Miracle-dz/UniFAR-FTUs huggingface dataset:
SPA1: A New Genetic Locus Involved in Phytochrome A–Specific Signal Transduction

To identify mutants potentially defective in signaling intermediates specific to phytochrome A (phyA), we screened for extragenic mutations that suppress the morphological phenotype exhibited by a weak phyA mutant (phyA-105) of Arabidopsis. A new recessive mutant, designated spa1 (for suppressor of phyA-105), was isolated and mapped to the bottom of chromosome 2. spa1 phyA-105 double mutants exhibit restoration of several responses to limiting fluence rates of continuous far-red light that are absent in the parental phyA-105 mutant, such as deetiolation, anthocyanin accumulation, and a far-red light–induced inability of seedlings to green upon subsequent transfer to continuous white light. spa1 mutations do not cause a phenotype in darkness, indicating that the suppression phenotype is light dependent. Enhanced photoresponsiveness was observed in spa1 seedlings in a wild-type PHYA background as well as in the mutant phyA-105 background but not in a mutant phyA null background. These results indicate that phyA is necessary in a non-allele-specific fashion for the expression of the spa1 mutant phenotype and that phyB to phyE are not sufficient for this effect. Taken together, the data suggest that spa1 mutations specifically amplify phyA signaling and therefore that the SPA1 locus encodes a component that acts negatively early in the phyA-specific signaling pathway.
Content-Based Quality Evaluation on Frame-Dropped and Blurred Video

In this paper, we present our work on developing perceptual quality metrics for low and very low bit-rate videos. At current stage, we've finished a number of subjective viewing experiments, and several video content-based models are built based on the experiments to measure the perceptual quality of frame-dropped and blurred video sequences. Experimental results show that the models can achieve very good performances.
Transducteurs à fenêtre glissante pour l’induction lexicale

Nous appliquons différents modèles de similarité graphique à la tâche de l’induction de lexiques bilingues entre un dialecte de Suisse allemande et l’allemand standard. Nous comparons des transducteurs stochastiques utilisant des fenêtres glissantes de 1 à 3 caractères, entraînés à l’aide de l’algorithme de maximisation de l’espérance avec des corpus d’entraînement de tailles différentes. Si les transducteurs à unigrammes donnent des résultats satisfaisants avec des corpus très petits, nous montrons que les transducteurs à bigrammes les dépassent à partir de 750 paires de mots d’entraînement. En général, les modèles entraînés nous ont permis d’améliorer la F-mesure de 7% à 15% par rapport à la distance de Levenshtein.
An introduction to coil array design for parallel MRI

The basic principles of radiofrequency coil array design for parallel MRI are described from both theoretical and practical perspectives. Because parallel MRI techniques rely on coil array sensitivities to provide spatial information about the sample, a careful choice of array design is essential. The concepts of coil array spatial encoding are first discussed from four qualitative perspectives. These qualitative descriptions include using coil arrays to emulate spatial harmonics, choosing coils with selective sensitivities to aliased pixels, using coil sensitivities with broad k‐space reception profiles, and relying on detector coils to provide a set of generalized projections of the sample. This qualitative discussion is followed by a quantitative analysis of coil arrays, which is discussed in terms of the baseline SNR of the received images as well as the noise amplifications (g‐factor) in the reconstructed data. The complications encountered during the experimental evaluation of coil array SNR are discussed, and solutions are proposed. A series of specific array designs are reviewed, with an emphasis on the general design considerations that motivate each approach. Finally, a set of special topics is discussed, which reflect issues that have become important, especially as arrays are being designed for more high‐performance applications of parallel MRI. These topics include concerns about the depth penetration of arrays composed of small elements, the use of adaptive arrays for systems with limited receiver channels, the management of inductive coupling between array elements, and special considerations required at high field strengths. The fundamental limits of spatial encoding using coil arrays are discussed, with a primary emphasis on how the determination of these limits impacts the design of optimized arrays. This review is intended to provide insight into how arrays are currently used for parallel MRI and to place into context the new innovations that are to come. Copyright © 2006 John Wiley & Sons, Ltd.
A new educational film control for use in studies of active mind-body therapies: acceptability and feasibility.

