Miracle-dz/UniFAR-FTUs huggingface dataset:
Dissecting the Molecular Basis of the Regulation of Wood Formation by Auxin in Hybrid Aspen[W]

Indole acetic acid (auxin) is a key regulator of wood formation, and an observed overlap between auxin concentration gradient and developing secondary xylem cells has led to the hypothesis that auxin regulates wood formation by acting as a morphogen. We dissected the role of auxin in wood formation by identifying the auxin-responsive transcriptome in wood-forming tissues and investigating alterations in wood formation in transgenic hybrid aspen plants (Populus tremula × Populus tremuloides) with perturbed auxin signaling. We showed that auxin-responsive genes in wood-forming tissues respond dynamically to changes in cellular auxin levels. However, the expression patterns of most of the auxin-responsive genes displayed limited correlation with the auxin concentration across this developmental zone. Perturbing auxin signaling by reducing auxin responsiveness reduced the cambial cell division activity, caused spatial deregulation of cell division of the cambial initials, and led to reductions in not only radial but also axial dimensions of fibers and vessels. We propose that, instead of acting as a morphogen, changes in auxin concentration in developing secondary xylem cells may provide important regulatory cues that modulate the expression of a few key regulators; these, in turn, may control the global gene expression patterns that are essential for normal secondary xylem development.
monogamous mammals Social structure influences extra-pair paternity in socially

Supplementary data ml http://rsbl.royalsocietypublishing. org/content/suppl/2009/02/27/rsbl.2008. 0760.DC1. ht "Data Supplement" References http://rsbl.royalsocietypublishing. org/content/5/3/313.full. html#ref-list-1 This article cites 12 articles, 2 of which can be accessed free Subject collections (502 articles) behaviour  Articles on similar topics can be found in the following collections Email alerting service here right-hand corner of the article or click Receive free email alerts when new articles cite this article sign up in the box at the top
Demystifying Privacy Policies with Language Technologies : Progress and Challenges

Privacy policies written in natural language are the predominant method that operators of websites and online services use to communicate privacy practices to their users. However, these documents are infrequently read by Internet users, due in part to the length and complexity of the text. These factors also inhibit the efforts of regulators to assess privacy practices or to enforce standards. One proposed approach to improving the status quo is to use a combination of methods from crowdsourcing, natural language processing, and machine learning to extract details from privacy policies and present them in an understandable fashion. We sketch out this vision and describe our ongoing work to bring it to fruition. Further, we discuss challenges associated with bridging the gap between the contents of privacy policy text and website users’ abilities to understand those policies. These challenges are motivated by the rich interconnectedness of the problems as well as the broader impact of helping Internet users understand their privacy choices. They could also provide a basis for competitions that use the annotated corpus introduced in this paper.
The Fingerprint of Anti-Bromodeoxyuridine Antibodies and Its Use for the Assessment of Their Affinity to 5-Bromo-2'-Deoxyuridine in Cellular DNA under Various Conditions

We have developed a simple system for the analysis of the affinity of anti-bromodeoxyuridine antibodies. The system is based on the anchored oligonucleotides containing 5-bromo-2'-deoxyuridine (BrdU) at three different positions. It allows a reliable estimation of the reactivity of particular clones of monoclonal anti-bromodeoxyuridine antibodies with BrdU in fixed and permeabilized cells. Using oligonucleotide probes and four different protocols for the detection of BrdU incorporated in cellular DNA, we identified two antibody clones that evinced sufficient reactivity to BrdU in all the tested protocols. One of these clones exhibited higher reactivity to 5-iodo-2'-deoxyuridine (IdU) than to BrdU. It allowed us to increase the sensitivity of the used protocols without a negative effect on the cell physiology as the cytotoxicity of IdU was comparable with BrdU and negligible when compared to 5-ethynyl-2'-deoxyuridine. The combination of IdU and the improved protocol for oxidative degradation of DNA provided a sensitive and reliable approach for the situations when the low degradation of DNA and high BrdU signal is a priority.
The research of personalized search engine based on users' access interest

