Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of genes (SPON2 and C20orf2) differentially expressed between cancerous and noncancerous lung cells by mRNA differential display.

mRNA differential display was applied to three small cell lung carcinoma (SCLC) cell lines, six non-small cell lung carcinoma (NSCLC) cell lines, and three normal lung tissues to identify genes differentially expressed between lung carcinoma cells and normal lung tissues and between SCLC cells and NSCLC cells. We isolated five differentially expressed genes, two that were novel and three that were already known. DIL-1 (differentially expressed in cancerous and noncancerous lung cells; HGMW-approved symbol SPON2) and pulmonary surfactant apoprotein A were expressed in normal lung tissues but not in lung carcinoma cell lines, whereas DIL-2 (HGMW-approved symbol C20orf2) and nm23-H1 were expressed in lung carcinoma cell lines but not in normal lung tissues. The remaining gene, Annexin II, was expressed at a lower level in SCLC than in NSCLC and normal lung tissues. These genes were also differentially expressed in primary lung cancers. One of the two novel genes, DIL-1, encodes a secreted protein homologous to the Mindin/F-spondin family. The other, DIL-2, encodes a protein with a putative ATP/GTP binding site motif. These data provide basic information necessary to understand the differences in gene expression profiles between lung carcinoma and normal lung and between SCLC and NSCLC. Further characterization of these genes will help to clarify the molecular mechanisms of human lung carcinogenesis.
Cloning, functional organization, transcript studies, and phylogenetic analysis of the complete nitrogenase structural genes (nifHDK2) and associated genes in the archaeon Methanosarcina barkeri 227

Determination of the nucleotide sequence of the nitrogenase structural genes (nifHDK2) from Methanosarcina barkeri 227 was completed in this study by cloning and sequencing a 2.7-kb BamHI fragment containing the 3' end of nifK2 and 1,390 bp of the nifE2-homologous genes. Open reading frame nifK2 is 1,371 bp long including the stop codon TAA and encodes a polypeptide of 456 amino acids. Phylogenetic analysis of the deduced amino acid sequences of the nifK2 and nifE2 gene products from M. barkeri showed that both genes cluster most closely with the corresponding nif-1 gene products from Clostridium pasteurianum, consistent with our previous analyses of nifH2 and nifD2. The nifE gene product is known to be homologous to that of nifD, and our analysis shows that the branching pattern for the nifE proteins resembles that for the nifD product (with the exception of vnfE from Azotobacter vinelandii), suggesting that a gene duplication occurred before the divergence of nitrogenases. Primer extension showed that nifH2 had a single transcription start site located 34 nucleotides upstream of the ATG translation start site for nifH2, and a sequence resembling the archaeal consensus promoter sequence [TTTA(A/T)ATA] was found 32 nucleotides upstream from that transcription start site. A tract of four T's, previously identified as a transcription termination site in archaea, was found immediately downstream of the nifK2 gene, and a potential promoter was located upstream of the nifE2 gene. Hybridization with nifH2 and nifDK2 probes with M. barkeri RNA revealed a 4.6-kb transcript from N2-grown cells, large enough to harbor nifHDK genes and their internal open reading frames, while no transcript was detected from NH4(+)-grown cells. These results support a model in which the nitrogenase structural genes in M. barkeri are cotranscribed in a single NH4(+)-repressed operon.
First‐trimester ultrasonographic diagnosis of Langer mesomelic dysplasia in a previouslyaffected family

