Miracle-dz/UniFAR-FTUs huggingface dataset:
The Genome-wide Transcriptional Responses of Saccharomyces cerevisiae Grown on Glucose in Aerobic Chemostat Cultures Limited for Carbon, Nitrogen, Phosphorus, or Sulfur*

Profiles of genome-wide transcriptional events for a given environmental condition can be of importance in the diagnosis of poorly defined environments. To identify clusters of genes constituting such diagnostic profiles, we characterized the specific transcriptional responses of Saccharomyces cerevisiaeto growth limitation by carbon, nitrogen, phosphorus, or sulfur. Microarray experiments were performed using cells growing in steady-state conditions in chemostat cultures at the same dilution rate. This enabled us to study the effects of one particular limitation while other growth parameters (pH, temperature, dissolved oxygen tension) remained constant. Furthermore, the composition of the media fed to the cultures was altered so that the concentrations of excess nutrients were comparable between experimental conditions. In total, 1881 transcripts (31% of the annotated genome) were significantly changed between at least two growth conditions. Of those, 484 were significantly higher or lower in one limitation only. The functional annotations of these genes indicated cellular metabolism was altered to meet the growth requirements for nutrient-limited growth. Furthermore, we identified responses for several active transcription factors with a role in nutrient assimilation. Finally, 51 genes were identified that showed 10-fold higher or lower expression in a single condition only. The transcription of these genes can be used as indicators for the characterization of nutrient-limited growth conditions and provide information for metabolic engineering strategies.
The Market Share Impact of Interpartner Learning in Alliances: Evidence from the Global Auto Industry

We investigate how inter-partner learning in alliances impacts the competitive positions of the involved partner firms. We identify two types of alliances: scale alliances in which the partner firms contribute similar resources to their joint endeavor, and link alliances in which the partners contribute complementary resources. Our study shows that the relative market share of the partners varies significantly more in link alliances than it does in scale alliances. This result suggests that "link" alliances lead to greater levels of inter-partner learning. A longitudinal study assessing 135 strategic alliances formed by competing firms in the global automotive industry from 1966 to 1995 supports this analysis.
Crowdsourcing using Mechanical Turk: quality management and scalability

I will discuss the repeated acquisition of "labels" for data items when the labeling is imperfect. Labels are values provided by humans for specified variables on data items, such as "PG-13" for "Adult Content Rating on this Web Page. " With the increasing popularity of micro-outsourcing systems, such as Amazon's Mechanical Turk, it often is possible to obtain less-than-expert labeling at low cost. We examine the improvement (or lack thereof) in data quality via repeated labeling, and focus especially on the improvement of training labels for supervised induction.
Current perspective on rituximab in rheumatic diseases

The steadily increasing knowledge regarding pathogenetic mechanisms in autoimmune rheumatic diseases has paved the way to different therapeutic approaches. In particular, the market entry of biologics has dramatically modified the natural history of rheumatic chronic inflammatory diseases with a meaningful impact on patients’ quality of life. Among the wide spectrum of available biological treatments, rituximab (RTX), first used in the treatment of non-Hodgkin’s lymphoma, was later approved for rheumatoid arthritis and anti-neutrophil cytoplasmic antibodies-associated vasculitis. Nowadays, in rheumatology, RTX is also used with off-label indications in patients with systemic sclerosis, Sjögren’s syndrome and systemic lupus erythematosus. RTX is a monoclonal antibody directed to CD20 molecules expressed on the surfaces of pre-B and mature B lymphocytes. It acts by causing apoptosis of these cells with antibody- and complement-dependent cytotoxicity. As inflammatory responses to cell-associated immune complexes are key elements in the pathogenesis of several autoimmune rheumatic diseases, such an approach might be effective in these patients. In fact, RTX, by promoting the rapid and long-term depletion of circulating and lymphoid tissue-associated B cells, leads to a lower recruitment of these effector cells at sites of immune complex deposition, thus reducing inflammation and tissue damage. RTX is of the most interest to rheumatologists as it represents an important additional therapeutic approach. Thus, the advent in clinical practice of approved RTX biosimilars, such as CT-P10, may be of help in improving treatment access as well as in reducing costs.
MDCHeS: Model-Driven Dynamic Composition of Heterogeneous Service

