Miracle-dz/UniFAR-FTUs huggingface dataset:
Anti-TNF treatment of chronic arthritis in clinical practice. New assessment method and predictors of efficacy and tolerability.

Abstract Treatment of chronic inflammatory arthritis has undergone major changes over the past years following introduction of targeted biological therapies. Tumour necrosis factor (TNF) blocking therapy has been the most important biological treatment of chronic arthritis to date. The overall objective of this thesis was to develop a new assessment method of efficacy of biological therapy in clinical practice. Further objectives were to study efficacy and tolerability and predictors thereof in anti-TNF treated patients with chronic arthritis in an open study setting. The thesis is based on four studies of patients with established rheumatoid arthritis (RA) and one study of patients with psoriatic arthritis (PsA). Patients included in the five studies were monitored according to a standardized clinical protocol of the South Swedish Arthritis Treatment Group (SSATG) developed at the Department of Rheumatology in Lund. The protocol included baseline characteristics such as diagnosis, disease duration, previous and ongoing disease modifying antirheumatic drugs (DMARDs), treatment start and termination. In addition efficacy measures used for calculating treatment response, i.e. EULAR and ACR response criteria, were collected at fixed time-points. Data were prospectively registered from March 1999. To overcome shortcomings of previous methods for reporting response data from long term observational cohorts, LUNDEX (LUND Efficacy indeX) was designed. LUNDEX adjusted response data combines the proportion of patients fulfilling a selected response criterion with the proportion of patients adhering to a particular therapy. LUNDEX applied on RA and PsA patients proved to be a valuable tool for evaluating drug efficacy in observational studies. It has the advantage of integrating both clinical response as well as adherence to therapy in a composite score. Predictors of drug survival in RA and PsA were studied using Cox regression models. The models showed that the risk for premature treatment termination was higher in infliximab compared to etanercept treated patients. Also, regression analysis showed that patients with higher baseline CRP-levels and concomitant MTX treatment had better overall treatment continuation. Good response to anti-TNF therapy in RA was associated with concomitant MTX or other DMARD treatment as well as low disability. Moreover, RA patients who failed their first course of anti-TNF treatment, showed response rates during second anti-TNF treatment course in the range of the initial treatment. In contrast, response to a third anti-TNF treatment was markedly reduced, suggesting that other treatment options should be tried. In conclusion, LUNDEX proved to be a practical and a potentially universal tool, valuable for assessing drug response in an open study setting. Important predictors of efficacy and tolerability of anti-TNF treatment were identified. (Less)
A Novel SIFT-Like-Based Approach for FIR-VS Images Registration

This paper presents a novel approach, based on a SIFT-like scale-space pyramidal scheme, for registering FarInfrared and Visible Spectrum images. The proposed approach consists of 3 stages. Initially, a key point detector is used to find interest points. This first stage is a SIFT-like based scale space representation. Then, each key point is characterized using an edge-oriented-histogram (EOH) in its neighborhood. Finally, a matching stage finds the nearest pairs in the couple of multispectral images. Experimental results are provided showing the validity of the proposed approach for registering such a kind of multispectral pair of images.
Parameter Estimation of Thermodynamic Models for Equilibrium of Proteins Solutions with salts

The main challenges of biomolecules production on an industrial scale can be divided into challenges in the upstream processes, which involve the product synthesis, and challenges in downstream processes involving the separation and purification of biomolecules. Among the unit operations employed in biotechnological processes, many of them need the knowledge of thermodynamic properties of the solutions, such as solubility and phase equilibrium of the system. In fact, the simulation of unit operations involved in protein purification, and therefore the prediction of the behavior of proteins in each unit operation, requires the understanding of both the phase behavior of systems and the chemical behavior of fluids in the processes. To do this, it is necessary the calculation of phase equilibrium, which can be quite complex, since it is possible to find systems with multiple phases in equilibrium, multiple chemical species distributed in phases, the presence of chemical reactions and the presence of partially or totally dissociated electrolytes. The accuracy of the results depends on model parameters that must be estimated and is fundamental for the correct process design. Usually, the numerical problem resulting of the resolution of the phase equilibrium equations corresponds to a nonlinear programming problem (NLP). In this context, the proposed paper presents an analysis of the utilization of different optimization methods for the problem of parameter estimation for the calculus of the equilibrium of solutions of proteins with salts. This optimization problem may present some particularities which difficult the utilization of traditional algorithms (e.g. multiple local optima). In this work more modern numerical techniques are employed to circumvent these obstacles.
19 / 09 Prenatal Care Utilization and Infant Health in Botswana by

