Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution of Tertiary Structure of Viral RNA Dependent Polymerases

Viral RNA dependent polymerases (vRdPs) are present in all RNA viruses; unfortunately, their sequence similarity is too low for phylogenetic studies. Nevertheless, vRdP protein structures are remarkably conserved. In this study, we used the structural similarity of vRdPs to reconstruct their evolutionary history. The major strength of this work is in unifying sequence and structural data into a single quantitative phylogenetic analysis, using powerful a Bayesian approach. The resulting phylogram of vRdPs demonstrates that RNA-dependent DNA polymerases (RdDPs) of viruses within Retroviridae family cluster in a clearly separated group of vRdPs, while RNA-dependent RNA polymerases (RdRPs) of dsRNA and +ssRNA viruses are mixed together. This evidence supports the hypothesis that RdRPs replicating +ssRNA viruses evolved multiple times from RdRPs replicating +dsRNA viruses, and vice versa. Moreover, our phylogram may be presented as a scheme for RNA virus evolution. The results are in concordance with the actual concept of RNA virus evolution. Finally, the methods used in our work provide a new direction for studying ancient virus evolution.
Development of a brief and effective temporomandibular disorder pain screening questionnaire: reliability and validity.

BACKGROUND Available screening instruments for identifying temporomandibular disorders (TMDs) exhibit methodological or logistic limitations. The authors conducted a study to develop and assess the validity of a self-report instrument in screening patients for pain-related TMDs. METHODS By using psychometric methods for item selection, the authors developed short (three-item) and long (six-item) versions of the questionnaire and evaluated them for validity among 504 participants. RESULTS Internal reliability was excellent, with coefficient α values of 0.87 and 0.93 for the short and long versions, respectively. When the authors dichotomized instrument scores at optimal thresholds, both versions had a sensitivity of 99 percent and a specificity of 97 percent for correct classification of the presence or absence of TMD. The specificity was at least 95 percent in the correct identification of people with nonpainful TMJ disorders or headahce without TMD pain. CONCLUSIONS With use of appropriate psychometric methodology, the selected items exhibited excellent content validity. The excellent levels of reliability, sensitivity and specificity demonstrate the validity and usefulness of this instrument. CLINICAL IMPLICATIONS Using this instrument will allow clinicians to identify more readily-and cost-effectively-most patients with painful TMD conditions for whom early and reliable identification would have a significant effect on diagnosis, treatment and prognosis.
Targeted therapy of human immunodeficiency virus‐related disease

Since the discovery of human immunodeficiency virus (HIV) as a pathogenic retrovirus linked to acquired immunodeficiency syndrome (AIDS), a number of potentially useful strategies for antiretroviral therapy of AIDS and its related diseases have emerged. One such strategy involves use of the broad family of 2′,3′‐dideoxynucleosides, to which 3′‐azido‐2′,3′‐dideoxythymidine (AZT) belongs. AZT has been shown to reduce the replication of HIV in vivo and to confer significant clinical benefits in patients in both early and advanced stages of infection. Other members of the family, 2′,3′‐dideoxycytidine (ddC), 2′,3′‐dideoxyinosine (ddI), and 2′,3′‐didehydro‐2′,3′‐dideoxythymidine (d4T), have also been reported to be active against HIV in short‐term clinical trials. The armamentarium of antiretroviral agents is rapidly growing. Various nonnucleoside agents have recently been identified to be active against HIV in vitro. HIV‐1 protease inhibitors are notable as possible new therapies for HIV‐1‐related diseases. However, we have faced several new challenges in the antiretroviral therapy in AIDS. These include long‐term drug‐related toxicities; emergence of drug‐resistant HIV variants; and development of various cancers, particularly as effective therapies prolong survival. Progress in understanding structure‐activity relations and clinical effectiveness will continue with dideoxynucleoside analogs. However, it seems certain that a variety of nonnucleoside analogs affecting multiple steps in viral replication will become available before long, and combination therapies using multiple antiretroviral drugs will be available. Such therapies will exert major effects against the moribidity and mortality caused by HIV. —Mitsuya, H. ; Yarchoan, R. ; Kageyama, S. ; Broder, S. Targeted therapy of human immunodeficiency virus‐related diseases. FASEB J. 5: 2369–2381; 1991.
The effects of trypan blue on chick embryos cultured in vitro.