In this research, users' access interests were introduced into the design of personalized search engine by using Web Mining technology. Firstly, the users' access interest transactions were gained by interest algorithm via mining the users' logs. Secondly, it presents a method to compute session similarity of transactional unit and transaction and sets up an interest similarity matrix for clustering by setting the suitable threshold value. At last, the result of clustering was applied in improving the PageRank algorithm for more accuracy. The personalized search engine can recommend pages which have more access interest to users who have similar interest with previous users. So the search engine's efficiency can be further improved and it can provide more accurate search service for users.
Risk Factors Associated with Peritoneal-Dialysis-Related Peritonitis

Background. Peritonitis represents a major complication of peritoneal dialysis (PD). The aim of this paper was to systematically collect data on patient-related risk factors for PD-associated peritonitis, to analyze the methodological quality of these studies, and to summarize published evidence on the particular risk factors. Methods. Studies were identified by searches of Pubmed (1990–2012) and assessed for methodological quality by using a modified form of the STROBE criteria. Results. Thirty-five methodologically acceptable studies were identified. The following nonmodifiable risk factors were considered valid and were associated with an increased risk of peritonitis: ethnicity, female gender, chronic lung disease, coronary artery disease, congestive heart failure, cardiovascular disease, hypertension, antihepatitis C virus antibody positivity, diabetes mellitus, lupus nephritis or glomerulonephritis as underlying renal disease, and no residual renal function. We also identified the following modifiable, valid risk factors for peritonitis: malnutrition, overweight, smoking, immunosuppression, no use of oral active vitamin D, psychosocial factors, low socioeconomic status, PD against patient's choice, and haemodialysis as former modality. Discussion. Modifiable and nonmodifiable risk factors analyzed in this paper might serve as a basis to improve patient care in peritoneal dialysis.
Lipopolysaccharide as trigger of platelet aggregation via eicosanoid over-production

Summary The effect of lipopolysaccharide (LPS) on platelet aggregation is still controversial. We performed in vitro and ex vivo studies in controls and in patients with community-acquired pneumonia (CAP) to assess the effect of LPS on platelet activation (PA). LPS (15–100 pg/ml) significantly increased PA only if combined with sub-threshold concentrations (STC) of collagen or ADP; this effect was associated with increased platelet H2O2 production, Nox2 activation, PLA2 phosphorylation, thromboxane (Tx)A2 and 8-iso-PGF2α-III, and was inhibited by aspirin, TxA2 receptor antagonist or by Toll-like receptor 4 blocking peptide (TLR4bp). Analysis of up-stream signalling potentially responsible for Nox2 and PLA2 activation demonstrated that LPS-mediated PA was associated with phosphorylation of AKT, p38 and p47phox translocation. In 10 consecutive CAP patients serum endotoxins were significantly higher compared to 10 controls (145 [115–187] vs 18 [6–21] pg/ml; p<0.01). Ex vivo study showed that agonist-stimulated platelets were associated with enhanced PA (p<0.01), Toll-like receptor 4 (TLR4) expression (p<0.05), TxA2 (p<0.01) and 8-iso-PGF2α-III (p<0.01) production in CAP patients compared to controls. The study provides evidence that LPS amplifies the platelet response to common agonists via TLR4-mediated eicosanoid production and suggests LPS as a potential trigger for PA in CAP. Supplementary Material to this article is available online at www.thrombosis-online.com
A short note on estimating intelligence from user profiles in the context of universal psychometrics: prospects and caveats

There has been an increasing interest in inferring some personality traits from users and players in social networks and games, respectively. This goes beyond classical sentiment analysis, and also much further than customer profiling. The purpose here is to have a characterisation of users in terms of personality traits, such as openness, conscientiousness, extraversion, agreeableness, and neuroticism. While this is an incipient area of research, we ask the question of whether cognitive abilities, and intelligence in particular, are also measurable from user profiles. However, we pose the question as broadly as possible in terms of subjects, in the context of universal psychometrics, including humans, machines and hybrids. Namely, in this paper we analyse the following question: is it possible to measure the intelligence of humans and (non-human) bots in a social network or a game just from their user profiles, i.e., by observation, without the use of interactive tests, such as IQ tests, the Turing test or other more principled machine intelligence tests?
CHAPTER 3 . 2 APPROACHES BASED ON SUPPORT VECTOR MACHINES TO CLASSIFICATION OF REMOTE SENSING DATA

