Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and characterization of a novel human papillomavirus type 6 DNA from an invasive vulvar carcinoma

Human papillomavirus type 6 (HPV-6) DNA was detected in a rapidly growing vulvar verrucous carcinoma and two recurrent tumor samples. The viral DNA (HPV-6vc) was molecularly cloned and found to have a high degree of DNA sequence homology to HPV-6b DNA. Comparison of restriction endonuclease cleavage patterns between HPV-6b and HPV-6vc genomes and DNA sequencing analysis demonstrated an additional 106 bases in the HPV-6vc genome. These additional nucleotides were located in the noncoding region of the viral genome which contains the putative viral DNA replication and early gene transcriptional control elements. Seventy-four of the additional 106 nucleotides were found as one insert in the purine-thymidine-rich region 3' to the end of the L1 open reading frame. This 74-base-pair addition had homology with viral sequences immediately upstream to it and to poly(dG-dT) sequences found in the human genome including the conserved repeated sequences in human DNA (EC1) and in the human cardiac muscle actin gene. Two smaller inserts, 19 and 15 nucleotides, were found upstream from the transcriptional control elements and demonstrate homology with regions of human alpha and gamma interferon genes.
The serine protease Esperase HPF inhibits the formation of multispecies biofilm

The antifouling (AF) potential of the serine protease Esperase HPF (subtilisin) was evaluated for the ability to prevent the formation of a four-species bacterial biofilm. The effects of enzyme activity, time and application of the enzyme were tested on the density and the oxidative metabolism of biofilm developed in microtiter wells. Esperase HPF did not inhibit the oxidative metabolism of the bacterial biofilm or planktonic growth, but the enzyme inhibited biofilm formation by its proteolytic activity as inactivated enzyme had no effect. The effective enzyme concentration was determined over a period of 72 h, as by then all the tested concentrations inhibited biofilm formation maximally. The effective concentrations of the enzymes in solution were the same regardless of time of application (ie before or after biofilm formation), but immobilisation of the enzymes caused a lower effective concentration. Esperase HPF is an attractive alternative to the biocidal compounds used in AF coatings today.
Diverse Antibody Genetic and Recognition Properties Revealed following HIV-1 Envelope Glycoprotein Immunization

Isolation of mAbs elicited by vaccination provides opportunities to define the development of effective immunity. Ab responses elicited by current HIV-1 envelope glycoprotein (Env) immunogens display narrow neutralizing activity with limited capacity to block infection by tier 2 viruses. Intense work in the field suggests that improved Env immunogens are forthcoming, and it is therefore important to concurrently develop approaches to investigate the quality of vaccine-elicited responses at a higher level of resolution. In this study, we cloned a representative set of mAbs elicited by a model Env immunogen in rhesus macaques and comprehensively characterized their genetic and functional properties. The mAbs were genetically diverse, even within groups of Abs targeting the same subregion of Env, consistent with a highly polyclonal response. mAbs directed against two subdeterminants of Env, the CD4 binding site and V region 3, could in part account for the neutralizing activity observed in the plasma of the animal from which they were cloned, demonstrating the power of mAb isolation for a detailed understanding of the elicited response. Finally, through comparative analyses of mAb binding and neutralizing capacity of HIV-1 using matched Envs, we demonstrate complex relationships between epitope recognition and accessibility, highlighting the protective quaternary packing of the HIV-1 spike relative to vaccine-induced mAbs.
Beyond GLMs: A Generative Mixture Modeling Approach to Neural System Identification

Generalized linear models (GLMs) represent a popular choice for the probabilistic characterization of neural spike responses. While GLMs are attractive for their computational tractability, they also impose strong assumptions and thus only allow for a limited range of stimulus-response relationships to be discovered. Alternative approaches exist that make only very weak assumptions but scale poorly to high-dimensional stimulus spaces. Here we seek an approach which can gracefully interpolate between the two extremes. We extend two frequently used special cases of the GLM—a linear and a quadratic model—by assuming that the spike-triggered and non-spike-triggered distributions can be adequately represented using Gaussian mixtures. Because we derive the model from a generative perspective, its components are easy to interpret as they correspond to, for example, the spike-triggered distribution and the interspike interval distribution. The model is able to capture complex dependencies on high-dimensional stimuli with far fewer parameters than other approaches such as histogram-based methods. The added flexibility comes at the cost of a non-concave log-likelihood. We show that in practice this does not have to be an issue and the mixture-based model is able to outperform generalized linear and quadratic models.
A Pill for the Ill? Patients’ Reports of Their Experience of the Medical Encounter in the Treatment of Depression