Web Service Composition provides an opportunity for enterprises to increase the ability to adapt themselves to frequent changes in users' requirements by integrating existing services. Our research has focused on proposing a framework to support dynamic composition and to use both SOAP-based and RESTful Web services simultaneously in composite services. In this paper a framework called "Model-driven Dynamic Composition of Heterogeneous Service" (MDCHeS) is introduced. It is elaborated in three different ways; each represents a particular view of the framework: data view, which consists of a Meta model and composition elements as well their relationships; process view, which introduces composition phases and used models in each phase; and component view, which shows an abstract view of the components and their interactions. In order to increase the dynamicity of MDCHeS framework, Model Driven Architecture and proxy based ideas are used.
Long-term follow-up after cryoablation for adolescent atrioventricular nodal reentrant tachycardia: recurrence is not predictable.

AIMS Data about the long-term outcome after cryoablation for atrioventricular nodal reentrant tachycardia (AVNRT) in the paediatric population indicate that recurrence rates are higher with cryo than with radiofrequency energy (RF). The purpose of this study was to review our institutional long-term outcome after cryoablation for AVNRT and to seek for predictors of recurrence. METHODS AND RESULTS Forty-nine patients (28 female, age 14 ± 2.7 years) undergoing slow-pathway modulation or ablation for AVNRT at our institution from 2004 to 2008 were included in the study. Acute success was obtained in all patients (100%) with a mean procedure time of 164 ± 50 min and a mean fluoroscopy time of 13 ± 8 min. During a follow-up time of 30 ± 1.9 months, AVNRT recurrence occurred in 11/49 patients (22.4%). Age, sex, number of cryomappings or ablations, catheter tip (4 mm vs. 6 mm), or ablation endpoint (slow-pathway ablation vs. modulation) were not predictive for recurrence. In eight patients, reablation using cryo was performed. All these patients remained free of arrhythmia symptoms during a follow-up of 30 ± 8 months following the second procedure. CONCLUSION Although cryoablation for the treatment for AVNRT in paediatric and adolescent patients is safe and associated with a high acute success rate, AVNRT recurrence occurs in 22% of patients during long-term follow-up without identifiable predictors for recurrence. A second cryoablation procedure leads to a success rate of 100% during long-term follow-up.
The United States' share of published research in neurosciences and clinical neurology

In most of the biomedical categories, the United States’ share of articles, along with other top-ranking countries, has declined in recent years. However, this trend has not yet been examined for neuroscience and clinical neurology journals. Relevant data were obtained from a total of 10 journals. Five neuroscience journals with the highest impact factors (Annual Review of Neuroscience, Neuron, Trends in Neurosciences, Progress in Neurobiology, and Current Opinion in Neurobiology) were selected from neurosciences category set by the Institute for Scientific Information. We excluded Nature Reviews Neuroscience, Nature Neuroscience, and Behavioral and Brain Sciences even though they had second, third, and seventh position in the Institute for Scientific Information ranking, respectively, because they were indexed in Medline database after 1994. With similar criteria, five clinical neurology journals (Brain, Annals of Neurology, Neurology, Neuroscience and Biobehavioral Reviews, and Stroke) were selected from the clinical neurology category. Medline database was searched to elicit the number of articles (journal articles) affiliated with different countries and published from 1994 through 2003. After that, the proportion of contribution of 10 top-ranking countries was ranked in descending order along with the trend over time. 2 test for trend was performed using SAS 9.1 (SAS Institute, Cary NC) to elicit any significant change over time. All tests of significance were two tailed and p values less than 0.05 were considered significant. In total, 5,998 and 17,085 articles were published from 1994 through 2003 in the selected neuroscience and clinical neurology journals, respectively. Shares of top-ranking 10 countries for each category are shown in the Table. In the past decade, although the United States’ share increased from 59.8 to 67.1% of the total for neuroscience articles (p 0.020), that for clinical neurology articles declined from 50.7 to 35.5% (p 0.001). Japan (p 0.001) and Germany (p 0.036) are the only other countries with a negative trend in clinical neurology and neurosciences, respectively. We found a significant positive trend in the share of neuroscience articles for Israel (p 0.028) and in the share of clinical neurology articles for the United Kingdom (p 0.001), Germany (p 0.001), Italy (p 0.001), France (p 0.023), Netherlands (p 0.001), and Australia (p 0.001). In conclusion, over the past decade, although the share of neuroscience articles from the United States has increased, that of clinical neurology articles from the United States has decreased contrary to the trend of most other countries.
A Simulation Platform for Evaluating RFID and WSN’s Energy Efficiencies