Despite the freely and publicly provided health care in Botswana, the proportion of low birth weight infants increased from 8% to 13% during 2000-2007 period. The latter rate was among the highest in the WHO African region and upper middle-income countries and may question the effectiveness of care. Using the 2007/08 Botswana Family Health Survey data collected by Statistics Botswana, the paper jointly estimates the adequate prenatal care utilization (input demand) and infant birth weight (outcome) functions through the treatment effect model, which accounts for the binary nature of the endogenous regressor. As birth weight information is not available for all infants, we also estimate a Heckman sample selection model to account for potential bias. Estimating models for rural and urban samples separately, we find that lower levels of mother`s education reduces the likelihood to both adequately utilize prenatal care and report infant birth weight. The likelihood for prenatal care utilization increases with the probability of a care facility being sufficiently close and availability of care facilities. Adequate prenatal care utilization is positively associated with birth weight and failing to account for endogeneity reduces its effect. On average, birth weight increases by 0.67, 0.73 and 0.64 kg in full, urban and rural samples respectively. JEL Classification: I11, I12, J13
Weber Sex-linked AFLP markers indicate a pseudoautosomal region in hemp ( Cannabis sativa L . )

In dioecious plants of hemp (Cannabis sativa L.), males are regarded as heterogametic XY and females as homogametic XX, although it is difficult to discriminate the X cytologically from the Y. The Y chromosome is somewhat larger than the X. Our aim was to analyse AFLP markers on X and Y, and to use them to gain some insight into the structure of the sex chromosomes. Markers located on the sex chromosomes can be grouped into different classes, depending on the presence or absence of a fragment on the X and/or the Y. They are detected by separately analysing male and female progenies of a single cross. Five markers were found to be located on both chromosomes. A few recombinants were observed for marker pairs of this class in the male progenies. Two completely linked markers located on the Y chromosome in the male parent show a recombination rate of r = 0.25 with sex. Recombination must have occurred between the sex chromosomes in the male parent. The recombination analysis led to the conclusion that there is a pseudoautosomal region (PAR) on the sex chromosomes, allowing recombination between the X and the Y chromosome. The other regions of the sex chromosomes show only a few recombination events, for the Y as well as for the X. These results are discussed in comparison to other dioecious plants.
3 1 OWNERSHIP STRUCTURE , CORPORATE CONTROL AND DIVIDEND PAYOUT IN CANADA

This paper examines the relationship between the structure of the ownership of equity in a company and the company’s dividend policy. For this purpose, a company’s dividend policy is characterised by the level and frequency of changes with regular dividend payments. A survey of the literature reveals that several hypotheses have been put forward regarding changes in dividend policy.Dividend policy is used to signal important information to potential investors, dividend policy can be used to increase or decrease the need for a company to resort to external capital markets, or dividend policy can serve the interests of major shareholders. The implications of these hypotheses are developed, and then compared to the actual behaviour of a sample of 600 Canadians in listed firms in order to examine which hypotheses are most useful in accounting for their behaviour. In using ordinary and logit regressions and conditional probability models to test the hypotheses, the results indicate that: (1) voting rights and equity ownership are highly concentrated in Canada; this result confirms those of Gadhoum (1999), Claessens et al. (2000), and La Porta et al. (2000); (2) large shareholders (in 81% of cases, a company) have a strong influence on dividend decisions; this result confirms that of Faccio et al. (2000) in Western Europe and East Asia; and (3) a firm with concentrated ownership pays more dividends because, in most cases, such payments are inter-company and non-taxable for the receiver. The latter effect, termed ‘tax effect’ in this paper, dominates the two known effects of dividends, namely signalling and agency costs. No prior reference to this tax effect has been found in the literature by the author of this paper.
The use of and training provision for healthcare assistants and support workers in the National Health Service in England.