OBJECTIVES The study objectives were to ascertain whether a novel educational film class is an acceptable and feasible comparison group for a randomized controlled trial regarding the effects of an active mind-body therapy on cardiovascular disease risk in postmenopausal women. METHODS Seventy-five (75) participants attended a baseline assessment visit and were randomly assigned to either a yoga group or an educational film (control) group. Both groups attended two 90-minute classes/week for 8 weeks, followed by a second assessment visit. Those not attending the second assessment were classified as dropouts. Over 60 films covering a range of topics relevant to the study population were evaluated; 15 were selected by consensus of at least 2 researchers and 1 layperson. Each film session followed the same format: an informal greeting period, viewing of the film, and a 15-minute postfilm discussion. To determine acceptability and feasibility of the film class, potential between-group differences in dropout and attendance were examined, and participant feedback given during class and on end-of-study questionnaires were evaluated. RESULTS The relation between group assignment and dropout was not significant (χ(2) [1, N = 75] = 0.14, p = 0.71). One-way analysis of variance (ANOVA) indicated no significant between-group difference in number of classes attended for the yoga (X = 13.67 ± 3.10) versus film group (13.26 ± 1.97), F(1,63) = 0.39, p = 0.53). Participant feedback regarding the film program was positive. CONCLUSIONS These findings support the feasibility and acceptability of this educational film control. Easy to standardize and tailor to a variety of populations, this film program may offer an attractive alternative to the more traditional educational control.
No-Pass Zone: Multidisciplinary Approach to Responding to Patient Needs

A nurse's need to juggle multiple priorities often leads to delays in responses to patient call lights, which may result in the patient's needs not being met quickly. Low patient satisfaction scores related to hospital staff responding to patient needs created urgency for this system to implement the No-Pass Zone, a multidisciplinary team approach to responding to call lights. A successful implementation of this intervention resulted in patients' needs being met more quickly as indicated by improved Hospital Consumer Assessment of Health Care Providers and Systems performance postimplementation.
miR-205 in situ expression and localization in head and neck tumors - a tissue array study.

BACKGROUND microRNAs are small non-coding RNA that control gene expression by mRNA degradation or translational inhibition. These molecules are known to play essential roles in many biological and physiological processes. miR-205 may be differentially expressed in head and neck cancers; however, there are conflicting data and localization of expression has yet to be determined. MATERIALS AND METHODS miR-205 expression was investigated in 48 cases of inflammatory, benign and malignant tumor tissue array of the neck, oronasopharynx, larynx and salivary glands by Locked Nucleic Acid in situ hybridization (LNA-ISH) technology. RESULTS miR-205 expression was significantly differentially expressed across all of the inflammatory, benign and malignant tumor tissues of the neck. A significant increase in miR-205 staining intensity (p<0.05) was observed from inflammation to benign and malignant tumors in head and neck tissue array, suggesting that miR-205 could be a biomarker to differentiate between cancer and non-cancer tissues. CONCLUSIONS LNA-ISH revealed that miR-205 exhibited significant differential cytoplasmic and nuclear staining among inflammation, benign and malignant tumors of head and neck. miR-205 was not only exclusively expressed in squamous epithelial malignancy. This study offers information and a basis for a comprehensive study of the role of miR-205 that may be useful as a biomarker and/or therapeutic target in head and neck tumors.
Staphylococcal glycocalyx activates macrophage prostaglandin E2 and interleukin 1 production and modulates tumor necrosis factor alpha and nitric oxide production

