Miracle-dz/UniFAR-FTUs huggingface dataset:
BCAR1/p130Cas expression in untreated and acquired tamoxifen‐resistant human breast carcinomas

High BCAR1/p130Cas expression in primary breast tumour cytosol predicts a poor chance of response recurrent disease to tamoxifen treatment in patients with oestrogen receptor (ER)–positive breast carcinomas. In this study, we assessed whether BCAR1/p130Cas expression is altered during acquisition of anti‐oestrogen resistance. BCAR1/p130Cas protein was quantitatively measured by chemiluminescent Western blot analysis in the cytosol of 34 predominantly ER+ carcinomas that initially responded to primary tamoxifen treatment and subsequently progressed (n = 22 ) or developed during adjuvant tamoxifen treatment (n = 12) and compared to 54 untreated ER+ human breast carcinomas. We did not detect significant differences in the level of BCAR1/p130Cas protein in untreated and acquired tamoxifen‐resistant carcinomas. Our results indicate that in tumour progression towards tamoxifen resistance, increase of BCAR1/p130Cas may be only one of the molecular mechanisms. Thus, high BCAR1/p130Cas protein levels appear to be a hallmark for intrinsic resistance to tamoxifen in breast carcinomas. Int. J. Cancer 89:465–468, 2000. © 2000 Wiley‐Liss, Inc.
Exploiting the query structure for efficient join ordering in SPARQL queries

The join ordering problem is a fundamental challenge that has to be solved by any query optimizer. Since the high-performance RDF systems are often implemented as triple stores (i.e., they represent RDF data as a single table with three attributes, at least conceptually), the query optimization strategies employed by such systems are often adopted from relational query optimization. In this paper we show that the techniques borrowed from traditional SQL query optimization (such as Dynamic Programming algorithm or greedy heuristics) are not immediately capable of handling large SPARQL queries. We introduce a new join ordering algorithm that performs a SPARQL-tailored query simplification. Furthermore, we present a novel RDF statistical synopsis that accurately estimates cardinalities in large SPARQL queries. Our experiments show that this algorithm is highly superior to the state-of-the-art SPARQL optimization approaches, including the RDF-3X’s original Dynamic Programming strategy.
Regulation of Tumor Necrosis Factor-related Apoptosis-inducing Ligand Expression in Primary Acute Leukemic Cells by Chemotherapeutics

Objective: The expression of the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) protein and its regulation by chemotherapeutics were analyzed in primary acute leukemic cells. Materials and Methods: Peripheral blood was collected from 16 patients with acute leukemia on days 0, 1, 3, and 5 of chemotherapy. The mononuclear cells were separated from the peripheral blood, and TRAIL expression was assessed by flow cytometry. The bone marrow mononuclear cells of patients with acute leukemia were separated before chemotherapy and cultured in vitro with VP-16 and/or interferon (IFN). The TRAIL expression level was detected after the cell culture. Results: TRAIL expression in the mononuclear cells of peripheral blood was significantly upregulated on day 1 (p<0.05) and then significantly decreased on day 5 after chemotherapy (p<0.05). Results from the in vitro culture revealed that VP-16 upregulated TRAIL expression in the bone marrow mononuclear cells of patients with acute leukemia, but the binding of VP-16 to IFN did not enhance TRAIL expression as compared with VP-16 alone (p>0.05). onclusion: OA single chemotherapy mechanism for leukemia may suffice to induce TRAIL expression and promote the apoptosis of leukemic cells. Conflict of interest:None declared.
The MADlib Analytics Library or MAD Skills, the SQL

MADlib is a free, open source library of in-database analytic methods. It provides an evolving suite of SQL-based algorithms for machine learning, data mining and statistics that run at scale within a database engine, with no need for data import/export to other tools. The goal is for MADlib to eventually serve a role for scalable database systems that is similar to the CRAN library for R: a community repository of statistical methods, this time written with scale and parallelism in mind. In this paper we introduce the MADlib project, including the background that led to its beginnings, and the motivation for its open source nature. We provide an overview of the library's architecture and design patterns, and provide a description of various statistical methods in that context. We include performance and speedup results of a core design pattern from one of those methods over the Greenplum parallel DBMS on a modest-sized test cluster. We then report on two initial efforts at incorporating academic research into MADlib, which is one of the project's goals. MADlib is freely available at this http URL, and the project is open for contributions of both new methods, and ports to additional database platforms.
A Note on the Validity of the Shannon Formulation for Fitts' Index of Difficulty

