Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel method for the detection of necrotic lesions in human cancers.

Data are presented in support of the hypothesis that malignant tumors, containing abnormally permeable, degenerating cells, can be selectively detected using monoclonal antibodies to intracellular antigens. Biodistribution, imaging, and autoradiographic studies were performed in nude mice transplanted with four different human tumor cell lines to demonstrate the binding of radiolabeled antinuclear monoclonal antibodies within bulky tumors containing necrotic lesions. For these studies, two monoclonal antibodies, designated TNT-1 (IgG2a) and TNT-2 (IgM) were chosen since they were found to bind to abundant nuclear antigens which are retained in permeable, dying cells. F(ab')2 fragments prepared by pepsin digestion were radiolabeled with iodine-125 or iodine-131 by the iodogen method for i.v. administration. Biodistribution studies in nontumor-bearing BALB/c mice at various time intervals revealed normal patterns of antibody excretion with no accumulation of antibody in healthy organs. In contrast, biodistribution studies performed on Day 3 in tumor-bearing nude mice showed high tumor to organ ratios in those animals bearing necrotic tumors. Necrotic regions dissected at necropsy gave tumor to blood ratios as high as 131:1. Transplants having little demonstrable necrosis were found to have low tumor to blood ratios (0.4:1). Sequential imaging studies confirmed the high tumor-to-organ ratios and showed positive tumor imaging as early as 4 h. Autoradiographic studies of excised tumors showed the presence of label selectively in necrotic areas with preferential labeling over the nuclei of degenerating cells. Because of the universal presence of these nuclear antigens and the known prevalence of necrosis in tumors, this approach may be of value for the imaging and treatment of a wide variety of cancers in humans.
Influence of Role Models and Mentors on Female Graduate Students’ Choice of Science as a Career

The purpose of this study was to examine the source, nature, and degree of influence of role models and mentors on female graduate students’ choice of science as a career. Also examined was the existence of gender or area-of-study (engineering, biological science, physical sciences) differences. Results of a factor analysis of the Influence of Others on Academic and Career Decisions Scale (IOACDS, Nauta & Kokaly, 2001) demonstrated that role models and mentors influenced students in distinct ways. Significant gender, area-of-study, and undergraduate country differences were found.
The Sparse Principal Component of a Constant-Rank Matrix

The computation of the sparse principal component of a matrix is equivalent to the identification of its principal submatrix with the largest maximum eigenvalue. Finding this optimal submatrix is what renders the problem NP-hard. In this paper, we prove that, if the matrix is positive semidefinite and its rank is constant, then its sparse principal component is polynomially computable. Our proof utilizes the auxiliary unit vector technique that has been recently developed to identify problems that are polynomially solvable. In addition, we use this technique to design an algorithm which, for any sparsity value, computes the sparse principal component with complexity O(ND+1), where N and D are the matrix size and rank, respectively. Our algorithm is fully parallelizable and memory efficient.
Event Driven Web Video Summarization by Tag Localization and Key-Shot Identification

With the explosive growth of web videos on the Internet, it becomes challenging to efficiently browse hundreds or even thousands of videos. When searching an event query, users are often bewildered by the vast quantity of web videos returned by search engines. Exploring such results will be time consuming and it will also degrade user experience. In this paper, we present an approach for event driven web video summarization by tag localization and key-shot mining. We first localize the tags that are associated with each video into its shots. Then, we estimate the relevance of the shots with respect to the event query by matching the shot-level tags with the query. After that, we identify a set of key-shots from the shots that have high relevance scores by exploring the repeated occurrence characteristic of key sub-events. Following the scheme in [6] and [22], we provide two types of summaries, i.e., threaded video skimming and visual-textual storyboard. Experiments are conducted on a corpus that contains 60 queries and more than 10 000 web videos. The evaluation demonstrates the effectiveness of the proposed approach.
Mechanisms Underlying the Very High Susceptibility of the Immature Mammary Gland to Carcinogenic Initiation.

