Miracle-dz/UniFAR-FTUs huggingface dataset:
Adverse Childhood Experiences and Adult Smoking, Nebraska, 2011

Introduction Smoking is a public health risk; the prevalence of smoking among adults in Nebraska is 18.4%. Studies indicate that maltreatment of children alters their brain development, possibly increasing risk for tobacco use. Previous studies have documented associations between childhood maltreatment and adult health behaviors, demonstrating the influence of adverse experiences on tobacco use. We examined prevalence and associations between adverse childhood experiences and smoking among Nebraskans. Methods We analyzed 2011 Nebraska Behavioral Risk Factor Surveillance System (Adverse Childhood Experience module) data, defining adverse childhood experience exposures as physical, sexual, and verbal abuse (ie, direct exposures), and household dysfunction associated with mental illness, substance abuse, divorce, domestic violence, and living with persons with incarceration histories (ie, environmental exposures). We estimated prevalence of exposures, taking into account the complex survey design. We used logistic regression with predicted margins to estimate adjusted relative risk for smoking by direct or environmental exposure. Results Approximately 51% of Nebraskans experienced 1 or more adverse childhood events; 7% experienced 5 or more. Prevalence of environmental exposures (42%) was significantly higher than that of direct exposures (31%). Prevalence of individual exposures ranged from 6% (incarceration of a household member) to 25% (verbal abuse). Adjusted relative risks of smoking for direct and environmental exposures were 1.5 and 1.8, respectively. Conclusion We present a new method of evaluating adverse childhood experience data. Prevalence of adverse childhood experiences is high among Nebraskans, and these exposures are associated with smoking. State-specific strategies to monitor adverse events among children and provide interventions might help to decrease the smoking rate in this population.
Hypoxia‐induced downregulation of miR‐30c promotes epithelial‐mesenchymal transition in human renal cell carcinoma

MicroRNAs (miRNAs), which negatively regulate protein expression by binding protein‐coding mRNAs, have been integrated into cancer development and progression as either oncogenes or tumor suppressor genes. miR‐30c was reported to be downregulated in several types of cancer. However, its role in human renal cell carcinoma (RCC) remains largely unknown. Here, we show that miR‐30c is significantly downregulated in human RCC tissues and cell lines. We found that miR‐30c downregulation could be induced by hypoxia in RCC cells in a hypoxia‐inducible factors (HIFs) dependent manner. Repression of miR‐30c through its inhibitor resulted in reduction of E‐cadherin production and promotion of epithelial‐mesenchymal transition (EMT), while overexpression of miR‐30c inhibited EMT in RCC cells. We identified Slug as a direct target of miR‐30c in RCC cells. Slug was upregulated in RCC tissues and its expression could be induced by hypoxia, which is consistent with downregulation of miR‐30c by hypoxia. Forced overexpression of Slug in 786‐O cells reduced E‐cadherin production, and promoted EMT as well as cell migration. Moreover, Slug overexpression abrogated the inhibitory role of miR‐30c in regulating EMT and cell migration, indicating miR‐30c regulates EMT through Slug in RCC cells. Our findings propose a model that hypoxia induces EMT in RCC cells through downregulation of miR‐30c, which leads to subsequent increase of Slug expression and repression of E‐cadherin production, and suggest a potential application of miR‐30c in RCC treatment.
The BINGO! System for Information Portal Generation and Expert Web Search

This paper presents the BINGO! focused crawler, an advanced tool for information portal generation and expert Web search. In contrast to standard search engines such as Google which are solely based on precomputed index structures, a focused crawler interleaves crawling, automatic classification, link analysis and assessment, and text filtering. A crawl is started from a user-provided set of training data and aims to collect comprehensive results for the given topics. The focused crawling paradigm has been around for a few years and many of our techniques are adopted from the information retrieval and machine learning literature. BINGO! is a system-oriented effort to integrate a suite of techniques into a comprehensive and versatile tool. The paper discusses its overall architecture and main components, important lessons from early experimentation and the resulting improvements on effectiveness and efficiency, and experimental results that demonstrate the usefulness of BINGO! as a next-generation tool for information organization and search.
Metabolism and Genetics of Helicobacter pylori: the Genome Era

