Miracle-dz/UniFAR-FTUs huggingface dataset:
Fold recognition, homology modeling, docking simulations, kinetics analysis and mutagenesis of ATP/CTP:tRNA nucleotidyltransferase from Methanococcus jannaschii

ATP/CTP:tRNA nucleotidyltransferases (NTases) and poly(A) polymerases (PAPs) belong to the same superfamily and their catalytic domains are remotely related. Based on the results of fold‐recognition analysis and comparison of secondary structure patterns, we predicted that these two NTase families share three domains, corresponding to “palm,” “fingers,” and “fingernails” in the PAP crystal structure. A homology model of tRNA NTase from Methanococcus jannaschii was constructed. Energy minimization calculations of enzyme‐nucleotide complexes and computer‐aided docking of nucleotides onto the enzyme's surface were carried out to explore possible ATP and CTP binding sites. Theoretical models were used to guide experimental analysis. Recombinant His‐tagged enzyme was expressed in Escherichia coli, and kinetic properties were characterized. The apparent KM for CTP was determined to be 38 μM, and the apparent KM for ATP was 21 μM. Three mutations of basic amino acids to alanine were created in a highly conserved region predicted to be in the vicinity of the nucleotide binding site. A deletion was also constructed to remove the C‐terminal structural domain defined by the model; it retained about 1% of wild type enzymatic activity using CTP as co‐substrate, confirming that detectable catalytic activity is exhibited by the N‐terminal domain, as defined by the model. Our results suggest a mechanism of differential ATP and CTP binding, which explains how the tRNA NTase, having only one catalytic site, utilizes different nucleotide triphosphates depending on the nature of the tRNA substrate. Proteins 2003;51:349–359. © 2003 Wiley‐Liss, Inc.
Style, Identity and Literacy: English in Singapore

Chapter 1: Social Practices and Linguistic Markets Chapter 2: Multilingualism in Late-Modern Singapore: A Portrait Chapter 3: Multilingualism in Late Modernity: Literacy as a Reflexive Performance of Identity Chapter 4: Some Data about our Data Chapter 5: Fandi and Ping: Literacy Practices and the Performance of Identities on Ambivalent Markets Chapter 6: Edwin, Wen and Yan: Styling Literacy Practices Inside and Outside the Classroom Chapter 7: Sha: A Comparison Chapter 8: Pedagogy, Literacy And Identity Chapter 9: The Dynamics of Language Distribution in Late-Modern Multilingual Singapore
Effect of valsartan compared with valsartan/hydrochlorothiazide on plasma levels of cellular adhesion molecules: the Val-MARC trial

Background: The Val-MARC trial showed that the angiotensin receptor blocker valsartan reduces high-sensitivity C reactive protein (hsCRP) levels, an effect that is independent of blood pressure, and seems to be neutralised by the addition of hydrochlorothiazide. Objective: To evaluate whether valsartan influences soluble intercellular adhesion molecule 1 (sICAM-1) or vascular cell adhesion molecule 1 (sVCAM-1). Design: Post-hoc analysis from a randomised trial. Setting: Val-MARC trial. Patients: 1188 patients with stage 2 hypertension. Intervention: Random allocation to either valsartan 320 mg (n = 607) or combination therapy with valsartan/hydrochlorothiazide 320 mg/12.5 mg (n = 581) for 6 weeks. Main outcome measure: Change in sICAM-1 and sVCAM-1 from baseline to 6 weeks of follow-up Results: After treatment, median (interquartile range) sICAM-1 levels were reduced by both valsartan alone (−4 (−25 to 16) ng/ml, p = 0.005) and valsartan/hydrochlorothiazide (−4 (−22 to 17) ng/ml, p = 0.028), such that the between-group difference was not significant (p = 0.7). The median percentage change from baseline was small in both groups (−1.6% and −1.3%). Median (interquartile range) sVCAM-1 levels were reduced by both valsartan alone (−13 (−70 to 42) ng/ml, p = 0.001) and valsartan/hydrochlorothiazide (−26 (−88 to 38), p<0.001); the between-group difference was of borderline significance (p = 0.051). The median percentage change from baseline was small (−2.1% and −4.4%). The reduction of sICAM-1 and sVCAM-1 was independent of blood pressure reduction (rs = 0.03 and rs = 0.06 for the relationship of change in systolic blood pressure with change in sICAM-1 and sVCAM-1, respectively). Conclusion: In contrast to hsCRP, both valsartan and valsartan/hydrochlorothiazide induced reductions of sICAM-1 and sVCAM-1 in the Val-MARC trial. These effects, although statistically significant, were small and independent of changes in blood pressure.
Global Information Assurance Certification Paper Interested in Learning More? Attributes of Malicious Files Attributes of Malicious Files 2

