility.
The magnetic field of IRAS 16293-2422 as traced by shock-induced H2O masers

Abstract H2O masers are important magnetic field tracers in very high density gas. We show one of the first magnetic field determinations at such high density in a low-mass protostar: IRAS 16293-2422. We used the Very Large Array (VLA) to carry out spectro-polarimetric observations of the 22 GHz Zeeman emission of H2O masers. A blend of at least three maser features can be inferred from our data. They are excited in zones of compressed gas produced by shocks between the outflows ejected by this source and the ambient gas. The post-shock particle density is in the range 1 - 3 × 109 cmt−3, and the line-of-sight component of the magnetic field is estimated as ~ 113 mG. The outflow dynamics is likely magnetically dominated.
Solving Vlasov-Poisson-Fokker-Planck Equations using NRxx method

We present a numerical method to solve the Vlasov-Poisson-Fokker-Planck (VPFP) system using the NRxx method proposed in [4, 7, 9]. A globally hyperbolic moment system similar to that in [23] is derived. In this system, the Fokker-Planck (FP) operator term is reduced into the linear combination of the moment coefficients, which can be solved analytically under proper truncation. The non-splitting method, which can keep mass conservation and the balance law of the total momentum, is used to solve the whole system. A numerical problem for the VPFP system with an analytic solution is presented to indicate the spectral convergence with the moment number and the linear convergence with the grid size. Two more numerical experiments are tested to demonstrate the stability and accuracy of the NRxx method when applied to the VPFP system. AMS subject classifications: 35Q83, 65L20, 78M05
CTLs for Cognate TCR Recognition and Properties Bypass the Requirement Superenhanced CD 8 Binding MHC Class I Molecules with

doi:10.4049/jimmunol.0902398 online Feb 26, 2010; 2010;184;3357-3366; originally published J. Immunol. Scott R. Burrows, David A. Price and Andrew K. Sewell K. Cole, Reno Debets, Cor Berrevoets, John J. Miles, Rachel E. Hewitt, Bruno Laugel, Emma Gostick, David Emily S. J. Edwards, Kristin Ladell, Julia Ekeruche, Linda Wooldridge, Mathew Clement, Anna Lissina, Nonspecifically Activate CTLs for Cognate TCR Recognition and Properties Bypass the Requirement Superenhanced CD8 Binding MHC Class I Molecules with
Hockey-stick vertical dome division technique for overprojected and broad nasal tips.

OBJECTIVES To discuss overprojected and broad nasal tips, to overview treatment options, and to relate our experience with the hockey-stick technique. DESIGN A retrospective review (1975-2005) was conducted. Patients were selected from a computerized rhinoplasty database of operative cases. The database was used to extract a subset population that had received the hockey-stick tip procedure and had follow-up data for 1 year or more after surgery. Medical records and photographs were also analyzed in this review of results and complications. RESULTS The hockey-stick modification of vertical dome division was used in 137 patients (9.9% of the rhinoplasties in the computerized database). Of these, 64 patients had 1 year or more of follow-up. Complications referable to the nasal tip (eg, bossae, persistent tip projection, and alar asymmetry) were seen in 8 patients (13%). Revisions for tip-related problems were performed in 4 patients (6%). CONCLUSIONS The hockey-stick technique is an effective method for nasal tip deprojection and narrowing via an endonasal approach. The length of follow-up in this patient population allows good long-term evaluation of this technique.
ManySense: An Extensible and Accessible Middleware for Consumer-Oriented Heterogeneous Body Sensor Networks

Consumer-oriented wearable sensors such as smart watches are becoming popular, but each manufacturer uses its own data access mechanism. At the same time, the need for inferred context data is increasing in context-aware applications. A system is needed to provide a unified access to heterogeneous wearable devices for context-aware application developers. We propose ManySense—an Android-based middleware for heterogeneous consumer-oriented BSNs. Extensibility is achieved through adapter interfaces which allow sensors and context inferencing algorithms to be coupled with the middleware. Accessibility of the middleware allows third party applications to access raw sensor data and inferred context data uniformly. This paper provides two main contributions which are divided into several outcomes: (1) design and implementation of the ManySense BSN middleware that allows low-effort addition of new sensors and context inferencing algorithms through adapter interfaces, provides unified access to optionally filtered sensor data and inferred context data for third party applications, mediates control queries to sensor adapters and context inferencing adapters, and facilitates adapter development through an SDK and (2) evaluation of ManySense by comparing its performance with manual sensor data acquisition, analysis of ManySense's extensibility through adapter interfaces, and analysis of ManySense's accessibility from third party applications.
Ca2+/Calmodulin-Dependent Protein Kinase Kinase-α Regulates Skeletal Muscle Glucose Uptake Independent of AMP-Activated Protein Kinase and Akt Activation

