Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel isolation method and structural stability of a eukaryotic chaperonin: The TCP‐1 ring complex from rabbit reticulocytes

In the course of removing a contaminant from preparations of aminoacyl‐tRNA synthetase complexes, a novel purification method has been developed for the eukaryotic cytoplasmic chaperonin known as TRiC or CCT. This method uses only three steps: ammonium sulfate precipitation, pelleting into a sucrose cushion, and heparin‐agarose chromatography. As judged by electrophoresis, sedimentation, and electron microscopy, the preparations are homogeneous. The particle is identified as a chaperonin from electrophoretic polypeptide pattern, electron microscopic images, direct mass measurement by sedimentation velocity analysis, amino‐terminal sequencing, and ATP‐dependent refolding of rhodanese and actin.
The diagnostic and prognostic value of first hour glycogen phosphorylase isoenzyme BB level in acute coronary syndrome.

BACKGROUND Evaluating patients with symptoms suggestive of acute coronary syndrome (ACS) is a time consuming, expensive and problematic process in the emergency department. This study aimed to evaluate the diagnostic and prognostic value of glycogen phosphorylase isoenzyme-BB (GP-BB) in ACS. METHODS A total of 72 patients (mean age 61.8 ± 11.6 years) with ACS were enrolled. The ELISA method for determining GP-BB level was performed and considered positive at 〉 10 ng/mL. Duration of angina, type of ACS, demographic features, myoglobin, creatinine kinase and troponin T (cTnT) were also assessed. The cTnT levels eight hours after pain onset was considered the gold standard test for the diagnosis of myocardial infarction. RESULTS The most sensitive biomarker at first hour of admission was GP-BB (95.8%). However, the specificity of GP-BB was low (43.7%). Receiver operating characteristics curve analysis of the GP-BB level for predicting myocardial infarction revealed the area under the curve value as 0.82 (SE 0.04; 95% CI 0.78-0.85). Positive treadmill exercise test (60% vs 17%, p = 0.047), coronary artery disease (CAD; 59% vs 19%, p = 0.007), percutaneous coronary intervention (44% vs 27%, p = 0.031) and 30-day mortality and/or readmission (33% vs 5%, p = 0.028) were found to be higher in unstable angina (UA) patients having GP-BB (+). CONCLUSIONS GP-BB is considerably cardiosensitive at the first hour of admission in patients with ACS, but the specificity of GP-BB is lower and it is elevated in nearly half of the patients with UA. However, in this group, GP-BB predicts significant CAD and the combined end-point of mortality and re-hospitalization.
Ketamine and amphetamine both enhance synaptic transmission in the amygdala–nucleus accumbens pathway but with different time‐courses

Excitatory glutamatergic fibers from limbic structures, such as the hippocampus and the basolateral amygdala, are known to converge on the same neurons in the nucleus accumbens. We have recently shown that ketamine, at a dose (25 mg/kg) that produces psychosis‐like behaviors in rats, decreases glutamatergic transmission between the hippocampus and the nucleus accumbens. Here we investigated whether ketamine also affects glutamatergic transmission between the basolateral amygdala and the nucleus accumbens. We also studied the effects of amphetamine (1.5 mg/kg), known to evoke psychosis‐like behaviors in rats. We found that each drug produced a long‐lasting (at least 30 min) potentiation of synaptic efficacy in the projection from the basolateral amygdala to the nucleus accumbens. However, while this synaptic potentiation developed shortly after ketamine injection (within 4 min), it occurred after a 30‐min delay in rats injected with amphetamine. These data reveal, in freely behaving rats, that ketamine has a more rapid and powerful effect on projection targets of the basolateral amygdala than does amphetamine. Synapse 57:61–65, 2005. © 2005 Wiley‐Liss, Inc.
WD40-Repeat Proteins in Plant Cell Wall Formation: Current Evidence and Research Prospects

