Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of the Arabidopsis REDUCED DORMANCY 2 Gene Uncovers a Role for the Polymerase Associated Factor 1 Complex in Seed Dormancy

The life of a plant is characterized by major phase transitions. This includes the agriculturally important transitions from seed to seedling (germination) and from vegetative to generative growth (flowering induction). In many plant species, including Arabidopsis thaliana, freshly harvested seeds are dormant and incapable of germinating. Germination can occur after the release of dormancy and the occurrence of favourable environmental conditions. Although the hormonal control of seed dormancy is well studied, the molecular mechanisms underlying the induction and release of dormancy are not yet understood. In this study, we report the cloning and characterization of the mutant reduced dormancy 2-1 (rdo2-1). We found that RDO2 is allelic to the recently identified dormancy gene TFIIS, which is a transcription elongation factor. HUB1, which was previously called RDO4, was identified in the same mutagenesis screen for reduced dormancy as rdo2-1 and was also shown to be involved in transcription elongation. The human homologues of RDO2 and HUB1 interact with the RNA Polymerase II Associated Factor 1 Complex (PAF1C). Therefore, we investigated the effect of other Arabidopsis PAF1C related factors; VIP4, VIP5, ELF7, ELF8 and ATXR7 on seed dormancy. Mutations in these genes resulted in reduced dormancy, similar to hub1-2 and rdo2-1. Consistent with a role at the end of seed maturation, we found that HUB1, RDO2 and VIP5 are upregulated during this developmental phase. Since mutants in PAF1C related factors are also described to be early flowering, we conclude that these components are involved in the regulation of both major developmental transitions in the plant.
Risk Estimation for Healthy Women from Breast Cancer Families

Risk estimation in breast cancer families is often estimated by use of the Claus tables. We analyzed the family histories of 196 counselees; compared the Claus tables with the Claus, the BRCA1/2, the BRCA1/2/ models; and performed linear regression analysis to extend the Claus tables with characteristics of hereditary breast cancer. Finally, we compared the Claus extended method with the Claus, the BRCA1/2, and the BRCA1/2/u models. We found 47% agreement for Claus table versus Claus model; 39% agreement for Claus table versus BRCA1/2 model; 48% agreement for Claus table versus BRCA1/2/u model; 37% agreement for Claus extended method versus Claus model; 44% agreement for Claus extended model versus BRCA1/2 model; and 66% agreement for Claus extended method versus BRCA1/2/u model. The regression formula (Claus extended method) for the lifetime risk for breast cancer was 0.08 + 0.40 ∗ Claus Table + 0.07 ∗ ovarian cancer + 0.08 ∗ bilateral breast cancer + 0.07 ∗ multiple cases. This new method for risk estimation, which is an extension of the Claus tables, incorporates information on the presence of ovarian cancer, bilateral breast cancer, and whether there are more than two affected relatives with breast cancer. This extension might offer a good alternative for breast cancer risk estimation in clinical practice.
The Role of the Five–factor Personality Traits in General Self–rated Health

Self–ratings of health (SRH) are widely used in large surveys and have been shown to predict mortality over and above more objective health measures. However, the debate still continues about what SRH actually represents and what the processes underlying people's assessments of their health are. The main aim of this study is to examine the role of the Five–Factor Model personality traits in general SRH assessment while controlling for the effects of objective health indicators, health–related quality of life and subjective well–being in a large population–based dataset of Estonian adults. A hierarchical linear regression analysis showed that only self–rated, but not informant–rated, neuroticism explained additional variance in SRH when the other aforementioned variables were taken into account. Our findings indicate that people's general SRH is a relatively good reflection of their objectively measured health status, but also that the way in which people experience and evaluate the quality of their lives—both in terms of subjective well–being and more specific aspects of health—plays a significant role in general SRH assessments. Copyright © 2016 European Association of Personality Psychology
Effect of Human Myotubes-Derived Media on Glucose-Stimulated Insulin Secretion

