Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanism of Product Chain Length Determination and the Role of a Flexible Loop in Escherichia coliUndecaprenyl-pyrophosphate Synthase Catalysis*

The Escherichia coliundecaprayl-pyrophosphate synthase (UPPs) structure has been solved using the single wavelength anomalous diffraction method. The putative substrate-binding site is located near the end of the βA-strand with Asp-26 playing a critical catalytic role. In both subunits, an elongated hydrophobic tunnel is found, surrounded by four β-strands (βA-βB-βD-βC) and two helices (α2 and α3) and lined at the bottom with large residues Ile-62, Leu-137, Val-105, and His-103. The product distributions formed by the use of the I62A, V105A, and H103A mutants are similar to those observed for wild-type UPPs. Catalysis by the L137A UPPs, on the other hand, results in predominantly the formation of the C70 polymer rather than the C55 polymer. Ala-69 and Ala-143 are located near the top of the tunnel. In contrast to the A143V reaction, the C30intermediate is formed to a greater extent and is longer lived in the process catalyzed by the A69L mutant. These findings suggest that the small side chain of Ala-69 is required for rapid elongation to the C55 product, whereas the large hydrophobic side chain of Leu-137 is required to limit the elongation to the C55product. The roles of residues located on a flexible loop were investigated. The S71A, N74A, or R77A mutants displayed 25–200-fold decrease in k cat values. W75A showed an 8-fold increase of the FPP K m value, and 22–33-fold increases in the IPP K m values were observed for E81A and S71A. The loop may function to bridge the interaction of IPP with FPP, needed to initiate the condensation reaction and serve as a hinge to control the substrate binding and product release.
Gait speed in Parkinson disease correlates with cholinergic degeneration

Objective: We investigated dopaminergic and cholinergic correlates of gait speed in Parkinson disease (PD) and non-PD control subjects to test the hypothesis that gait dysfunction in PD may result from multisystem degeneration. Methods: This was a cross-sectional study. Subjects with PD but without dementia (n = 125, age 65.6 ± 7.3 years) and elderly subjects without PD (n = 32, age 66.0 ± 10.6 years) underwent [11C]dihydrotetrabenazine dopaminergic and [11C]methyl-4-piperidinyl propionate acetylcholinesterase PET imaging, and cognitive and clinical testing, including an 8.5-m walk in the dopaminergic “off” state. The fifth percentile of cortical cholinergic activity in the elderly without PD was used to define normal-range activity in the subjects with PD. Results: Normal-range cortical cholinergic activity was present in 87 subjects with PD (69.6%). Analysis of covariance using gait speed as the dependent variable demonstrated a significant model (F = 6.70, p < 0.0001) with a significant group effect (F = 3.36, p = 0.037) and significant slower gait speed in the low cholinergic PD subgroup (0.97 ± 0.22 m/s) with no significant difference between the normal-range cholinergic PD subgroup (1.12 ± 0.20 m/s) and control subjects (1.17 ± 0.18 m/s). Covariate effects were significant for cognition (F = 6.58, p = 0.011), but not for striatal dopaminergic innervation, sex, or age. Conclusion: Comorbid cortical cholinergic denervation is a more robust marker of slowing of gait in PD than nigrostriatal denervation alone. Gait speed is not significantly slower than normal in subjects with PD with relatively isolated nigrostriatal denervation.
Theories for ecological restoration in changing environment: Toward ‘futuristic’ restoration