SUMMARY The publication of the complete sequence of Helicobacter pylori 26695 in 1997 and more recently that of strain J99 has provided new insight into the biology of this organism. In this review, we attempt to analyze and interpret the information provided by sequence annotations and to compare these data with those provided by experimental analyses. After a brief description of the general features of the genomes of the two sequenced strains, the principal metabolic pathways are analyzed. In particular, the enzymes encoded by H. pylori involved in fermentative and oxidative metabolism, lipopolysaccharide biosynthesis, nucleotide biosynthesis, aerobic and anaerobic respiration, and iron and nitrogen assimilation are described, and the areas of controversy between the experimental data and those provided by the sequence annotation are discussed. The role of urease, particularly in pH homeostasis, and other specialized mechanisms developed by the bacterium to maintain its internal pH are also considered. The replicational, transcriptional, and translational apparatuses are reviewed, as is the regulatory network. The numerous findings on the metabolism of the bacteria and the paucity of gene expression regulation systems are indicative of the high level of adaptation to the human gastric environment. Arguments in favor of the diversity of H. pylori and molecular data reflecting possible mechanisms involved in this diversity are presented. Finally, we compare the numerous experimental data on the colonization factors and those provided from the genome sequence annotation, in particular for genes involved in motility and adherence of the bacterium to the gastric tissue.
The Dual‐microfacet Model for Capturing Thin Transparent Slabs

We present a new model, called the dual‐microfacet, for those materials such as paper and plastic formed by a thin, transparent slab lying between two surfaces of spatially varying roughness. Light transmission through the slab is represented by a microfacet‐based BTDF which tabulates the microfacet's normal distribution (NDF) as a function of surface location. Though the material is bounded by two surfaces of different roughness, we approximate light transmission through it by a virtual slab determined by a single spatially‐varying NDF. This enables efficient capturing of spatially variant transparent slices. We describe a device for measuring this model over a flat sample by shining light from a CRT behind it and capturing a sequence of images from a single view. Our method captures both angular and spatial variation in the BTDF and provides a good match to measured materials.
Differentiation of human embryonal carcinoma cells induces human immunodeficiency virus permissiveness which is stimulated by human cytomegalovirus coinfection

Human immunodeficiency virus (HIV) replicates in differentiated but not undifferentiated NTERA-2 human embryonal carcinoma cells; neither cell type expresses CD4. Susceptibility of the differentiated cells is enhanced by coinfection with cytomegalovirus. HIV infection induces lactoseries glycolipids, suggesting a mechanism whereby HIV might interfere with normal embryogenesis.
Axiomatic Analysis of Cross-Language Information Retrieval

A major challenge in Cross-Language Information Retrieval (CLIR) is the adoption of translation knowledge in retrieval models, as it affects the term weighting which is known to highly impact the retrieval performance. In this paper, we present an analytical study of using translation knowledge in CLIR. In particular, by adopting axiomatic analysis framework, we formulate the impacts of translation knowledge on document ranking as constraints that any cross-language retrieval model should satisfy. We then consider the state-of-the-art CLIR methods and check whether they satisfy these constraints. Finally, we show through empirical evaluation that violating one of the constraints harms the retrieval performance significantly which calls for further investigation.
Advances in Brief MCF 7 / LCC 2 : A 4-Hydroxytamoxifen Resistant Human Breast Cancer Variant That Retains Sensitivity to the Steroidal Antiestrogen ICI 182 , 78 o 1

