Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and characterization of an organotypic model of Barrett's esophagus

Understanding the molecular and cellular processes underlying the development, maintenance, and progression of Barrett's esophagus (BE) presents an empirical challenge because there are no simple animal models and standard 2D cell culture can distort cellular processes. Here we describe a three‐dimensional (3D) cell culture system to study BE. BE cell lines (CP‐A, CP‐B, CP‐C, and CP‐D) and esophageal squamous keratinocytes (EPC2) were cultured on a matrix consisting of esophageal fibroblasts and collagen. Comparison of growth and cytokeratin expression in the presence of all‐trans retinoic acid or hydrochloric acid was made by immunohistochemistry and Alcian Blue staining to determine which treatments produced a BE phenotype of columnar cytokeratin expression in 3D culture. All‐trans retinoic acid differentially affected the growth of BE cell lines in 3D culture. Notably, the non‐dyplastic metaplasia‐derived cell line (CP‐A) expressed reduced squamous cytokeratins and enhanced columnar cytokeratins upon ATRA treatment. ATRA altered the EPC2 squamous cytokeratin profile towards a more columnar expression pattern. Cell lines derived from patients with high‐grade dysplasia already expressed columnar cytokeratins and therefore did not show a systematic shift toward a more columnar phenotype with ATRA treatment. ATRA treatment, however, did reduce the squamoid‐like multilayer stratification observed in all cell lines. As the first study to demonstrate long‐term 3D growth of BE cell lines, we have determined that BE cells can be cultured for at least 3 weeks on a fibroblast/collagen matrix and that the use of ATRA causes a general reduction in squamous‐like multilayered growth and an increase in columnar phenotype with the specific effects cell‐line dependent. J. Cell. Physiol. 227: 2654–2659, 2012. © 2011 Wiley Periodicals, Inc.
Changes in myofibrillar protein composition of human diaphragm elicited by congestive heart failure.

We describe the changes in proportions of myofibrillar proteins elicited by chronic congestive heart failure in the costal diaphragm (DIA) of humans using one and two-dimensional electrophoretic techniques. Three myosin heavy chain (MHC) isoforms were found in the DIA from control subjects: slow MHC I (43 +/- S.E. 2%), fast MHC IIa (41 +/- 2%) and fast MHC IIb (17 +/- 1%). In heart failure DIA, the percentage of MHC I was increased to 57 +/- 2%, while that of MHC IIb was decreased to 8 +/- 2 (P < 0.001 for both cases). Similarly, this DIA had higher molar ratios (%) of the slow myosin light chain isoforms (i.e. 1sa, 1sb, and 2s), and lower molar ratios of the fast isoforms (i.e. 1f, 2f, and 3f) than control DIA. Heart failure DIA also contained lower proportions of both alpha-tropomyosin and fast isoforms of troponin-T, I and C than control DIA. These results indicate that heart failure elicits fast-to-slow transformations of both myosin and regulatory proteins of human costal DIA. These changes can be viewed as an increase in slow-twitch characteristics of the DIA and differ from the adaptations elicited by heart failure in limb muscles.
Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data

Small RNA sequencing can be used to gain an unprecedented amount of detail into the microRNA transcriptome. The relatively high cost and low throughput of sequencing bases technologies can potentially be offset by the use of multiplexing. However, multiplexing involves a trade-off between increased number of sequenced samples and reduced number of reads per sample (i.e., lower depth of coverage). To assess the effect of different sequencing depths owing to multiplexing on microRNA differential expression and detection, we sequenced the small RNA of lung tissue samples collected in a clinical setting by multiplexing one, three, six, nine, or 12 samples per lane using the Illumina HiSeq 2000. As expected, the numbers of reads obtained per sample decreased as the number of samples in a multiplex increased. Furthermore, after normalization, replicate samples included in distinct multiplexes were highly correlated (R > 0.97). When detecting differential microRNA expression between groups of samples, microRNAs with average expression >1 reads per million (RPM) had reproducible fold change estimates (signal to noise) independent of the degree of multiplexing. The number of microRNAs detected was strongly correlated with the log2 number of reads aligning to microRNA loci (R = 0.96). However, most additional microRNAs detected in samples with greater sequencing depth were in the range of expression which had lower fold change reproducibility. These findings elucidate the trade-off between increasing the number of samples in a multiplex with decreasing sequencing depth and will aid in the design of large-scale clinical studies exploring microRNA expression and its role in disease.
- 1-Word Association Norms , Mutual Information , and Lexicography

