Miracle-dz/UniFAR-FTUs huggingface dataset:
A Genome-Wide Study of Cytogenetic Changes in Colorectal Cancer Using SNP Microarrays: Opportunities for Future Personalized Treatment

In colorectal cancer (CRC), chromosomal instability (CIN) is typically studied using comparative-genomic hybridization (CGH) arrays. We studied paired (tumor and surrounding healthy) fresh frozen tissue from 86 CRC patients using Illumina's Infinium-based SNP array. This method allowed us to study CIN in CRC, with simultaneous analysis of copy number (CN) and B-allele frequency (BAF) - a representation of allelic composition. These data helped us to detect mono-allelic and bi-allelic amplifications/deletion, copy neutral loss of heterozygosity, and levels of mosaicism for mixed cell populations, some of which can not be assessed with other methods that do not measure BAF. We identified associations between CN abnormalities and different CRC phenotypes (histological diagnosis, location, tumor grade, stage, MSI and presence of lymph node metastasis). We showed commonalities between regions of CN change observed in CRC and the regions reported in previous studies of other solid cancers (e.g. amplifications of 20q, 13q, 8q, 5p and deletions of 18q, 17p and 8p). From Therapeutic Target Database, we identified relevant drugs, targeted to the genes located in these regions with CN changes, approved or in trials for other cancers and common diseases. These drugs may be considered for future therapeutic trials in CRC, based on personalized cytogenetic diagnosis. We also found many regions, harboring genes, which are not currently targeted by any relevant drugs that may be considered for future drug discovery studies. Our study shows the application of high density SNP arrays for cytogenetic study in CRC and its potential utility for personalized treatment.
Usefulness of a Clinician Rating Scale in Identifying Preschool Children With ADHD

Objective: To ascertain the psychometric properties and clinical utility of the Behavioral Rating Inventory for Children (BRIC), a novel clinician inventory for preschoolers. Method: Completion of the BRIC for 214 preschoolers follows 2 evaluation sessions, generally separated by less than 2 weeks. Items are submitted to a Principal Components Analysis (PCA) with Varimax rotation. Test-retest reliability and validity relative to other measures are assessed. Results: PCA yields a 2-factor solution representing a “Symptom Triad” and a “Mood/Sociability Factor. ” Test-retest reliability of the triad and factor are . 78 (p <.001) and . 55 (p < .001), respectively. Correlations between parent and teacher ratings of ADHD-related behaviors and the Symptom Triad range from . 39-. 47 (all p <.001); similar correlations are found with laboratory measures of activity level (r = .35-.49, all p <.001). Conclusion: The Symptom Triad of the BRIC appears to be a reliable and valid tool that may assist researchers and clinicians in studying and diagnosing ADHD in preschoolers, particularly in cases where teacher ratings are unavailable. J. of Att. Dis. 2010; 13(5) 479-488
Hybrid phage displaying SLAQVKYTSASSI induces protection against Candida albicans challenge in BALB/c mice

The polymorphic fungus Candida albicans (C. albicans) can live as an aggressive pathogen and cause many diseases in hosts, for which no effective vaccine exists. The secreted aspartyl proteinase 2 (Sap2) plays a protective role in systemically infected BALB/c mice. Protective cellular immune responses can be preferentially induced when antigens are displayed on small particles. Therefore, the emphasis is placed on developing new phage vaccine to inhibit C. albicans infection. In this study, the ability of the hybrid phage displaying the epitope SLAQVKYTSASSI and recombinant protein of Sap2 (rSap2) for inducing immune protective responses against C. albicans infection was evaluated by lymphoproliferative assay, to gather cytokine and antibody measurements in BALB/c mice. Our results showed that, strong cellular and humoral immune responses were induced in a mouse model immunized with hybrid phage or rSap2. Furthermore, the protection against lethal challenge with C. albicans was observed in mice vaccinated hybrid phage without adjuvant. These findings demonstrate that the hybrid phage displaying the epitope SLAQVKYTSASSI might be a potential vaccine against C. albicans infections.
EFFECT OF THERAPEUTIC TOUCH ON PAIN RELATED PARAMETERS IN PATIENTS WITH CANCER: A RANDOMIZED CLINICAL TRIAL