Background Starting in the 1960s, a broad-based patients’ rights movement began to question doctors’ paternalism and to demand disclosure of medical information, informed consent, and active participation by the individual in personal health care. According to scholars, these changes contributed to downplay the biomedical approach in favor of a more patient-oriented perspective. The Swedish non-profit organization Consumer Association for Medicines and Health (KILEN) has offered the possibility for consumers to report their perceptions and experiences from their use of medicines in order to strengthen consumer rights within the health care sector. Methodology In this paper, qualitative content analysis was used to analyze 181 KILEN consumer reports of adverse events from antidepressant medications in order to explore patients’ views of mental ill health symptoms and the doctor-patient interaction. Principal Findings Overall, the KILEN stories contained negative experiences of the patients’ medical encounters. Some reports indicated intense emotional outrage and strong feelings of abuse by the health care system. Many reports suggested that doctors and patients had very different accounts of the nature of the problems for which the patient was seeking help. Although patients sought help for problems like tiredness and sleeplessness (often with a personal crisis of some sort as a described cause), the treating doctor in most cases was exceptionally quick in both diagnosing depression and prescribing antidepressant treatment. When patients felt they were not being listened to, trust in the doctor was compromised. This was evident in the cases when the doctor tried to convince them to take part in medical treatment, sometimes by threatening to withdraw their sick-listing. Conclusions Overall, this study suggests that the dynamics happening in the medical encounter may still be highly affected by a medical dominance, instead of a patient-oriented perspective. This may contribute to a questionable medicalization and/or pharmaceuticalization of depression.
Physical reproduction of materials with specified subsurface scattering

We investigate a complete pipeline for measuring, modeling, and fabricating objects with specified subsurface scattering behaviors. The process starts with measuring the scattering properties of a given set of base materials, determining their radial reflection and transmission profiles. We describe a mathematical model that predicts the profiles of different stackings of base materials, at arbitrary thicknesses. In an inverse process, we can then specify a desired reflection profile and compute a layered composite material that best approximates it. Our algorithm efficiently searches the space of possible combinations of base materials, pruning unsatisfactory states imposed by physical constraints. We validate our process by producing both homogeneous and heterogeneous composites fabricated using a multi-material 3D printer. We demonstrate reproductions that have scattering properties approximating complex materials.
On the Myth of Automatic Semantic Activation in Reading

Visual word recognition is widely considered to be automatic in the sense that activation of meaning occurs both in the absence of intent and despite the reader's intent to not read the word. New evidence from the semantic priming paradigm and the Stroop paradigm undermines this view. Semantic processing depends strongly on attentional control over how activation is distributed across different levels of representation.
Variation in Heterozygosity Predicts Variation in Human Substitution Rates between Populations, Individuals and Genomic Regions

The “heterozygote instability” (HI) hypothesis suggests that gene conversion events focused on heterozygous sites during meiosis locally increase the mutation rate, but this hypothesis remains largely untested. As humans left Africa they lost variability, which, if HI operates, should have reduced the mutation rate in non-Africans. Relative substitution rates were quantified in diverse humans using aligned whole genome sequences from the 1,000 genomes project. Substitution rate is consistently greater in Africans than in non-Africans, but only in diploid regions of the genome, consistent with a role for heterozygosity. Analysing the same data partitioned into a series of non-overlapping 2 Mb windows reveals a strong, non-linear correlation between the amount of heterozygosity lost “out of Africa” and the difference in substitution rate between Africans and non-Africans. Putative recent mutations, derived variants that occur only once among the 80 human chromosomes sampled, occur preferentially at the centre of 2 Kb windows that have elevated heterozygosity compared both with the same region in a closely related population and with an immediately adjacent region in the same population. More than half of all substitutions appear attributable to variation in heterozygosity. This observation provides strong support for HI with implications for many branches of evolutionary biology.
Validity and Teacher Inference

The authors examine inferences made by a beginning teacher and illustrate that traditional notions of validity as presented by Cronbach and Cook and Campbell are inadequate for judging their validity. These traditional notions of validity depend on a regularity theory of causation, although Cronbach's and Cook and Campbell's particular conceptions are quite different. The relationships between causation and validity are discussed. A different theory of causation, an intentional theory of causation, is explicated. Such a view runs counter to the principles of the regularity theory but makes intuitive sense and seems particularly sensible in understanding teachers' causal inferences. The authors advocate an expanded, pluralistic conception of validity that allows that inferences made in a variety of ways can be valid.
The Social Construction of Europe

