Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Hendra Virus G Glycoprotein Residues That Are Critical for Receptor Binding

ABSTRACT Hendra virus (HeV) is an emerging paramyxovirus capable of infecting and causing disease in a variety of mammalian species, including humans. The virus infects its host cells through the coordinated functions of its fusion (F) and attachment (G) glycoproteins, the latter of which is responsible for binding the virus receptors ephrinB2 and ephrinB3. In order to identify the receptor binding site, a panel of G glycoprotein constructs containing mutations was generated using an alanine-scanning mutagenesis strategy. Based on a predicted G structure, charged amino acids residing in regions that could be homologous to those in the measles virus H attachment glycoprotein known to be involved in its protein receptor interaction were targeted. Using a coprecipitation-based assay, seven single-amino-acid substitutions in HeV G were identified as having significantly impaired binding to both the ephrinB2 and ephrinB3 viral receptors: D257A, D260A, G439A, K443A, G449A, K465A, and D468A. The impairment of receptor interaction conferred a concomitant diminution in their abilities to promote membrane fusion when coexpressed with F. The G glycoprotein mutants were also recognized by three or more conformation-dependent monoclonal antibodies of a panel of five, were expressed on the cell surface, and retained their abilities to bind and coprecipitate F. Interestingly, some of these mutant G glycoproteins coprecipitated with F more efficiently than wild-type G. Taken together, these data provide strong biochemical and functional evidence that some of these residues could be part of a conformation-dependent, discontinuous, and overlapping ephrinB2 and -B3 binding domain within the HeV G glycoprotein.
Geographical variations in the morphology of the small intestinal mucosa in apparently healthy individuals.

Macroscopic and microscopic photographs of seven jejunal biopsies illustrating the range of morphological changes found in southern Indian control subjects were circulated, together with a questionaire, to observers in different parts of the world. There was general agreement among the observers regarding the ‘normality’ of the biopsy showing the least changes and the abnormality of the two showing the most marked changes, but considerable disagreement over those intermediate between these two extremes. Opinion regarding the prevalence of the different biopsy appearances in control subjects varied significantly between temperate and tropical areas. A hierarchy of abnormality has been drawn up ranking countries in decreasing order of prevalence of the two most abnormal biopsies. Possible factors in the pathogenesis of the morphological changes in the jejunal mucosa in the tropics are discussed.
Heparan sulfate: growth control with a restricted sequence menu.

The growth and differentiation of cells and their organization into organs and tissues are complex processes, largely determined by the concerted actions of the ECM and small, soluble “effector” proteins in the pericellular milieu. Cells respond to the instructive potential of their microenvironment by means of specialized plasma membrane receptors, which elicit intracellular signals when activated by cognate ECM or soluble peptide ligands. In many receptor systems, ligand binds first to an abundant, low-affinity receptor, which draws the ligand onto the cell surface and then transfers it to a second, high-affinity receptor that transduces the appropriate signal into the cell. The most common and widely acting low-affinity receptors are the heparan sulfate proteoglycans (HSPGs), which play central roles in the reception and modulation of a wide range of growth factors, morphogens, and chemokines (1–3). They also act in combination with membrane integrins to control cell adhesion and migration in the ECM (4). The question arises as to how the structure and properties of the HSPGs enable them to fulfill such diverse and fundamental roles. These issues are the subject of intense experimental study, and a growing body of data has been published on the protein recognition properties of HSPGs and their association with signaling receptor complexes. However, more questions are being raised than problems solved by these analyses, perhaps as a result of the unusual properties of the HS chains that determine the majority of the interactions of PGs with external proteins. HS polysaccharides display a versatility in conformation and orientation of functional groups that permits them to employ different modes of binding with any individual protein or protein complex. Here, I argue that this versatility could offset the need for the controlled synthesis of a vast repertoire of defined sequences for exclusive binding of individual proteins.
Psychological treatment of depression in children and adolescents