Advances in the wireless, RFID and sensor technologies has given rise to a plethora of diverse WSN motes that can be used in association with numerous applications. Experimenting with new MAC algorithms and various functionalities on a real sensor network to obtain energy efficiency is both time consuming and expensive especially when these different mote platforms are deployed in one application. Generally Simulators are used to approximate the performance of MAC protocols. Out of the numerous simulators available, none can simulate the energy efficiencies given different types of motes and environments in one application. Hence, the need of a simulation platform for a mix deployment of different types of WSNs and RFIDs is felt to access application performance requirements while curtailing energy consumption to enhance application lifetime. In this paper, we presents an extension of our effort EnergySim [1], which is a simulation platform developed dedicatedly for evaluating energy efficiencies. In this paper we have discussed the simulation modes, methodology and architecture of our proposed simulator with some future extensions presented at the end of the paper.
Probing the fate of interstitial water in bulk bioactive glass by ab initio simulations

As also observed for conventional silicate glasses, water can be incorporated in the bulk interstitial regions of a bioactive glass (BG) matrix during the glass preparation and/or upon exposure to an aqueous environment. However, in the case of BGs, very little is known about the effect of hydration on the bulk structure, and then on key properties of these materials, such as biodegradation and bioactivity, that depend on the bulk structure itself. Here we employ a combination of atomistic simulation techniques to explore the nature and effects of water–BG interactions in the bulk of a bioactive glass. The fate of water inserted in the bulk interstitial region of 45S5 bioglass has been studied by ab initio geometry relaxations and Molecular Dynamics (AIMD) simulations. We probed the interaction of a water molecule with silica rings and cages of different size, as well as the stability of potentially relevant configurations involving manually dissociated water and opened rings. The local stability of selected configurations was further assessed by subjecting them to AIMD runs, in order to overcome possible kinetic barriers for water diffusion and dissociation. Small rings do not appear as favourable absorption sites in the bulk of a bioactive glass as they are for bioinert glasses. Moreover, water dissociation through rupture of Si–O bonds of silica rings formed in the bulk was thermodynamically unfavourable. However, a high-temperature AIMD run led to a dissociated state involving no broken Si–O bonds and a free hydroxyl: because re-optimization of this state produced the most favourable hydration energy identified in this study, dissociative absorption through this mechanism appears a likely outcome of the water–45S5 interaction at low water content. We discuss the structural and dynamical basis for the stability of this and other water–glass adducts identified, and the potential consequences of these interactions for the behaviour of the glass in a biological context.
Site-directed mutagenesis of the gag-myc gene of avian myelocytomatosis virus 29: biological activity and intracellular localization of structurally altered proteins