Langer mesomelic dysplasia (LMD, MIM #249 700) is a rare dwarfism characterized by the shortening of the middle segment of the limbs, aplasia or hypoplasia of the ulna and fibula, and variable hypoplasia of the mandible (Langer, 1967). LMD represents the homozygous form of the Leri Weill Syndrome (LWS), a bone dysplasia characterized by disproportionate short stature with mesomelic shortening of arms and legs associated with the typical feature of Madelung deformity (radial bowing and dorsal distal ulna dislocation) (Rappold et al., 2007). LWS and LMD are respectively caused by heterozygous or homozygous loss-of-function mutations in the SHOX gene, which is localized on the pseudoautosomal region 1 (PAR1) of the X chromosome (Belin et al., 1998). In the pathogenesis of both diseases, PAR1 deletions downstream the coding region of SHOX, involving the 3′ enhancer region of the gene, have been described (Benito-Sanz et al., 2005). In 2007, we have reported a consanguineous LWS family, in which we retrospectively showed a homozygous deletion in the 3′ enhancer region in a previously aborted fetus with a clinical ultrasonographic diagnosis of LMD at the 22nd week of pregnancy (Bertorelli et al., 2007). From the same family, we presently document that the LMD phenotype is readily recognizable at the end of the first trimester of pregnancy. The proband, a 30 years old quintigravida quartipara, was referred at the 12th week of pregnancy for ultrasonographic follow-up and prenatal diagnosis. The proband and her husband, first cousins, had already been characterized for their mutational status, and both are known to have a heterozygous deletion of the enhancer region of the SHOX gene (Bertorelli et al., 2007). Of the two living children (additional one daughter deceased in a car accident), one, at the age of 2.2 years was affected by LWS, having inherited the parental mutation in a heterozygote fashion (his stature is 82.5 cm, between the 2nd and the 5th centile of the
Dynamic contrast enhanced MRI for investigation of the blood-brain barrier in an experimental model of communicating hydrocephalus

L. Fanea, S. Rashid, J. P. McAllister, J. Li, H. Benveniste, M. Yu, and M. E. Wagshul Department of Radiology, SUNY Stony Brook, Stony Brook, NY, United States, Division of Pediatric Neurosurgery, Primary Children's Hospital, University of Utah, Salt Lake City, UT, United States, Department of Pediatric Neurosurgery, Children's Hospital of Michigan, Detroit, MI, United States, Medical Department, Brookhaven National Laboratory, Upton, NY, United States
Amphiphysin-positive paraneoplastic myelitis and stiff-person syndrome

Finding the underlying etiology of transverse myelitis (TM) can be challenging, as several disorders, including multiple sclerosis (MS), neuromyelitis optica, acute disseminated encephalomyelitis, postvaccine myelitis, Sjögren disease, neurosarcoidosis, infectious myelopathies, or idiopathic TM, may be causative.1 Paraneoplastic myelopathy, another differential diagnosis, is associated with a broad range of neoplasms and bears a severe risk to develop disability.2 Stiff-person syndrome (SPS) can occur as a result of some neoplasms and is characterized by skeletal muscle rigidity and spasms.
A computer vision approach for detection and counting of motorcycle riders in university campus

Essential tasks of automatic traffic monitoring are a vehicle classification and a vehicle or passenger counting system. These tasks provide useful data in planning transportation system. This paper presents an automatic system to classify a motorcycle and count riders on it. The system extracts moving objects and classifies them as a motorcycle or other moving objects based on features derived from their region properties using K-Nearest Neighbor (KNN) classifier. The heads of the riders on the recognized motorcycle are then counted based on projection profiling. Experiment results show an average correct motorcycle classification at 95.31% and correct rider count at 83.82%.
La conception : de la résolution de problèmes à la construction de représentations

De nombreuses publications d’orientation cognitiviste sur la conception vehiculent la presupposition, explicitee ou non, qu’il est possible de parler de « la » conception, independamment de sa situation de mise en œuvre. Dans cet esprit, Goel et Pirolli (1989) ont propose le concept de « conception generique ». Nous proposons ici un double developpement des propositions des deux auteurs : d’abord une extension de la vue sur la conception effectuee par divers auteurs dans des etudes sur la conception, notamment dans le domaine de l’ergonomie cognitive de la conception ; ensuite un changement de perspective sur la conception, qui consiste a analyser celle-ci comme une activite de construction de representations, plutot qu’une activite de resolution de problemes, approche heritee de Simon (1969/1996).
Influence of the deposition process on the bandgap and electrical properties of TiO2 solar cells