Introduction: In patients with cancer, pain may influence their life style, and feeling of satisfaction and comfort, leading to fatigue, and cause impairment of their quality of life, personal relationships, sleep and daily activities. The aim of this study was to evaluate the effect of therapeutic touch (TT) on pain related parameters of in patients with cancer. Methods: In a randomized clinical trial a total of 90 male patients referring to Specialized Oncology Hospital in Mashhad, were conveniently selected and randomly divided into three intervention, placebo, and control groups. The intervention consisted of TT in 7 sessions for a 4-week period. The data were collected using a demographic questionnaire along with the Brief Pain Inventory, which were then analyzed and compared using Kruskal-Wallis and Mann-Whitney tests. Results: By comparing scores parameters of pain scales (general activity, mood, walking ability, relations with other people and sleep) in the three groups, there was no significant difference at the beginning of the first session. However, a significant difference was observed at the end of TT sessions between the three groups (p= 0.001). Furthermore, the groups were compared two-by-two by using Mann-Whitney test and Bonferroni correction, and the result indicated significant differences between the two intervention and placebo groups as well as between the two intervention and control groups. Conclusion: The results of the study showed that TT had a positive impact on the positive management of pain related parameters in cancer patients. Therefore, TT is suggested to be used by healthcare providers as a complementary method for managing pain and its parameters.
Quantifying Transmission Investment in Malaria Parasites

Many microparasites infect new hosts with specialized life stages, requiring a subset of the parasite population to forgo proliferation and develop into transmission forms. Transmission stage production influences infectivity, host exploitation, and the impact of medical interventions like drug treatment. Predicting how parasites will respond to public health efforts on both epidemiological and evolutionary timescales requires understanding transmission strategies. These strategies can rarely be observed directly and must typically be inferred from infection dynamics. Using malaria as a case study, we test previously described methods for inferring transmission stage investment against simulated data generated with a model of within-host infection dynamics, where the true transmission investment is known. We show that existing methods are inadequate and potentially very misleading. The key difficulty lies in separating transmission stages produced by different generations of parasites. We develop a new approach that performs much better on simulated data. Applying this approach to real data from mice infected with a single Plasmodium chabaudi strain, we estimate that transmission investment varies from zero to 20%, with evidence for variable investment over time in some hosts, but not others. These patterns suggest that, even in experimental infections where host genetics and other environmental factors are controlled, parasites may exhibit remarkably different patterns of transmission investment.
Pharmacokinetics, Clinical Indications, and Resistance Mechanisms in Molecular Targeted Therapies in Cancer

The strategy for discovery and development of new cancer drugs has shifted the field from cytotoxic agents to therapies that selectively target oncogenic drivers. In the last decade, a number of targeted cancer therapies have been discovered and proven effective in a variety of hematological and solid malignancies. In this article, we review clinical pharmacokinetic characteristics of the U.S. Food and Drug Administration–approved targeted therapies and provide an overview of key clinical trials that led to approval of these drugs. The major limiting factor of targeted treatment is the development of resistance. We describe general principles of resistance and specific, clinically confirmed mechanisms of resistance to several therapies in different malignancies.
Staging Dynamic Programming Algorithms

Applications of dynamic programming (DP) algorithms are numerous, and include genetic engineering and operations research problems. At a high level, DP algorithms are specified as a system of recursive equations implemented using memoization. The recursive nature of these equations suggests that they can be written naturally in a functional language. However, the requirement for memoization poses a subtle challenge: memoization can be implemented using monads, but a systematic treatment introduces several layers of
Factors for Effective Use of Deployed Design Patterns

Design patterns have been advocated by many researchers and practitioners as a means to produce better solutions and reduce efforts in software maintenance. Previous studies use controlled experiments to compare the maintenance efforts by developers having different work experience with and without deployed design patterns. Many experiments primarily focus on the effect of one or two human factors, and have not explored the effects of many other relevant factors. We have performed an empirical study to investigate the relative importance of several factors that may affect the effective use of deployed design patterns. In this paper, we report our findings of the study involving 118 subjects to perform three change tasks on JHotDraw. Interestingly, we find that among the factors examined, both the level of expertise on design patterns and proficiency of the programming language are not significant in terms of maintenance time, while factors such as the familiarity with the application under maintenance are notably more important.
A 10b 25MS/s 4.8mW 0.13um CMOS ADC for Digital Multimedia Broadcasting Applications

A 10b two-stage pipeline ADC implemented in a 0.13mum CMOS operates at dual sampling clock rates of 25MS/s and 10MS/s based on a switched-bias power-reduction technique for low-power system applications. The prototype ADC shows a maximum SNDR and SFDR of 56dB and 65dB at all sampling rates up to 25MS/s. The ADC occupies an active die area of 0.8mm2 and consumes 4.8mW at 25MS/s and 2.4mW at 10MS/s, respectively, at a 1.2V supply
Health consequences of visceral obesity