Transfection of chicken embryo cells with pMC29, a plasmid vector containing the sequences for the acute transforming virus MC29, and a cloned transformation-defective helper virus, p delta Mst, resulted in morphological transformation, the synthesis of P110gag-myc (the product of the gag-myc oncogene), and the production of infectious virus. MC29 mutants bearing site-directed deletions within the gag-specific sequences or within the middle portion of the myc sequences efficiently induced transformation of chicken embryo cells in culture. However, variants containing deletions of sequences in the amino-terminal half or carboxy-terminal portion of the myc gene were defective for transformation. The gag-myc proteins encoded by these variants efficiently localized to the cell nucleus. Premature termination mutants were isolated which encoded gag-myc proteins lacking the carboxy-terminal 185 residues; these truncated proteins localized to both the nucleus and the cytoplasm. Deletion of as few as 11 residues within the middle of the myc-specific sequences (residues Ile-239 to Glu-249) significantly reduced the efficiency of chicken hematopoietic cell transformation.
Post Marketing Surveillance Study to Assess Safety and Efficacy of Cyclosporine Micro-Emulsion (Neoral ® ) Treatment in Psoriasis Patients

Background: To assess efficacy and safety of Cyclosporine micro-emulsion (Neoral ® ) in psoriasis treatment Material and Methods: A total of 102 patients (mean age: 42.1 ± 11.2; 51.0% were males) who were considered appropriate for Cyclosporine micro-emulsion (Neoral ® ) treatment by study investigators were enrolled in this multicentre post marketing surveillance study (COLO400CTR05) at 2 different centers in Turkey between September 2005 – June 2009. Data were collected at a total of 17 visits in 12 months for each patient. Efficacy was evaluated in terms of PASI and DLQI scores, while alteration in blood pressure and serum creatinine levels together with adverse events were recorded to evaluate safety during follow up. Results: Of 102 patients 87.3% completed the 3rd month visit. Psoriasis vulgaris was the leading diagnosis (90.2%) and the average duration of psoriasis was 15.2±8.6 years. When compared to values obtained in the last visit, a significant but steady decline was observed in PASI as well as DLQI scores at each consecutive visit performed during the course of the study (p<0.05 for PASI scores and p<0.001 for DLQI scores). Relapse was identified in 8.8% of patients. Adverse events were reported to be mild in 60.0% of patients while the relation of adverse events to the study medication was considered to be suspicious in 86.0% of cases. Conclusion: In conclusion, offering steady state and graduated resolution of extent and severity of disease and positive impact on quality of life, cyclosporine therapy in micro-emulsion form seems to be associated with low relapse rate as well as high patient compliance in severe psoriasis treatment for up to 12 months of follow up performed in accordance with therapeutic guidelines.
Chinese Named Entity Recognition with Conditional Probabilistic Models

This paper describes the work on Chinese named entity recognition performed by Yahoo team at the third International Chinese Language Processing Bakeoff. We used two conditional probabilistic models for this task, including conditional random fields (CRFs) and maximum entropy models. In particular, we trained two conditional random field recognizers and one maximum entropy recognizer for identifying names of people, places, and organizations in unsegmented Chinese texts. Our best performance is 86.2% F-score on MSRA dataset, and 88.53% on CITYU dataset.
Complications associated with anemia and blood transfusion in patients with aneurysmal subarachnoid hemorrhage