The development of resistance to the antiestrogen tamoxifen occurs in a high percentage of initially responsive patients. We have developed a new model in which to investigate acquired resistance to triphenylethylenes. A stepwise in vitro selection of the hormone-independent human breast cancer variant MCF-7/LCC1 against 4-hydroxytamoxifen pro duced a stable resistant population designated MCF7/LCC2. MCF7/LCC2 cells retain levels of estrogen receptor expression comparable to the pa rental MCF7/LCC1 and MCF-7 cells. Progesterone receptor expression remains estrogen inducible in MCF7/LCC2 cells, although to levels sig nificantly lower than observed in MCF-7 and MCF7/LCC1 cells. MCF7/ LCC2 cells form tumors in ovariectomized nude mice without estrogen supplementation, and these tumors are tamoxifen resistant but can be estrogen stimulated. Significantly, MCF7/LCC2 cells have retained sensi tivity to the steroidal antiestrogen ICI 182,780. These data suggest that some breast cancer patients who acquire resistance to tamoxifen may not develop cross-resistance to treatment with steroidal antiestrogens.
First Order Methods beyond Convexity and Lipschitz Gradient Continuity with Applications to Quadratic Inverse Problems

We focus on nonconvex and nonsmooth minimization problems with a composite objective, where the differentiable part of the objective is freed from the usual and restrictive global Lipschitz gradient continuity assumption. This longstanding smoothness restriction is pervasive in first order methods (FOM), and was recently circumvent for convex composite optimization by Bauschke, Bolte and Teboulle, through a simple and elegant framework which captures, all at once, the geometry of the function and of the feasible set. Building on this work, we tackle genuine nonconvex problems. We first complement and extend their approach to derive a full extended descent lemma by introducing the notion of smooth adaptable functions. We then consider a Bregman-based proximal gradient methods for the nonconvex composite model with smooth adaptable functions, which is proven to globally converge to a critical point under natural assumptions on the problem's data. To illustrate the power and potential of our general framework and results, we consider a broad class of quadratic inverse problems with sparsity constraints which arises in many fundamental applications, and we apply our approach to derive new globally convergent schemes for this class.
The Exclusion of Afro-Guyanese Hucksters in Micro-Banking

At the 1997 Microcredit Summit in Washington DC, the primary goal of microfinance agreed to was that it was a tool to upset conventional banking and to make financial services inclusive; yet this is not the case for microfinance in Guyana. Educated Indo-Guyanese lenders admitted to their own personal biases against Afro-Guyanese as clients without remorse in this case study of 93 people. I argue in this paper that micro-banking managers and staff hold onto historically-rooted prejudices which interfere with the allocation of loans. Race is seemingly the issue that divides the populace; however, I found issues of racial, class and gender bias intertwined in the lending process that deny poor Afro-Guyanese women loans. Personal bias can affect the management of economic development pro-grammes for the poor and it should not be assumed that microfinance helps everyone. Resumen: La exclusion de los ‘hucksters’ afroguyaneses en la microbanca En la Cumbre de Microcredito celebrada en Washington DC en 1997, se acordo que el objetivo principal de las microfinanzas era servir como herramienta para desbaratar la banca convencional y hacer inclusivos los servicios financieros; sin embargo, este no es el caso de las microfinanzas en Guyana. Prestamistas indoguyaneses con una buena formacion se deja-ron llevar sin reparos por sus propios prejuicios personales contra los afroguyaneses como clientes en este estudio de caso de 93 personas. En este documento sostengo que los directores y el personal de la microbanca se aferran a prejuicios enraizados historicamente que interfieren en la concesion de prestamos. Aparentemente la raza es la cuestion que divide al pueblo; sin embargo, identifique prejuicios raciales, de clase y de genero entrelazados en el proceso crediticio por los que se deniegan prestamos a mujeres afroguyanesas pobres. Los prejuicios personales pueden afectar a la gestion de los programas de desarrollo economico para los pobres y no se debe asumir que las microfinanzas ayudan a todo el mundo.
Geodesic trajectory generation on learnt skill manifolds