Studies in nonmuscle cells have demonstrated that Ca2+/calmodulin-dependent protein kinase kinases (CaMKKs) are upstream regulators of AMP-activated protein kinase (AMPK) and Akt. In skeletal muscle, activation of AMPK and Akt has been implicated in the regulation of glucose uptake. The objective of this study was to determine whether CaMKKα regulates skeletal muscle glucose uptake, and whether it is dependent on AMPK and/or Akt activation. Expression vectors containing constitutively active CaMKKα (caCaMKKα) or empty vector were transfected into mouse muscles by in vivo electroporation. After 2 weeks, caCaMKKα was robustly expressed and increased CaMKI (Thr177/180) phosphorylation, a known CaMKK substrate. In muscles from wild-type mice, caCaMKKα increased in vivo [3H]-2-deoxyglucose uptake 2.5-fold and AMPKα1 and -α2 activities 2.5-fold. However, in muscles from AMPKα2 inactive mice (AMPKα2i), caCaMKKα did not increase AMPKα1 or -α2 activities, but it did increase glucose uptake 2.5-fold, demonstrating that caCaMKKα stimulates glucose uptake independent of AMPK. Akt (Thr308) phosphorylation was not altered by CaMKKα, and caCaMKKα plus insulin stimulation did not increase the insulin-induced phosphorylation of Akt (Thr308). These results suggest that caCaMKKα stimulates glucose uptake via insulin-independent signaling mechanisms. To assess the role of CaMKK in contraction-stimulated glucose uptake, isolated muscles were treated with or without the CaMKK inhibitor STO-609 and then electrically stimulated to contract. Contraction increased glucose uptake 3.5-fold in muscles from both wild-type and AMPKα2i mice, but STO-609 significantly decreased glucose uptake (∼24%) only in AMPKα2i mice. Collectively, these results implicate CaMKKα in the regulation of skeletal muscle glucose uptake independent of AMPK and Akt activation.
Cognitive function and apolipoprotein E in very old adults: findings from the Nun Study.

OBJECTIVES The epsilon4 allele of apolipoprotein E (APOE) has been associated with Alzheimer' s disease and with milder forms of cognitive impairment. We investigated the possibility that the absence of the epsilon4 allele may predict the maintenance of high cognitive function among very old individuals. METHODS Our data are from the Nun Study, a longitudinal study of aging and Alzheimer's disease in 678 Catholic sisters. All sisters participate in annual functional exams that include the Consortium to Establish a Registry for Alzheimer's Disease (CERAD) battery of cognitive tests. High cognitive function was defined as intact scores on five of the CERAD tests. A total of 241 participants aged 75 to 98 met this criterion at the first exam. RESULTS Findings showed that 62% of the 241 participants maintained intact scores on the five CERAD tests throughout their participation in the study. Life table analyses indicated that those without the APOE epsilon4 allele spent more time with intact cognitive function than those with the epsilon4 allele (p = .007). Cox regression analyses indicated that those without the epsilon4 allele had half the risk of losing their intact status during the study when compared with those with the epsilon4 allele (p < .01). DISCUSSION Our findings suggest that the APOE epsilon4 allele may be included among the variables that predict high cognitive function in cognitively intact, very old adults. Although the presence or absence of the epsilon4 allele is known to be related to the risk of dementia, it also appears to be related to maintaining high levels of cognitive function in old age.
Parametric Study of an Electroosmotic Micromixer with Heterogeneous Charged Surface Patches