Objective:Patients with subarachnoid hemorrhage (SAH) frequently develop delayed cerebral ischemia and may be especially vulnerable to the effects of anemia. However, the potentially harmful effects of allogeneic red blood cells are increasingly being recognized. The optimal transfusion threshold is unknown, but current practice most often uses a liberal approach. We assessed the association between anemia or transfusion and subsequent adverse outcomes. Design:Retrospective cohort study. Setting:Neuroscience intensive care unit of a university hospital. Patients:A total of 245 consecutive patients with aneurysmal SAH. Interventions:None. Measurements:Logistic regression models were used to adjust for baseline differences in age, severity of neurologic impairment, and amount of blood on computed tomography. Patients were dichotomized based on whether symptomatic vasospasm was diagnosed. Main Results:Individually, anemia (nadir hemoglobin <10 g/dL) and the use of transfusions were both associated with the combined outcome of death, severe disability, or delayed infarction (odds ratio [OR] for anemia, 2.7; 95% confidence interval [CI] 1.5–5; p < .01; OR for transfusion, 4.8; 95% CI, 2.5–9.1; p < .01). When both variables were together introduced into a logistic regression model, only transfusion remained significantly predictive (OR, 4.3; 95% CI, 1.5–9.3; p < .01). The relationship between anemia and adverse outcomes was stronger among patients diagnosed with vasospasm, whereas for transfusion, it was stronger among patients without vasospasm. Transfusion also was associated with the development of nosocomial infections (OR, 3.2; 95% CI, 1.7–5.5; p < .01). There was no statistically significant difference in complications based on the duration of blood storage before transfusion. Conclusions:Although anemia is predictive of adverse outcomes in patients with SAH, this observation cannot be considered justification for a liberal transfusion strategy. Appropriate transfusion thresholds may vary depending on the presence or absence of clinical vasospasm. Randomized trials that compare liberal and restrictive transfusion strategies in patients with SAH are needed.
The Role of Investments in Export Growth: Evidence from a Middle-Income Country

In this work we follow the recent strand of work linking innovation, productivity and exports. We test the hypothesis that a rise in investment favors entrance in export markets and increases exports among previously exporting firms. We address causal links through impact evaluation techniques for observational data. We examine the binary case as well as continuous treatment analysis for investment as treatment. The analysis is conducted for a panel of Uruguayan manufacturing firms for the period 1997-2008. To the best of our knowledge, this is the first study of our approach for a Latin American economy, and the relatively long time span of our data makes it possible a better characterization of new entrants and firms with changing export behavior. Also, our data appears to be richer, including information to estimate total factor productivity, and R&D and training investments, which provide better controls for confounding factors. We find evidence that investments "cause" exports and export orientation, which provides a rationale for carefully designing investment promotion policies rather than focusing on other export support policies.
Institutional Logics and Status: Strategic Patenting in the Legal Service Sector

Professional service firms adhere to at least two often conflicting institutional logics - serving their clients and serving as a gatekeeper of societal institutions, but the literature says little about under which conditions professional service firms align their actions with each of these conflicting logics. Simultaneously, a large literature emphasizes that the behavior of professional service firms are driven by status dynamics, however, this literature has yet to consider how status dynamics affect firms' adherence to institutional logics. We bring these two previously separate literatures together by investigating law firms' tendency to aid their clients with strategic patenting. Drawing on a large dataset of patent applications from the European Patent Office we first show that status is a strong predictor of following a client logic. Yet, the effect of status wanes as firms gain more experience with patenting. This paper contributes to the literature on institutional logics by specifying the conditions that influence firms' adherence to conflicting institutional logics. We also discuss the impact of our results for the literature on status.
Identification of available and desirable indicators for patent systems, patenting processes and patent rights: research project for the German Patent and Trademark Office

In 2004 the German Patent and Trademark Office commissioned the Ifo Institute to deliver a research report on the topic "Identification of Available and Desirable Indicators for Patent Systems, Patenting Processes and Patent Rights". - The report provides an extensive overview of the existing literature about the valuation of patents, mainly from an economic point of view but also giving consideration to legal and business aspects. This includes the valuation of the patent system itself, the valuation of the patenting process and the valuation of the assigned patent rights. Looking at the relevant literature, however, it reveals immeadiately that a quantification of these patent related issues is not easy. The economic literature relies heavily on the valuation of patent rights, as this gives a possible measurement of innovation output.
Equalization of OFDM-systems by interference cancellation techniques

Intercarrier interference can be a dominant source of errors in OFDM-systems, requiring some sort of equalization. We show that serial and parallel interference cancellation techniques, which were originally developed for CDMA multiuser techniques, can be used for OFDM equalization and are much more efficient than a brute force inversion of the channel matrix. Maximum excess delays of up to 70% of the OFDM block duration can be handled without loss of performance.