Ecological restoration is one of the fastest growing fields in applied ecology providing new ideas and opportunities for biological conservation and natural resource management. Despite countless attempts in the past, large portions of restoration projects have been considered unsuccessful mainly due to: unrealistic goals; inadequate restoration plans based on an ad-hoc approach; lack of explicit and quantified evaluation criteria for restoration success; lack of ecological understanding; social, economic, and political constraints; or combinations of these factors. Existing ecological theories, particularly succession theories, may provide a conceptual framework for a restoration trajectory. However, projecting a ‘desirable’ trajectory and outcome is often challenged by the unpredictability of ecological communities in the changing environment. Particularly, the sustainability of reconstructed ‘historic’ ecosystems appears to be an unlikely goal in the ever-changing and unpredictable future environment. This paper calls for a shift in the restoration paradigm from ‘historic’ to ‘futuristic. ’ A ‘futuristic’ restoration is: (i) to set realistic and dynamic (instead of static) goals for future, instead of past, environment; (ii) to assume multiple trajectories acknowledging the unpredictable nature of ecological communities and ecosystems; (iii) to take an ecosystem or landscape approach, instead of ad-hoc gardening, for both function and structure; (iv) to evaluate the restoration progress with explicit criteria, based on quantitative inference; and (v) to maintain long-term monitoring of restoration outcomes. A theoretical framework for ‘futuristic’ restoration, in terms of goals, trajectories, evaluation criteria, and monitoring, along with a historical perspective is presented in this paper.
Swimming lessons, swimming ability, and the risk of drowning

Drowning is a leading cause of injury related death in many countries. Strategies to prevent these deaths depend upon characteristics of the victim and the specific circumstances surrounding the event. One preventive strategy that may be beneficial for persons of all ages and under nearly all circumstances is increased swimming ability, through some form of swimming instruction. However, a clear protective relationship between increased swimming ability and the risk of drowning has never been demonstrated. Studies focused on children, suggest that swimming ability may confer some protection, although the data are far from conclusive. This paper (1) reviews the current evidence regarding the relationship between swimming ability, swimming lessons and the risk of drowning, (2) reviews the past and present recommendations for swimming instruction and (3) outlines future research needs.
Le rôle des métriques d’évaluation dans le processus de recherche en TAL [The role of evaluation metrics in the NLP research process]

Le traitement automatique des langues (TAL) releve a la fois de la demarche scientifique et de la demarche technologique. Dans les deux cas, l'evaluation des systemes informatiques implementes est indispensable pour estimer le succes d'une recherche. S'inspirant du cadre ISO pour l'evaluation des logiciels, et utilisant une typologie des systemes de TAL fondee sur la place de la langue parmi les donnees d'entree ou de sortie, cet article analyse le role central des metriques d'evaluation a plusieurs etapes du processus de recherche en TAL. L'accent est mis sur les metriques qui comparent un resultat produit avec des resultats corrects attendus. L'analyse de plusieurs situations d'evaluation, en particulier le cas des systemes de traduction automatique, illustre l'importance d'un choix coherent des metriques et de l'utilisation conjointe de plusieurs metriques. L'influence du contexte d'utilisation sur le choix des metriques et le cas des systemes interactifs sont discutes en conclusion. Research in natural language processing (NLP) has both scientific and technological dimensions. In both cases, it is necessary to evaluate the implemented systems in order to assess the success of a study. This article, grounded in the ISO framework for software evaluation, introduces a typology of NLP systems based on the role of language as input or output data, in order to analyze the central role of evaluation metrics at several stages of the NLP research process. The article focuses on the evaluation metrics that compare the response of a system to a set of correct responses. The analysis of several evaluation examples, in particular the case of machine translation systems, shows the importance of a coherent choice of metrics and of the joint use of several metrics. The influence of the context of use on the set of metrics and the case of interactive systems are discussed as a conclusion.
Small RNA-mediated chromatin silencing directed to the 3′ region of the Arabidopsis gene encoding the developmental regulator, FLC