Humanoid robots are appealing due to their inherent dexterity. However, these potential benefits may only be realized if the corresponding motion synthesis procedure is suitably flexible. This paper presents a flexible trajectory generation algorithm that utilizes a geometric representation of humanoid skills (e.g., walking) - in the form of skill manifolds. These manifolds are learnt from demonstration data that may be obtained from off-line optimization algorithms (or a human expert). We demonstrate that this model may be used to produce approximately optimal motion plans as geodesics over the manifold and that this allows us to effectively generalize from a limited training set. We demonstrate the effectiveness of our approach on a simulated 3-link planar arm, and then the more challenging example of a physical 19-DoF humanoid robot. We show that our algorithm produces a close approximation of the much more computationally intensive optimization procedure used to generate the data. This allows us to present experimental results for fast motion planning on a realistic - variable step length, width and height - walking task on a humanoid robot.
Tutorial: stream processing optimizations

This tutorial starts with a survey of optimizations for streaming applications. The survey is organized as a catalog that introduces uniform terminology and a common categorization of optimizations across disciplines, such as data management, programming languages, and operating systems. After this survey, the tutorial continues with a deep-dive into the fission optimization, which automatically transforms streaming applications for data-parallelism. Fission helps an application improve its throughput by taking advantage of multiple cores in a machine, or, in the case of a distributed streaming engine, multiple machines in a cluster. While the survey of optimizations covers a wide range of work from the literature, the in-depth discussion of fission relies more heavily on the presenters' own research and experience in the area. The tutorial concludes with a discussion of open research challenges in the field of stream processing optimizations.
Implementation of evidence‐based practice in optometry

Evidence‐based practice in health care requires that treatment decisions be supported by high‐quality clinical evidence, preferably involving well‐designed large‐scale clinical trials of the various treatment options. How does this relate to everyday primary‐care optometry? This article provides a background to the emergence of the ‘evidence‐based’ movement and investigates areas where the efficacy of clinical optometry might be improved by an evidence‐based approach. It is argued that evidence‐based practice is appropriate for all aspects of optometry but it may be most useful in the selection of treatments with topical therapeutic agents and in optometry’s growing public health role in the detection and management of sight‐threatening disease.
Draft Genome Sequence of a New Shigella flexneri Subserotype, 4S BJ10610

ABSTRACT Shigella flexneri is of great concern in the prevalence of shigellosis and resistance to many antibiotics in developing countries. Here, we report the draft genome sequence of a new S. flexneri subserotype, 4S BJ10610, isolated from the stool specimens of a patient in Beijing, China.
Prediction of Ligand Binding Using an Approach Designed to Accommodate Diversity in Protein-Ligand Interactions

Computational determination of protein-ligand interaction potential is important for many biological applications including virtual screening for therapeutic drugs. The novel internal consensus scoring strategy is an empirical approach with an extended set of 9 binding terms combined with a neural network capable of analysis of diverse complexes. Like conventional consensus methods, internal consensus is capable of maintaining multiple distinct representations of protein-ligand interactions. In a typical use the method was trained using ligand classification data (binding/no binding) for a single receptor. The internal consensus analyses successfully distinguished protein-ligand complexes from decoys (r 2, 0.895 for a series of typical proteins). Results are superior to other tested empirical methods. In virtual screening experiments, internal consensus analyses provide consistent enrichment as determined by ROC-AUC and pROC metrics.
Prediction the Substrate Specificities of Membrane Transport Proteins Based on Support Vector Machine and Hybrid Features

Membrane transport proteins and their substrate specificities play crucial roles in a variety of cellular functions. Identifying the substrate specificities of membrane transport proteins is closely related to the protein-target interaction prediction, drug design, membrane recruitment, and dysregulation analysis. However, experimental methods to this aim are time consuming, labor intensive, and costly. Therefore, we proposed a novel method basing on support vector machine (SVM) to predict substrate specificities of membrane transport proteins by integrating features from position-specific score matrix (PSSM), PROFEAT, and Gene Ontology (GO). Finally, jackknife cross-validation tests were adopted on a benchmark and independent datasets to measure the performance of the proposed method. The overall accuracy of 96.16 and 80.45 percent were obtained for two datasets, which are higher (from 2.12 to 20.44 percent) than that by the state-of-the-art tool. Comparison results indicate that the proposed model is more reliable and efficient for accurate prediction the substrate specificities of membrane transport proteins.
Training design for doubly-selective channel estimation