The metabolic complexity of living organisms relies on supramolecular protein structures which ensure vital processes, such as signal transduction, transcription, translation and cell wall synthesis. In eukaryotes WD40-repeat (WDR) proteins often function as molecular “hubs” mediating supramolecular interactions. WDR proteins may display a variety of interacting partners and participate in the assembly of complexes involved in distinct cellular functions. In plants, the formation of lignocellulosic biomass involves extensive synthesis of cell wall polysaccharides, a process that requires the assembly of large transmembrane enzyme complexes, intensive vesicle trafficking, interactions with the cytoskeleton, and coordinated gene expression. Because of their function as supramolecular hubs, WDR proteins could participate in each or any of these steps, although to date only few WDR proteins have been linked to the cell wall by experimental evidence. Nevertheless, several potential cell wall-related WDR proteins were recently identified using in silico approaches, such as analyses of co-expression, interactome and conserved gene neighborhood. Notably, some WDR genes are frequently genomic neighbors of genes coding for GT2-family polysaccharide synthases in eukaryotes, and this WDR-GT2 collinear microsynteny is detected in diverse taxa. In angiosperms, two WDR genes are collinear to cellulose synthase genes, CesAs, whereas in ascomycetous fungi several WDR genes are adjacent to chitin synthase genes, chs. In this Perspective we summarize and discuss experimental and in silico studies on the possible involvement of WDR proteins in plant cell wall formation. The prospects of biotechnological engineering for enhanced biomass production are discussed.
Baseline quality of life before intensive care: A comparison of patient versus proxy responses

Objective:To compare acute lung injury patients' self-reported, retrospective baseline quality of life before their intensive care hospitalization with population norms and retrospective proxy estimates. Design:Prospective cohort study using the Short Form 36 quality-of-life survey. Setting:Thirteen intensive care units at four teaching hospitals in Baltimore, Maryland. Patients:One hundred thirty-six acute lung injury survivors and their designated proxies. Interventions:Both patients and proxies were asked to estimate patient baseline quality of life before hospital admission using the Short Form 36 survey. Measurements and Main Results:Compared with population norms, quality-of-life scores were lower in acute lung injury patients across all eight domains, but the difference was significantly greater than the minimum clinically important difference in only two of eight domains (Physical Role and General Health). The mean paired difference between patient and proxy responses revealed no clinically important difference. However, &kgr; statistics demonstrated only fair to moderate agreement for all domains. Bland-Altman analysis revealed that, for all domains, proxies tended to overestimate quality of life when patient scores were low and underestimate the quality of life when patient scores were high. Conclusion:Retrospective assessment of quality of life before hospitalization revealed that acute lung injury patients' scores were consistently lower than population norms, but the magnitude of this difference may not be clinically important. Proxy assessments had only fair to moderate agreement with patient assessments. Across all eight Short Form 36 quality-of-life domains, proxy responses represented an attenuation of patient quality-of-life estimates.
Sources for Metals in the Intergalactic Medium

We present a discussion of possible sources of C, O, and Si in the intergalactic medium (IGM) using the yields of very massive stars (VMSs) and Type II supernovae (SNe II). The chemical evolution of the IGM is considered on the basis of analytical phenomenological models of hierarchical structure formation and the required metal production rates. Two regimes are considered: one for gas expulsion by VMSs and SNe II in low-mass halos prior to dissociation of H2 molecules and reionization, and the other for later SN II-driven outflows from intermediate-mass halos. We use recent data on the abundances of C, O, and Si in the IGM inferred from two UV background (UVB) models. We show that the values of [C/O]IGM and [Si/C]IGM inferred from the UVB model using quasars only cannot be explained by any existing stellar models. To account for the elemental ratios in the IGM by stellar models requires that a softer UVB model be used in calculating the elemental abundances from the data on ionic species. This then permits a solution using the yields of VMSs and SNe II. The results, in particular [Si/C]IGM, show that VMSs must provide ≳15% of the C in the IGM. The preferred scenario is that VMSs in low-mass halos provided between 15% and 60% of the C in the regime of very high redshift (z ≳ 15) and that galactic outflows provided the remainder during later epochs (4 < z ≲ 6). Thus, there is a large gap in z between metal production by VMSs very early in the chemical evolution of the IGM and subsequent contributions from galactic outflows. It is not possible to explain the observations by just SN II sources associated with galactic outflows. The observational estimate of [O/H]IGM implies a high [Fe/H]IGM ≥ -3 for all cases considered (including the case of a pure VMS source). This raises problems with regard to observations of metal-poor stars in the Galaxy. In addition, the [O/Fe] values for SN II models are in conflict with stellar observations, which indicate that the calculated average Fe yields of SNe II are a factor of ~2 too high. These issues and the general problem of relating abundances in the IGM to those in metal-poor stars remain to be investigated.
Link-alike: using wireless to share network resources in a neighborhood

