Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional plasticity through differential assembly of a multiprotein activation complex

Cell adaptation to the environment often involves induction of complex gene expression programs under the control of specific transcriptional activators. For instance, in response to cadmium, budding yeast induces transcription of the sulfur amino acid biosynthetic genes through the basic-leucine zipper activator Met4, and also launches a program of substitution of abundant glycolytic enzymes by isozymes with a lower content in sulfur. We demonstrate here that transcriptional induction of PDC6, which encodes a pyruvate decarboxylase isoform with low sulfur content, is directly controlled by Met4 and its DNA-binding cofactors the basic-helix–loop–helix protein Cbf1 and the two homologous zinc finger proteins Met31 and Met32. Study of Cbf1 and Met31/32 association with PDC6 allowed us to find a new mechanism of recruitment of Met4, which allows PDC6 being differentially regulated compared to sulfur amino acid biosynthetic genes. Our findings provide a new example of mechanism allowing transcriptional plasticity within a regulatory network thanks to a definite toolbox comprising a unique master activator and several dedicated DNA-binding cofactors. We also show evidence suggesting that integration of PDC6 to the Met4 regulon may have occurred recently in the evolution of the Saccharomyces cerevisiae lineage.
Some pragmatic functions of conversational facial gestures1

Conversational facial gestures are not emotional expressions (Ekman, 1997). Facial gestures are co-speech gestures – configurations of the face, eyes, and/or head that are synchronized with words and other co-speech gestures. Facial gestures are the most frequent facial actions in dialogue, and the majority serve pragmatic (meta-communicative) rather than referential functions. A qualitative microanalysis of a close-call story illustrates three pragmatic facial gestures in their macro- and micro-context: (a) The narrator’s thinking faces (Goodwin & Goodwin, 1986) occurred as the narrator was getting started, and they accompanied verbal collateral signals of delay, such as “uh” or “um”. (b) The narrator pointed at his hand gestures with his head and eyes (Streeck, 1993), drawing the addressee’s attention to depictions that would later be crucial to the close call. (c) The meta-communicative functions of smiles included marking the narrator’s description of danger as ironic or humorous, hinting at key elements, and acknowledging errors.
Emergence of Parkinson's disease in essential tremor: A study of the clinical correlates in 53 patients

Patients with essential tremor (ET) may develop Parkinson's disease (PD); however, few studies have examined the clinical features of this combination syndrome. Fifty‐three patients with ET‐PD were studied and compared to 53 PD and 150 ET patients. Although the latency from onset of ET to PD was brief (<5 years) in 38.5%, in a sizable proportion (30.8%), it was very long (>20 years). The gender distribution of ET‐PD (67.9% male) was identical to that of PD (67.9% male), yet differed from that of ET (50.0% male) (P = 0.02). The initial cardinal sign of PD was rest tremor in 100% of patients. In ET‐PD, the side of greatest initial ET severity usually matched that of greatest PD severity (P < 0.05). In ET‐PD, male gender predominated and the sidedness of the ET and PD usually matched. The co‐occurrence of the two diagnoses in the same patient may be mechanistically related. © 2008 Movement Disorder Society
CLIMATE , WIND STORMS , AND THE RISK OF VALLEY FEVER ( COCCIDIOIDOMYCOSIS )

Rego RF, Moraes LR, Dourado I. Diarrhoea and garbage disposal in Salvador, Brazil. Trans R Soc Trop Medi Hyg. 2005;99:48–54. Stiratelli R, Laird N, Ware JH. Random-effects models for serial observations with binary response. Biometrics. 1984;40:961–971. Trostle JA, Hubbard A, Scott J, et al. Raising the level of analysis of food-borne outbreaks. Epidemiology. 2008;19(3):384–390. Tumwine JK, Thompson J, Katua-Katua M, et al. Diarrhoea and effects of different water sources, sanitation and hygiene behaviour in East Africa. Trop Med Int Health. 2002;7:750–756. Wallace D, Wallace R. A plague on your houses: How New York was burned down and national public health crumbled. New York: Verso; 1998. Wallace R. A Synergism of plagues: “Planned shrinkage,” contagious housing destruction, and AIDS in the Bronx. Environmental Research. 1988;47(1):1–33. WHO. Persistent diarrhoea in children in developing countries: Memorandum from a WHO meeting. Bulletin of the World Health Organization. 1988;66:709–717.
Police perceptions of restorative justice: Findings from a small‐scale study

This paper considers the views and perceptions of police officers and staff from a local police force in England, on the training provided in, and use of, restorative justice. These views were obtained through the use of an online questionnaire as well as the recording of comments made by police officers and staff after one training session. While the overall sample is too small to draw any concrete conclusions, participants appeared to share views expressed in similar, larger studies. This study adds to the literature on restorative justice as police views in this area are underresearched in England and Wales.
- 1-Price Dispersion and Differentiation in On-Line Travel : An Empirical Investigation forthcoming , Management Science