The article introduces constructivist approaches to research on European integration. While stressing middle-range theory, it recognizes that meta-theoretical choices also matter for theorizing and analysing European integration. Tracing developments in the philosophy of science and in international relations theory, social constructivism is introduced as a way of establishing the 'middle ground' in juxtaposition to rationalism and reflectivism - not as a grand theory for the study of European integration. Crucial aspects of the integration process - polity formation through rules and norms, the transformation of identities, the role of ideas and the uses of language - are thereby opened up to systematic inquiry.
Analysis of cautious adaptive RED (CARED)

Internet in the present scenario has become a gigantic source of information. There has been a tremendous rise in the variety of Internet applications with each application demanding a specific performance criteria to be satisfied. Routers presently use Passive Queue Management (PQM) mechanisms and hence, merely have any control over the queue occupancy. Therefore, there has been an increased interest in exploring Active Queue Management (AQM) in Internet routers so as to reduce the queue latency and meet the demands of time sensitive applications. In this paper, we mainly focus on analyzing the AQM mechanism which we proposed recently, named Cautious Adaptive Random Early Detection (CARED). We study the effectiveness of CARED by carrying out simulations in ns-2 and comparing its performance with Adaptive RED (ARED) and Refined Adaptive RED (Re-ARED) in a wide variety of Internet scenarios. Based on the simulation results obtained, we highlight the advantages of CARED in terms of throughput, packet drop rate and the stability of the average queue size.
Transcriptome of a Nitrosomonas europaea Mutant with a Disrupted Nitrite Reductase Gene (nirK)

ABSTRACT Global gene expression was compared between the Nitrosomonas europaea wild type and a nitrite reductase-deficient mutant using a genomic microarray. Forty-one genes were differentially regulated between the wild type and the nirK mutant, including the nirK operon, genes for cytochrome c oxidase, and seven iron uptake genes. Relationships of differentially regulated genes to the nirK mutant phenotype are discussed.
Pronominal case and verbal finiteness contingencies in child English

ABSTRACT Child English speakers use nonnominative pronouns in subject position but do not tend to use these types of pronouns with finite verbs. Recent findings demonstrate that knowledge of the pronoun paradigm is relevant to pronoun case errors below the 60% correct finiteness marking level but irrelevant above it. We use a receptive test with children who are above the 60% correct finiteness marking level and show that judgments of nominative case and verb finiteness correlate (r = .549, p < .001, n = 49), consistent with the predictions of case theory. Children at this level of finiteness marking show no asymmetry in feminine versus masculine nonnominative errors, but they do allow third singular –s with nonnominatives, which is problematic for both agreement tense omission model and constructivist priming accounts.
EC Application HELPING CUSTOMERS NAVIGATE THE WEB SITE AND INCREASE SALES AT CAMPMOR The Problem

Content Helping Customers Navigate the Web Site and Increase Sales at Campmor 19.1 Major E-Commerce Applications and Their Functionalities 19.2 A Five-Step Approach to Developing an E-Commerce Landscape 19.3 Development Options for E-Commerce Applications 19.4 Criteria for Selecting a Development Approach 19.5 E-Commerce Software Packages and Suites 19.6 Connecting to Databases and Other Enterprise Systems 19.7 Vendor and Software Selection 19.8 Usage Analysis and Site Management Managerial Issues Real-World Case: Molding a New Vision for E-Commerce at D-M-E Upon completion of this chapter, you will be able to: 1. Discuss the major steps in developing an EC application. 2. Describe the major EC applications and list their major functionalities. 3. List the major EC application development options along with their benefits and limitations. 4. Discuss various EC application outsourcing options, including application service providers (ASPs), software as a service (SaaS), and utility computing. 5. Discuss the major EC software packages and EC application suites. 6. Describe various methods for connecting an EC application to back-end systems and databases. 7. Discuss the value and technical foundation of Web Services and their evolution into secondgeneration tools in EC applications. 8. Understand service-oriented architecture (SOA) and virtualization and their relationship to EC application development. 9. Describe the criteria used in selecting an outsourcing vendor and package. 10. Understand the value and uses of EC application log files. 11. Discuss the importance of usage analysis and site management. Learning Objectives
SELECTION OF THE NUMBER OF NEIGHBOURS OF EACH DATA POINT FOR THE LOCALLY LINEAR EMBEDDING ALGORITHM