The term word association is used in a very particular sense in the psycholinguistic literature. (Generally speaking, subjects respond quicker than normal to the word nurse if it follows a highly associated word such as doctor.) We will extend the term to provide the basis for a statistical description of a variety of interesting linguistic phenomena, ranging from semantic relations of the doctor/nurse type (content word/content word) to lexico-syntactic co-occurrence constraints between verbs and prepositions (content word/function word). This paper will propose an objective measure based on the information theoretic notion of mutual information, for estimating word association norms from computer readable corpora. (The standard method of obtaining word association norms, testing a few thousand subjects on a few hundred words, is both costly and unreliable.) The proposed measure, the association ratio, estimates word association norms directly from computer readable corpora, making it possible to estimate norms for tens of thousands of words. 1. Meaning and Association It is common practice in linguistics to classify words not only on the basis of their meanings but also on the basis of their co-occurrence with other words. Running through the whole Firthian tradition, for example, is the theme that ‘‘You shall know a word by the company it keeps’’ (Firth, 1957). ‘‘On the one hand, bank co-occurs with words and expression such as money, notes, loan, account, investment, clerk, official, manager, robbery, vaults, working in a, its actions, First National, of England, and so forth. On the other hand, we find bank co-occurring with river, swim, boat, east (and of course West and South, which have acquired special meanings of their own), on top of the, and of the Rhine. ’’ [Hanks (1987), p. 127] The search for increasingly delicate word classes is not new. In lexicography, for example, it goes back at least to the ‘‘verb patterns’’ described in Hornby’s Advanced Learner’s Dictionary (first edition 1948). What is new is that facilities for the computational storage and analysis of large bodies of natural language have developed significantly in recent years, so that it is now becoming possible to test and apply informal assertions of this kind in a more rigorous way, and to see what company our words do keep. 2. Practical Applications The proposed statistical description has a large number of potentially important applications, including: (a) constraining the language model both for speech recognition and optical character recognition (OCR), (b) providing disambiguation cues for parsing highly ambiguous syntactic structures such as noun compounds, conjunctions, and prepositional phrases, (c) retrieving texts from large databases (e.g., newspapers, patents), (d) enhancing the productivity of computational linguists in compiling lexicons of lexico-syntactic facts, and (e) enhancing the productivity of lexicographers in identifying normal and conventional usage.
Approche connexionniste du contrôle optimal

Les algorithmes connexionnistes sont inspires de la maniere dont le cerveau traite l'information : ils impliquent un grand nombre d'unites simples fortement interconnectees, manipulant des informations numeriques de maniere distribuee et massivement parallele. Le controle optimal est une theorie computationnelle qui permet d'ecrire l'interaction entre un agent et un environnement : elle permet de formaliser precisement le probleme consistant a atteindre un certain nombre de buts via l'interaction. Si le controle optimal caracterise un "but" (l'optimisation d'un critere), l'approche connexionniste suggere, elle, une "maniere" de calculer. Nous decrivons plusieurs problematiques s'inscrivant dans le cadre du controle optimal et montrons qu'elles admettent des solutions qui sont connexionnistes : 1) Le controle optimal et sa variante adaptative (l'apprentissage par renforcement) dans un petit espace d'etats 2) L'apprentissage d'une representation pour approximer le probleme de controle optimal ayant un grand espace d'etats.
Mixed H2/H∞ control with pole placement: state feedback case