A T-shaped micromixer featuring electroosmotic flow with heterogeneous charged surface patches on the channel walls was analyzed, and an improved design was proposed to enhance mixing performance. Numerical analysis was performed using steady Navier-Stokes equations with an additional electrokinetic body force. The numerical results for species concentration were validated with available experimental data. A parametric analysis of the micromixer was performed by varying channel height, channel width, patch width, and externally applied voltage. The effects of these parameters on the flow structure and mixing performance were analyzed in detail. A quantitative measurement based upon the mass variance was employed to quantify the mixing performance. Numerical results of the parametric study were used to propose an improved micromixer design with spacing between adjacent charged patches. The proposed design provided a more favorable flow structure to allow for enhanced mixing performance.
A methodological combined framework for roadmapping biosensor research: a fault tree analysis approach within a strategic technology evaluation frame

Abstract Biosensor technology began in the 1960s to revolutionize instrumentation and measurement. Despite the glucose sensor market success that revolutionized medical diagnostics, and artificial pancreas promise currently the approval stage, the industry is reluctant to capitalize on other relevant university-produced knowledge and innovation. On the other hand, the scientific literature is extensive and persisting, while the number of university-hosted biosensor groups is growing. Considering the limited marketability of biosensors compared to the available research output, the biosensor field has been used by the present authors as a suitable paradigm for developing a methodological combined framework for “roadmapping” university research output in this discipline. This framework adopts the basic principles of the Analytic Hierarchy Process (AHP), replacing the lower level of technology alternatives with internal barriers (drawbacks, limitations, disadvantages), modeled through fault tree analysis (FTA) relying on fuzzy reasoning to count for uncertainty. The proposed methodology is validated retrospectively using ion selective field effect transistor (ISFET) – based biosensors as a case example, and then implemented prospectively membrane biosensors, putting an emphasis on the manufacturability issues. The analysis performed the trajectory of membrane platforms differently than the available market roadmaps that, considering the vast industrial experience in tailoring and handling crystallic forms, suggest the technology path of biomimetic and synthetic materials. The results presented herein indicate that future trajectories lie along with nanotechnology, and especially nanofabrication and nano-bioinformatics, and focused, more on the science-path, that is, on controlling the natural process of self-assembly and the thermodynamics of bioelement-lipid interaction. This retained the nature-derived sensitivity of the biosensor platform, pointing out the differences between the scope of academic research and the market viewpoint.
Simple linguistic methods for improving a word alignment algorithm

This paper approaches word alignment problems and aims to show how some linguistic methods can combine with the statistical ones in order to get better results. In this sense, the system that participated in the shared task HLT/NAACL 2003 is presented in its actual version including the improvements the paper focuses on. This system, called TREQ-AL, works on parallel bilingual texts and needs some common pre-processing, such as tokenization, sentence-alignment, tagging, which are also shortly presented. In order to fulfill the word-alignment task, TREQ-AL relies on the output of a statistical translation-equivalence extractor along with which is described in a main section of the paper. The linguistic improvements taken into account are shown in another section and they refer to the cognate detection, the precedence constraint, pair assignments, collocations and language-specific rules. Instead of conclusions, graphical evaluation data are offered in the final section of the paper.
Biochemical Characterization of the Pseudomonas aeruginosa 101/1477 Metallo-β-Lactamase IMP-1 Produced byEscherichia coli

ABSTRACT The blaIMP gene coding for the IMP-1 metallo-β-lactamase produced by a Pseudomonas aeruginosaclinical isolate (isolate 101/1477) was overexpressed via a T7 expression system in Escherichia coli BL21(DE3), and its product was purified to homogeneity with a final yield of 35 mg/liter of culture. The structural and functional properties of the enzyme purified from E. coli were identical to those of the enzyme produced by P. aeruginosa. The IMP-1 metallo-β-lactamase exhibits a broad-spectrum activity profile that includes activity against penicillins, cephalosporins, cephamycins, oxacephamycins, and carbapenems. Only monobactams escape its action. The enzyme activity was inhibited by metal chelators, of which 1,10-o-phenanthroline and dipicolinic acid were the most efficient. Two zinc-binding sites were found. The zinc content of the P. aeruginosa 101/1477 metallo-β-lactamase was not pH dependent.
Smart Web Filtering