Abstract : The overall goal of this project remains to explore the toxic effects of physical and chemical carcinogens on the immature mammary gland as compared to these effects on the young adult mammary gland using a rat model. During the second grant year we have: (1) shown that as with radiation, the rat mammary carcinogen NMU is more cytotoxic in the immature in situ mammary gland than it is in the mature gland, (2) established the "Big Blue" mutagenesis assay in the laboratory and are in the process of adapting it to the mammary gland, (3) have set up our first long term carcinogenesis study, (4) have established the "Comet assay" for DNA damage in the lab and are adapting it to mammary cells, and (5) have established subtraction libraries to identify genes which are either under or overexpressed in the immature mammary gland. We are currently analyzing members of these libraries. We feel that these studies will help mechanistically define the epidemiological observation in women which suggests that the immature mammary gland is more susceptible to environmental carcinogens than is the adult gland.
Efficacy of the antiphospholipid score for the diagnosis of antiphospholipid syndrome and its predictive value for thrombotic events.

OBJECTIVE To define the antiphospholipid score (aPL-S) by testing multiple antiphospholipid antibodies (aPL) and to evaluate its efficacy for the diagnosis of antiphospholipid syndrome (APS) and predictive value for thrombosis. METHODS This study comprised 2 independent sets of patients with autoimmune diseases. In the first set of patients (n = 233), the aPL profiles were analyzed. Five clotting assays for testing lupus anticoagulant and 6 enzyme-linked immunosorbent assays (IgG/IgM anticardiolipin antibodies, IgG/IgM anti-β(2)-glycoprotein I, and IgG/IgM phosphatidylserine-dependent antiprothrombin antibodies) were included. The association of the aPL-S with a history of thrombosis/pregnancy morbidity was assessed. In the second set of patients (n = 411), the predictive value of the aPL-S for thrombosis was evaluated retrospectively. Two hundred ninety-six of these patients were followed up for >2 years. The relationship between the aPL-S and the risk of developing thrombosis was analyzed. RESULTS In the first set of patients, the aPL-S was higher in those with thrombosis/pregnancy morbidity than in those without manifestations of APS (P < 0.00001). For the aPL-S, the area under the receiver operating characteristic curve value was 0.752. In the second set of patients, new thromboses developed in 32 patients. The odds ratio (OR) for thrombosis in patients with an aPL-S of ≥30 was 5.27 (95% confidence interval [95% CI] 2.32-11.95, P < 0.0001). By multivariate analysis, an aPL-S of ≥30 appeared to be an independent risk factor for thrombosis (hazard ratio 3.144 [95% CI 1.383-7.150], P = 0.006). CONCLUSION The aPL-S is a useful quantitative index for diagnosing APS and may be a predictive marker for thrombosis in autoimmune diseases.
How to Classify Influenza A Viruses and Understand Their Severity

As an application of the chaos degree introduced in the framework of information adaptive dynamics, we study the classification of the Influenza A viruses. What evolutional processes determine the severity and the ability for transmission among human of influenza A viruses? We performed phylogenetic classifications of influenza A viruses that were sampled between 1918 and 2009 by using a measure called entropic chaos degree, that was developed through the study of chaos in information dynamics. The phylogenetic analysis of the internal protein (PB2, PB1, PA, NS, M1, M2, NS1, and NS2) indicated that Influenza A viruses adapting to human and transmitting among human were clearly distinguished from swine lineage and avian lineage. Furthermore, the HA, NA, and internal proteins of the influenza strain that caused a pandemic or a severe epidemic with high mortality were phylogenetically different from those from previous pandemic and severe epidemic strains. We have come to the conclusion that the internal protein has a significant impact on the ability for transmission among human. Based of this study, we are convinced that entropic chaos degree is very useful as a measure of understanding the classification and severity of an isolated strain of influenza A virus.
Reprinted from C. P. Gibson "Colour coded vs Monochrome Electronic Displays", Her Majesty's Stationery Office, London, 1984 REACTION TIME AS A MEASURE OF THE DISCRIMINABILITY OF LARGE COLOUR DIFFERENCES