The profile of healthcare assistants and support workers [HCA/SWs] continues to grow within the National Health Service [NHS] in England and policy steadfastly moves towards greater labour substitution between HCA/SWs and qualified registered nurses. With the emphasis on HCA/SWs, the focus of the thesis is the interface between these two healthcare labour groups. Preliminary analysis of the non-medical workforce census indicated variability in the use of HCA/SWs across the NHS which has implications for patient safety and for quality of care. Opportunities for effective skill mix change are raised by appropriate training and the observed differences in the use of trained/trainee HCAs across the NHS implies inequalities in the training provision for the non-registered workforce. Thus, two key questions arise: what is the current training provision for these workers and how does it differ across the NHS Trusts? Two empirical studies are presented. The first explores the variability in use of HCA/SWs through panel data compiled from the non-medical workforce census on 99 Health Authorities over a sevenyear period 1995 2001. Using fixed effects models, variables including local labour market factors, competition, and population densities are investigated. The second study presents the results from a survey of all NHS Trusts on their training organisation and expenditure; induction and certificated training programmes; outcomes and rewards to training. Results confirm that variability in the use of HCA/SWs is influenced by the size of the local NHS and population densities whilst use of trained HCAs is affected by local labour markets, that definitional latitude exists for HCA/SWs, that there appears no systematic and universal approach to training across the Trusts and that rewards to training although motivational, are not guaranteed. Hence, policy to increase standardisation may be necessary. Finally, an agenda for future research in this area is outlined.
Comparison of models to predict the effect of background speech on work performance in open-plan offices

There are different models to estimate the relationships between measurable acoustical parameters and office workers’ perception, well-being and performance. These models are based on speech transmission index (STI), fluctuation strength (FS) or percentile level statistics. Whilst STI requires a loudspeaker and is measured in unoccupied conditions, other metrics, such as FS or percentile level statistics, can be determined in situ during usual working hours. Nonetheless, the established models have some shortcomings. STI can estimate the effect of one simulated speech source on short-term memory performance but it cannot assess the effect of office noise exposure in occupied offices. FS correlates with the impact of temporal-spectral variability of a background sound on short-term memory performance but it depends on the sound pressure level which does not have an effect on the short-term memory performance. Percentile level statistics correlate with the speech-to-noise ratio: higher differences between the 10th and 90th percentile levels measured with fast time weighting lead to lower number recall performances. As part of this study 110 sound conditions under which subjects have to complete a number recall task are evaluated with respect to their relationships with these three acoustical parameters. A cross-validation reveals comparable prediction qualities of the models.
CharBiDAF with Self-Attention for SQuAD

The Stanford Question Answering Dataset (SQuAD) is a reading comprehension dataset designed to challenge systems in “understanding" text. Given a paragraph and a question about the paragraph, the goal of the SQuAD challenge is to answer the question correctly. This paper explores the effectiveness of using a bi-directional attention flow (BiDAF) model with character-level embeddings and a self-attention mechanism on the SQuAD challenge. We additionally experimented with varying the hyperparameters of the model. On our best model, we were able to achieve an F1 Score: 64.938 and a EM Score: 61.302 on the test set in the non-PCE division.
Award Number: W81XWH-10-1-0707 TITLE: Targeted Magnetic Hyperthermia for Lung Cancer PRINCIPAL INVESTIGATOR:

Cancer stem cells (CSCs) are a subpopulation of cancer cells that have stem cell-like properties and are thought to be responsible for tumor drug resistance and relapse. Therapies that can effectively eliminate CSCs will, therefore, likely inhibit tumor recurrence. The objective of our study was to determine the susceptibility of CSCs to magnetic hyperthermia, a treatment that utilizes superparamagnetic iron oxide nanoparticles placed in an alternating magnetic field to generate localized heat and achieve selective tumor cell kill. SPIO NPs having a magnetite core of 12 nm were used to induce magnetic hyperthermia in A549 and MDA-MB-231 tumor cells. Multiple assays for CSCs, including side population phenotype, aldehyde dehydrogenase expression, mammosphere formation, and in vivo xenotransplantation, indicated that magnetic hyperthermia reduced or, in some cases, eliminated the CSC subpopulation in treated cells. Interestingly, conventional hyperthermia, induced by subjecting cells to elevated temperature (46 °C) in a water bath, was not effective in eliminating CSCs. Our studies show that magnetic hyperthermia has pleiotropic effects, inducing acute necrosis in some cells while stimulating reactive oxygen species generation and slower cell kill in others. These results suggest the potential for lower rates of tumor recurrence after magnetic hyperthermia compared to conventional cancer therapies.
Title Dynamically and Observationally Constrained Estimates of Water-Mass Distributions and Ages in the Global Ocean Permalink

A data-constrained ocean circulation model is used to characterize the distribution of water masses and their ages in the global ocean. The model is constrained by the time-averaged temperature, salinity, and radiocarbon distributions in the ocean, as well as independent estimates of the mean sea surface height and sea surface heat and freshwater fluxes. The data-constrained model suggests that the interior ocean is ventilated primarily by water masses forming in the Southern Ocean. Southern Ocean waters, including those waters forming in the Antarctic and subantarctic regions, make up about 55% of the interior ocean volume and an even larger percentage of the deep-ocean volume. In the deep North Pacific, the ratio of Southern Ocean to North Atlantic waters is almost 3:1. Approximately 65% of interior ocean waters make first contact with the atmosphere in the Southern Ocean, further emphasizing the central role played by the Southern Ocean in the regulation of the earth’s climate. Results of the age analysis suggest that the mean ventilation age of deep waters is greater than 1000 yr throughout most of the Indian and Pacific Oceans, reaching a maximum of about 1400–1500 yr in the middepth North Pacific. The mean time for deep waters to be reexposed at the surface also reaches a maximum of about 1400–1500 yr in the deep North Pacific. Together these findings suggest that the deep North Pacific can be characterized as a ‘‘holding pen’’ of stagnant and recirculating waters.
C9orf72 Proteins Regulate Autophagy and Undergo Autophagosomal or Proteasomal Degradation in a Cell Type-Dependent Manner

Dysfunctional autophagy or ubiquitin-proteasome system (UPS) are suggested to underlie abnormal protein aggregation in neurodegenerative diseases. Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS)-associated C9orf72 is implicated in autophagy, but whether it activates or inhibits autophagy is partially controversial. Here, we utilized knockdown or overexpression of C9orf72 in mouse N2a neuroblastoma cells or cultured neurons to elucidate the potential role of C9orf72 proteins in autophagy and UPS. Induction of autophagy in C9orf72 knockdown N2a cells led to decreased LC3BI to LC3BII conversion, p62 degradation, and formation of LC3-containing autophagosomes, suggesting compromised autophagy. Proteasomal activity was slightly decreased. No changes in autophagy nor proteasomal activity in C9orf72-overexpressing N2a cells were observed. However, in these cells, autophagy induction by serum starvation or rapamycin led to significantly decreased C9orf72 levels. The decreased levels of C9orf72 in serum-starved N2a cells were restored by the proteasomal inhibitor lactacystin, but not by the autophagy inhibitor bafilomycin A1 (BafA1) treatment. These data suggest that C9orf72 undergoes proteasomal degradation in N2a cells during autophagy. Lactacystin significantly elevated C9orf72 levels in N2a cells and neurons, further suggesting UPS-mediated regulation. In rapamycin and BafA1-treated neurons, C9orf72 levels were significantly increased. Altogether, these findings corroborate the previously suggested regulatory role for C9orf72 in autophagy and suggest cell type-dependent regulation of C9orf72 levels via UPS and/or autophagy.
Reactive Extraction of Itaconic acid using Natural non-toxic solvent