This paper considers state feedback mixed H2/H∞ control with pole placement via convex optimization. A generalized Riccati equation and a change of variable technique are employed in order to convexify the design problem. The resulting convex optimization problem is shown to be reducable to Generalized Eigenvalue Minimization Problem.
ECONOMIC GROWTH AND THE REAL EXCHANGE RATE : REVISITING THE BALASSA-SAMUELSON EFFECT

Introduction This paper has much of the flavor of an assigned essay. In a meeting at The Higher School of Economics late last year, the conversation turned to the topic of how economic growth influences the real exchange rate. I had earlier (1991) briefly investigated this topic and had reported those results here in Russia. Briefly, the results were that it was hard to detect any systematic connection between economic growth on the one hand and real exchange rate changes on the other. When I mentioned this, one or two members of the group asked how my results could be reconciled with the well-known Balassa-Samuelson effect, which asserts that in the process of growth real cost reduction comes faster in the tradables goods than in nontradables, hence prices of tradables tend to fall relative to nontradables, which implies that the real price of the dollar will also tend to fall through time (with a fixed exchange rate the prices of tradables in rubles will move with their prices in dollars, but the consumer price index and the GDP will rise, relative to tradables prices because these indexes have an important component of nontradables prices). At some point in the conversation that followed Professor Yasin said “this would be a fine topic for your presentation at our Conference next April”-thus creating my assigned topic.
Ex vivo expansion of hematopoietic progenitor cells is associated with downregulation of α4 integrin- and CXCR4-mediated engraftment in NOD/SCID β2-microglobulin-null mice

This study shows that ex vivo culture of hematopoietic stem cells is associated with downregulation of both α4 and CXCR4-mediated engraftment. Background Several studies indicate that ex vivo cytokine-supported expansion induces defective hematopoietic stem cell engraftment. We investigated the role of α4 integrin, α5 integrin and CXCR4 in engraftment of unmanipulated and cytokine-treated human cord blood CD34+ cells. Design and Methods Uncultured or expanded CD34+ cells were infused in NOD/SCID-β2microglobulin-null mice. The function of α4, and α5 integrins and CXCR4 was assessed by incubating cells with specific neutralizing antibodies, prior to transplant. The activation state of α4 integrin was further tested by adhesion and migration assays. Results Neutralization of either α4 integrin or CXCR4 abolished engraftment of uncultured CD34+ cells at 6 week spost-transplant, while α5 integrin neutralization had no significant effect. However, after short-term ex vivo culture, blocking α4 integrin or CXCR4 did not affect repopulating activity whereas neutralization of α5 integrin inhibited engraftment. Using soluble vascular cell adhesion molecule-1 binding assays, we observed that α4 integrin affinity in fresh CD34+ cells was low and susceptible to stimulation while in cultured CD34+ cells, it was high and insensitive to further activation. In addition, stromal cell-derived factor-1 stimulated migration across vascular cell adhesion molecule-1 in fresh CD34+ cells but not in cultured CD34+ cells. Conclusions Our data show that ex vivo culture of hematopoietic progenitor cells is associated with downregulation of both α4 integrin- and CXCR4-mediated engraftment. Further investigations suggest that this is caused by supraphysiological increase of α4 integrin affinity, which impairs directional migration across vascular cell adhesion molecule-1 in response to stromal cell-derived factor-1. Such changes may underlie the engraftment defect of cytokine-stimulated CD34+ cells.
Traffic Accidents Analysis using Self-Organizing Maps and Association Rules for Improved Tourist Safety

Traffic accidents is the most common cause of injury among tourists. This paper presents a method and a tool for analysing historical traffic accident records using data mining techniques for the development of an application that warns tourist drivers of possible accident risks. The knowledge necessary for the specification of the application is based on patterns distilled from spatiotemporal analysis of historical accidents records. Raw accident obtained from Police records, underwent pre-processing and subsequently was integrated with secondary traffic-flow data from a mesoscopic simulation. Two data mining techniques were applied on the resulting dataset, namely, clustering with self-organizing maps (SOM) and association rules. The former was used to identify accident black spots, while the latter was applied in the clusters that emerged from SOM to identify causes of accidents in each black spot. Identified patterns were utilized to develop a software application to alert travellers of imminent accident risks, using characteristics of drivers along with real-time feeds of drivers’ geolocation and environmental conditions.
Serum resistance in Escherichia coli strains causing acute pyelonephritis and bacteraemia