Asymmetric broadband connections in the home provide a limited upstream pipe to the Internet. This limitation makes various applications, such as remote backup and sharing high definition video, impractical. However, homes in a neighborhood often have high bandwidth wireless networks, whose bandwidth exceeds that of a single wired uplink. Moreover, most (wired and wireless) connections are idle most of the time. In this paper, we examine the fundamental requirements of a system that aggregates upstream broadband connections in a neighborhood using wireless communication between homes. A scheme addressing this problem must operate efficiently in an environment that is: i) highly lossy; ii) broadcast in nature; and iii) half-duplex. We propose a novel scheme, Link-alike, that addresses those three challenges using opportunistic wireless reception, a novel wireless broadcast rate control scheme, and preferential use of the wired downlink. Through analytical and experimental evaluation, we demonstrate that our approach provides significantly better throughput than previous solutions based on TCP or UDP unicast.
Interpretation and Transformation for Abstracting Conversations

We address the challenge of automatically abstracting conversations such as face-to-face meetings and emails. We focus here on the stages of interpretation, where sentences are mapped to a conversation ontology, and transformation, where the summary content is selected. Our approach is fully developed and tested on meeting speech, and we subsequently explore its application to email conversations.
Scleroderma in children: an update

Purpose of reviewScleroderma, in its localized and systemic presentation, represents the third most frequent rheumatic condition in childhood after juvenile idiopathic arthritis and systemic lupus erythematosus. Early diagnosis, appropriate assessment and effective treatment are crucial to improve the long-term outcome. Recent findingsRecent studies, concerning histopathology and clinical associations with other conditions, open new horizons on the etiopathogenesis of scleroderma. New developments have been also reached in the field of outcome measures. In juvenile localized scleroderma (JLS), new techniques such as Doppler and laser Doppler imaging have shown their usefulness for the daily monitoring of the patients. In juvenile systemic sclerosis (JSSc), a new severity score has been developed and needs to be validated in future trials. Finally, a randomized, double-blind controlled trial, a multicenter consensus statement and long-term follow-up studies have confirmed the important role of methotrexate (MTX) for the treatment of JLS. SummaryStudies over recent years highlighted the role of imaging as outcome measures for JLS and introduced a severity score for JSSc. New studies on MTX confirmed its important role for the treatment of JLS.
Answering Aggregation Queries in a Secure System Model

As more sensitive data is captured in electronic form, security becomes more and more important. Data encryption is the main technique for achieving security. While in the past enterprises were hesitant to implement database encryption because of the very high cost, complexity, and performance degradation, they now have to face the ever-growing risk of data theft as well as emerging legislative requirements. Data encryption can be done at multiple tiers within the enterprise. Different choices on where to encrypt the data offer different security features that protect against different attacks. One class of attack that needs to be taken seriously is the compromise of the database server, its software or administrator. A secure way to address this threat is for a DBMS to directly process queries on the ciphertext, without decryption. We conduct a comprehensive study on answering SUM and AVG aggregation queries in such a system model by using a secure homomorphic encryption scheme in a novel way. We demonstrate that the performance of such a solution is comparable to a traditional symmetric encryption scheme (e.g., DES) in which each value is decrypted and the computation is performed on the plaintext. Clearly this traditional encryption scheme is not a viable solution to the problem because the server must have access to the secret key and the plaintext, which violates our system model and security requirements. We study the problem in the setting of a read-optimized DBMS for data warehousing applications, in which SUM and AVG are frequent and crucial.
Mutants of Escherichia coli with High Minimal Temperatures of Growth