Visceral obesity is associated with metabolic abnormalities that increase the risk of type 2 diabetes and coronary heart disease. Obese patients with a substantial accumulation of visceral adipose tissue are characterized by higher insulinaemic and glycaemic responses during an oral glucose challenge as well as by a deteriorated plasma lipoprotein-lipid profile compared with individuals with normal body weights or obese subjects with low levels of visceral adipose tissue. Results of the Quebec Cardiovascular Study have shown that the cluster of metabolic disturbances observed among subjects with visceral obesity (hyperinsulinaemia, hyperapolipoprotein B and small, dense low-density lipoprotein (LDL) particles) is associated with a 20-fold increase in the risk of coronary heart disease in a sample of middle-aged men followed over 5 years. Therefore, we have developed a simple screening approach in order to help physicians and health professionals identify at low cost individuals who would be characterized by this cluster of atherogenic abnormalities. We found that the simultaneous presence of an elevated waist girth combined with moderate hypertriglyceridaemia (‘hypertriglyceridaemic waist’) could adequately identify a large proportion (-80%) of carriers of the above triad of atherogenic metabolic abnormalities (hyperinsulinaemia, hyperapolipoprotein B and small, dense LDL particles). Finally, there is evidence suggesting that the risk of an acute coronary syndrome in these viscerally obese patients may not always be related to the extent of coronary artery stenosis, providing further support to the notion that additional markers of thrombosis/inflammation should be considered. Thus, the stabilization of the atherosclerotic plaque, rather than its regression may even become a more legitimate and feasible therapeutic objective for the management of the coronary heart disease risk in the viscerally obese patient. Although these notions are based on a plausible metabolic rationale, randomized trials with proper end-points will be needed to determine the clinical benefits associated with the management of visceral obesity and related metabolic complications.
Biometric access control for wireless nodes

The most important requirements of Wireless Sensor Network (WSN) security are confidentiality, authentication and integrity. User authentication is necessary for legitimate access control in WSNs. These sensors have limited processing power, bandwidth, memory and limited communication abilities. Assume that WSN is deployed in a hospital, a university campus, or a smart home, to permit legal users to query and receive the particular response from any of this sensor node of WSN. Significantly, the system must produce authentication method for confirming if the user is legal or not. We present a solution based on biometric for this problem and also adapt it for WSN environment. The proposed protocol involves simple operations and light computations.
How to formalize variation : Stochastic ot models and /S/ deletion in Spanish

The existence of variability, i.e., when multiple surface forms correspond to a single underlying representation, is a significant problem for many formal theories of phonology, which are often treated as strictly deterministic. Many theorists simply regard the different surface forms as free variants and use optional rules to formalize the variation (see Chomsky & Halle 1968). Others argue that the choice of surface variants is a performance phenomenon, and has no place in a model of grammatical competence (e.g., Bickerton 1971). However, following Labov's early work (e.g., his 1969 article on the copula in AAVE) which demonstrated that the choice of surface variants is conditioned in a consistent and probabilistic manner by several factors, most variationist sociolinguists have assumed inherent variability in the grammar. That is, a speaker's grammatical competence contains knowledge of all of the surface variants, as well as knowledge of how frequently they occur. While variationists working under this paradigm do not always attempt to formalize their empirical findings, when they do, the model they use most commonly is the variable rule (see Labov 1969 and Cedergren & Sankoff 1974 for early formulations). The locus of variation in a speaker's grammar has remained a contentious issue to the present day (see, for example, the exchange between Newmeyer 2003 and Bybee 2005). Recently, however, many phonologists, especially those working within the framework of Optimality Theory (OT), have begun to explore ways in which to extend their formal models to account for variation. Some of the formalisms that have been proposed are Partially Ordered
DSM-III Diagnoses in Chronic Pain: Confusion or Clarity?

The assessment of patients with chronic pain is receiving increasing attention by psychiatrists. Recent publications have put forward the concept of the “pain-prone disorder” as a variant of depressive illness. This study describes a series of 50 consecutive patients with chronic pain in terms of the five axes of the DSM-III nosology. Diagnoses were made after a 90- to 120-minute psychiatric interview, and a check on diagnostic reliability was made on a small subsample. Psychological factors affecting physical condition were diagnosed in 34% and dysthymic disorder was diagnosed in 28%, while major depression, psychogenic pain disorder, somatization disorder, and anxiety disorders were each respectively diagnosed in 8%. Only 6% had no diagnosis on axis I and 4% had no diagnosis on axis III. Personality disorder was diagnosed in 40%, and traits of dependence, compulsiveness, and anxiety were common. Overall, the patients had experienced a high degree of psychosocial stress with fair to poor adaptive functioning. The notion of chronic pain as a variant of depressive disease is questioned on the basis of these findings. The author suggests that although pain-proneness is a useful psychodynamic concept, the case for its establishment as a new psychobiological disorder is not proven. Furthermore, the concepts of pain-proneness, depression, and psychogenic pain have become confused. The author argues that the current classification is adequate to deal with the varieties of depression associated with chronic pain and that psychogenic pain disorder should be remerged with conversion disorder for the sake of clarity.
Effect of age and asthma duration upon elastase and α1-antitrypsin levels in adult asthmatics