The capacity of Escherichia coli to resist the bactericidal action of serum was examined in 367 clinical isolates obtained from children with acute pyelonephritis (n = 57), adults with acute pyelonephritis (n = 55), non‐diabetic patients with bacteraemia (n = 101), diabetic patients with bacteraemia (n = 65) and from the faecal flora of healthy controls (n = 89). The incidence of serum‐resistant E. coli strains was significantly higher in pyelonephritogenic strains from children and adults (93% and 82%) as compared to faecal control strains (57%, p < 0.001 and p< 0.005 respectively). Strains causing bacteraemia in non‐diabetic and diabetic patients were more often serum resistant (72% and 80%) as compared to control strains (p < 0.05 and p < 0.001 respectively). The frequency of serum‐sensitive strains was similar in diabetic patients with decreased renal fuction or proteinuria compared to those with normal renal function. There were no significant correlations between serum resistance of E. coli and expression of P fimbriae, type I fimbriae or mannose‐resistant haemagglutination, cell surface hydrophobic properties, production of aerobactin, haemolysin or cytotoxic necrotizing factor in 53 pyelonephritogenic strains from adult patients.
Near-Infrared Spectroscopy and Geostatistical Analysis for Modeling Spatial Distribution of Analytical Constituents in Bulk Animal By-Product Protein Meals

Control and inspection operations within the context of safety and quality assessment of bulk foods and feeds are not only of particular importance, they are also demanding challenges, given the complexity of food/feed production systems and the variability of product properties. Existing methodologies have a variety of limitations, such as high costs of implementation per sample or shortcomings in early detection of potential threats for human/animal health or quality deviations. Therefore, new proposals are required for the analysis of raw materials in situ in a more efficient and cost-effective manner. For this purpose, a pilot laboratory study was performed on a set of bulk lots of animal by-product protein meals to introduce and test an approach based on near-infrared (NIR) spectroscopy and geostatistical analysis. Spectral data, provided by a fiber optic probe connected to a Fourier transform (FT) NIR spectrometer, were used to predict moisture and crude protein content at each sampling point. Variographic analysis was carried out for spatial structure characterization, while ordinary Kriging achieved continuous maps for those parameters. The results indicated that the methodology could be a first approximation to an approach that, properly complemented with the Theory of Sampling and supported by experimental validation in real-life conditions, would enhance efficiency and the decision-making process regarding safety and adulteration issues.
The Applicability of DNA Techniques in Investigations of Hospital Malpractices

DNA analysis has been used successfully in a number of parentage cases and for the purposes of identification. However DNA typing is still not generally integrated efficiently into hospital systems in India. I report here the use of DNA evidence in a parentage dispute that arose as a result of a bizarre sequence of events in a maternity ward of General Hospital, Chandigarh, India. The changing standards of hospital practice and social attitudes such as gender bias are likely to augment medico-legal problems in India. There is good reason for DNA profiling methods to be introduced into the hospitals.
ISOKINETIC KNEE MUSCLE STRENGTH PROFILE IN BRAZILIAN MALE SOCCER, FUTSAL, AND BEACH SOCCER PLAYERS: A CROSS-SECTIONAL STUDY.