Background This paper reviews research on the psychological treatment of depression in children. Method Manual and computer literature searches were performed. Results The most promising psychological interventions for depression in children are individual rather than family therapies. Cognitive – behavioural therapy seems to be an effective treatment for depressive symptoms and mild depressive disorders. It may also be a useful preventive intervention, though this remains to be conclusively demonstrated. There have been no systematic studies comparing psychological treatments with medication. Conclusions Studies comparing psychological treatments and medication are now required.
Modest inhibition of the growth hormone axis does not affect mitochondrial reactive oxygen species generation or redox state, unlike calorie restriction

Aim: Modest inhibition of the growth hormone (GH) axis by overexpression of the antisense GH gene in male Wistar rats reduced food intake and body weight, and lengthened the lifespan, even if fed ad libitum (AL). These findings were comparable with those induced by 30% calorie restriction (CR) in wild‐type (WT) rats, suggesting importance of the GH signal pathway in the effect of CR. The present study evaluated the effects of GH inhibition and CR on mitochondrial oxidative stress and redox state in the liver.
Patent mining : combining dictionary-based and machine-learning approaches

Exploration of the chemical patent space is essential for early-stage medicinal chemistry activities. The BioCreative CHEMDNER-patents task focuses on the recognition of chemical compounds in patents. This includes recognition of chemical named entities in patents (CEMP), classification of chemical-related patent titles and abstracts (CPD), and recognition of genes and proteins in patent abstracts (GPRO). In this study we tackled the CEMP and CPD tasks. We investigated an ensemble system where a dictionary-based approach is combined with a machine-learning approach to extract compounds from text. For this the performance of several lexical resources was assessed using Peregrine, our open source indexing engine. We combined our dictionarybased results on the patent corpus with the results of tmChem, a CRF-based chemical recognizer. To improve the performance of tmChem, three additional feature types where introduced (POS tags, lemmas, and word-vector clusters). When evaluated on the training data, our final system obtained an F-score of 85.21% for the CEMP task, and an accuracy of 91.53% for the CPD task. On the test set, our system ranked sixth among 21 teams for CEMP with an F-score of 86.82%, and second for CPD with an accuracy of 94.23%.
A simple and illustrative analytical model for the performance analysis of queuing systems loaded with mpeg streams

This paper consists of three parts. In the first one, we present a statistical analysis of experimental MPEG video sources and we discuss some modeling issues relevant to the performance evaluation of a queuing system loaded with such bit streams. In the second one, we propose a modeling approach (basic model) that considers the particular structure of MPEG streams and gives accurate results in a well-defined set of the queuing system parameters. In the third part, we introduce an extension of the basic model to take into account Long Range Dependences (LRD). This extension enlarges the range of applicability of the basic model. Our results show that the impact on the performance of the particular structure of MPEG sequences and the relevant bit rate distribution is always significant, while the impact of long term correlations is important only for large buffer sizes and high loads. These cases do not correspond often to realistic scenarios. The proposed model is validated with simulation results produced by using many experimental video sequences (both MPEG1 and MPEG2).
Whole-genome characterisation of Chikungunya virus from Aedes albopictus collected in Thailand