In this paper the bandgap variation have been studied as a function to the deposition temperature, annealing temperature and water ratio. High temperature during deposition or annealing has yielded in a low bandgap, while increasing water concentration has increase it. I-V characteristics for different thicknesses demonstrates a better Isc for a thicker sample. Conversion efficiency at a higher temperatures gave a better response towards the midrange of the UV spectrum. High temperature response in these cells can be considered as an advantage over that of conventional solar cells. We concluded that deposition parameters play a very important role in the optical and electrical characteristics of TiO2 nano materials, theses results reflected positively in producing TiO2 solar cells.
The Prognostic Value of Cell-Free DNA in Advanced Non-Small-Cell Lung Cancer

Background: Cell-free DNA (cfDNA) holds promise as a tumor marker of clinical importance. We aimed to investigate the prognostic value of baseline cfDNA in non small-cell lung cancer (NSCLC). Material and Methods: During a three-year period, patients with newly diagnosed, previously untreated advanced NSCLC were included in a consecutive, prospective marker-trial. Plasma was isolated from a pre-treatment peripheral blood sample and the level of total cfDNA was measured by an in-house assay qPCR-method. The treatment comprised carboplatin (AUC 5) intravenously day 1), and vinorelbine (30 mg/m2 intravenously day 1 and 60 mg/m2 perorally day 8) q3w for a maximum of six cycles. The primary end-point was overall survival (OS). Secondary end-points were progression free survival (PFS) and overall response rate (ORR). Results: 245 patients were included and received a minimum of 1 cycle of chemotherapy (median 4). The median OS was 8.9 months, the median PFS by intention to treat 5.4 months and the ORR was 25%. The patients were divided into four groups based on quartiles of cfDNA and subsequently dichotomized by the 75th percentile revealing a significantly worse prognosis for patients in the upper 75th percentile (median OS 4.9 months) compared to patients with lower levels (10.0 months) (HR 2.1, 95%CI 1.4 - 3.1, p 0.0001). A multivariate analysis confirmed the independent prognostic value of cfDNA. A subgroup analysis of patients with high cfDNA and poor performance status (PS = 2) identified a group of patients with even worse prognosis (median OS 2.0 versus 9.1 months, HR 3.6, 95%CI 1.4 - 9.2, p 0.0001). Similar and significant results were found when comparing level of cfDNA and PFS. Conclusions: High pre-treatment level of cfDNA seems to have a strong prognostic impact in patients with newly diagnosed advanced NSCLC. Combined with PS it identifies a patient group with minimal or no benefit of chemotherapy.
Efficient monitoring of large scale infrastructure as a service clouds

Cloud computing has had a transformative effect upon distributed systems research. It has been one of the precursors of supposed big data revolution and has amplified the scale of software, networks, data and deployments. Monitoring tools have not, however, kept pace with these developments. Scale is central to cloud computing but it is not its chiefly defining property. Elasticity, the ability of a cloud deployment to rapidly and regularly change in scale and composition, is what differentiates cloud computing from alternative paradigms of computation. Older tools originating from cluster, grid and enterprise computing predominantly lack designs which allow them to tolerate huge scale and rapid elasticity. This has led to the development of monitoring as a service tools; third party tools which abstract the intricacies of the monitoring process from the end user. These tools rely upon an economy of scale in order to deploy large numbers of VMs or servers which monitor multiple users’ infrastructure. These tools have restricted functionality and trust critical operations to third parties, which often lack reliable SLAs and which often charge significant costs. We therefore contend that an alternative is necessary. This thesis investigates the domain of cloud monitoring and proposes Varanus, a new cloud monitoring tool, which eschews conventional architectures in order to outperform current tools in a cloud setting. We compare a number of aspects of performance including monitoring latency, resource usage and elasticity tolerance. Through investigation of current monitoring approaches in conjunction with a thorough examination of cloud computing we derive a design for a new tool which leverages peer to peer and autonomic computing in order to build a tool well suited to the requirements of cloud computing. Through a detailed evaluation we demonstrate how this tool withstands the effects of scale and elasticity which impair current tools and how it employs a novel architecture which reduces fiscal costs. We demonstrate that Varanus maintains a low, near 1 second monitoring latency, regardless of both scale and elasticity and does so without imparting significant computational costs. We conclude that this design embodied by this tool represents a successful alternative to current conventional and monitoring as a service tools.
Algoritmo de classificação de especialistas em áreas na base de currículos Lattes