Small RNA-mediated chromatin silencing is well characterized for repeated sequences and transposons, but its role in regulating single-copy endogenous genes is unclear. We have identified two small RNAs (30 and 24 nucleotides) corresponding to the reverse strand 3′ to the canonical poly(A) site of FLOWERING LOCUS C (FLC), an Arabidopsis gene encoding a repressor of flowering. Genome searches suggest that these RNAs originate from the FLC locus in a genomic region lacking repeats. The 24-nt small RNA, which is most abundant in developing fruits, is absent in mutants defective in RNA polymerase IVa, RNA-DEPENDENT RNA POLYMERASE 2, and DICER-LIKE 3, components required for RNAi-mediated chromatin silencing. The corresponding genomic region shows histone 3 lysine 9 dimethylation, which was reduced in a dcl2,3,4 triple mutant. Investigations into the origins of the small RNAs revealed a polymerase IVa-dependent spliced, antisense transcript covering the 3′ FLC region. Mutation of this genomic region by T-DNA insertion led to FLC misexpression and delayed flowering, suggesting that RNAi-mediated chromatin modification is an important component of endogenous pathways that function to suppress FLC expression.
Cloning and Functional Expression of the Mucrosobin Protein, a β-Fibrinogenase of Trimeresurus mucrosquamatus (Taiwan Habu)

A venom-specific cDNA encoding for a thrombin-like enzyme designated as mucrosobin has been cloned and sequenced from the cDNA library of the venomous gland of Trimeresurus mucrosquamatus. The full-length cDNA of mucrosobin was assembled by oligonucleotide screening and 5′-rapid amplification of cDNA ends. The amino acid sequence deduced from the cDNA consists of 257 amino acid residues with a putative signal peptide of 24 residues. It is highly homologous to the other thrombin-like enzymes (batroxobin, mucofirase, and calobin), suggesting that it is a serine proteinase with a conserved catalytic triad of His41, Asp84 and Ser179 in the deduced form of mucrosobin protein. Northern blot analysis revealed that the mucrosobin gene encodes an mRNA of 1.5 kb and suggested a tissue-specific expression in the venomous gland. In an effort to study the biological property of mocrosobin, we have expressed the 28-kDa protein as inclusion bodies in Escherichia coli. For analyzing enzymatic activity, the inclusion bodies were solubilized and the recombinant protein was refolded with a two-step dialysis protocol. The refolded recombinant protein exhibited a specific β-fibrinogenolytic activity. This study offers a possibility of using genetic engineering to acquirie a functional snake venom protein with therapeutic potential.
The Alabama Preterm Birth Prevention Project

A preterm birth prevention program consisting of risk scoring, intensive weekly observation including cervical examinations, and detailed education about preterm labor signs and symptoms was tested in a predominantly black, indigent population. One thousand high-risk women were randomized to treatment or control groups. Although more preterm labor was diagnosed and treated in the treatment group, there were no significant differences between the groups with respect to mean birth weight or gestational age, spontaneous preterm delivery rates, or low or very low birth weight rates. The rates of respiratory distress syndrome and fetal and neonatal mortality, although greater in the treatment group, were not statistically different. However, the treatment-group infants had significantly more intracranial hemorrhages and spent more days on ventilators. At this institution, the preterm birth prevention program was not effective.
Direct muscle stimulation in acute quadriplegic myopathy

We have previously found that muscle is electrically inexcitable in severe acute quadriplegic myopathy (AQM). In contrast, muscle retains normal electrical excitability in peripheral neuropathy. To study the relationship between muscle electrical excitability and all types of flaccid weakness occurring in the intensive care unit, we identified 14 critically ill, weak patients and measured the amplitude of compound muscle action potentials (CMAPs) obtained with direct muscle stimulation (dmCMAP) and with nerve stimulation (neCMAP). In 11 of 14 patients dmCMAP amplitudes were reduced and the ratio of the neCMAP amplitude to the dmCMAP amplitude (nerve/muscle ratio) was indicative of loss of muscle electrical excitability. In 2 other patients, the nerve/muscle ratio indicated neuropathy. Direct muscle stimulation may allow differentiation of AQM from neuropathy even in comatose or encephalopathic critically ill patients. AQM may be more common than has previously been appreciated. © 1997 John Wiley & Sons, Inc. Muscle Nerve, 20, 665–673, 1997.
DNA‐adduct levels as a predictor of outcome for NSCLC patients receiving daily cisplatin and radiotherapy