Chikungunya fever (CHIKF) is an important public-health problem in several countries. The causative agent, Chikungunya virus (CHIKV), is an enveloped, singlestranded RNA virus in the genus Alphavirus, of the family Togaviridae, and was initially discovered 58 years ago, in Tanzania (Ross, 1956; Griffin, 2001). The clinical signs and symptoms of CHIKF include high fever, arthralgia, myalgia, headache and rash (Jupp and McIntosh, 1988; Johnston and Peters, 1996), with the arthralgia, which can persist for several months or even years, more specific to CHIKF than any of the other symptoms (Rianthavorn et al., 2010). Some cases may also show haemorrhagic signs, such as epistaxis or gingivorrhagia (Schuffenecker et al., 2006). The first known outbreak of CHIKF in Thailand was confirmed, by antibody testing, in the 1960s (Hammon and Sather, 1964). Since then, there have been outbreaks reported in many of the country’s provinces, especially in the south, where the latest epidemic began in late 2008 (Thavara et al., 2009; Theamboonlers et al., 2009; http:// 203.157.15.4/chikun/; www.promedmail.org/ pls/apex/f? p52400:1202:4499468516694014:: NO::F2400_P1202_CHECK_DISPLAY,F2400_ P1202_PUB_MAIL_ID:X,74552). The two species of mosquito that are considered to be the main vectors of CHIKV, Aedes aegypti and Ae. albopictus, are both abundant in the southern provinces of Thailand, especially in the many rubber-tree plantations. Aedes albopictus may be the most important vector generally (Charrel et al., 2007; Thavara et al., 2009). Although the CHIKV that were recently isolated from patients in the southern part of Thailand harbored a mutation — A226V in their E1 genes — that enhances the transmissibility of the virus by this species (Pongsiri et al., 2010; Rianthavorn et al., 2010), little is known about the CHIKV carried by mosquitoes in Thailand. In this study, the entire genome of CHIKV isolated from Ae. albopictus collected in Uthai Thani province, in western–central Thailand (Fig. 1), was characterised, allowing the viral isolates from the mosquitoes to be compared with those previously collected from humans in the south of Thailand (Pongsiri et al., 2010).
Contribuciones a la dependencia y dimensionalidad en cópulas

El concepto de dependencia aparece por todas partes en nuestra tierra y sus habitantes de manera profunda. Son innumerables los ejemplos de fenomenos interdependientes en la naturaleza, asi como en aspectos medicos, sociales, politicos, economicos, entre otros. Mas aun, la dependencia es obviamente no deterministica, sino de naturaleza estocastica. Es por lo anterior que resulta sorprendente que conceptos y medidas de dependencia no hayan recibido suficiente atencion en la literatura estadistica. Al menos hasta 1966, cuando el trabajo pionero de E.L. Lehmann probo el lema de Hoeffding. Desde entonces, se han publicado algunas generalizaciones de este. Nosotros hemos obtenido una generalizacion multivariante para funciones de variacion acotada que agrupa a las planteadas anteriormente, al establecer la relacion entre los planteamiento presentados por Quesada-Molina (1992) y Cuadras (2002b) y extendiendo este ultimo al caso multivariante. Uno de los conceptos importante en la interpretacion estadistica esta relacionada con la dimension. Es por eso que hemos definido la dimensionalidad geometrica de una distribucion conjunta H en funcion del cardinal del conjunto de correlaciones canonicas de H, si H se puede representar mediante una expansion diagonal. La dimensionalidad geometrica ha sido obtenida para algunas de las familias de copulas mas conocidas. Para determinar la dimensionalidad de algunas de las copulas, se utilizaron metodos numericos. De acuerdo con la dimensionalidad, hemos clasificado a las copulas en cuatro grupos: las de dimension cero, finita, numerable o continua. En la mayoria de las copulas se encontro que poseen dimension numerable. Con el uso de dos funciones que satisfacen ciertas condiciones de regularidad, se ha obtenido una extension generalizada para la copula Gumbel-Barnett, a la que hemos deducido sus principales propiedades y medidas de dependencia para algunas funciones en particular. La copula FGM es una de las copulas con mas aplicabilidad en campos como el analisis financiero, y a la que se le han obtenido un gran numero de generalizaciones para el caso simetrico. Nosotros hemos obtenido dos nuevas generalizaciones. La primera fue obtenida al adicionar dos distribuciones auxiliares y la segunda generalizacion es para el caso asimetrico. En esta ultima caben algunas de las generalizaciones existentes. Para ambos casos se han deducido los rangos admisibles de los parametros de asociacion, las principales propiedades y las medidas de dependencia. Demostramos que si se conocen las funciones canonicas de una funcion de distribucion, es posible aproximarla a otra funcion de distribucion a traves de combinaciones lineales de las funciones canonicas. Como ejemplo, consideramos la copula FGM en dos dimensiones, en el sentido geometrico, debido a que se conocen sus funciones canonicas, y hemos comprobado numericamente que su aproximacion a otras copulas con dimension numerable es aceptablemente bueno.
Map-Matching Integrity Using Multihypothesis Road-Tracking