1Assistant Professor, Department of Chemical Engineering, Priyadarshini Institute of Engineering and Technology, Nagpur (M.S.)440019 INDIA 2M.Tech 4thsem, Department of Chemical Engineering, Priyadarshini Institute of Engineering and Technology, Nagpur (M.S.) 440019 INDIA Abstract A problem in the use of reactive extraction to recover carboxylic acids from bioreactors is the toxicity of extractants and diluents used. Selection of anextractant and diluent for reactive extraction should be on the basis of minimal toxicity and maximum capacity. Due to the increasing petroleum costs, these acids are largely produced by fermentation route. Reactive extraction is a promising method to recover carboxylic acid but suffers from toxicity problems of the diluent and extractant employed. Present paper focuses on reactive extraction of itaconic acid using tri-n-butyl phosphate in natural non-toxic sesame oil. Results were presented in terms of distribution coefficients loading ratio and degree of extraction.
Toward a Classification Framework for Software Architectural Smells

Architectural decay is a commonly occurring phenomenon in long-lived software systems. During a system’s lifetime, its architecture gradually degrades via the appearance of architectural “bad smells”, which are instances of poorly thoughtthrough design decisions. To date, there has been limited in-depth study of this phenomenon, its root causes, its characteristics, or the trends it may follow. Instead, both researchers and practitioners have relied on folklore, and their own intuitions and experiences, when referring to architectural smells and their negative impact on software systems. Two key reasons for the absence of large-scale studies of architectural smells are the lack of a systematic categorization of smells and further the absence of algorithms for automatically detecting smells. In this paper, we propose a framework (1) to classify architectural smells based on their characteristics and (2) to detect the smells based on their symptoms. The categorization includes five different classes of smells, of which we focus on four that can be readily detected with the help of existing architecture recovery and analysis techniques. We illustrate the framework with 11 distinct architectural smells across the four categories. We formally define each smell, present a detection algorithm for it, and illustrate it with an example from real systems.
Joint Scale-Lag Diversity in Mobile Wideband Systems

We consider the effect of mobility on a wideband direct seque nce spread spectrum (DSSS) communication system, and study a scale-lag Rake receiver capa ble of leveraging the diversity that results from mobility. A wideband signal has a large bandwidth-to-c enter frequency ratio, such that the typical narrowband Doppler spread assumptions do not apply to mobil e channels. Instead, we assume a more general temporal scaling phenomenon, i.e., a dilation of th e transmitted signal’s time support. Based on a uniform ring of scatterers model, we determine that the wid eband scattering function, which quantifies the average scale spreading, has a “bathtub-shaped” scale p rofil . We compare the performances of a scale-lag Rake and a frequency-lag Rake, each capable of lev eraging the diversity that results from mobility. Such analysis applies, for example, to ultra-wid eband (UWB) radio frequency channels and underwater wideband acoustic channels. A. Margetts is currently with MIT Lincoln Laboratory in Lexi ngton, MA. P. Schniter is with the Department of Electrical and Compute r Engineering at The Ohio State University, Columbus, OH. A. Swami is with the Army Research Laboratory, Adelphi, MD. ∗Please direct all correspondence to Adam R. Margetts, MIT Li ncoln Laboratory, 244 Wood Street, Lexington, MA 02420. e-mail: margetts@ieee.org, phone 781.981. 0571, fax 781.9 81.3 05. This work was supported by the Ohio Space Grant Consortium an d by the Office of Naval Research. Portions of this work were presented at the 2004 Asilomar Con fere ce on Signals, Systems, and Computers, and at the 2005 International Conference on Acoustics, Speech, and Signal Processing. SUBMITTED TO IEEE TRANSACTIONS ON WIRELESS COMMUNICATIONS 2