Este trabalho propoe um algoritmo para construir um ranking de especialistas da base de curriculos Lattes. Para isto, foi elaborado um algoritmo composto por tres estagios de processamento: Score Alfa, que analisa os titulos dos documentos baseado na ontologia definida para selecionar os assuntos e importâncias destes assuntos para cada publicacao; Score Beta, que analisa a qualidade das publicacoes utilizando conceitos definidos pela CAPES para beneficiar producoes publicadas em veiculos mais importantes; e Score Propagated, que analisa a importância de estar bem conectado a demais pesquisadores especialistas propagando o conhecimento obtido. Para o teste de precisao do algoritmo, utilizaram-se dados reais da area de Nanotecnologia.
User Profile Selection by Means of Ontology Reasoning

Service delivery platforms in telecommunication environments aim to host multiple services and to provide context-awareness and personalization features. This calls for an appropriate management of user profiles containing general user information as well as situation-dependent user preferences for the contextual personalization of these services. We present a user profile selection approach that decides on the selection of matching situation-dependent user preferences concerning the user's current situation. The presented approach takes advantage of ontology reasoning and is compared to other approaches. The comparison shows that our ontology reasoning based approach allows for more expressiveness concerning the specification of situation-dependent user preferences and hence leads to an added value for platform users.
Economic Policy Uncertainty & Asset Price Volatility

We document that fear about misspecified economic and central bank policies explain 45% of variations in bond option implied volatilities and interest rate volatilities. We endogenize this empirical pattern with a parsimonious equilibrium asset pricing model. In equilibrium, volatility is endogenously driven by fear of not knowing the data generating process that drives future economic and future central bank policies. An increase in either of these two uncertainties steepens the yield curve and increases the volatility in asset and option markets. A structural estimation of the equilibrium model explains the upward sloping term structures of interest rates, bond volatility, and option volatility, with only four in real-time observable economic and central bank related risk and uncertainty factors. The study ends with highlighting an inverse relationship between interest rates and volatility disparity from fundamentals during the policy hiking period of 2004-2007 and during QE1.
A Large Family of Putative Transmembrane Receptors Homologous to the Product of the Drosophila Tissue Polarity Gene frizzled(*)

In Drosophila melanogaster, the frizzled gene plays an essential role in the development of tissue polarity as assessed by the orientation of cuticular structures. Through a combination of random cDNA sequencing, degenerate polymerase chain reaction amplification, and low stringency hybridization we have identified six novel frizzled homologues from mammals, at least 11 from zebrafish, several from chicken and sea urchin, and one from Caenorhabditis elegans. The complete deduced amino acid sequences of the mammalian and nematode homologues share with the Drosophila frizzled protein a conserved amino-terminal cysteine-rich domain and seven putative transmembrane segments. Each of the mammalian homologues is expressed in a distinctive set of tissues in the adult, and at least three are expressed during embryogenesis. As hypothesized for the Drosophila frizzled protein, the frizzled homologues are likely to act as transmembrane receptors for as yet unidentified ligands. These observations predict the existence of a family of signal transduction pathways that are homologous to the pathway that determines tissue polarity in Drosophila.
Activation pathway of Src kinase reveals intermediate states as targets for drug design

Unregulated activation of Src kinases leads to aberrant signalling, uncontrolled growth and differentiation of cancerous cells. Reaching a complete mechanistic understanding of largescale conformational transformations underlying the activation of kinases could greatly help in the development of therapeutic drugs for the treatment of these pathologies. In principle, the nature of conformational transition could be modelled in silico via atomistic molecular dynamics simulations, although this is very challenging because of the long activation timescales. Here we employ a computational paradigm that couples transition pathway techniques and Markov state model-based massively distributed simulations for mapping the conformational landscape of c-src tyrosine kinase. The computations provide the thermodynamics and kinetics of kinase activation for the first time, and help identify key structural intermediates. Furthermore, the presence of a novel allosteric site in an intermediate state of c-src that could be potentially used for drug design is predicted. DOI: 10.1038/ncomms4397
Substroke approach to HMM-based on-line Kanji handwriting recognition