We aimed to investigate whether biological factors related to radiosensitivity and chemosensitivity have prognostic significance in non‐small‐cell‐lung‐cancer (NSCLC) patients treated with daily low doses of cisplatin and radiotherapy. We treated 27 NSCLC patients with concomitant daily low‐dose cisplatin and radiotherapy between 1993 and 1995. Tumour specimens were analyzed for p53 and bcl‐2 expression, and for cell proliferation using antibodies against ki‐67. In addition, apoptosis was measured by an end‐labeling technique (TUNEL). Finally, cisplatin‐induced DNA modification in buccal cells was assessed immunocytochemically using a specific anti‐serum. Univariate and multivariate analyses were performed to assess the association between the different variables and survival. The median follow‐up was 41 months, and 21 patients (78%) have died. In a univariate analysis, age, tumour stage and cisplatin‐DNA‐adduct staining were the only factors significantly associated with survival (p < 0.05, log‐rank test). p53, bcl‐2, Ki‐67 and apoptosis showed no relationship with outcome. Multivariate analysis revealed that cisplatin‐DNA‐adduct staining remained an independent prognostic factor (hazard ratio, 0.10, 95% CI, 0.02–0.49), with shorter survival times for patients with low adduct staining. Int. J. Cancer (Pred. Oncol.) 89:160–166, 2000. © 2000 Wiley‐Liss, Inc.
Socialization to dying: social determinants of death acknowledgement and treatment among terminally ill geriatric patients.

Although the vast majority of deaths occur among terminally ill geriatric patients, little is known about the etiology of these patients' death acknowledgement and ultimate type of treatment. Based on interviews with 76 triads composed of physicians, terminally ill patients, and primary caregivers, this study uses the socialization perspective to identify the actors and actions that most strongly affect the patient's death acknowledgment and receipt of exclusively palliative care (i.e., socialization to the dying role). Whereas patient preferences and sociodemographic characteristics do not influence significantly the patient's odds of death acknowledgment, these odds are increased if their primary caregivers accept death, their physicians are not affiliated with a teaching hospital, and the terminal prognosis is disclosed to them and disclosed "matter-of-factly. " Patients who acknowledge death, whose agents value pain alleviation over life-prolongation, and whose physicians are not affiliated with a teaching hospital, are substantially more likely to receive exclusively palliative rather than curative terminal treatment.
Social norms campaigns: examining the relationship between changes in perceived norms and changes in drinking levels.

OBJECTIVE This study examined changes in drinking as a function of changes in perceived drinking norms following a social norms marketing campaign to correct normative misperceptions of college student drinking among residence hall students. The researchers expected students to reduce their estimates of typical student drinking following the social marketing campaign and that reductions in perceived norms would be associated with reduced drinking. METHOD Perceived norms and self-reported frequency and quantity of alcohol consumption were assessed before and after a social norms marketing campaign among 474 residence hall students. RESULTS Paired samples t tests revealed reduced perceptions of typical student drinking frequency and quantity. In addition, among nonabstainers, drinking quantity went down from pre- to postintervention. Further examination revealed that reductions in drinking were evident only among students whose perceived norms were reduced. CONCLUSIONS Results suggest that social norms marketing in residence halls can effectively reduce overestimates of typical student drinking and that reduction of perceived drinking norms are associated with reduced drinking.
An algorithm of improved association rules mining

In this paper, in order to reduce the times of scanning database when presented algorithms compute support of candidate frequent itemsets, in order to improve the method of computing support of candidate frequent itemsets, and in order to further improve the efficiency of algorithm, based on up search strategy of Apriori, we propose an algorithm of association rules mining based on sequence number. The algorithm would use the method of binary Boolean calculation to generate candidate frequent itemsets of binary form, and gain support of candidate frequent itemsets by computing Sequence Number Degree (SND), which is gained through computing these Sequence Number (SN) of all these items contained by candidate frequent itemsets. The algorithm only need scan once all these transactions in database to indeed improve the efficiency of algorithm. The experiment indicates the efficiency of this algorithm is faster and more efficient than presented algorithms.
Role of mitochondrial and cytoplasmic serine hydroxymethyltransferase isozymes in de novo purine synthesis in Saccharomyces cerevisiae.