This paper deals with a method, called locally linear embedding. It is a nonlinear dimensionality reduc- tion technique that computes low-dimensional, neighbourhood preserving embeddings of high dimensional data and attempts to discover nonlinear structure in high dimensional data. The implementation of the algorithm is fairly straightforward, as the algorithm has only two control parameters: the number of neighbours of each data point and the regularisation parameter. The mapping quality is quite sensitive to these parameters. In this paper, we propose a new way for selecting the number of the nearest neighbours of each data point. Our approach is experimentally verified on two data sets: artificial data and real world pictures.
The influence of muscles activation on the dynamical behaviour of the tympano-ossicular system of the middle ear

The human ear is a complex biomechanical system and is divided into three parts: outer, middle and inner ear. The middle ear is formed by ossicles (malleus, incus and stapes), ligaments, muscles and tendons, which transfers sound vibrations from the eardrum to the inner ear, linking with mastoid and Eustachian tube. In this work, a finite element modelling of the tympano-ossicular system of the middle ear was developed. A dynamic study based on a structural response to harmonic vibrations, for a sound pressure level (SPL) of 110, 120 and 130 dB SPL applied in the eardrum, is presented. The connection between the ossicles is made using a contact formulation. The model includes the different ligaments considering its hyperelastic behaviour. The activation of the muscles is based on the constitutive model proposed by previous work. The harmonic responses of displacement and pressure obtained on the stapes footplate, for a frequency range between 100 Hz and 10 kHz, are obtained simulating the muscle activation. The results are compared considering the passive and active states. The results are discussed and they are in accordance with audiological data published with reference to the effects of the middle ear muscles contraction.
Infrared Properties of Nearby Interacting Galaxies: from Spirals to ULIRGs

Abstract I present a brief review of some of the mid-infrared properties of interacting galaxies as these were revealed using observations from the Infrared Space Observatory and Spitzer Space Telescope over the last decade. The variation of the infrared spectral energy distribution in interacting galaxies can be used as an extinction free tracer not only of the location of the star formation activity but also of the physical mechanism dominating their energy production. ‡.
What Do Development Banks Do? Evidence from BNDES, 2002-2009

While some authors view development banks as an important tool to alleviate capital constraints in scarce credit markets and unlock productive investments, others see those banks as conduits of cheap loans to politically-connected firms that could obtain capital elsewhere. We test these contrasting views using data on loans and equity allocations in the period 2002-2009 by the Brazilian National Development Bank (BNDES), one of the largest development banks in the world. In our fixed effect regressions, we find that BNDES’ allocations do not seem to affect firm-level operational performance and investment decisions, although they do reduce firm-level cost of capital due to the governmental subsidies accompanying loans. Next, examining the selection process through which BNDES’ capital is allocated to firms, we find that BNDES apparently selects firms with good operational performance but also provides more capital to firms with political connections (measured as campaign donations to politicians who won an election). Yet, we do not find evidence that BNDES is systematically bailing out firms. In general, BNDES appears to be generally selecting firms with capacity to repay their loans, as regular commercial banks would do.
Receptor arrays optimized for natural odor statistics

Significance Natural odors typically consist of many molecules at different concentrations, which together determine the odor identity. This information is collectively encoded by olfactory receptors and then forwarded to the brain. However, it is unclear how the receptor activity can encode both the composition of the odor and the concentrations of its constituents. We study a simple model of the olfactory receptors from which we derive design principles for optimally communicating odor information in a given natural environment. We use these results to discuss biological olfactory systems, and we propose how they can be used to improve artificial sensor arrays. Natural odors typically consist of many molecules at different concentrations. It is unclear how the numerous odorant molecules and their possible mixtures are discriminated by relatively few olfactory receptors. Using an information theoretic model, we show that a receptor array is optimal for this task if it achieves two possibly conflicting goals: (i) Each receptor should respond to half of all odors and (ii) the response of different receptors should be uncorrelated when averaged over odors presented with natural statistics. We use these design principles to predict statistics of the affinities between receptors and odorant molecules for a broad class of odor statistics. We also show that optimal receptor arrays can be tuned to either resolve concentrations well or distinguish mixtures reliably. Finally, we use our results to predict properties of experimentally measured receptor arrays. Our work can thus be used to better understand natural olfaction, and it also suggests ways to improve artificial sensor arrays.
Young people’s views about their involvement in decision‐making

This paper reports on research conducted over a two‐year period in a large Educational Psychology Service (EPS) in England. Researchers were keen to ascertain the views of young people and EPS members about young people being directly involved in educational decision‐making and how their genuine involvement in such decision‐making might be best achieved. Focus groups were employed as a means of gathering data which were analysed using Content Analysis. Young people and EPS members ultimately identified “culture”, “attitudes”, “environment”, and “systems” as being the most important factors in ensuring the genuine involvement of young people in decision‐making.