O'Donovan, Gerard A. (University of California, Davis), Catherine L. Kearney, and John L. Ingraham. Mutants of Escherichia coli with high minimal temperatures of growth. J. Bacteriol. 90:611–616. 1965. —Three general classes of mutants showing increased minimal temperatures of growth have been isolated from Escherichia coli. These mutants do not grow at temperatures below 20 C, although their parents can grow at temperatures as low as 8 C. The first class of mutants (K-I) cannot grow below 20 C in either complex or minimal medium, but grows at nearly normal rates at 37 C on both types of media. Normal growth rate at 20 C can be conferred on these mutants by infection at a low multiplicity with a transducing phage grown on the parent. The second class of mutants (K-II) fails to grow only in minimal medium at 20 C. These mutants are characterized by their singular response to specific nutrients in minimal medium at 20 C. The third class of mutants (K-III) grows normally in minimal medium at all temperatures with either glucose or glycerol as the carbon source, but does not grow at 20 C with lactose as the carbon source.
Performance Evaluation of Hybrid Multipath Progressive Routing Protocol for MANETs

Researchers has been developed various routing protocols for Mobile Ad-hoc Networks (MANETs). Each protocol proposed and designed so far has its own merits and demerits. Researchers are trying continuously to develop advance routing protocols that can route messages towards their destination in an efficient way while consuming minimum amount of bandwidth and battery. In this work we are considering two well known MANET routing protocols, (1) Ad-hoc On-demand Distance Vector routing protocol, (2) Optimized Link State Routing protocol, and we have combined their preferred properties to formulate a new Hybrid routing protocol. In this paper we have proposed a routing protocol in hybrid category with the target of increasing the packet delivery ratio (PDR), throughput and decreasing endto-end delay. Our extensive simulation based experimental studies shows that the performance of proposed Hybrid Multipath Progressive Routing Protocol is better than the AODV, OLSR and ZRP on above and many other parameters. We have simulated the results on Exata Cyber 1.1.
Payoff Shares in Two-Player Contests

In imperfectly discriminating contests with symmetric valuations, equilibrium payoffs are positive shares of the value of the prize. In contrast to a bargaining situation, players’ shares sum to less than one because a residual share of the value is lost due to rent dissipation. In this paper, we consider contests with two players and investigate the relationship between these equilibrium shares and the parameters of a class of asymmetric Tullock contest success functions. Our main finding is that any players’ shares that sum up to less than one can arise as the unique outcome of a pure-strategy Nash equilibrium for appropriate parameters.
Finite countermodels for safety verification of parameterized tree systems

In this paper we deal with verification of safety properties of parameterized systems with a tree topology. The verification problem is translated to a purely logical problem of finding a finite countermodel for a first-order formula, which further resolved by a generic finite model finding procedure. A finite countermodel method is shown is at least as powerful as regular tree model checking and as the methods based on monotonic abstraction and backwards symbolic reachability. The practical efficiency of the method is illustrated on a set of examples taken from the literature.
Implementing a partial group based routing for homogeneous fat tree network on chip architecture

As the growing consumer electronic market imposes constraint such as compact product design and strict time to market, the traditional method of chip designing failed miserably to satisfy these constraints. With the evolution of Network-on-Chip, researchers have made an honest effort to resolve such issues but designing a network which encourages reusability of components and also scalable still remains an area where more refinement is necessary. In this paper we present before you a fat tree based network on chip. The entire design of the network with the nodes and switches has been described in details. The proposed architecture has been implemented and analyzed in a C++ based simulator. The analysis results have been presented at the end of the paper.
Symbol Grounding is an Empirical Problem: Neural Nets are Just a Candidate Component