The three most common variations of Fitts’ index of difficulty are the Fitts formulation, the Welford formulation, and the Shannon formulation. A recent paper by Hoffmann [1] critiqued the three and concluded that the Fitts and Welford formulations are valid and that the Shannon formulation is invalid. In this paper, we challenge Hoffmann’s position regarding the Shannon formulation. It is argued that the issue of validity vs. invalidity is ill-conceived, given that Fitts’ law is a “model by analogy” with no basis in human motor control. The relevant questions are of utility: Does a model work? How well? Is it useful? Where alternative formulations exist, they may be critiqued and compared for strengths and weaknesses, but validity is an irrelevant construct. In a reanalysis of data from Fitts’ law experiments, models built using the Shannon formulation are (re)affirmed to be as good as, and generally better than, those built using the Fitts or Welford formulation.
Ubiquitin ligase TRIM3 controls hippocampal plasticity and learning by regulating synaptic γ-actin levels

TRIM3 regulates synaptic γ-actin levels. TRIM3-deficient mice consequently have higher hippocampal spine densities, increased long-term potentiation, and enhanced contextual fear memory consolidation, indicating that temporal control of ACTG1 levels by TRIM3 is required to constrain hippocampal plasticity within physiological boundaries.
Sampling and reconstruction in sparse atomic spaces

This paper provides a quantitative notion of the sparsity for infinite dimensional atomic spaces, which play an important role in many signal processing applications. This notion of sparsity is defined as the ratio of the number of redundant samples (not necessary to recover any signal in the atomic space) to the number of all available samples of a particular canonical sampling system. It is shown that the so defined sparsity can be expressed in terms of the support of the spectral density of the sequence which generates the atomic space.
CNTRICS final task selection: executive control.

The third meeting of the Cognitive Neuroscience Treatment Research to Improve Cognition in Schizophrenia (CNTRICS) was focused on selecting promising measures for each of the cognitive constructs selected in the first CNTRICS meeting. In the domain of executive control, the 2 constructs of interest were "rule generation and selection" and "dynamic adjustments in control. " CNTRICS received 4 task nominations for each of these constructs, and the breakout group for executive control evaluated the degree to which each of these tasks met prespecified criteria. For rule generation and selection, the breakout group for executive control recommended the intradimensional/extradimensional shift task and the switching Stroop for translation for use in clinical trial contexts in schizophrenia research. For dynamic adjustments in control, the breakout group recommended conflict and error adaptation in the Stroop and the stop signal task for translation for use in clinical trials. This article describes the ways in which each of these tasks met the criteria used by the breakout group to recommend tasks for further development.
Prevention of Earlobe Keloid Recurrence with Postoperative Corticosteroid Injections Versus Radiation Therapy A Randomized, Prospective Study and Review of the Literature

BACKGROUND Simple excision of earlobe keloids can result in recurrence rates approaching 80%. Many modalities have been suggested to reduce the risk of recurrence postoperatively, including intralesional steroids and radiotherapy. OBJECTIVE In order to determine the most reliable method to prevent keloid recurrence, we have conducted the first randomized, prospective trial comparing corticosteroid injections versus radiation therapy. RESULTS Thirty‐one keloids were treated and followed for a minimum of 12.0 months. Two of 16 keloids (12.5%) recurred after surgery and radiation therapy, while 4 of 12 (33%) recurred after surgery and steroid injections. No alteration of skin pigmentation, wound dehiscence, chronic dermatitis, or neoplastic changes was observed in any patient in either group. Although a statistically significant difference was not observed, radiotherapy appeared to be more effective than steroid injections in preventing keloid recurrence. CONCLUSIONS Radiotherapy is a simpler treatment modality with better patient compliance, and patients were much more likely to complete treatment than with corticosteroid injections. We believe that radiotherapy can play an important role in the prevention of earlobe keloid recurrences, and that with current techniques, complications can be minimized. Further randomized study with additional patients is needed to compare the effectiveness of corticosteroid injections and radiotherapy in preventing keloid recurrence.
Boosting Algorithms for Maximizing the Soft Margin