The discriminability of colours along two axes in chromaticity space has been studied by measuring the time that a normal observer requires to decide whether two colours are identical or different. By means of a multidimensional scaling program, these data were used to generate a space in which the distance between pairs of colours increases as the response time decreases. The results of this analysis suggest that colours that lie along straight lines in the C.1. E. -(ul,v') diagram lie on curves in discriminability space; and that conventional representations of colour space overestimate the discriminability of red from green. When targets are of small area and brief duration, reaction times are particularly long for colours that lie along a tritanopic confusion line (roughly, a line from yellow to violet). Combinations of these colours should therefore be avoided when choosing colours for colour-coding applications.
Regulation of the NADPH Oxidase and Associated Ion Fluxes During Phagocytosis

The production of reactive oxygen species (ROS) within immune cell phagosomes is critical for antimicrobial activity and for correct antigen processing, and influences signaling pathways that direct host responses to infection and inflammation. Because excess oxidants can cause tissue damage and oxidative stress, phagocytes must precisely control both the location and timing of NADPH oxidase activity. How differential regulation is achieved at phagosomes is not well understood. Recent studies have revealed that the PI(3)P phosphoinositide plays an important role in locally boosting phagosomal NADPH oxidase activity through its binding to the p40phox NADPH oxidase subunit. Furthermore, phox subunit dynamics at phagosomes may regulate the timing of the oxidative burst. Novel elements regulating catalytic core trafficking include Rab27 and SNAP‐23. In addition to trafficking events, the activity of the electrogenic oxidase is also governed by ionic fluxes, which are constrained at phagosomes owing to low intraphagosomal volume and dynamic display of channels, transporters, and pumps. New insights on the interdependence of phagosomal pH and ROS have been recently elucidated, and chloride channels important for microbicidal functions, including CFTR, and CLIC family channels, have been identified. Finally, periphagosomal calcium microdomains and calcium‐dependent S100A8/9 protein recruitment may help fine‐tune spatiotemporal regulation of NADPH oxidase activation for an effective immune response.
Empowering 21 st Century Biology Gene

Several lists of grand challenges in biology have been published recently, highlighting the strong need to answer fundamental questions about how life evolves and is governed, and how to apply this knowledge to solve the pressing problems of our times. To succeed in addressing the challenges of 21st century biology, scientists need to generate, have access to, interpret, and archive more information than ever before. But for many important questions in biology, progress is stymied by a lack of essential tools. Discovering and developing necessary tools requires new technologies, applications of existing technologies, software, model organisms, and social structures. Such new social structures will promote tool building, tool sharing, research collaboration, and interdisciplinary training. Here we identify examples of the some of the most important needs for addressing critical questions in biology and making important advances in the near future.
Influence Maximization with an Unknown Network by Exploiting Community Structure

In many real world applications of influence maximization, practitioners intervene in a population whose social structure is initially unknown. We formalize this problem by introducing exploratory influence maximization, in which an algorithm queries individual network nodes to learn their links. The goal is to locate a seed set nearly as influential as the global optimum using very few queries. We show that this problem is intractable for general graphs. However, real world networks typically have community structure, in which nodes are arranged in densely connected subgroups. We present the ARISEN algorithm, which leverages community structure to find an influential seed set by querying only a fraction of the network. Experiments on real world networks of homeless youth, village populations in India, and others validate ARISEN’s performance.
Single-neuron diversity generated by Protocadherin-β cluster in mouse central and peripheral nervous systems