We have examined the effect of staphylococcal glycocalyces on the ability of murine peritoneal macrophages to produce prostaglandin E2 (PGE2) and the inflammatory cytokines interleukin 1 (IL-1) and tumor necrosis factor alpha (TNF-alpha) and to generate nitric oxide. Glycocalyx partially purified under endotoxin-free conditions from defined liquid medium cultures of Staphylococcus lugdunensis or Staphylococcus epidermidis was a strong stimulator of PGE2 and IL-1 production. The addition of 10 to 100 micrograms of glycocalyx per ml induced levels of IL-1 and PGE2 production similar to that induced by 0.1 to 1 micrograms of Escherichia coli lipopolysaccharide (LPS) per ml. In contrast, glycocalyx induced ninefold less TNF-alpha and three- to fourfold less nitrite than LPS. A modulatory effect was suggested by the observation that the amount of TNF-alpha and nitrite generated remained constant whether the macrophages were stimulated with 10 or 100 micrograms of glycocalyx per ml. A selective modulation of macrophage activation was confirmed by the demonstration that costimulation of macrophages with both glycocalyx and LPS resulted in a reduction in TNF-alpha and nitrite generation relative to stimulation with LPS alone even though costimulation had no effect on PGE2 production and increased IL-1 production. Involvement of PGE2 in this modulatory effect was suggested by the ability of indomethacin to augment glycocalyx-stimulated TNF-alpha production and to reverse the inhibitory effect of glycocalyx on LPS induction of TNF-alpha production. However, the inability of indomethacin to reverse the inhibitory effect of glycocalyx on LPS-induced nitric oxide generation suggests that the selective modulation of macrophage function by glycocalyx may be more complex than increased sensitivity to PGE2 feedback inhibition.
From prepared speech to spontaneous speech recognition system: a comparative study applied to French language

Automatic speech recognition systems (ASR) have more trouble processing spontaneous speech (e.g. debates) than prepared speech (e.g. broadcast news). These difficulties are due to peculiarities of spontaneous speech (false start, repetition, schwa, etc.). In this paper, we highlight some of these peculiarities, especially in French. We show that the use of manual transcriptions having no link with the focused application, but which contains only transcriptions of very spontaneous speech, allows to estimate a better language model, strongly decreasing perplexity and significantly decreasing the word error rate on spontaneous speech. But other knowledge bases used by the ASR have to be adapted. For example, our work shows that adding specific pronunciation variants seems useful, but has to be constrained and modelized. Finally, we compare errors of our CMU Sphinx-based ASR system on spontaneous vs. prepared speech.
Stone Bead Technologies and Early Craft Specialization: Insights from Two Neolithic Sites in Eastern Jordan

Abstract What social groups were involved in Neolithic craft production? What was the nature of early forms of craft specialization, long before urban economies evolved? One way to look at this is to investigate manufacture of Neolithic prestige goods. Seasonal camps in Wadi Jilat (eastern Jordan) revealed unusually detailed evidence for manufacture of stone beads: debris, blanks, finished beads, and tools for drilling, sawing and abrasion. The material is 'Dabba Marble', a metamorphic rock of which the major source is nearby. This article describes lapidary technology at Jilat 13 and Jilat 25, equivalent in age to the Pre-Pottery Neolithic C (PPNC). Mineral-chemical characterization data on Dabba Marble are presented. These sites raise issues about early craft specialization. These beadmakers seem to have been master craftsmen/women. We suggest that these sites illustrate a particular form of 'site specialization', namely sites located in remote territories and focused on special materials and intensive production of prestige goods. However, these craft activities were also embedded in hunting, herding and, perhaps, ritual, as suggested by figurines and pillars.
The importance of molecular markers for diagnosis and selection of targeted treatments in patients with cancer

The past 30 years have seen the introduction of a number of cancer therapies with the aim of restricting the growth and spread of primary and metastatic tumours. A shared commonality among these therapies is their targeting of various aspects of the cancer hallmarks, that is traits that are essential to successful tumour propagation and dissemination. The evolution of molecular‐scale technology has been central to the identification of new cancer targets, and it is not a coincidence that improved therapies have emerged at the same time as gene expression arrays and DNA sequencing have enhanced our understanding of cancer genetics. Modern tumour pathology is now viewed at the molecular level ranging from IHC biomarkers, to gene signature classifiers and gene mutations, all of which provide crucial information about which patients will respond to targeted therapy regimens. In this review, we briefly discuss the general types of targeted therapies used in a clinical setting and provide a short background on immunohistochemical, gene expression and DNA sequencing technologies, before focusing on three tumour types: breast, lung and colorectal cancers. For each of these cancer types, we provide a background to the disease along with an overview of the current standard therapies and then focus on the relevant targeted therapies and the pathways they inhibit. Finally, we highlight several strategies that are pivotal to the successful development of targeted anti‐cancer drugs.
Nanoformulations of curcumin: an emerging paradigm for improved remedial application