One-carbon units are essential to a variety of anabolic processes which yield necessary cellular components including purines, pyrimidines, amino acids, and lipids. Serine hydroxymethyltransferase (SHMT) is the major provider of one-carbon units in the cell. The other product of this reaction is glycine. Both of these metabolites are required in de novo purine biosynthesis. In Saccharomyces cerevisiae, mitochondrial and cytoplasmic SHMT isozymes are encoded by distinct nuclear genes (SHM1 and SHM2). Molecular genetic analyses have begun to define the roles of these two isozymes in folate-mediated one-carbon metabolism [McNeil, J. B. , et al. (1996) Genetics 142, 371-381]. In our study, the SHM1 and SHM2 genes were disrupted singly and in combination to investigate the contributions of the two SHMT isozymes to the production of glycine and one-carbon units required in purine biosynthesis. Cell subfractionation experiments indicated that while only 5% of total activity was localized in the mitochondria, the specific activity in that compartment was much higher than in the cytoplasm. Growth and 13C NMR experiments indicate that the two isozymes function in different directions, depending on the nutritional conditions of the cell. When yeast was grown on serine as the primary one-carbon source, the cytoplasmic isozyme was the main provider of glycine and one-carbon groups for purine synthesis. When grown on glycine, the mitochondrial SHMT was the predominant isozyme catalyzing the synthesis of serine from glycine and one-carbon units. However, when both serine and glycine were present, the mitochondrial SHMT made a significant contribution of one-carbon units, but not glycine, for purine synthesis. Finally, NMR data are presented that suggest the existence of at least two sites of de novo purine biosynthesis in growing yeast cells, each being fed by distinct pools of precursors.
HpaB from Xanthomonas campestris pv. vesicatoria acts as an exit control protein in type III‐dependent protein secretion

The hrp (hypersensitive response and pathogenicity) gene cluster of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria encodes a type III secretion (TTS) system, which injects bacterial effector proteins into the plant cell. Here, we characterized hpaB (hpa, hrp‐associated), which encodes a pathogenicity factor with typical features of a TTS chaperone. We show that HpaB is important for the efficient secretion of at least five effector proteins but is dispensable for the secretion of non‐effectors such as XopA and the TTS translocon protein HrpF. GST pull‐down assays revealed that HpaB interacts with two unrelated effector proteins, AvrBs1 and AvrBs3, but not with XopA. The HpaB‐binding site is located within the first 50 amino acids of AvrBs3. This region also contains the targeting signal for HpaB‐dependent secretion, which is missing in HrpF and XopA. Intriguingly, the N‐termini of HrpF and XopA target the AvrBs3Δ2 reporter for translocation in a ΔhpaB mutant but not in the wild‐type strain. This indicates that HpaB plays an essential role in the exit control of the TTS system. Our data suggest that HpaB promotes the secretion of a large set of effector proteins and prevents the delivery of non‐effectors into the plant cell.
Trace Attack against Biometric Mobile Applications

With the exponential increase in the dependence on mobile devices in everyday life, there is a growing concern related to privacy and security issues in the Gulf countries; therefore, it is imperative that security threats should be analyzed in detail. Mobile devices store enormous amounts of personal and financial information, unfortunately without any security. In order to secure mobile devices against different threats, biometrics has been applied and shown to be effective. However, biometric mobile applications are also vulnerable to several types of attacks that can decrease their security. Biometric information itself is considered sensitive data; for example, fingerprints can leave traces in touched objects and facial images can be captured everywhere or accessed by the attacker if the facial image is stored in the mobile device (lost or stolen). Hence, an attacker can easily forge the identity of a legitimate user and access data on a device. In this paper, the effects of a trace attack on the sensitivity of biometric mobile applications are investigated in terms of security and user privacy. Experimental results carried out on facial and fingerprint mobile authentication applications using different databases have shown that these mobile applications are vulnerable to the proposed attack, which poses a serious threat to the overall system security and user privacy.