Various malformations in rats and mice have been observed to be caused by administration of the vital dye, Trypan blue (Gillman, Gilbert, Gillman, & Spence, 1948; Fox & Goss, 1956, 1957; Hamburgh, 1952, 1954; Waddington & Carter, 1952, 1953). Recently Waddington & Perry (1956) reported a teratogenic effect of Trypan blue on Amphibian embryos. The present paper deals with the effects of this dye on cultured chick embryos. Hen9s eggs were incubated at 38°C. to the desired stage of development. Cultures were set up according to the ring technique described by New (1955). Precautions to maintain sterile conditions were observed throughout. An aqueous 1 per cent, solution of Gurr9s vital Trypan blue was diluted with Pannett Compton saline to 0·05 per cent. , which had been found to be a suitable concentration. A few drops of the dye solution were placed on the upper surface of the treated blastoderms.
Identification of a Novel Human ADP Receptor Coupled to Gi *

We have cloned and expressed a novel human G-protein-coupled receptor closely related to the human P2Y12 receptor. It corresponds to the orphan receptor called GPR86. GPR86 proved to be a Gi-coupled receptor displaying a high affinity for ADP, similar to the P2Y12receptor and can therefore be tentatively called P2Y13. In 1321N1 cells, the P2Y13 receptor coupled to the phosphoinositide pathway only when coexpressed with Gα16. Inositol trisphosphate formation was stimulated equipotently by nanomolar concentrations of ADP and 2MeSADP, whereas 2MeSATP and ATP were inactive. In CHO-K1 cells expressing the P2Y13 receptor, ADP and 2MeSADP had a biphasic effect on the forskolin-stimulated accumulation of cAMP: inhibition at nanomolar concentrations and potentiation at micromolar levels. In the same cells, ADP and 2MeSADP also stimulated the phosphorylation of Erk1 and Erk2, in a pertussis toxin-sensitive way. The tissue distribution of P2Y13 was investigated by reverse transcriptase-polymerase chain reaction, and the predominant signals were obtained in spleen and brain. Although these can be discriminated by tissue distribution and some pharmacological features, the P2Y12and P2Y13 receptors form a subgroup of related P2Y subtypes that is structurally different from the other P2Y subtypes but share coupling to Gi and a high affinity for ADP.
Versatile Action of Picomolar Gradients of Progesterone on Different Sperm Subpopulations

High step concentrations of progesterone may stimulate various sperm physiological processes, such as priming and the acrosome reaction. However, approaching the egg, spermatozoa face increasing concentrations of the hormone, as it is secreted by the cumulus cells and then passively diffuses along the cumulus matrix and beyond. In this context, several questions arise: are spermatozoa sensitive to the steroid gradients as they undergo priming and the acrosome reaction? If so, what are the functional gradual concentrations of progesterone? Do spermatozoa in different physiological states respond differentially to steroid gradients? To answer these questions, spermatozoa were confronted with progesterone gradients generated by different hormone concentrations (1 pM to 100 µM). Brief exposure to a 10 pM progesterone gradient stimulated priming for the acrosome reaction in one sperm subpopulation, and simultaneously induced the acrosome reaction in a different sperm subpopulation. This effect was not observed in non-capacitated cells or when progesterone was homogeneously distributed. The results suggest a versatile role of the gradual distribution of very low doses of progesterone, which selectively stimulate the priming and the acrosome reaction in different sperm subpopulations.
Geraniales flowers revisited: evolutionary trends in floral nectaries