Efficient and reliable map-matching algorithms are essential for Advanced Driver Assistance Systems. While most existing solutions fail to provide trustworthy outputs when the situation is ambiguous (such as at road intersections, at roundabouts, or when roads are parallel), we present a new map-matching method that overcomes this limitation. It is based on multihypothesis road-tracking that takes advantage of the geographical database road connectivity to provide a reliable road-matching solution with a confidence indicator that can be used for integrity-monitoring purposes. The presented multihypothesis road-tracking method combines proprioceptive sensors (odometers and gyrometers) with global positioning system and map information. While usually the algorithmic complexity of a multihypothesis method is exponential, because each hypothesis can generate new hypotheses at each sampling step, we propose using road connectivity information to overcome this drawback, so that new hypotheses are created only when they are really necessary. The proposed decision rule of the integrity monitoring strategy takes account of the estimated location with the map, as well as the respective probabilities of the different hypotheses to handle ambiguity zones. The performance of the method presented in this article is illustrated by tests that were carried out in real-world road conditions.
Downregulation of the KIP family members p27KIP1 and p57KIP2 by SKP2 and the role of methylation in p57KIP2 inactivation in nonsmall cell lung cancer

Knowing the status of molecules involved in cell cycle control in cancer is vital for therapeutic approaches aiming at their restoration. The p27KIP1 and p57KIP2 cyclin‐dependent kinase inhibitors are nodal factors controlling normal cell cycle. Their expression in normal lung raises the question whether they have a mutual exclusive or redundant role in nonsmall cell lung cancer (NSCLC). A comparative comprehensive analysis was performed in a series of 70 NSCLCs. The majority of cases showed significantly reduced expression of both members compared to normal counterparts. Low KIP protein levels correlated with increased proliferation, which seems to be histological subtype preponderant. At mechanistic level, degradation by SKP2 was demonstrated, in vivo and in vitro, by siRNA‐methodology, to be the most important downregulating mechanism of both KIPs in NSCLC. Decreased p57KIP2‐transcription complements the above procedure in lowering p57KIP2‐protein levels. Methylation was the main cause of decreased p57KIP2‐mRNA levels. Allelic loss and imprinting from LIT1 mRNA contribute also to decreased p57KIP2 transcription. In vitro recapitulation of the in vivo findings, in A549 lung cells (INK4A‐B(−/−)), suggested that inhibition of the SKP2‐degradation mechanism restores p27KIP1 and p57KIP2 expression. Double siRNA treatments demonstrated that each KIP is independently capable of restraining cell growth. An additional demethylation step is required for complete reconstitution of p57KIP2 expression in NSCLC. © 2006 Wiley‐Liss, Inc.
Micro fluidic device to analyze the effect of cadmium on Caenorhabditis elegans

To analyze the condition of Caenorhabditis elegans (C. elegans) as a bioindicator, a micro fluidic device is developed. It can culture C. elegans and measure its capacitance change to assess the body volume of C. elegans; it is one of the characteristics to analyze the condition of C. elegans and directly measured from its capacitance change because the capacitance has a correlation with the body volume of C. elegans. The proposed micro fluidic device was implemented using a PDMS layer and a glass substrate that were bonded together. The PDMS layer has valves to control the position of C. elegans. Inside a chamber, it can culture and analyze the C. elegans. A pair of electrodes is used to measure the capacitance change. In this study, total of 10 L4 larval stage C. elegans were introduced into a chamber to be cultured and measured their capacitance change over 24 h. It was confirmed the correlation between the capacitance change and the body volume of C. elegans; r = 0.918 (p < 0.05) and the possibility of the proposed micro fluidic device that can analyze the condition of C. elegans as a bioindicator.
A leucine‐to‐phenylalanine substitution in the acetylcholine receptor ion channel in a family with the slow‐channel syndrome