A new method is proposed for online handwriting recognition of Kanji characters. The method employs substroke HMM as minimum units to constitute Japanese Kanji characters and utilizes the direction of pen motion. The main motivation is to fully utilize the continuous speech recognition algorithm by relating sentence speech to Kanji character phonemes to substrokes, and grammar to Kanji structure. The proposed system consists input feature analysis, substroke HMM, a character structure dictionary and a decoder. The present approach has the following advantages over the conventional methods that employ whole character HMM. 1) Much smaller memory requirement for dictionary and models. 2) Fast recognition by employing efficient substroke network search. 3) Capability of recognizing characters not included in the training data if defined as a sequence of substrokes in the dictionary. 4) Capability of recognizing characters written by various different stroke orders with multiple definitions per one character in the dictionary. 5) Easiness in HMM adaptation to the user with a few sample character data.
Talmudic Methodology and Aristotelian Logic: David ibn Bilia's Commentary on the Thirteen Hermeneutic Principles

This article analyzes the commentary of R. David Ibn Bilia (Portugal, first half of the fourteenth century) on the Thirteen Hermeneutic Principles enumerated in the introduction to the Sifra. The commentary’s originality lies in its comprehensive and consistent application of Aristotelian logic to the realm of Talmudic-rabbinic methodology. Ibn Bilia’s project can be considered a Maimonidean interpretation of Jewish sources, although it deviates from the Maimonidean line by applying allegorical interpretation to the realm of the law. It is most likely that Ibn Bilia’s goal in his commentary was to defend the authority of the Talmud against the critique of contemporary radical rationalists, by demonstrating the affinities between Talmudic methods and Aristotelian principles of logic, and also to show that logic and philosophy were indispensable for the proper understanding of Jewish law. In the context of the controversy concerning the relationship between wisdom and tradition, Ibn Bilia’s commentary should be seen as voicing a middle position between two warring camps. From a hermeneutical point of view Ibn Bilia seems to have regarded Talmudic sources as having two layers of meaning – the plain-outer and the philosophical-inner. The first layer This article analyzes the historical and cultural significance of Ibn Bilia’s commentary, its sources in the Talmudic and Aristotelian literature, and its hermeneutical methods.
Heterocosmica: Fiction and Possible Worlds

"The universe of possible worlds is constantly expanding and diversifying thanks to the incessant world-constructing activity of human minds and hands. Literary fiction is probably the most active experimental laboratory of the world-constructing enterprise. "-from the author's Preface The standard contrast between fiction and reality, notes Lubomir Dolezel, obscures an array of problems that have beset philosophers and literary critics for centuries. Commentators usually admit that fiction conveys some kind of truth-the truth of the story of Faust, for instance. They acknowledge that fiction usually bears some kind of relation to reality-for example, the London of Dickens. But both the status of the truth and the nature of the relationship have baffled, frustrated, or repelled a long line of thinkers. In Heterocosmica, Lubomir Dolezel offers nothing less than a complete theory of literary fiction based on the idea of possible worlds. Beginning with a discussion of the extant semantics and pragmatics of fictionality-by Leibniz, Russell, Frege, Searle, Auerbach, and others-he relates them to literature, literary theory, and narratology. He also investigates theories of action, intention, and literary communication to develop a system of concepts that allows him to offer perceptive reinterpretations of a host of classical, modern, and postmodern fictional narratives-from Defoe through Dickens, Dostoevsky, Huysmans, Bely, and Kafka to Hemingway, Kundera, Rhys, Plenzdorf, and Coetzee. By careful attention to philosophical inquiry into possible worlds, especially Saul Kripke's and Jaakko Hintikka's, and through long familiarity with literary theory, Dolezel brings us an unprecedented examination of the notion of fictional worlds.