Background and Aims The detailed relationships in Geraniales in their current circumscription have only recently been clarified. The disparate floral morphologies and especially the nectaries of the corresponding group have consequently not previously been studied in a phylogenetic context. Methods The present study investigates floral and especially nectary morphology and structure for representatives of 12 of the 13 currently accepted genera in the five families of the Geraniales. Flowers were studied using light microscopy and scanning electron microscopy. Key Results The data demonstrate the derivation of even the most disparate floral morphologies from a basic pentamerous and pentacyclic organization, with an obdiplostemonous androecium and receptacular nectaries associated with the antesepalous stamens. Divergent morphologies are explained by modifications of merosity (tetramerous flowers), symmetry (several transitions to zygomorphic flowers) and elaboration of the nectaries into variously shaped outgrowths and appendages, especially in Francoaceae. The divergent development of nectar glands ultimately leads to either a reduction in their number (to one in some Geraniaceae and Melianthaceae) or their total loss (some Vivianiaceae). Conclusions Floral morphology of the Geraniales shows a high degree of similarity, despite the variation in overall floral appearance and nectary morphology. A hypothesis on the transformation of the nectaries within the Geraniales is presented.
Design exploration with an application-specific instruction-set processor for ELA deinterlacing

Achievable performance gains, when accelerating applications using ASIPs, with a good sequence of specialized instructions, depends on the applications' available parallelism, and possibilities for optimizations and transformations. The type and number of operations, and the number of data transfers of the application are also critical factors. Much progress has been done on ASIP customized instruction-identification and selection research; they are usually based on operation clustering. In this paper, we propose to minimize the number of data transfers during execution of specialized instructions sequence by storing temporary values in user-defined registers. The method avoids costly data transfers and allows parallel processing of demanding computations. This method is applied to the design of an ASIP dedicated to edge line average deinterlacing, an algorithm used in HDTV. Experimental results show that our design method applied to this application, yields a speedup factor larger than 18
Stability of FRP Beams under Three-point Loading and LRFD Approach

This article presents the results of an experimental and theoretical study of I-section fiber-reinforced plastic (FRP) beams subjected to a gradually increasing midspan load. The load is applied about the beam major axis from the compression flange side through a point below the shear center. The boundary conditions are flexurally and torsionally pinned. A 4 2 1/4 in. 3 pultruded I-section is adopted for the study and beam span lengths of 108, 96, 84, and 72 in. are used. The flexural-torsional response of the FRP beams is studied experimentally up to the maximum loadcarrying capacity. The experimental peak loads are compared with those arrived at theoretically using an equilibrium approach and are found to be in good agreement. To obtain a design expression for estimating the beam buckling load, an elastic buckling moment expression from the load and resistance factor design (LRFD) specification of the American Institute of Steel Construction is first modified. Next, a LRFD approach for the beam is outlined and its use demonstrated through analysis and design examples.
Implementation and evaluation of a low-literacy diabetes education computer multimedia application.

OBJECTIVE To evaluate a clinic-based multimedia intervention for diabetes education targeting individuals with low health literacy levels in a diverse population. RESEARCH DESIGN AND METHODS Five public clinics in Chicago, Illinois, participated in the study with computer kiosks installed in waiting room areas. Two hundred forty-four subjects with diabetes were randomized to receive either supplemental computer multimedia use (intervention) or standard of care only (control). The intervention includes audio/video sequences to communicate information, provide psychological support, and promote diabetes self-management skills without extensive text or complex navigation. HbA(1c) (A1C), BMI, blood pressure, diabetes knowledge, self-efficacy, self-reported medical care, and perceived susceptibility of complications were evaluated at baseline and 1 year. Computer usage patterns and implementation barriers were also examined. RESULTS Complete 1-year data were available for 183 subjects (75%). Overall, there were no significant differences in change in A1C, weight, blood pressure, knowledge, self-efficacy, or self-reported medical care between intervention and control groups. However, there was an increase in perceived susceptibility to diabetes complications in the intervention group. This effect was greatest among subjects with lower health literacy. Within the intervention group, time spent on the computer was greater for subjects with higher health literacy. CONCLUSIONS Access to multimedia lessons resulted in an increase in perceived susceptibility to diabetes complications, particularly in subjects with lower health literacy. Despite measures to improve informational access for individuals with lower health literacy, there was relatively less use of the computer among these participants.
Character-Level Machine Translation Evaluation for Languages with Ambiguous Word Boundaries