Previous research has examined whether price dispersion exists in theoretically highly efficient Internet markets. However, much of the previous work has been focused on industries with low cost and undifferentiated products. In this paper, we examine the presence of price dispersion and product differentiation using data on the airline ticket offerings of online travel agents (OTAs). We find that different OTAs offer tickets with substantially different prices and characteristics when given the same customer request. Some of this variation appears to be due to product differentiation -different OTAs specialize by systematically offering different tradeoffs between ticket price and ticket quality (minimizing the number of connections, matching requested departure and return time). However, even after accounting for differences in ticket quality, ticket prices vary by as much as 18% across OTAs. In addition, OTAs return tickets that are strictly inferior to the ticket offered by another OTA for the same request between 2.2% and 28% of the time. Overall, this suggests the presence of both price dispersion and product differentiation in the online travel market.
Understanding Online Community User Participation: A Social Influence Perspective

Purpose – The purpose of this study is to examine the determinants of online community user participation from a social influence perspective.Design/methodology/approach – Based on 450 valid responses collected from a survey questionnaire, structural equation modeling (SEM) technology was employed to examine the research model.Findings – The results show that both social identity and group norm have significant effects on user participation. In addition, group norm affects social identity. It was not possible to find the effect of subjective norm on participation intention.Research limitations/implications – This research is limited to a particular sample: students. Thus the results need to be generalized to other samples, such as working professionals.Originality/value – Extant research has mainly focused on the effects of user motivations such as perceived usefulness, trust and commitment on online community user behavior, and seldom considered the effects of social processes including compliance, ident.
Social Capital, Human Capital, and Economic Well-Being in the Knowledge Economy: Results from Canada's General Social Survey

Beginning in the mid-1990s, the Canadian welfare state’s devolutionary transformation ushered in an era which potentially increased the importance of social capital and human capital as mechanisms for promoting socio-economic advancement. In this study, the authors analyze data from Canada’s General Social Survey to assess how social capital and human capital influence the reported incomes of the Canadian population. The primary findings were that both social and human capital influenced income and that human capital had a larger effect on economic mobility than did social capital. The implications the study’s findings have for policy and programmatic interventions within the 21st century knowledge-based economy are discussed, and future studies which can further understanding in the area of social and human capital are also proposed.
Building Artistic Computer Colleagues with an Enactive Model of Creativity

This paper reports on the theory, design, and implementation of an artistic computer colleague that improvises and collaborates with human users in real-time. Our system, Drawing Apprentice, is based on existing theories of art, creative cognition, and collaboration synthesized into an enactive model of creativity. The implementation details of the Drawing Apprentice are provided along with early collaborative artwork created with the system. We present the enactive model of creativity as a potential theoretical framework for designing creative systems involving continuous improvisational collaboration between a human and computer.
Global regularity and scattering for general non-linear wave equations II. (4+1) dimensional Yang-Mills equations in the Lorentz gauge

We continue here with previous investigations on the global behavior of general type nonlinear wave equations for a class of small, scale-invariant initial data. In particular, we show that the (4 + 1) dimensional Yang-Mills equations are globally well posed with asymptotically free behavior for a wide class of initial data sets which include general charges. The method here is based on the use of a new set of Strichartz estimates for the linear wave equation which incorporates extra weighted smoothness assumptions with respect to the angular variable, along with the construction of appropriate micro-local function spaces which take into account this type of additional regularity.
Blocking TLR2 Activity Attenuates Pulmonary Metastases of Tumor

Background Metastasis is the most pivotal cause of mortality in cancer patients. Immune tolerance plays a crucial role in tumor progression and metastasis. Methods and Findings In this study, we investigated the potential roles and mechanisms of TLR2 signaling on tumor metastasis in a mouse model of intravenously injected B16 melanoma cells. Multiple subtypes of TLRs were expressed on B16 cells and several human cancer cell lines; TLR2 mediated the invasive activity of these cells. High metastatic B16 cells released more heat shock protein 60 than poor metastatic B16-F1 cells. Importantly, heat shock protein 60 released by tumor cells caused a persistent activation of TLR2 and was critical in the constitutive activation of transcription factor Stat3, leading to the release of immunosuppressive cytokines and chemokines. Moreover, targeting TLR2 markedly reduced pulmonary metastases and increased the survival of B16-bearing mice by reversing B16 cells induced immunosuppressive microenvironment and restoring tumor-killing cells such as CD8+ T cells and M1 macrophages. Combining an anti-TLR2 antibody and a cytotoxic agent, gemcitabine, provided a further improvement in the survival of tumor-bearing mice. Conclusions and Significance Our results demonstrate that TLR2 is an attractive target against metastasis and that targeting immunosuppressive microenvironment using anti-TLR2 antibody is a novel therapeutic strategy for combating a life-threatening metastasis.
Pathological and molecular mechanisms of prostate carcinogenesis: Implications for diagnosis, detection, prevention, and treatment