Malware has become a common component to most modern intrusions. Confirming a system is infected or finding the attacker-­‐planted backdoor can be a daunting task. To BLOCKIN BLOCKIN compound BLOCKIN BLOCKIN the BLOCKIN BLOCKIN situation, BLOCKIN BLOCKIN attackers BLOCKIN BLOCKIN are BLOCKIN BLOCKIN taking BLOCKIN BLOCKIN steps BLOCKIN BLOCKIN to BLOCKIN BLOCKIN actively BLOCKIN BLOCKIN evade BLOCKIN BLOCKIN traditional detection mechanisms. The foundations laid in this paper begin to develop an alternate and supplementary approach for identifying malware through detecting anomalies in the low-­‐level attributes of malicious files. Over 2.5 million malicious samples were analyzed and compared with a control set of non-­‐malicious files to develop the indicators presented.
Picture naming in typically developing and language-impaired children: the role of sustained attention.

BACKGROUND Children with specific language impairment (SLI) have problems not only with language performance but also with sustained attention, which is the ability to maintain alertness over an extended period of time. Although there is consensus that this ability is impaired with respect to processing stimuli in the auditory perceptual modality, conflicting evidence exists concerning the visual modality. AIMS To address the outstanding issue whether the impairment in sustained attention is limited to the auditory domain, or if it is domain-general. Furthermore, to test whether children's sustained attention ability relates to their word-production skills. METHODS & PROCEDURES Groups of 7-9 year olds with SLI (N = 28) and typically developing (TD) children (N = 22) performed a picture-naming task and two sustained attention tasks, namely auditory and visual continuous performance tasks (CPTs). OUTCOMES & RESULTS Children with SLI performed worse than TD children on picture naming and on both the auditory and visual CPTs. Moreover, performance on both the CPTs correlated with picture-naming latencies across developmental groups. CONCLUSIONS & IMPLICATIONS These results provide evidence for a deficit in both auditory and visual sustained attention in children with SLI. Moreover, the study indicates there is a relationship between domain-general sustained attention and picture-naming performance in both TD and language-impaired children. Future studies should establish whether this relationship is causal. If attention influences language, training of sustained attention may improve language production in children from both developmental groups.
The significance of sampling time in therapeutic drug monitoring of clozapine

Therapeutic drug monitoring (TDM) of clozapine is standardized to 12‐h postdose samplings. In clinical settings, sampling time often deviates from this time point, although the importance of the deviation is unknown. To this end, serum concentrations (s‐) of clozapine and its metabolite N‐desmethyl‐clozapine (norclozapine) were measured at 12 ± 1 and 2 h postdose.
Clomiphene Citrate as a New Treatment for SUNCT: Hormonal Manipulation for Hypothalamic‐Influenced Trigeminal Autonomic Cephalalgias

We present a patient with treatment refractory short‐lasting unilateral neuralgiform headache attacks with conjunctival injection and tearing (SUNCT) who was found to have low levels of serum testosterone supporting the hypothalamic connection to this trigeminal autonomic cephalalgia. Clomiphene citrate therapy induced a significant elevation of testosterone levels (by its effect on hypothalamic estrogen receptors) and led to a dramatic reduction in SUNCT attacks. Hormonal manipulation may be a treatment strategy for hypothalamic‐influenced trigeminal autonomic cephalalgias.
The Prevalence and Incidence of Convulsive Disorders in Children