The generation of complex neural circuits depends on the correct wiring of neurons with diverse individual characteristics. To understand the complexity of the nervous system, the molecular mechanisms for specifying the identity and diversity of individual neurons must be elucidated. The clustered protocadherins (Pcdh) in mammals consist of approximately 50 Pcdh genes (Pcdh-α, Pcdh-β, and Pcdh-γ) that encode cadherin-family cell surface adhesion proteins. Individual neurons express a random combination of Pcdh-α and Pcdh-γ, whereas the expression patterns for the Pcdh-β genes, 22 one-exon genes in mouse, are not fully understood. Here we show that the Pcdh-β genes are expressed in a 3′-polyadenylated form in mouse brain. In situ hybridization using a pan-Pcdh-β probe against a conserved Pcdh-β sequence showed widespread labeling in the brain, with prominent signals in the olfactory bulb, hippocampus, and cerebellum. In situ hybridization with specific probes for individual Pcdh-β genes showed their expression to be scattered in Purkinje cells from P10 to P150. The scattered expression patterns were confirmed by performing a newly developed single-cell 3′-RACE analysis of Purkinje cells, which clearly demonstrated that the Pcdh-β genes are expressed monoallelically and combinatorially in individual Purkinje cells. Scattered expression patterns of individual Pcdh-β genes were also observed in pyramidal neurons in the hippocampus and cerebral cortex, neurons in the trigeminal and dorsal root ganglion, GABAergic interneurons, and cholinergic neurons. Our results extend previous observations of diversity at the single-neuron level generated by Pcdh expression and suggest that the Pcdh-β cluster genes contribute to specifying the identity and diversity of individual neurons.
Variable training: effects on velocity and accuracy in the tennis serve

Abstract Variable practice has been shown to be an effective strategy to improve open motor skills. However, the usefulness of this procedure in closed motor skills remains controversial. The following study has the objective of analysing the effects of variability practice in the improvement of a closed skill. The skill studied has been the tennis serve. Thirty young tennis players (13 ± 1.52 years), divided in two groups, took part in this study. One group practiced in variable conditions and the other group in consistency conditions. Both groups performed 12 training sessions (60 serves/session). The variable practice group improved their accuracy significantly compared with the consistency group (F3.25 = 3.078; P = 0.035). The velocity of serve increased after training in both groups (F3.25 = 15.890; P = 0.001). The practice in variable conditions seems to be effective in improving the performance of the tennis serve.
A system of categorization and classification based on certain criteria

This paper proposes a new system of categorization and classification using data mining techniques based on certain criteria/topics. We describe the design and implementation of proposed system that automatically categorizes a restaurant as being good or bad, using data mining techniques, based on users' reviews. For this study we took a data set consisting of approximately 9,000 reviews for 2,355 restaurants in Romania. The categorization was done on four criteria/topics: food, service, prices, atmosphere, and the results are represented as a range for each topic separately.
Interactive Modeling of Mechanical Objects

Objects with various types of mechanical joints are among the most commonly built. Joints implement a vocabulary of simple constrained motions (kinematic pairs) that can be used to build more complex behaviors. Defining physically correct joint geometry is crucial both for realistic appearance of models during motion, as these are typically the only parts of geometry that stay in contact, and for fabrication. Direct design of joint geometry often requires more effort than the design of the rest of the object geometry, as it requires design of components that stay in precise contact, are aligned with other parts, and allow the desired range of motion. We present an interactive system for creating physically realizable joints with user‐controlled appearance. Our system minimizes or, in most cases, completely eliminates the need for the user to manipulate low‐level geometry of joints. This is achieved by automatically inferring a small number of plausible combinations of joint dimensions, placement and orientation from part geometry, with the user making the final high‐level selection based on object semantic. Through user studies, we demonstrate that functional results with a satisfying appearance can be obtained quickly by users with minimal modeling experience, offering a significant improvement in the time required for joint construction, compared to standard modeling approaches.
Targeting Intermediary Metabolism in the Hypothalamus as a Mechanism to Regulate Appetite