We present a novel boosting algorithm, called SoftBoost, designed for sets of binary labeled examples that are not necessarily separable by convex combinations of base hypotheses. Our algorithm achieves robustness by capping the distributions on the examples. Our update of the distribution is motivated by minimizing a relative entropy subject to the capping constraints and constraints on the edges of the obtained base hypotheses. The capping constraints imply a soft margin in the dual optimization problem. Our algorithm produces a convex combination of hypotheses whose soft margin is within δ of its maximum. We employ relative entropy projection methods to prove an O(ln N/δ2) iteration bound for our algorithm, where N is number of examples. We compare our algorithm with other approaches including LPBoost, Brown-Boost, and SmoothBoost. We show that there exist cases where the number of iterations required by LPBoost grows linearly in N instead of the logarithmic growth for SoftBoost. In simulation studies we show that our algorithm converges about as fast as LPBoost, faster than BrownBoost, and much faster than SmoothBoost. In a benchmark comparison we illustrate the competitiveness of our approach.
Further Comments on the Measurement of Carotid Stenosis From Angiograms

Three different methods for estimating the percentage of reduction in the diameter of the internal carotid artery (ie, stenosis) have been proposed in the literature. Further comparisons of the methods were carried out with the intent of recommending a current standard for determining the percentage of stenosis from angiograms. Methods Angiograms from 112 patients were obtained. For each angiogram, stenosis was estimated in the manner of the European Carotid Surgery Trial (ECST method), the North American Symptomatic Carotid Endarterectomy Trial (NASCET method), and by a method using the common carotid artery lumen diameter (CC method). Results Although there is much discrepancy among the estimates of stenosis arising from the three different methods for any particular patient, it is possible to predict (on average) the percentage of stenosis from one method to another. The relationship between the NASCET and CC methods is linear, with a mean ratio of distal internal carotid artery to common carotid diameter of 0.62 (SD of 0.11). The variability in the diameter of the common carotid artery lumen stabilizes only beyond 2.5 common carotid diameter units (approximately 20 to 30 mm by conventional angiography) proximal to the bifurcation. Unexpectedly, the relationships between both the ECST and NASCET methods and ECST and CC methods were parabolic (P<.001). The reasons underlying these departures from linearity are uncertain. Conclusions The comparability of our results with those reported in the literature regarding the CC and NASCET methods provides further evidence of the reproducibility of methods measuring anatomic features that can be visualized on an angiogram. Disease of the internal carotid artery is one of the important causes of ischemic symptoms. Measuring the narrowest portion of the internal artery relative to the normal portion of the same artery, well beyond the bulb, is a logical method. Moreover, benefits of carotid endarterectomy for patients with 70% to 99% stenosis as determined by the NASCET method have been well established in a clinical trial. Converting from the NASCET method to the CC method, given that the CC method is neither superior nor easier to calculate, is not recommended.
M2-Polarized tumor-associated macrophages are associated with poor prognoses resulting from accelerated lymphangiogenesis in lung adenocarcinoma