Summary: Each year, about 150,000 children and adolescents in the United States will come to medical attention for evaluation of a newly occurring seizure disorder of some type. Between 2% and 4% of all children in Europe and the United States experience at least one convulsion associated with a febrile illness before the age of 5 years. The cumulative incidence of febrile convulsions among children ranges from about 1% in China to more than 8% in Japan and 14% in Guam. The peak incidence of a first febrile convulsion occurs in the second year of life. Between 0.5% and 1% of children and adolescents experience a seizure associated with other acute metabolic or neurologic insults; most of these occur in the neonatal period. The incidence of epilepsy (recurrent unprovoked seizures) in children and adolescents seems relatively consistent across all populations studied, ranging from 50 to 100/100,000. The highest incidence of epilepsy is in the first year of life. West syndrome accounts for about 2% of all childhood epilepsy, Lennox‐Gastaut syndrome for 1–2%, childhood absence epilepsy (pyknolepsy) for 10–15%, juvenile myoclonic epilepsy for 5%, and idiopathic localization‐related epilepsy for 10%. Between 0.5 and 1% of children experience a nonrecurrent, single, unprovoked convulsive episode. Following are the estimated numbers of children and adolescents with newly diagnosed convulsive disorders in the United States for the year 1990: febrile seizures, 100,000; neonatal seizures, 4,000; other provoked seizures, 6,000; single unprovoked seizures, 10,000; and epilepsy, 30,000.
Stereochemistry and size of sugar head groups determine structure and phase behavior of glycolipid membranes: densitometric, calorimetric, and X-ray studies.

The role carbohydrate moieties play in determining the structure and energetics of glycolipid model membranes has been investigated by small- and wide-angle X-ray scattering, differential scanning densitometry (DSD), and differential scanning microcalorimetry (DSC). The dependence of a variety of thermodynamic and structural parameters on the stereochemistry of the OH groups in the pyranose ring and on the size of the sugar head group has been studied by using an homologous series of synthetic stereochemically uniform glyceroglycolipids having glucose, galactose, mannose, maltose, or trimaltose head groups and saturated ether-linked alkyl chains with 10, 12, 14, 16, or 18 carbon atoms per chain. The combined structural and thermodynamic data indicate that stereochemical changes of a single OH group in the pyranose ring can cause dramatic alterations in the stability and in the nature of the phase transitions of the membranes. The second equally important determinant of lipid interactions in the membrane is the size of the head group. A comparison of lipids with glucose, maltose, or trimaltose head groups and identical hydrophobic moieties has shown that increasing the size of the neutral carbohydrate head group strongly favors the bilayer-forming tendency of the glycolipids. These experimental results provide a verification of the geometric model advanced by Israelachvili et al. (1980) [Israelachvili, J. N. , Marcelja, S. , & Horn, R. G. (1980) Q. Rev. Biophys. 13, 121-200] to explain the preferences lipids exhibit for certain structures. Generally galactose head groups confer highest stability on the multilamellar model membranes as judged on the basis of the chain-melting transition. This is an interesting aspect in view of the fact that galactose moieties are frequently observed in membranes of thermophilic organisms. Glucose head groups provide lower stability but increase the number of stable intermediate structures that the corresponding lipids can adopt. Galactolipids do not even assume a stable intermediate L alpha phase for lipids with short chain length but perform only Lc----HII transitions in the first heating. The C2 isomer, mannose, modifies the phase preference in such a manner that only L beta----HII changes can occur. Maltose and trimaltose head groups prevent the adoption of the HII phase and permit only L beta----L alpha phase changes. The DSD studies resulted in a quantitative estimate for the volume change associated with the L alpha----HII transition of 14-Glc. The value of delta v = 0.005 mL/g supports the view that the volume difference between L alpha and HII is minute. (ABSTRACT TRUNCATED AT 400 WORDS)
Distributed schemes for fair throughput in infrastructure-based IEEE 802.11 mesh networks

This paper studies throughput fairness among different basic service sets (BSSs) in infrastructure-based IEEE 802.11 mesh networks, where inter-BSS interference is unavoidable because of the difficulty in frequency and coverage planning and the limited number of non-overlapping frequency channels available for IEEE 802.11 networks. Two approaches are proposed for achieving fair throughput among the co-channel BSSs: (i) dynamic network allocation vectors (DNAV), which dynamically adjusts the co-channel interference by temporarily stopping transmissions in some BSSs using network allocation vectors (NAVs), and (ii) forced handoffs (FHO), which forces mobile stations (MSs) to handoff between neighboring BSSs. An optimization problem is formulated as well as a distributed scheme is proposed for each of the approaches for achieving the required throughput fairness while keeping high transmission throughput in the BSSs. Our results show that (i) the DNAV scheme can always achieve the required throughput fairness; (ii) performance of throughput fairness using the FHO scheme depends on coverage overlapping between the BSSs, and when there is strong coverage overlapping among the BSSs, the scheme achieves a higher throughput than the DNAV while achieving the required throughput fairness; and (iii) the converged throughput performance of the proposed distributed schemes is very close to the corresponding optimized one.
An in-situ measurement approach for IEEE 802.11 wireless multihop networks