This chapter presents an extensive and critical rev iew on the use of kernel methods and in particular of support vector machine s (SVMs) in the classification of remote-sensing (RS) data. The cha pter recalls the mathematical formulation and the main theoretical concepts relat ed to SVMs, and discusses the motivations at the basis of the use of SVMs in remote sensing. A review on the main applications of SVMs in classification of remote sensing is given, presenting a literature survey on the use of SVMs f or the analysis of different kinds of RS images. In addition, the most recent me thodological developments related to SVM-based classification techniques in R S are illustrated by focusing on semisupervised, domain adaptation, and context s nsitive approaches. Finally, the most promising research directions on SVM in RS are identified and discussed.
ENHANCING TEXT REPRESENTATION FOR CLASSIFICATION TASKS WITH SEMANTIC GRAPH STRUCTURES

To represent the textual knowledge more expressively, a kind of semantic-based graph structure is proposed, in which more semantic and ordering information among terms as well as the structural information of the text are incorporated. Such model can be constructed by extracting representative terms from texts and their mutually semantic relationships. Afterward, it is represented as a graph, whose nodes are the selected terms and whose edges are the corresponding relationships respectively. More-over, the weight is assigned to each edge so that the strength of relationship between two terms can be measured. Furthermore, for this weighted directed graph structure, a novel graph similarity algorithm is developed by extracting the maximum common subgraph between two concerned graphs, which can therefore be used to measure the distance be-tween two graph structures, i.e., two texts, and further be applied to classi(cid:12)cation tasks. Finally, some experiments have been conducted with the Chinese benchmark corpus for validation. The experimental results have proved the better performance of the proposed textual knowledge representation model in terms of its precision and recall.
Hare TRIM5α Restricts Divergent Retroviruses and Exhibits Significant Sequence Variation from Closely Related Lagomorpha TRIM5 Genes

ABSTRACT TRIM5α proteins recruit and restrict incoming cytoplasmic retroviruses. Primate TRIM5α sequence diversity underlies species-specific restriction and is likely caused by selective pressure from ancient pathogenic infections. Here we show that TRIM5α from the European brown hare restricts diverse retroviruses. Furthermore, it differs significantly in sequence from TRIM5α from the closely related rabbit, suggesting evolutionary changes in the last 12 million years since these species diverged. We propose that, like primates, lagomorphs have been subject to selective pressure from TRIM5-sensitive viruses, possibly related to the endogenous lentivirus RELIK found in both rabbits and hares.
Degraded EEG decoding of wrist movements in absence of kinaesthetic feedback

A major assumption of brain–machine interface research is that patients with disconnected neural pathways can still volitionally recall precise motor commands that could be decoded for naturalistic prosthetic control. However, the disconnected condition of these patients also blocks kinaesthetic feedback from the periphery, which has been shown to regulate centrally generated output responsible for accurate motor control. Here, we tested how well motor commands are generated in the absence of kinaesthetic feedback by decoding hand movements from human scalp electroencephalography in three conditions: unimpaired movement, imagined movement, and movement attempted during temporary disconnection of peripheral afferent and efferent nerves by ischemic nerve block. Our results suggest that the recall of cortical motor commands is impoverished in the absence of kinaesthetic feedback, challenging the possibility of precise naturalistic cortical prosthetic control. Hum Brain Mapp 36:643–654, 2015. © 2014 The Authors. Human Brain Mapping Published by Wiley Periodicals, Inc.
A promoter-hijack strategy for conditional shutdown of multiply spliced essential cell cycle genes