Prostate cancer is an increasing threat throughout the world. As a result of a demographic shift in population, the number of men at risk for developing prostate cancer is growing rapidly. For 2002, an estimated 189,000 prostate cancer cases were diagnosed in the U.S., accompanied by an estimated 30,200 prostate cancer deaths [Jemal et al., 2002 ]. Most prostate cancer is now diagnosed in men who were biopsied as a result of an elevated serum PSA (>4 ng/ml) level detected following routine screening. Autopsy studies [Breslow et al., 1977 ; Yatani et al., 1982 ; Sakr et al., 1993 ], and the recent results of the Prostate Cancer Prevention Trial (PCPT) [Thompson et al., 2003 ], a large scale clinical trial where all men entered the trial without an elevated PSA (<3 ng/ml) were subsequently biopsied, indicate the prevalence of histologic prostate cancer is much higher than anticipated by PSA screening. Environmental factors, such as diet and lifestyle, have long been recognized contributors to the development of prostate cancer. Recent studies of the molecular alterations in prostate cancer cells have begun to provide clues as to how prostate cancer may arise and progress. For example, while inflammation in the prostate has been suggested previously as a contributor to prostate cancer development [Gardner and Bennett, 1992 ; Platz, 1998 ; De Marzo et al., 1999 ; Nelson et al., 2003 ], research regarding the genetic and pathological aspects of prostate inflammation has only recently begun to receive attention. Here, we review the subject of inflammation and prostate cancer as part of a “chronic epithelial injury” hypothesis of prostate carcinogenesis, and the somatic genome and phenotypic changes characteristic of prostate cancer cells. We also present the implications of these changes for prostate cancer diagnosis, detection, prevention, and treatment. © 2003 Wiley‐Liss, Inc.
Stellar Orbits in Triaxial Clusters around Black Holes in Galactic Nuclei

We investigate the orbital structure of a model triaxial star cluster, centered around a supermassive black hole (BH), appropriate to galactic nuclei. Sridhar & Touma proved in 1999 that the presence of the BH enforces some regularity in the dynamics within the radius of influence of the BH. We employ their averaging method to reduce the degrees of freedom from 3 to 2. Numerical orbit integrations, together with Poincaré surfaces of section, allow us to draw a global portrait of the orbital structure; in our calculations we employ a model cluster potential that is triaxial and harmonic. The averaged dynamics of the axisymmetric case is integrable, and we present a detailed comparison of orbits in oblate and prolate axisymmetric potentials. Both cases support resonant orbits with fixed values of eccentricity, inclination, and periapsis, whose lines of nodes rotate steadily. We then systematically explore significantly triaxial potentials possessing small oblateness or prolateness. Resonant orbits and their families are studied both numerically and through secular perturbation theory. Chaos appears to be suppressed for all the cases we studied, and we obtain effective third integrals. Some of the orbits appear to reinforce the shape of the potential; we provide phase-space as well as real-space portraits of these orbits. A particularly promising resonant orbit exists in highly prolate, triaxial potentials.
A Survey of User Interaction for Spontaneous Device Association

In a wireless world, users can establish ad hoc virtual connections between devices that are unhampered by cables. This process is known as spontaneous device association. A wide range of interactive protocols and techniques have been demonstrated in both research and practice, predominantly with a focus on security aspects. In this article, we survey spontaneous device association with respect to the user interaction it involves. We use a novel taxonomy to structure the survey with respect to the different conceptual models and types of user action employed for device association. Within this framework, we provide an in-depth survey of existing techniques discussing their individual characteristics, benefits, and issues.
A 53‐year‐old woman with muscular atrophy showing hypersomnia and respiratory failure