Fasting to postprandial transition requires a tight adjustment of insulin secretion to its demand, so tissue (e.g., skeletal muscle) glucose supply is assured while hypo-/hyperglycemia are prevented. High muscle glucose disposal after meals is pivotal for adapting to increased glycemia and might drive insulin secretion through muscle-released factors (e.g., myokines). We hypothesized that insulin influences myokine secretion and then increases glucose-stimulated insulin secretion (GSIS). In conditioned media from human myotubes incubated with/without insulin (100 nmol/L) for 24 h, myokines were qualitatively and quantitatively characterized using an antibody-based array and ELISA-based technology, respectively. C57BL6/J mice islets and Wistar rat beta cells were incubated for 24 h with control and conditioned media from noninsulin- and insulin-treated myotubes prior to GSIS determination. Conditioned media from insulin-treated versus nontreated myotubes had higher RANTES but lower IL6, IL8, and MCP1 concentration. Qualitative analyses revealed that conditioned media from noninsulin- and insulin-treated myotubes expressed 32 and 23 out of 80 myokines, respectively. Islets incubated with conditioned media from noninsulin-treated myotubes had higher GSIS versus control islets (p < 0.05). Meanwhile, conditioned media from insulin-treated myotubes did not influence GSIS. In beta cells, GSIS was similar across conditions. In conclusion, factors being present in noninsulin-stimulated muscle cell-derived media appear to influence GSIS in mice islets.
Business Process Lines to Deal with the Variability

Variability proved to be a central concept in different domains, manufacturing, software development etc. in order to develop solutions that can be easily adapted to different organizational settings and different sets of customers at a low price. We argue that families of business process models can facilitate the installation of situated models in different organizations. We propose a representation system called Map to capture variability in process models expressed in an intentional manner through business goals and strategies. The paper presents an intentional view of the business process variability and illustrates it in an excerpt of a real case in the Electricity Supply Industry. The kernel of an organizational level model is also introduced to allow the organizational implementation of each variant.
Bridging the Gap of Network Management and Anomaly Detection through Interactive Visualization

Large-scale networks have become increasingly challenging to manage. It is vital for a system administrator or network manager to be able to analyze the vast amount of log data in order to detect suspicious behaviors or patterns, possibly due to malicious users/applications or faulty devices. While an intrusion detection system (IDS) log can provide a large number of warnings, exactly which alarms are true while the others are false, and more importantly what are the underlying causes are still difficult to know. To bridge the gap between network log and anomaly discovery, we design and implement a visualization tool that combines multiple commodity visualizations with minimum learning curve. While each individual view is well understood, the effects of such views in analyzing network anomalies are not well studied. Since each visualization technique has advantages as well as limitations in addressing a particular task, we show that these views, when combined and linked together, may provide an effective and lightweight network anomaly analysis tool. The web-based open platform may simplify network administration as well as promote collaborative analysis among researchers.
Low-Cost Software Countermeasures Against Fault Attacks : Implementation and Performances Trade Offs

In this paper we present software countermeasures specifically designed to counteract fault attacks during the execution of a software implementation of a cryptographic algorithm and analyze their efficiency. We propose two approaches that are based on the insertion of redundant computations and checks, which in their general form, are suitable for any cryptographic algorithm. In particular, we focus on selective instruction duplication, employed to detect single errors, instruction triplication to support also error correction, and parity checking to detect corruption of a stored value. We developed a framework to automatically add the desired countermeasure, and we support the possibility to apply the selected redundancy to either all the instructions of the cryptographic routine or restrict it to the most sensitive ones, such as table lookups and key fetching. Considering an ARM processor as a target platform and AES as a target algorithm, we evaluate the overhead of each proposed countermeasure while keeping the robustness of the implementation high enough to thwart most or all the known fault attacks. Experimental results show that in the considered architecture, the fastest solution is per-instruction selective doubling and checking, and that the instruction triplication is a viable alternative if very high levels of fault resistance are required. Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Copyright 20XX ACM X-XXXXX-XX-X/XX/XX . $10.00.
Power Analysis of WEP Encryption