In this work, we introduce the TESLA-CELAB metric (Translation Evaluation of Sentences with Linear-programming-based Analysis -- Character-level Evaluation for Languages with Ambiguous word Boundaries) for automatic machine translation evaluation. For languages such as Chinese where words usually have meaningful internal structure and word boundaries are often fuzzy, TESLA-CELAB acknowledges the advantage of character-level evaluation over word-level evaluation. By reformulating the problem in the linear programming framework, TESLA-CELAB addresses several drawbacks of the character-level metrics, in particular the modeling of synonyms spanning multiple characters. We show empirically that TESLA-CELAB significantly outperforms character-level BLEU in the English-Chinese translation evaluation tasks.
Development of vehicular-collision avoidance support system by inter-vehicle communications - VCASS

In order to achieve a safe automotive society, it is necessary to develop an on-board intelligent system with inter-vehicle communications (IVC). We want to avoid vehicle collisions under most situations, such as intersections, highways, and blind corners, by using IVC technology through wireless ad hoc networks. The paper describes a vehicular collision avoidance support system (VCASS), and shows its performance by various experiments with two real vehicles. We have installed personal computers, telecommunication equipment, and GPS in the vehicles. A vehicle exchanges location information and velocity vectors with the other by a UDP broadcast, and calculates the relative position/speed. Vehicles warn the drivers of the possibility of collision. We verify the validity and effectiveness of VCASS by experiments.
The structure and mechanics of cork

The excellence of cork for stopping bottles, for thermal and sound insulation, and as a shock-absorbing material for flooring and packaging is due to the special shape, size and structure of its cells. When loaded, the cell walls bend or buckle, giving large recoverable deflexions and large energy absorption. We have investigated the structure of cork and have measured its moduli and other mechanical characteristics. These can be broadly explained in terms of cell-wall deformation.
Cognitive externalism meets bounded rationality

When proponents of cognitive externalism (CE) turn to empirical studies in cognitive science to put the framework to use and to assess its explanatory success, they typically refer to perception, memory, or motor coordination. In contrast, not much has been said about reasoning. One promising avenue to explore in this respect is the theory of bounded rationality (BR). To clarify the relationship between CE and BR, we criticize Andy Clark's understanding of BR, as well as his claim that BR does not fit his version of CE. We then propose and defend a version of CE—“scaffolded cognition”—that is not committed to constitutive claims about the mind, but still differs from mainstream internalism. Finally, we analyze BR from our own CE perspective, thereby clarifying its vague appeals to the environment, and argue that cognitive internalism cannot explain important aspects of the BR program.
Paternal age as an independent factor does not affect embryo quality and pregnancy outcomes of testicular sperm extraction‐intracytoplasmic sperm injection in azoospermia

This study was performed to evaluate the independent influence of paternal age affecting embryo development and pregnancy using testicular sperm extraction (TESE)‐intracytoplasmic sperm injection (ICSI) in obstructive azoospermia (OA) and nonobstructive azoospermia (NOA). Paternal patients were divided into the following groups: ≤30 years, 31–35 years, 36–40 years, 41–45 years and ≥46 years. There were no differences in the rates of fertilisation or embryo quality according to paternal and maternal age. However, clinical pregnancy and implantation rates were significantly lower between those ≥46 years of paternal age compared with other age groups. Fertilisation rate was higher in the OA than the NOA, while embryo quality, pregnancy and delivery results were similar. Clinical pregnancy and implantation rates were significantly lower for patients ≥46 years of paternal age compared with younger age groups. In conclusion, fertilisation using TESE in azoospermia was not affected by the independent influence of paternal age; however, as maternal age increased concomitantly with paternal age, rates of pregnancy and delivery differed between those with paternal age <41 years and ≥46 years. Therefore, paternal age ≥46 years old should be considered when applying TESE‐ICSI in cases of azoospermia, and patients should be advised of the associated low pregnancy rates.
A New Approximation Algorithm for the Steiner Tree Problem with Performance Ratio 5/3

In this paper we present an RNC approximation algorithm for the Steiner tree problem in graphs with performance ratio 5/3 and RNC approximation algorithms for the Steiner tree problem in networks with performance ratio 5/3+? for all ? 0. This is achieved by considering a related problem, the minimum spanning tree problem in weighted 3-uniform hypergraphs. For that problem we give a fully polynomial randomized approximation scheme. Our approach also gives rise to conceptually much easier and faster (though randomized) sequential approximation algorithms for the Steiner tree problem than the currently best known algorithms from Karpinski and Zelikovsky which almost match their approximation factor.
Expression of collagen, interstitial collagenase, and tissue inhibitor of metalloproteinases-1 in restenosis after carotid endarterectomy.