A wireless multihop network is a communications network composed of nodes equipped with wireless interfaces and organized in an ad hoc manner. It has become an attractive and practical solution for providing flexible and extended wireless coverage over large areas. Measurement of physical layer quantities can provide useful information in the design of networking protocols and cross-layer optimization. In this paper, we present a cost-effective approach of performing physical-layer and link-layer measurements by exploiting the capabilities of inexpensive commercial-off-the-shelf (COTS) wireless routers and open-source software tools. Our experimental results show that the measurements made using inexpensive wireless routers are consistent with theoretical models and hence reliable. It is therefore possible to utilize the measurements to devise models or algorithms that will improve the performance of networking protocols.
A new algorithm for through wall human respiration monioring using GPR

The ground penetrating radar (GPR) are widely used in recent years due to its potential applications and unique capabilities, especially in the earthquake search or rescue. In this paper, a novel adaptive line enhancer (ALE) algorithm for human respiration monitoring through obstacle with low-power GPR is presented. The results of through wall experiments show that it is feasible to use this algorithm to monitor the respiration of human target through the obstacle. The correlation of the human target's breathing rate between the simultaneously measured results obtained by our method and by the contact respiratory chest band using Biopac mpl50 measurement system is very good.
A parallel decomposition algorithm for training multiclass kernel-based vector machines

We present a decomposition method for training Crammer and Singer's multiclass kernel-based vector machine model. A new working set selection rule is proposed. Global convergence of the algorithm based on this selection rule is established. Projected gradient method is chosen to solve the resulting quadratic subproblem at each iteration. An efficient projection algorithm is designed by exploiting the structure of the constraints. Parallel strategies are given to utilize the storage and computational resources available on the multiprocessor system. Numerical experiment on benchmark problems demonstrates that the good classification accuracy and remarkable time saving can be achieved.
A highly efficient method for long-chain cDNA synthesis using trehalose and betaine.

Obtaining full-length cDNA is important for many molecular biology methods like cDNA library construction or RACE-PCR (rapid amplification of cDNA ends). We have found that the inclusion of betaine alone and in combination with trehalose in reverse transcription results in longer cDNA synthesis products. As shown on the 14-kb long clarithrin mRNA with real-time PCR, a combination of 2 M betaine and 0.6 M trehalose leads to almost 9 times more cDNA with a length of 12.5 kb. This is due to the ability of betaine to resolve secondary structures of the RNA, thereby decreasing its melting temperature. The application of betaine in combination with trehalose should prove useful in all laboratory methods relying on full-length cDNA. (USA).
Cell-Based Regenerative Strategies for Treatment of Diabetic Skin Wounds, a Comparative Study between Human Umbilical Cord Blood-Mononuclear Cells and Calves' Blood Haemodialysate

Background Diabetes-related foot problems are bound to increase. However, medical therapies for wound care are limited; therefore, the need for development of new treatment modalities to improve wound healing in diabetic patients is essential and constitutes an emerging field of investigation. Methods Animals were randomly divided into 8 groups (I–VIII) (32 rats/group), all were streptozotocin (STZ)-induced diabetics except groups III and VIII were non-diabetic controls. The study comprised two experiments; the first included 3 groups. Group I injected with mononuclear cells (MNCs) derived from human umbilical cord blood (HUCB), group II a diabetic control group (PBS i.v). The second experiment included 5 groups, groups IV, V, and VI received topical HUCB-haemodialysate (HD), calves' blood HD, and solcoseryl, respectively. Group VII was the diabetic control group (topical saline). Standard circular wounds were created on the back of rats. A sample of each type of HD was analyzed using the high performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) system. Wound area measurement and photography were carried out every 4 days. Plasma glucose, catalase (CAT), malondialdehyde (MDA), nitric oxide (NO) and platelets count were assessed. Wound samples were excised for hydroxyproline (HP) and histopathological study. Results Treatment with HUCB MNCs or HUCB-HD resulted in wound contraction, increased CAT, NO, platelets count, body weights, and HP content, and decreased MDA and glucose. Conclusion Systemic administration of HUCB MNCs and topical application of the newly prepared HUCB-HD or calves' blood HD significantly accelerated the rate of diabetic wound healing and would open the possibility of their future use in regenerative medicine.
Genome Sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T, the Type Strains of Two Marine Roseobacter Genera