Curcumin is a natural polyphenol and essential curcuminoid derived from the rhizome of the medicinal plant Curcuma longa (L.) is universally acknowledged as “Wonder drug of life”. It is a vital consumable and restorative herb, commonly keened for several ailments such as cancer, arthritis, pain, bruises, gastrointestinal quandaries, swelling and much more. Despite its enormous curative potential, the poor aqueous solubility and consequently, minimal systemic bioavailability with rapid degradation are some of the major factors which restrict the utilization of curcumin at medical perspective. However, to improve its clinically relevant parameters, nanoformulation of curcumin is emerging as a novel substitute for their superior therapeutic modality. It enhances its aqueous solubility and targeted delivery to the tissue of interest that prompts to enhance the bioavailability, better drug conveyance, and more expeditious treatment. Subsequent investigations are endeavored to enhance the bio-distribution of native curcumin by modifying with felicitous nano-carriers for encapsulation. In this review, we specifically focus on the recent nanotechnology based implementations applied for overcoming the innate constraints of native curcumin and additionally the associated challenges which restrict its potential therapeutic applications both in vivo and in-vitro studies, as well as their detailed mechanism of action, have additionally been discussed.
Learning finite-state machines: statistical and algorithmic aspects

The present thesis addresses several machine learning problems on generative and predictive models on sequential data. All the models considered have in common that they can be de ned in terms of nite-state machines. On one line of work we study algorithms for learning the probabilistic analog of Deterministic Finite Automata (DFA). This provides a fairly expressive generative model for sequences with very interesting algorithmic properties. State-merging algorithms for learning these models can be interpreted as a divisive clustering scheme where the "dependency graph" between clusters is not necessarily a tree. We characterize these algorithms in terms of statistical queries and a use this characterization for proving a lower bound with an explicit dependency on the distinguishability of the target machine. In a more realistic setting, we give an adaptive state-merging algorithm satisfying the stringent algorithmic constraints of the data streams computing paradigm. Our algorithms come with strict PAC learning guarantees. At the heart of state-merging algorithms lies a statistical test for distribution similarity. In the streaming version this is replaced with a bootstrap-based test which yields faster convergence in many situations. We also studied a wider class of models for which the state-merging paradigm also yield PAC learning algorithms. Applications of this method are given to continuous-time Markovian models and stochastic transducers on pairs of aligned sequences. The main tools used for obtaining these results include a variety of concentration inequalities and sketching algorithms. In another line of work we contribute to the rapidly growing body of spectral learning algorithms. The main virtues of this type of algorithms include the possibility of proving nite-sample error bounds in the realizable case and enormous savings on computing time over iterative methods like Expectation-Maximization. In this thesis we give the rst application of this method for learning conditional distributions over pairs of aligned sequences de ned by probabilistic nite-state transducers. We also prove that the method can learn the whole class of probabilistic automata, thus extending the class of models previously known to be learnable with this approach. In the last two chapters we present works combining spectral learning with methods from convex optimization and matrix completion. Respectively, these yield an alternative interpretation of spectral learning and an extension to cases with missing data. In the latter case we used a novel joint stability analysis of matrix completion and spectral learning to prove the rst generalization bound for this type of algorithms that holds in the non-realizable case. Work in this area has been motivated by connections between spectral learning, classic automata theory, and statistical learning; tools from these three areas have been used.
Redox imaging using genetically encoded redox indicators in zebrafish and mice