The central nervous system mediates energy balance (energy intake and energy expenditure) in the body; the hypothalamus has a key role in this process. Recent evidence has demonstrated an important role for hypothalamic malonyl CoA in mediating energy balance. Malonyl CoA is generated by the carboxylation of acetyl CoA by acetyl CoA carboxylase and is then either incorporated into long-chain fatty acids by fatty acid synthase, or converted back to acetyl-CoA by malonyl CoA decarboxylase. Increased hypothalamic malonyl CoA is an indicator of energy surplus, resulting in a decrease in food intake and an increase in energy expenditure. In contrast, a decrease in hypothalamic malonyl CoA signals an energy deficit, resulting in an increased appetite and a decrease in body energy expenditure. A number of hormonal and neural orexigenic and anorexigenic signaling pathways have now been shown to be associated with changes in malonyl CoA levels in the arcuate nucleus (ARC) of the hypothalamus. Despite compelling evidence that malonyl CoA is an important mediator in the hypothalamic ARC control of food intake and regulation of energy balance, the mechanism(s) by which this occurs has not been established. Malonyl CoA inhibits carnitine palmitoyltransferase-1 (CPT-1), and it has been proposed that the substrate of CPT-1, long-chain acyl CoA(s), may act as a mediator(s) of appetite and energy balance. However, recent evidence has challenged the role of long-chain acyl CoA(s) in this process, as well as the involvement of CPT-1 in hypothalamic malonyl CoA signaling. A better understanding of how malonyl CoA regulates energy balance should provide novel approaches to targeting intermediary metabolism in the hypothalamus as a mechanism to control appetite and body weight. Here, we review the data supporting an important role for malonyl CoA in mediating hypothalamic control of energy balance, and recent evidence suggesting that targeting malonyl CoA synthesis or degradation may be a novel approach to favorably modify appetite and weight gain.
Potential Therapeutic Targets for Cardiac Fibrosis: TGF&bgr;, Angiotensin, Endothelin, CCN2, and PDGF, Partners in Fibroblast Activation

Fibrosis is one of the largest groups of diseases for which there is no therapy but is believed to occur because of a persistent tissue repair program. During connective tissue repair, “activated” fibroblasts migrate into the wound area, where they synthesize and remodel newly created extracellular matrix. The specialized type of fibroblast responsible for this action is the &agr;-smooth muscle actin (&agr;-SMA)–expressing myofibroblast. Abnormal persistence of the myofibroblast is a hallmark of fibrotic diseases. Proteins such as transforming growth factor (TGF)&bgr;, endothelin-1, angiotensin II (Ang II), connective tissue growth factor (CCN2/CTGF), and platelet-derived growth factor (PDGF) appear to act in a network that contributes to myofibroblast differentiation and persistence. Drugs targeting these proteins are currently under consideration as antifibrotic treatments. This review summarizes recent observations concerning the contribution of TGF&bgr;, endothelin-1, Ang II, CCN2, and PDGF and to fibroblast activation in tissue repair and fibrosis and the potential utility of agents blocking these proteins in affecting the outcome of cardiac fibrosis.
The Effect of Exercise on Bone Mineral Density, Bone Markers and Postural Stability in Subjects with Osteoporosis

1.1. 1 Factors affecting osteoporosis incidence The diagnosis of osteoporosis is based on the measurement of bone mineral density (BMD), which accounts for 70% of the bone strength, and is, therefore, a good indicator of an impending risk of fracture (Wilkins & Birge, 2005). According to World Health Organization, BMD values are divided into three groups: normal BMD (T-score up to -1.0 standard deviation (SD)), osteopenia (T-score between -1.0 and -2.4 SD), osteoporosis (T-score -2.5 SD and below). Wilkins and Birge (2005) presented these factors as contributing to reduced BMD: nonmodifiable – advanced age, female sex, white/asian race, family history of osteoporosis, family history of hip fracture, lactose intolerance, metabolic disorders affecting the skeleton, certain malignancies (myeloma, lymphoma), and modifiable – smoking, low calcium intake, low vitamin D intake/sunlight exposure, sedentary lifestyle, low body weight, stress/depression, surgical or drug induced hypogonadism, and glucocorticoid therapy. The risk of fracture is considered as age-related. There are two main reasons: age-related decrease in bone mineral density of the proximal femur and the age-related increase in falls which is associated with worsening balance (Dontas & Yiannakopoulos, 2007).