We describe a method for the isolation of conditional knockouts of essential multiply spliced genes in which the entire body of the gene downstream of the ATG start codon is left untouched but can be switched off rapidly and completely by adding tetracycline to the culture medium. The approach centers on a “promoter-hijack” strategy in which the gene's promoter is replaced with a minimal promoter responsive to the tetracycline-repressible transactivator (tTA). Elsewhere in the genome, a cloned fragment of the gene's promoter is used to drive expression of a tTA. Thus, the gene is essentially regulated by its own promoter but through the intermediary tTA. Using this strategy, we generated a conditional knockout of chromokinesin KIF4A, an important mitotic effector protein whose mRNA is multiply spliced and whose cDNA is highly toxic when overexpressed in cells. We used chicken DT40 cells, but the same strategy should be applicable to ES cells and, eventually, to mice.
Multi Drug and Other Forms of Drug Resistant Tuberculosis Are Uncommon among Treatment Naïve Tuberculosis Patients in Tanzania

Background Surveillance and effective management of drug resistance is important to sustaining tuberculosis (TB) control efforts. We aimed to determine resistance rates to first line anti tuberculosis drugs and to describe factors associated with the resistance to any of the first line anti tuberculosis drugs in Dar es Salaam Tanzania. Materials Newly diagnosed, TB patients with neither history of tuberculosis treatment nor isoniazid prophylaxis were included into the study. Sputum specimens were cultured on either mycobacteria growth indicator tube 960 (MGIT 960) or Lowenstein Jenstein (LJ) medium supplemented with either glycerol (GLJ) or pyruvate (PLJ). Drug susceptibility for isoniazid, rifampicin, streptomycin and ethambutol was determined by either Lowenstein–Jensen (LJ) medium or mycobacteria growth indicator tube 960 (MGIT 960). Results A total of 933 newly diagnosed TB patients, were included into the study. Multi drug resistance (MDR) tuberculosis was detected among 2 (0.2%) patients. Resistance to any of the four tested drugs was detected among 54 (5.8%) patients. Mono-resistance to isoniazid, rifampicin, streptomycin and ethambutol were 21(2.3%), 3 (0.3%), 13 (1.4%), 9 (1.0%) respectively. Conclusion Primary resistance to first line anti tuberculosis drugs is still low in this setting. Continued vigilance including periodic national surveillance of anti-tuberculosis resistance is recommended.
Gamma Interferon-Induced Interferon Regulatory Factor 1-Dependent Antiviral Response Inhibits Vaccinia Virus Replication in Mouse but Not Human Fibroblasts

ABSTRACT Vaccinia virus (VACV) replicates in mouse and human fibroblasts with comparable kinetics and efficiency, yielding similar titers of infectious progeny. Here we demonstrate that gamma interferon (IFN-γ) but not IFN-α or IFN-β pretreatment of mouse fibroblasts prior to VACV infection induces a long-lasting antiviral state blocking VACV replication. In contrast, high doses of IFN-γ failed to establish an antiviral state in human fibroblasts. In mouse fibroblasts, IFN-γ impeded the viral replication cycle at the level of late gene transcription and blocked the multiplication of VACV genomes. The IFN-γ-induced antiviral state invariably prevented the growth of different VACV strains but was not effective against the replication of ectromelia virus. The IFN-γ effect required intact IFN-γ receptor signaling prior to VACV infection through Janus kinase 2 (Jak2) and signal transducer and activator of transcription 1 (STAT1). The permissive state of IFN-γ-treated human cells was unrelated to the VACV-encoded IFN decoy receptors B8 and B18 and associated with a complete disruption of STAT1 homodimer formation and DNA binding. Unlike human fibroblasts, mouse cells responded with long-lasting STAT1 activation which was preserved after VACV infection. The deletion of the IFN regulatory factor 1 (IRF-1) gene from mouse cells rescued efficient VACV replication, demonstrating that IRF-1 target genes have a critical role in VACV control. These data have implications for the understanding of VACV pathogenesis and identify an incongruent IFN-γ response between the human host and the mouse model.
PRODUCT AND PROCESS DEVELOPMENT INTENSITY IN PROCESS INDUSTRY: A CONCEPTUAL AND EMPIRICAL ANALYSIS OF THE ALLOCATION OF COMPANY RESOURCES FOR THE DEVELOPMENT OF PROCESS TECHNOLOGY