Abstract Redox signals have emerged as important regulators of cellular physiology and pathology. The advent of redox imaging in vertebrate systems now provides the opportunity to dynamically visualize redox signaling during development and disease. In this review, we summarize recent advances in the generation of genetically encoded redox indicators (GERIs), introduce new redox imaging strategies, and highlight key publications in the field of vertebrate redox imaging. We also discuss the limitations and future potential of in vivo redox imaging in zebrafish and mice.
Regulation of spo0H, a gene coding for the Bacillus subtilis sigma H factor

The Bacillus spo0H gene codes for sigma H, which, as part of the RNA polymerase holoenzyme E sigma H, is responsible for the transcription of several genes which are expressed at the beginning of the sporulation process. In this communication, we examined the regulation of the spo0H gene of Bacillus subtilis by using lacZ reporter gene assays, quantitative RNA determinations, and Western immunoassay. The expression of the spo0H gene increases as the culture enters the mid-logarithmic stage of growth. This increased expression requires the genes spo0A, spo0B, spo0E, and spo0F, and the requirement for at least spo0A and spo0B can be bypassed when the abrB gene is mutated. The expression of the spo0H gene is constitutive in the presence of the abrB mutation, being expressed at higher levels during vegetative growth. In addition, the sof-1 mutation, in the spo0A structural gene, can bypass the need for spo0F in spo0H expression. The transcriptional start site of spo0H was determined by using RNA made in vivo as well as in vitro. These studies indicate that spo0H is transcribed by the major vegetative RNA polymerase, E sigma A. spo0H RNA and sigma H levels during growth are not identical to each other or to the pattern of expression of spoVG, a gene transcribed by E sigma H. This suggests that spo0H is regulated posttranscriptionally and also that factors in addition to sigma H levels are involved in the expression of genes of the E sigma H regulon.
SHP-1 Binds and Negatively Modulates the c-Kit Receptor by Interaction with Tyrosine 569 in the c-Kit Juxtamembrane Domain

ABSTRACT The SH2 domain-containing SHP-1 tyrosine phosphatase has been shown to negatively regulate a broad spectrum of growth factor- and cytokine-driven mitogenic signaling pathways. Included among these is the cascade of intracellular events evoked by stem cell factor binding to c-Kit, a tyrosine kinase receptor which associates with and is dephosphorylated by SHP-1. Using a series of glutathioneS-transferase (GST) fusion proteins containing either tyrosine-phosphorylated segments of the c-Kit cytosolic region or the SH2 domains of SHP-1, we have shown that SHP-1 interacts with c-Kit by binding selectively to the phosphorylated c-Kit juxtamembrane region and that the association of c-Kit with the larger of the two SHP-1 isoforms may be mediated through either the N-terminal or C-terminal SHP-1 SH2 domain. The results of binding assays with mutagenized GST-Kit juxtamembrane fusion proteins and competitive inhibition assays with phosphopeptides encompassing each c-Kit juxtamembrane region identified the tyrosine residue at position 569 as the major site for binding of SHP-1 to c-Kit and suggested that tyrosine 567 contributes to, but is not required for, this interaction. By analysis of Ba/F3 cells retrovirally transduced to express c-Kit receptors, phenylalanine substitution of c-Kit tyrosine residue 569 was shown to be associated with disruption of c-Kit–SHP-1 binding and induction of hyperproliferative responses to stem cell factor. Although phenylalanine substitution of c-Kit tyrosine residue 567 in the Ba/F3–c-Kit cells did not alter SHP-1 binding to c-Kit, the capacity of a second c-Kit-binding tyrosine phosphatase, SHP-2, to associate with c-Kit was markedly reduced, and the cells again showed hyperproliferative responses to stem cell factor. These data therefore identify SHP-1 binding to tyrosine 569 on c-Kit as an interaction pivotal to SHP-1 inhibitory effects on c-Kit signaling, but they indicate as well that cytosolic protein tyrosine phosphatases other than SHP-1 may also negatively regulate the coupling of c-Kit engagement to proliferation.