"Symbol Grounding" is beginning to mean too many things to too many people. My own construal has always been simple: Cognition cannot be just computation, because computation is just the systematically interpretable manipulation of meaningless symbols, whereas the meanings of my thoughts don't depend on their interpretability or interpretation by someone else. On pain of infinite regress, then, symbol meanings must be grounded in something other than just their interpretability if they are to be candidates for what is going on in our heads. Neural nets may be one way to ground the names of concrete objects and events in the capacity to categorize them (by learning the invariants in their sensorimotor projections). These grounded elementary symbols could then be combined into symbol strings expressing propositions about more abstract categories. Grounding does not equal meaning, however, and does not solve any philosophical problems.
Trapping an Activated Conformation of Mammalian Carbamyl-phosphate Synthetase*

The amidotransferase or glutaminase domain (GLN domain) of mammalian carbamyl-phosphate synthetase II (CPSase II) catalyzes glutamine hydrolysis and transfers ammonia to the synthetase domain (CPS domain), where carbamyl phosphate formation is catalyzed in three consecutive reactions. The GLN and CPS domains are part of a single polypeptide and are connected via a 29-amino acid chain segment (GC linker). In contrast, the two comparable domains ofEscherichia coli CPSase are not fused, but are separate, noncovalently associated subunits. To establish the function of the GC linker in mammalian CPSase, it was deleted, and the two domains were directly fused. The deletion mutant not only catalyzed glutamine-dependent carbamyl phosphate synthesis, but was activated 10-fold relative to its wild-type counterpart. However, ammonia-dependent synthesis of carbamyl phosphate was abolished, indicating that ammonia no longer had access to the active site on the CPS domain. The mutant was still sensitive to inhibition by the allosteric effector UTP, but was no longer activated by the allosteric effector phosphoribosyl pyrophosphate, although evidence indicated that the latter could bind to the enzyme. The linker appears to serve as a spacer that allows the complex to cycle between two conformations, an open low activity form in which the ammonia site on the CPS domain is accessible and an activated conformation in which the ammonia generated in situ from glutamine is directly channeled to the CPS active site and access to exogenous ammonia is blocked.
Distributed Power Control for Spectrum-Sharing Femtocell Networks Using Stackelberg Game

In this paper, we investigate the distributed power allocation strategies for a spectrum-sharing femtocell network, where a central macrocell underlaid with several femtocells. Assuming that the macrocell protects itself by pricing the interference from the femtocells, a Stackelberg game is formulated to jointly consider the utility maximization of the macrocell and the femtocells. Then, the Stackelberg equilibrium for the proposed game is studied, and an effective distributed interference price bargaining algorithm with guaranteed convergency is proposed to achieve the equilibrium. Numerical examples are then presented to verify the proposed studies. It is shown that the algorithm is effective in distributed power allocation and macrocell protection requiring minimal network overhead for spectrum-sharing-based two-tier femtocell networks.
Essential Yeast Protein with Unexpected Similarity to Subunits of Mammalian Cleavage and Polyadenylation Specificity Factor (CPSF)

The 3′ ends of most eukaryotic messenger RNAs are generated by internal cleavage and polyadenylation. In mammals, there is a strict dependence of both reactions on the sequence AAUAAA, which occurs upstream of polyadenylation [poly(A)] sites and which is recognized by CPSF. In contrast, cis-acting signals for yeast 3′-end generation are highly divergent from those of mammals, suggesting that trans-acting factors other than poly(A) polymerase would not be conserved. The essential yeast protein Brr5/Ysh1 shows sequence similarity to subunits of mammalian CPSF and is required for 3′-end processing in vivo and in vitro. These results demonstrate a structural and functional conservation of the yeast and mammalian 3′-end processing machineries despite a lack of conservation of the cis sequences.