In Process Industry, process development traditionally takes a large part of the company's total development efforts, but has nevertheless not received much attention in academic studies. As a part of a larger research project concerning process development in Process Industry, the allocation of company resources to R&D, and to process development in particular, has been investigated in an exploratory survey to R&D managers in European Process Industry (Mining & Mineral Industry, Food & Beverage Industry, Pulp & Paper Industry, Chemical Industry, Basic Metal Industry, and Other Process Industry). The results show that of the total resources for R&D, 40% was allocated to process development, and over 60% of the companies expected this figure to increase in the future. This figure not only shows the future importance of process development, but also indicates that the importance of product development in this group of companies is at present still rated higher than process development. The results from the study do not fit the most widely used theoretical models, and it is concluded that there is a need for better models with more explanatory power. The new concepts of product and process development intensity are introduced. The product and process development intensities can be looked upon as aggregated measures of individual development efforts by a company, and it is thus argued that they are of overall company strategic importance.
The Influence of Psychosocial Immaturity, Age, and Mental State Beliefs on Culpability Judgments About Juvenile Offenders

Juvenile offenders are treated harshly in that they receive adult-like punishment and are incarcerated when alternatives to incarceration are possible. Research on adolescent offenders suggests that they are less mature than their adult counterparts and that they suffer psychosocial setbacks as a result of incarceration. We examined the effect of psychosocial immaturity information on culpability judgments about juvenile offenders. In Study 1, we provided information about limitations in adolescents’ abilities to control their impulses, weigh risks and benefits, and consider the future consequences of their behavior. Compared with a control condition, those in the immaturity conditions attributed less responsibility to the offender. In Study 2, we manipulated both immaturity information and an actor’s mental state beliefs about the consequences of his action. We found that mental beliefs weighed more heavily in judgments about responsibility and guilt than information about immaturity. Discussion focuses on implications of this research for juvenile justice.
A differential excitation based rotational invariance for convolutional neural networks

Deep Learning (DL) methods extract complex set of features using architectures containing hierarchical set of layers. The features so learned have high discriminative power and thus represents the input to the network in the most efficient manner. Convolutional Neural Networks (CNN) are one of the deep learning architectures, extracts structural features with little invariance to smaller translational, scaling and other forms of distortions. In this paper, the learning capabilities of CNN's are explored towards providing improvement in rotational invariance to its architecture. We propose a new CNN architecture with an additional layer formed by differential excitation against distance for the improvement of rotational invariance and is called as RICNN. Moreover, we show that the proposed method is giving superior performance towards invariance to rotations against the original CNN architecture (training samples with different orientations are not considered) without disturbing the invariance to smaller translational, scaling and other forms of distortions. Different profiles like training time, testing time and accuracies are evaluated at different percentages of training data for comparing the performance of the proposed configuration with original configuration.
Transporters Buffer Synaptically Released Glutamate on a Submillisecond Time Scale

The role of transporters in clearing free glutamate from the synaptic cleft was studied in rat CA1 hippocampal neurons cultured on glial microislands. The time course of free glutamate in the cleft during a synaptic event was estimated by measuring the extent to which the rapidly dissociating AMPA receptor antagonist kynurenate (KYN) was replaced by glutamate during a synaptic response. Dose inhibition of the AMPA receptor EPSC by KYN was less than predicted by the equilibrium affinity of the antagonist, and the rise time of AMPA receptor miniature EPSCs (mEPSCs) was slowed by KYN. Both results indicated that KYN dissociated from AMPA receptors and was replaced by synaptically released transmitter. When transporters were blocked byd,l-threo-β-hydroxyaspartic acid (THA) or Li+, the mEPSC rise time in the presence of KYN was slowed further, indicating that transporters affect the glutamate concentration in the first few hundred microseconds of the synaptic response. The glutamate transient necessary to cause these effects was determined by developing a detailed kinetic model of the AMPA receptor. The model replicated the effects of KYN on the amplitude and rise time of the synaptic responses when driven by glutamate transients that were similar to previous estimates (Clements et al., 1992; Clements, 1996). The effects of THA were replicated by slowing and enlarging the slower phase of the dual component transient by about 20% or by prolonging the single component by almost 40%. Because transport is too slow to account for these effects, it is concluded that transporters buffer glutamate in the synaptic cleft.