OBJECTIVES: Tumor-associated macrophages have been implicated in promoting tumor growth, progression and metastasis. However, the activated phenotype (M1 or M2) of tumor-associated macrophages remains unknown in solid tumors. Therefore, this study examined the density and prognostic significance of M2-polarized tumor-associated macrophages in lung adenocarcinoma. METHODS: Tumor specimens from 65 lung adenocarcinoma patients were assessed by ELISA for Th1/Th2 cytokine concentrations. The activated phenotype (M1 or M2) of tumor-associated macrophages was determined utilizing immunofluorescence staining. Additionally, to evaluate lymphangiogenesis, peritumoral lymphatic microvessel density was measured using D2-40. The correlation between tumor-associated macrophage subtype and overall patient survival was analyzed using the Kaplan-Meier method and compared using the log-rank test. RESULTS: A shift toward Th2 cytokine expression was detected within lung adenocarcinoma microenvironments. Approximately 79.71±16.27% of tumor-associated macrophages were M2 polarized; the remaining 20.35±5.31% were M1 polarized. The infiltration of M2-polarized macrophages was significantly associated with P-TNM staging and lymph node metastasis. The peritumoral lymphatic microvessel density was significantly higher in the high M2-polarized tumor-associated macrophage group than in the low M2-polarized tumor-associated macrophage group. A significant difference in overall patient survival was detected not only between patients with tumors with high and low macrophage counts but also between patients with tumors with high and low counts of M2-polarized macrophages. CONCLUSION: Tumor-associated macrophages in lung adenocarcinoma have an M2-polarized subtype and are associated with poor prognoses, perhaps resulting from accelerated lymphangiogenesis and lymph node metastasis.
Parental ADHD Symptomology and Ineffective Parenting: The Connecting Link of Home Chaos

SYNOPSIS Objective. This study examines links between maternal and paternal attention-deficit/hyperactivity disorder (ADHD) symptoms and parenting practices that require inhibition of impulses, sustained attention, and consistency; the role of home chaos in these associations is also assessed. Design. ADHD symptoms, the level of home chaos, and parenting practices (e.g., involvement, inconsistent discipline, supportive and nonsupportive responses to children's negative emotions, and positive parenting) were assessed through self-reports of 311 mothers and 149 fathers of middle-childhood children. Teachers assessed the child ADHD symptoms. Results. Mothers reported higher home chaos when they or their children had higher levels of ADHD symptoms; for fathers, only their own ADHD symptoms predicted higher levels of home chaos. Mothers' ADHD symptoms were positively associated with inconsistent discipline and nonsupportive responses to children's negative emotions, and these associations were mediated by home chaos. Higher levels of fathers' ADHD symptoms predicted more inconsistent discipline, low involvement, and a low level of supportive and a high level of nonsupportive responses to children's negative emotions. Home chaos moderated the link between paternal ADHD and inconsistent discipline and mediated the link between paternal ADHD and involvement. Overall, positive aspects of parenting, and those that require attention and ability to control one's impulses, may be compromised in fathers with high levels of ADHD symptoms. Conclusions. Effectiveness of specific parenting practices for both mothers and fathers may be compromised in parents with ADHD symptoms. In certain cases, parental ADHD symptoms translate into ineffective parenting through disorganized homes.
Impact of the 2009 influenza pandemic on pneumococcal pneumonia hospitalizations in the United States.

BACKGROUND Infection with influenza virus increases the risk for developing pneumococcal disease. The A/H1N1 influenza pandemic in autumn 2009 provided a unique opportunity to evaluate this relationship. METHODS Using weekly age-, state-, and cause-specific hospitalizations from the US State Inpatient Databases of the Healthcare Cost and Utilization Project 2003-2009, we quantified the increase in pneumococcal pneumonia hospitalization rates above a seasonal baseline during the pandemic period. RESULTS We found a significant increase in pneumococcal hospitalizations from late August to mid-December 2009, which corresponded to the timing of highest pandemic influenza activity. Individuals aged 5-19 years, who have a low baseline level of pneumococcal disease, experienced the largest relative increase in pneumococcal hospitalizations (ratio, 1.6 [95% confidence interval {CI}, 1.4-1.7]), whereas the largest absolute increase was observed among individuals aged 40-64 years. In contrast, there was no excess disease in the elderly. Geographical variation in the timing of excess pneumococcal hospitalizations matched geographical patterns for the fall pandemic influenza wave. CONCLUSIONS The 2009 influenza pandemic had a significant impact on the rate of pneumococcal pneumonia hospitalizations, with the magnitude of this effect varying between age groups and states, mirroring observed variations in influenza activity.
Organization of the autoantibody repertoire in healthy newborns and adults revealed by system level informatics of antigen microarray data