Article abstract—The slow-channel syndrome is one of several congenital myasthenic syndromes that result from inherited abnormalities of the ion channel of the skeletal muscle acetylcholine receptor (AChR). The ion channel is formed by the second transmembrane domains (M2) of the four AChR subunits. We screened the genomic DNA of one family with the slow-channel syndrome for mutations in the coding sequences for the M2 domains of the four AChR subunits and report the identification of a missense mutation that causes a leucine-to-phenylalanine substitution at position 269 of the E subunit in three affected members of a family with the slow-channel syndrome. We propose that this mutation may be responsible for the disease.
Efficient secure channel coding scheme based on low-density Lattice codes

In this study, the authors introduce an efficient secure channel coding (joint cryptography-channel coding) scheme based on Latin square low-density lattice codes (Latin square LDLCs) over unconstrained power additive white Gaussian noise channel. They benefit the properties of Latin square LDLCs to dramatically reduce the key size of the proposed scheme while having an acceptable level of security compared with previous similar schemes. To reduce the key size, they consider two approaches: (i) saving the generating sequence of parity-check matrix of used Latin square LDLC as the part of secret key set; (ii) employing the Hermite normal form of the generator matrix of used Latin square LDLC as the encryption matrix. To provide an acceptable level of security, they consider three other strategies: (i) applying two hard problems related to lattices, i.e. shortest basis problem and closest vector problem; (ii) using a random rational vector as the perturbation (error) vector; (iii) exploiting the special joint encryption/LDLC encoding and joint decryption/LDLC decoding algorithms. Besides, the study discusses other efficiency analysis results consisting error performance and computational complexity of the proposed scheme.
Border-Flow Control by means of Phase Shifting Transformers

In this paper, a control scheme is demonstrated that regulates multiple phase shifting transformers (PSTs) to equally load the interconnectors of a border. A crucial step in the development of the control scheme is the derivation of phase shifter distribution factors (PSDFs), which indicate the influence of a PST on the active power flow on a certain line. Based on these PSDFs, the Linear Least Squares (LLS) method is used to calculate the optimal PST settings. The degree to which an even repartition can be obtained, depends on the number of PSTs in relation to the number of interconnectors. As a case- study, simulations are performed involving the Dutch and Belgian interconnectors.
Incubation Damage in the Radioimmunoassay for Human Plasma Glucagon and Its Prevention with “Trasylol”

Extremely high values for endogenous glucagon in fasting human plasma have been reported recently from several laboratories employing the radioimmunoassay for glucagon. The present report presents evidence that spuriously high values may result from damage to glucagon. Im which occurs during incubation with human plasma. After incubation with human plasma at 40C for four days, evidence of marked damage to glucagon-Im was present. The trichloracetic acid-precipitable fraction fell 65%, the chromatographically non-migrating fraction fell 11%, and the immunoreactive fraction declined 60% Dilution of plasma up to 1:8 failed to prevent this damage completely, but the addition of Trasylol, a proteinase inhibitor, prevented it almost completely. A plasma specimen which measured 0.7 mμ/ml of glucagon in a Trasylol-containing assay system, measured 2.0 mμg/ml in a Trasylol-free assay system; the apparently higher glucagon value obtained in the latter system could be accounted for entirely by a reduction in immunoreactive glucagon-Im. It is concluded that failure to prevent incubation damage to glucagon-Im during the radioimmunoassay of glucagon can lead to high values and that the addition of Trasylol to the assay system prevents this damage and results in lower values.
Extracting significant features based on candlestick patterns using unsupervised approach

This paper proposes algorithms for the extraction of features from candlestick patterns for technical analysis of share indices. The significant features consist of: the direction of candlestick, the gap between CLOSE and OPEN price of two candlesticks, the body level of current and previous candlesticks, and the length of the candlesticks. K-Means clustering approach is applied for solving the unclearly defined length of Upper Shadow, Body and Lower Shadow. The Thai SET index OHLC data from 1990 to 2017 are used as the experimental dataset. The results show the similarity between the candlestick chart from raw data and decoding data, which is applied by the proposed algorithms. The output result from the approach can be used as the input to other machine learning methods such as Artificial Neuron Networks, Reinforcement Learning, or Content Based Image Retrieval (CBIR).