We address the problem of estimating time-varying channels using two different basis expansion models (BEMs): the complex exponential (CE)-BEM, and the discrete prolate spheroidal (DPS)-BEM. The frequencies of both of these BEMs are limited to [-fmax,fmax], where fmax is the maximum Doppler spread. The coefficients of the BEM are estimated using pilot clusters that are time-division multiplexed with the data. For a fixed number of pilot symbols, we attempt to optimize the power and placement of the pilot symbols used in transmission, and then optimize the BEM parameters used in channel estimation, in the sense of minimizing the mean-square estimation error (MSE) at the receiver. These optimum values depend on the statistics of the channel, the signal-to-noise ratio (SNR), and other system parameters. Simulation results confirm that for a wide range of SNR and Doppler spread values, this optimization greatly reduces the MSE, and the bit-error rate.
Molecular Biology And

Alterations in cell survival may contribute to tumour development, influence tumour biology and its response to chemotherapy. Apoptosis may be triggered by p53-dependent or p53-independent mechanisms that share downstream biochemical pathways. P53-dependent apoptosis is stimulus specific. In several cell types wild-type p53 protein is necessary for induction of apoptosis after defects in p53-dependent apoptotic response may contribute to malignant transformation, tumour progression and tumour resistance to DNA damage-inducing therapy. P53-mediated apoptosis involves transcriptional repression of bcl-2, activation of bax and bcl-xL, as well as immediate interaction with proteins – mediators of apoptosis Bcl-2 and bcl-x L proteins are inhibitors of programmed cell death, while bax belongs to promotors. It is suggested that both bcl-2 and bax proteins may participate in mitochondrial pore formation, and thus influence the execution step of apoptosis. Bcl-2 and bcl-x L anti-apoptotic proteins may be blocked by complex formation with bax (Reed, 1997). Little is known on apoptosis regulation in vivo. p53 gene alterations are very frequent in ovarian cancer – they have been found in 81% of serous type tumours in our own material, and are rather an early step in the development of ovarian cancer (Kupryjanczyk et al, 1993, 1995a; reviewed in Kupryjanczyk, 1996). One may expect that p53 gene mutations will negatively influence p53-dependent spontaneous and induced apoptosis. It is assumed that poor response to DNA-damage in tumours bearing a p53 gene mutation may cause genomic instability and tumour progression, as well as resistance to DNA damage-inducing therapy. However, studies on p53 status and response to cisplatin-based chemotherapy have not given so far equivocal results (Righetti et al, 1996; De Feudis et al, 1997). To our knowledge, spontaneous apoptosis has not been evaluated in relation to p53 gene mutation neither in ovarian or other tumour samples. Also, nothing is known about possible prognostic value of spontaneous apoptosis in ovarian Spontaneous apoptosis in ovarian carcinomas: a positive association with p53 gene mutation is dependent on growth fraction Summary Changes in cell survival contribute to tumour development, influence tumour biology and its response to chemotherapy. p53 gene alterations should negatively affect apoptosis by impaired p53-dependent apoptotic response. We looked for associations between spontaneous apoptosis, p53 gene mutation, p53 protein accumulation, growth fraction, bcl-2 expression and histological parameters in 64 ovarian, four tubal and three peritoneal carcinomas. Apoptotic cells were detected with the TUNEL method. p53 gene variants were detected by the single-strand conformation polymorphism and …
Exploring the Empty Spaces of Organizing: How Improvisational Jazz Helps Redescribe Organizational Structure

This paper uses jazz as a metaphoric vehicle for redescribing (Rorty 1989) the concept of organizational structure in ways that fit within the emerging vocabulary of organization studies. It begins with a description of some basic elements of jazz performance soloing, comping, trading fours, listening and responding, groove and feel and builds on these to redescribe organizational structure as ambiguous, emotional and temporal. In reflexive fashion, the paper not only demonstrates the concepts it engages, but presents a jazz-like performance of Rorty's method of redescription via metaphor.