The internet consists of a range of different undesired information. Besides advertising or spam there is also other content, which specific users do not want to read about. While some do not want to see spoilers about the last episode of Game of Thrones, others may watch the finals of the European Championship one day later and therefore do not want to be informed about the result. Apart from that, there is a lot of annoying and uninteresting information as well, for example news about the private life of some celebrities. We introduce a web filter that takes undesired topics of the user as input and finds related terms using Wikidata. After applying our filtering algorithm, unwanted content is hidden and the user can decide to unhide it, if he wants to see it anyway. Our system managed to hide nearly 90% of chosen undesired topics of different types on 200 web pages. By only considering topics of specific types the system was able to filter 97% of the unwanted content.
From Design to Invariants: Detecting Attacks on Cyber Physical Systems

An approach is proposed to derive state-based invariants that, when programmed into a controller, proved to be effective in detecting cyber attacks on an Industrial Control System (ICS). The proposed approach begins with the ICS design and models its process dynamics using an extended hybrid automata from which the invariants are derived. Each invariant is programmed and inserted into an appropriate Programmable Logic Controller (PLC) as a companion to the control code. The invariant is active during ICS operation and serves to check on the validity of the system state in accordance with the system design. This approach, referred to as D2I for Design to Invariants, was evaluated on a fully operational 6-stage water treatment plant that uses a distributed process control system.
L-Glutamic acid and glutamine: Exciting molecules of clinical interest

Glutamine is one of the most abundant amino acids and participates in a variety of physiological functions, namely - as a major fuel source for enterocytes, as a substrate for neoglucogenesis in kidney, lymphocytes, and monocytes, a nutrient/substrate in muscle protein metabolism in response to infection, inflammation, and muscle trauma. Studies evaluating the role of glutamine have confirmed it's participation in maintaining mucosal integrity of the gastrointestinal tract following it's administration in patients with major bowel surgery. The role of glutamine as a protective agent in hepatobiliary dysfunction and as a supplement in total parenteral nutrition is well established, particularly, in patients under intensive care. L-Glutamic acid (L-GA) physiologically exists as glutamate. Glutamate along with glutamine plays a major role in amino acid metabolism and thus in maintaining nitrogen balance in the body. Glutamate is a well-established excitatory neurotransmitter in the central nervous system. There has been convincing evidence on protective activity of L-GA and a-ketoglutarate in vincristine-induced neurotoxicity. Based on the above information, a large number of studies have been carried out. The findings of recent clinical studies are presented below. Looking at the wide profile of activity, it has been proposed that though L-GA and glutamine were once considered nonessential for health, may now be considered as - 'conditionally essential' amino acids. While complete therapeutic role is yet to be elucidated, it may be anticipated that L-GA and glutamine may prove to be exciting molecules of interest to clinicians. The future research may therefore be directed at confirming the above activities and at investigating their role in other clinical conditions.
Candidate high-z protoclusters among the Planck compact sources, as revealed by Herschel-SPIRE

By determining the nature of all the Planck compact sources within 808.4 deg(2) of large Herschel surveys, we have identified 27 candidate protoclusters of dusty star-forming galaxies (DSFGs) that are at least 3 sigma overdense in either 250, 350, or 500 mu m sources. We find roughly half of all the Planck compact sources are resolved by Herschel into multiple discrete objects, with the other half remaining unresolved by Herschel. We find a significant difference between versions of the Planck catalogues, with earlier releases hosting a larger fraction of candidate protoclusters and Galactic cirrus than later releases, which we ascribe to a difference in the filters used in the creation of the three catalogues. We find a surface density of DSFG candidate protoclusters of (3.3 +/- 0.7) x 10(-2) sources deg(-2), in good agreement with previous similar studies. We find that a Planck colour selection of S-857/S-545 1. Our candidate protoclusters are a factor of 5 times brighter at 353 GHz than expected from simulations, even in the most conservative estimates. Further observations are needed to confirm whether these candidate protoclusters are physical clusters, multiple protoclusters along the line of sight, or chance alignments of unassociated sources.
Data exploration in meta‐analysis with smooth latent distributions

Meta‐analysis with discrete outcomes is interpreted as the estimation (in one or two dimensions) of a non‐parametric smooth latent distribution of event probabilities (or rates). A simple but efficient EM algorithm is presented. A fine grid is used and fast smoothing is done by penalized least squares. Data exploration is the primary goal, but the estimated distribution can also be used to compute useful statistics of treatment effects. Copyright © 2007 John Wiley & Sons, Ltd.