Extracellular matrix is the principal component of the fibrous caps of atherosclerotic plaques and intimal hyperplastic lesions of reconstructed arteries. Interstitial collagen form an important part of the matrix, and the balance between collagen synthesis and degradation by interstitial collagenase (matrix metalloproteinase-1, MMP-1) may determine whether plaques rupture or vessels develop stenosis. We examined type I procollagen gene expression in human atherosclerotic and restenotic carotid arteries using in situ messenger RNA (mRNA) hybridization and the expression of MMP-1 and its endogenous inhibitor (tissue inhibitor of metalloproteinases-1, TIMP-1) by immunohistochemistry. Compared with normal arteries, atherosclerotic plaques bed increased expression of immunoreactive MMP-1 and TIMP-1 with modest increase of type 1 procollagen mRNA. Early restenotic lesions (< 1.5 years) contained abundant type I procollagen mRNA but little immunoreactive MMP-1 and TIMP-1. Late restenotic lesions (> 4 years) resembled atheroma and exhibited increased immunoreactive MMP-1 and TIMP-1 as well as abundant type I procollagen mRNA. Compared with atherosclerotic plaques, type I procollagen is increased and MMP-1 is decreased in early restenotic lesions. MMP-1 and TIMP-1 expressions are upregulated in lesions with a clear atheroma. These findings suggest that the balance between proteolysis and matrix synthesis may influence both the stability of atheromatous plaques and the development of restenotic lesions.
Medicinal and edible lignicolous fungi as natural sources of antioxidative and antibacterial agents

The antioxidant activity of organic extracts of eight fungal species, Ganoderma lucidum, Ganoderma applanatum, Meripilus giganteus, Laetiporus sulphureus, Flammulina velutipes, Coriolus versicolor, Pleurotus ostreatus and Panus tigrinus, was evaluated for free radical (DPPH· and OH·) scavenging capacity and an effect on lipid peroxidation, and the antibacterial activity was tested by the agar well diffusion method. The highest DPPH· scavenging activity was found in the methanol extract of G. applanatum (12.5 μg/mL, 82.80%) and the chloroform extract of G. lucidum (510.2 μg/mL, 69.12%). The same extracts also showed the highest LP inhibition (91.83%, 85.09%) at 500 μg/mL, while the methanol extracts of G. applanatum and L. sulphureus showed the highest scavenging effect on OH· radicals (68.47%, 57.06%, respectively) at 400 μg/mL. A strong antibacterial activity against Gram‐positive bacteria was also manifested. The antioxidative potencies correlated generally with the total phenol content (0.19–9.98 mg/g). The HPLC determination showed that the majority of analysed species contained gallic and protocatechic acids. Consequently, these fungi are shown to be potential sources of antioxidative and antibacterial agents. Copyright © 2010 John Wiley & Sons, Ltd.
Prediction of Long-Term Performance and Durability of BFRP Bars under the Combined Effect of Sustained Load and Corrosive Solutions

AbstractUnlike carbon-fiber-reinforced polymer (CFRP) bars and the maturely developed glass FRP (GFRP) bars, the long-term performance of the newly developed basalt-fiber reinforced polymer (BFRP) bars under severe environmental conditions remains unclear. This paper evaluates the residual tensile properties of unstressed and stressed BFRP bars exposed to four types of simulated harsh environments: alkaline solution, salt solution, acid solution, and de-ionized water at 25, 40, and 55°C. Microstructural analysis using scanning electronic microscopy (SEM) was also conducted to reveal the inherent degradation mechanism of BFRP bars in alkaline environment. The residual tensile strength of unstressed BFRP bars exposed to alkaline solution was used for long-term performance prediction based on Arrhenius theory. The results showed that the effect on the durability of BFRP bars exposed to acid, salt, and deionized water was less than that for bars exposed to alkaline solution. The effects of sustained stress on.