ABSTRACT Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T represent two marine genera in the globally significant Roseobacter clade of the Alphaproteobacteria. Here, we present the genome sequences of these organisms, isolated from the Sargasso Sea using dilution-to-extinction culturing, which offer insight into the genetic basis for the metabolic and ecological diversity of this important group.
Expression of the SUC2 Gene of Saccharomyces cerevisiae is Induced by Low Levels of Glucose

High levels of glucose repress expression of the SUC2 gene in the yeast Saccharomyces cerevisiae. We have discovered that low levels of glucose are required for maximal transcription of SUC2: SUC2 expression is induced about five‐ to ten‐fold in cells growing on low levels of glucose (0.1%) compared to cells growing on galactose or glycerol. Two pieces of evidence suggest that this low‐glucose‐induced expression is mediated by a repression mechanism that involves an upstream repression site in the SUC2 promoter (URSSUC2). First, deletion of the URSSUC2 results in expression of the SUC2 gene in the absence of glucose, and second the URSSUC2 mediates a six‐fold repression of a reporter gene when inserted into a heterologous promoter. However, this URSSUC2‐mediated repression occurs on all tested carbon sources, suggesting that this URS element acts in concert with all other promoter elements to respond to low concentrations of glucose. This repression requires the general repressor Ssn6p. SNF3, which encodes a glucose transporter that appears to be a sensor of low levels of glucose, is also required for low‐glucose‐induced expression of SUC2. ©1997 John Wiley & Sons, Ltd.
On Achieving Capture Power Safety in At-Speed Scan-Based Logic BIST

The applicability of at-speed scan-based logic built-in self-test (BIST) is being severely challenged by excessive capture power that may cause erroneous test responses for good chips. Different from conventional low-power BIST, this paper is the first that has explicitly focused on achieving capture power safety with a practical scheme called capture-power-safe BIST (CPS-BIST). The basic idea is to identify all possibly erroneous test responses and use the well-known technique of mask (partial-mask or full-mask) to block them from reaching the MISR. Experiments with large benchmark and industrial circuits show that CPS-BIST can achieve capture power safety with negligible impact on both test quality and area overhead.
Expertise localization discovered through correlation of key term distribution and community detection in co-author networks

We present an efficient and effective automatic method for determining the research focus of scientific communities found in co-authorship networks. It utilizes bibliographic data from a database to form the network, followed by fastgreedy community detection to identify communities within large connected components of the network. Text analysis techniques are used to identify community-specific significant terms which represent the topic of the community. In order to greatly reduce computation time, the `Topics' field of each publication in the network is analyzed rather than its entire text. Using this text analysis approach requires a certain level of statistical confidence,therefore analyzing very small communities is not effective with this technique. We find a minimum community size threshold of 8 coauthored papers; below this value, the community's topic cannot be reliably identified with this method. Additionally, we consider the implications this study has regarding factors involved in the formation of scientific communities in co-authorship networks.
Dendritic Cell Development: Multiple Pathways to Nature's Adjuvants

Dendritic cells are a system of bone marrow‐derived antigen‐presenting cells specialized for interaction with T lymphocytes and essential for initiating primary T cell immune responses. Recent investigation indicates that dendritic cells are of diverse origin, with at least two types of myeloid precursors and a lymphoid precursor implicated in their generation. Mature dendritic cell subtypes, while sharing the capacity to activate T cells, show additional functional specialization. Some dendritic cells are equipped with additional mechanisms to regulate the response of the T cells they activate, while others are able to interact with B cells and modify B cell responses.