A 53-year-old female patient noticed weakness and wasting of limb muscles at age 30 years.Over the following years, the sternocleidomastoid muscles became atrophic and wasted, with frontal baldness. At age 43, her eyesight began to fail because of bilateral cataracts. She had experienced increasing sleepiness since adolescence. She was always very apt to drop off to sleep and always had difficulty in getting up in the morning. Examination at age 45 years revealed a hatchet face with frontal baldness,bilateral ptosis, grasp and percussion myotonia, and muscular atrophy of the four limbs, greater distally, and at the sternocleidomastoid. Pulmonary function tests revealed ventilatory insufficiency of a restrictive type with reduction of vital capacity (1800 mL, 55% of predicted), total lung capacity (2500 mL) and maximum breathing capacity (24 I/min, 25% of predicted). The ratio of the forced expiratory volume in 1 second to the forced vital capacity was 80%, showing no sign of airway obstruction. Arterial gas analysis values at rest while awake showed marked hypercapnea and hypoxia with respiratory acidosis (PaO2 40 mmHg; PaCO2 68 mmHg; pH 7.29). The maximum inspiratory and expiratory pressure (71.3 cmH2O and 83.2 cmH2O) and the diffusion capacity for CO (15.3 mL/min/ mmHg) revealed no abnormality.The ventilatory response to CO2 inhalation was markedly impaired. However, voluntary hyperventilation lowered the CO2 by 23 mmHg. Mental changes such as inattention, apathy and memory defect, which were not noticed in her childhood, were observed. Her IQ was 48. Brain CT scan disclosed enlargement of the lateral ventricles. At age 46, the patient experienced sudden respiratory insufficiency caused by local anesthesia for a cataract operation.She died of acute pneumonia at 53 years of age.
Determining the Optimal Challenge Point for Motor Skill Learning in Adults With Moderately Severe Parkinson's Disease

Objective. To test the predictions of the Challenge Point Framework (CPF) for motor learning in individuals with Parkinson's disease (PD) by manipulating nominal task difficulty and conditions of practice. Methods. Twenty adults with PD and 20 nondisabled controls practiced 3 variations of a laboratory-based goal-directed arm movement over 2 days. A between-group (PD, nondisabled) 2-factor design compared 2 levels of nominal task difficulty (low, high) and 2 levels of practice condition (low, high demand). Learning was assessed with a no-feedback recall test 1 day after practice. Performance was quantified using a root mean square error difference between the goal and participant-generated movement. Results. All participants improved with practice. Under the low-demand practice condition, adults with PD demonstrated comparable learning to that of controls when nominal task difficulty was low but not high. In contrast, under the high-demand practice condition, adults with PD demonstrated preserved motor learning for both levels of task difficulty, but only if recall was tested under the same context as that used during practice. Conclusions. In general, the predictions of CPF were supported. Together, the level of nominal task difficulty and the inherent demand of the practice condition played a critical role in determining the optimal challenge point for motor learning in individuals with PD. More important, and in contrast to the predictions of CPF, a high-demand practice condition appeared to have a facilitative effect on motor learning. However, this benefit revealed the context specificity of motor learning in adults with PD.
SERIMI: Class-based Disambiguation for Effective Instance Matching over Heterogeneous Web Data

matching has been studied with focus on the single- domain setting, while less attention is given to the hetero- geneous environment of the Web, where data comes from dierent domains and are associated with dierent schemas. For this heterogeneous setting, we propose an unsupervised schema-agnostic approach that focuses on the renement (disambiguation) of candidate instances (resulting from block- ing). Given instances of a source dataset that belong to a class, it computes candidates in the target datasets and re- nes them such that the remaining matches correspond to the source instances at the class level. However, no schema knowledge and explicit correspondences between classes in the source and target datasets are required for this. Rather, the disambiguation is performed based on an instance-based representation of classes computed online. We evaluated our work using experiments on large-scale real-world datasets provided by a benchmark. The proposed solution outper- formed two alternative approaches for instance matching in 70% of the cases, and in those cases we improved average F-measure by 10%.
Functional Associations by Response Overlap (FARO), a Functional Genomics Approach Matching Gene Expression Phenotypes

The systematic comparison of transcriptional responses of organisms is a powerful tool in functional genomics. For example, mutants may be characterized by comparing their transcript profiles to those obtained in other experiments querying the effects on gene expression of many experimental factors including treatments, mutations and pathogen infections. Similarly, drugs may be discovered by the relationship between the transcript profiles effectuated or impacted by a candidate drug and by the target disease. The integration of such data enables systems biology to predict the interplay between experimental factors affecting a biological system. Unfortunately, direct comparisons of gene expression profiles obtained in independent, publicly available microarray experiments are typically compromised by substantial, experiment-specific biases. Here we suggest a novel yet conceptually simple approach for deriving ‘Functional Association(s) by Response Overlap’ (FARO) between microarray gene expression studies. The transcriptional response is defined by the set of differentially expressed genes independent from the magnitude or direction of the change. This approach overcomes the limited comparability between studies that is typical for methods that rely on correlation in gene expression. We apply FARO to a compendium of 242 diverse Arabidopsis microarray experimental factors, including phyto-hormones, stresses and pathogens, growth conditions/stages, tissue types and mutants. We also use FARO to confirm and further delineate the functions of Arabidopsis MAP kinase 4 in disease and stress responses. Furthermore, we find that a large, well-defined set of genes responds in opposing directions to different stress conditions and predict the effects of different stress combinations. This demonstrates the usefulness of our approach for exploiting public microarray data to derive biologically meaningful associations between experimental factors. Finally, our results indicate that FARO is more powerful in associating mutants in common pathways than existing methods such as co-expression analysis.