Background Anterior cruciate ligament injury is higher in soccer athletes as compared to athletes of other sports. Risk factors for anterior cruciate ligament injury include low knee hamstring/quadriceps strength ratio and bilateral strength deficits. Purpose To investigate isokinetic thigh muscles strength, hamstring/quadriceps strength ratio, and bilateral strength comparisons in athletes who participate in professional soccer, futsal, and beach soccer. Study Design Cross-sectional study. Methods Brazilian professional soccer (n=70), futsal (n=30), and beach soccer (n=12) players were isokinetically assessed to examine strength of knee extensors and flexors at 60 degrees/second in concentric mode, to measure peak torque of dominant and non-dominant limbs. Results In the dominant limb, for extensors muscles, futsal players presented significantly lower peak torque values (223.9 ± 33.4 Nm) than soccer (250.9 ± 43.0 Nm; p=0.02) and beach soccer players (253.1 ± 32.4 Nm; p=0.03). Peak torque for extensor muscles in the non-dominant limb was significantly lower in futsal (224.0 ± 35.8 Nm) than in beach soccer players (256.8 ± 39.8 Nm; p=0.03). Hamstring/quadriceps strength ratio for dominant limbs for futsal (57.6 ± 10.1%), soccer (53.5 ± 8.8%), and beach soccer (56.3 ± 8.4%) players presented no significant differences between groups; however, the mean values were lower than recommended values found in the literature. There were no strength deficits for any of the evaluated groups when compared bilaterally. Conclusions Futsal athletes presented lower values for quadriceps strength than soccer and beach soccer athletes. Futsal, soccer, and beach soccer players presented no strength asymmetries, but they presented with strength imbalance in hamstring/quadriceps strength ratio. Level of Evidence 3.
Three Dimensional Model for N-Terminal A Domain of DmpR (2-Dimethylphenol) Protein Based on Secondary Structure Prediction and Fold Recognition

DmpR (dimethylphenol regulatory protein) is a member of the NtrC family of transcriptional activators and controls the transcription of the dmp operons in response to aromatic effector compounds. Secondary structure and fold recognition prediction of N-terminal A domain of this protein (210 amino acid) was performed in Genesilico Metaserver and 3DJury. The consensus result from these servers suggested MJ_1460 as a template. Three dimensional structures were generated from the sequence structure alignments of the template and target protein with MODELLER. The results suggested that the N-terminal A domain of DmpR belongs to Muramoyl pentapeptide carboxypeptidase domain family. The binding interaction sites of the known effectors were predicted using protein-ligand docking. The proposed active site of N-terminal A domain of DmpR comprises of key residues such as Phe93, Glu127, Phe132, Ser160, Phe163, Met164, Arg166 and Pro189. The findings provide some direction to the experimental studies that aim to broaden the range of phenolic derivative which can be sensed by N-DmpR in order to improve the biodegradation potential.
Quantum Theory of Coherence and Polarization of Light

When we open our eyes on earth for the first time, light generates the sensation of vision in our mind. If there was no light, our way of thinking would undoubtedly be quite different. Therefore, it is natural to ask the question, what is light? Our early inquisitiveness about light is documented in many stories and characters from almost all religions and cultures. Later, with the development of science, we tried to use more rigorous techniques to understand the nature of light. However, regardless of intense investigations for centuries on this subject, we are far from obtaining a convincing answer to the question “what is light? ” Einstein seems to have put it best1:
Preconditioned Iterative Solves in Model Reduction of Second Order Linear Dynamical Systems

Recently a new algorithm for model reduction of second order linear dynamical systems with proportional damping, the Adaptive Iterative Rational Global Arnoldi (AIRGA) algorithm, has been proposed. The main computational cost of the AIRGA algorithm is in solving a sequence of linear systems. These linear systems do change only slightly from one iteration step to the next. Here we focus on efficiently solving these systems by iterative methods and the choice of an appropriate preconditioner. We propose the use of relevant iterative algorithm and the Sparse Approximate Inverse (SPAI) preconditioner. A technique to cheaply update the SPAI preconditioner in each iteration step of the model order reduction process is given. Moreover, it is shown that under certain conditions the AIRGA algorithm is stable with respect to the error introduced by iterative methods. Our theory is illustrated by experiments. It is demonstrated that SPAI preconditioned Conjugate Gradient (CG) works well for model reduction of a one dimensional beam model with AIRGA algorithm. Moreover, the computation time of preconditioner with update is on an average 2/3 rd of the computation time of preconditioner without update. With average timings running into hours for very large systems, such savings are substantial.