The immune system is essential to body defense and maintenance. Specific antibodies to foreign invaders function in body defense, and it has been suggested that autoantibodies binding to self molecules are important in body maintenance. Recently, the autoantibody repertoires in the bloods of healthy mothers and their newborns were studied using an antigen microarray containing hundreds of self molecules. It was found that the mothers expressed diverse repertoires for both IgG and IgM autoantibodies. Each newborn shares with its mother a similar repertoire of IgG antibodies, which cross the placental but its IgM repertoire is more similar to those of other newborns. Here, we took a system-level approach and analyzed the correlations between autoantibody reactivities of the previous data and extended the study to new data from newborns at birth and a week later, and from healthy young women. For the young women, we found modular organization of both IgG and IgM isotypes into antigen cliques—subgroups of highly correlated antigen reactivities. In contrast, the newborns were found to share a universal congenital IgM profile with no modular organization. Moreover, the IgG autoantibodies of the newborns manifested buds of the mothers' antigen cliques, but they were noticeably less structured. These findings suggest that the natural autoantibody repertoire of humans shows relatively little organization at birth, but, by young adulthood, it becomes sorted out into a modular organization of subgroups (cliques) of correlated antigens. These features revealed by antigen microarrays can be used to define personal states of autoantibody organizational motifs.
An Integrated Self-Organizing Map for the Traveling Salesman Problem

As a representative combinatorial optimization problem, the Traveling Salesman Problem (TSP) has attracted extensive research. In this paper, we develop a new Self-Organizing Map (SOM) network for the TSP and call it the Integrated SOM (ISOM) network. Its learning rule embodies the effective mechanisms of three typical learning rules. In its single learning activity, the excited neuron first is dragged close to the input city, and then is expanded towards the convex-hull of the TSP, and finally, it is drawn close to the middle point of its two neighbor neurons. The elaborate cooperation among these three learning mechanisms is evolved by a genetic algorithm. The simulation results show that the finally established ISOM can generate more promising solutions, with similar computation time, than other neural networks like the SOM network, the Expanded SOM, and the Convex Elastic Net. Key-Words: Self-organizing map, Traveling salesman problem, Genetic algorithms, Convex-hull
Regulation of B- and T-cell Mediated Xenogeneic Transplant Rejection by Interleukin 12

Background. Xenotransplantation may provide a solution to the increasing shortage of donor organs. Acute vascular rejection and cell-mediated rejection remain the primary barriers to successful xenotransplantation. In animal models where acute vascular rejection can be attenuated, xenografts succumb to cell-mediated rejection. The mechanisms of acute vascular rejection and cell-mediated rejection are poorly understood. Methods. Using a heterotopic rat-to-mouse cardiac transplantation model, we demonstrate that IL-12p40 attenuates both allogeneic and xenogeneic acute vascular rejection pathology by suppressing B-cell activation and anti-rat isotype switching. To study the mechanism of xenogeneic cell-mediated rejection, we use B-cell deficient mice that only develop cell-mediated rejection pathology. To elucidate the role of IL-12 in cell-mediated rejection, we generated B cell/ IL-12p40 double knockout mice. Results. We demonstrate that xenogeneic cell-mediated rejection is mediated by CD4+ T cells, and is accompanied by elevated FasL and granzyme mRNA expression. Strikingly, by generating B cell/IL-12p40 double knockout mice, we demonstrate that xenogeneic cell-mediated rejection is IL-12p40 dependent. In contrast, we demonstrate that allogeneic cellular rejection is IL-12p40 independent. Conclusions. We conclude that IL-12 plays a dual role in xenotransplantation by driving xenogeneic CD4+ T cell responses but suppressing both allogeneic and xenogeneic B cell responses. Therefore, the mechanism of allogeneic and xenogeneic transplantation rejection is differentially regulated by IL-12.