In asthmatic subjects an imbalance between elastase and α1‐antitrypsin (α1‐PI) exists. This study aims to evaluate whether ageing per se affects the levels of elastase. Both young and elderly asthmatics with comparable severity and duration of disease, as well as young and elderly healthy subjects, underwent an induced sputum procedure to measure levels of elastase and α1‐PI. The percentage of sputum neutrophils and eosinophils was higher in young and elderly asthmatics than in young and elderly controls. The levels of both total and active elastase were significantly higher in young and elderly asthmatics than in young and elderly controls, and directly correlated with the percentage of neutrophils. In addition, in both young and elderly asthmatics the levels of total and active elastase were negatively correlated with forced expiratory volume in one second values, but positively correlated with the duration of the disease. This study indicates that ageing per se does not necessarily lead to a progressive elastase/α1‐antitrypsin imbalance in asthma, and suggests that an important variable in the development of airway remodelling in both young and elderly asthmatics is represented by the duration of the disease.
Surmounting barriers: The benefit of hydrodynamic interactions

We experimentally and theoretically investigate the collective behavior of three colloidal particles that are driven by a constant force along a toroidal trap. Due to hydrodynamic interactions, a characteristic limit cycle is observed. When we additionally apply a periodic sawtooth potential, we find a novel caterpillar-like motional sequence that is dominated by hydrodynamic interactions and promotes the surmounting of potential barriers by the particles.
What Works to Prevent Partner Violence? An Evidence Overview.

Lori Heise reviews the empirical evidence of what works in low- and middle-income countries to prevent violence against women by their husbands and other male partners. The review focuses on prevention programmes rather than responses or services, and on research-based evaluations rather than insights from practice. Individual chapters cover: changing gender norms, childhood exposure to violence, excessive alcohol use, women’s economic empowerment, law and justice system reform. Heise summarises the evidence that links each factor with the risk of partner violence as well as the effectiveness of prevention programmes.
Indoleamine 2,3‐dioxygenase in T‐cell tolerance and tumoral immune escape

Summary: Indoleamine 2, 3‐dioxygenase (IDO) degrades the essential amino acid tryptophan in mammals, catalyzing the initial and rate‐limiting step in the de novo biosynthesis nicotinamide adenine dinucleotide (NAD). Broad evidence implicates IDO and the tryptophan catabolic pathway in generation of immune tolerance to foreign antigens in tissue microenvironments. In particular, recent findings have established that IDO is overexpressed in both tumor cells and antigen‐presenting cells in tumor‐draining lymph nodes, where it promotes the establishment of peripheral immune tolerance to tumor antigens. In the normal physiologic state, IDO is important in creating an environment that limits damage to tissues due to an overactive immune system. However, by fostering immune suppression, IDO can facilitate the survival and growth of tumor cells expressing unique antigens that would be recognized normally as foreign. In preclinical studies, small‐molecule inhibitors of IDO can reverse this mechanism of immunosuppression, complementing classical cytotoxic cancer chemotherapeutic agents' ability to trigger regression of treatment‐resistant tumors. These results have encouraged the clinical translation of IDO inhibitors, the first of which entered phase I clinical trials in the fall of 2007. In this article, we survey the work defining IDO as an important mediator of peripheral tolerance, review evidence of IDO dysregulation in cancer cells, and provide an overview of the development of IDO inhibitors as a new immunoregulatory treatment modality for clinical trials.
Measuring the Level of Transfer Learning by an AP Physics Problem-Solver

Transfer learning is the ability of an agent to apply knowledge learned in previous tasks to new problems or domains. We approach this problem by focusing on model formulation, i.e., how to move from the unruly, broad set of concepts used in everyday life to a concise, formal vocabulary of abstractions that can be used effectively for problem solving. This paper describes how the Companions cognitive architecture uses analogical model formulation to learn to solve AP Physics problems. Our system starts with some basic mathematical skills, a broad common sense ontology, and some qualitative mechanics, but no equations. Our system uses worked solutions to learn how to use equations and modeling assumptions to solve AP Physics problems. We show that this process of analogical model formulation can facilitate learning over a range of types of transfer, in an experiment administered by the Educational Testing Service.
3D reconstruction with uncalibrated cameras using the six-line conic variety

We present new algorithms for the recovery of the Euclidean structure from a projective calibration of a set of cameras with square pixels but otherwise arbitrarily varying intrinsic and extrinsic parameters. Our results, based on a novel geometric approach, include a closed-form solution for the case of three cameras and two known vanishing points and an efficient one-dimensional search algorithm for the case of four cameras and one known vanishing point. In addition, an algorithm for a reliable automatic detection of vanishing points on the images is presented. These techniques fit in a 3D reconstruction scheme oriented to urban scenes reconstruction. The satisfactory performance of the techniques is demonstrated with tests on synthetic and real data.