This paper examines the power consumption in Wired Encryption Privacy (WEP) encryption and decryption. This topic has long been neglected, as the power consumption inside an access point of base station that uses WEP is often not a factor, as designers often assume a reliable power source. We are exploring power consumption within the Information and Communication Technology framework, which seeks to close the digital divide between the digitally empowered and the digitally poor. Specifically, we hope that low power access points and base stations will allow Internet access to become a reality for the rural poor in developing areas. Targeting software WEP encryption and decryption, we show significant power consumption can be achieved using software and hardware optimizations. By utilizing loop unrolling, we are able to increase the efficiency of the processor and reduce the power consumed by up to 5.8%. Similarly, with hardware cache optimizations, we show that power consumption can be reduced by 10.5%.
Image quality assessment based on Structure Similarity

Image Structure Similarity (SSIM) and its extended versions have been successfully used in image quality assessment. In this paper, we propose a similarity metric to evaluate image quality by extracting image sparse structure from natural scene image. A sparse dictionary trained on the data contains the basic elements for representing sparse structures, and it is insensitive to different databases. The sparse structure similarity of testing image pairs is calculated with this dictionary. The final score of image quality is obtained by counting the changed number of elements in sparse structure vector between distorted image and reference image. Experiments demonstrate that the proposed method could assess image quality effectively and outperform existing SSIM based methods.
PRATA : A System for XML Publishing , Integration and View Maintenance

We present PRATA, a system that supports the following in a uniform framework: (a) XML publishing, i.e., converting data from databases to an XML document, (b) XML integration, i.e., extracting data from multiple, distributed databases, and integrating the data into a single XML document, and (c) incremental maintenance of published or integrated XML data (view), i.e., in response to changes to the source databases, efficiently propagating the source changes to the XML view by computing the corresponding XML changes. A salient feature of the system is that publishing, integration and view maintenance are schema-directed: they are conducted strictly following a user-specified (possibly recursive and complex) XML schema, and guarantee that the generated or modified XML document conforms to the predefined schema. We discuss techniques underlying PRATA and report the current status of the system.
Serum brain-derived neurotrophic factor (BDNF) levels in schizophrenia: A systematic review

Background There is increasing interest in the role of brain-derived neurotrophic factor (BDNF) in the onset and course of schizophrenia, but there are conflicting reports about serum levels of BDNF in patients with schizophrenia. Aim Conduct a meta-analysis combining studies from China and other countries that have evaluated the relationship of serum BDNF levels to schizophrenia. Method We used Cochrane methodology and RevMan 5.1 software to identify and pool the results of studies. Electronic searches of western and Chinese registries and follow-up assessment of references located 268 potential articles. Twenty-five articles (20 in English and 5 in Chinese) published before December 2011 that used case-control methods, included patients with schizophrenia who had no concurrent disorders, and used ELISA technology to assess serum BDNF were included in the analysis. The main outcome was the pooled standardized mean difference (SMD) between cases and controls. The quality of the studies was independently assessed by two raters using the GRADE system. The heterogeneity, sensitivity and potential publication bias of the studies was evaluated using RevMan. Results The pooled sample included 1663 patients with schizophrenia and 1355 controls. Fifteen of the included studies were rated as ‘poor quality’ and 10 were rated as ‘very poor quality’. The results of the studies were quite heterogenous (I2=95%) but subgroup analyses found that the heterogeneity was not related to country of origin, sample size, age, gender, prior use of antipsychotic medication, or study quality. The pooled SMD (computed using a random-effect model because of study heterogeneity) was -0.74 (95% CI, -0.99∼-0.50; Z=5.99, p<0.001). Sensitivity analysis found that the result was stable and there was no evidence of publication bias. Conclusion Despite the robust statistical findings of lower serum BDNF in patients with schizophrenia than in controls, given the low quality of the available studies and the substantial heterogeneity between studies, the evidence of lower serum BDNF in patients with schizophrenia must be considered ‘weak’. The potential use of serum BDNF as a biomarker for schizophrenia must wait until higher-quality prospective studies that follow patients over time and that use uniform selection and monitoring procedures confirm these preliminary results.
Area and power efficient network on chip router architecture

In System on Chip, buses and point to point links are used as a communication infrastructure between one IP to another, but these cannot provide efficient interconnect from performance point of view. So NoC architecture was proposed to provide communication in multiprocessor SoC and overcome the limitations. This paper has implemented a 5-port 32-bit and 64-bit router architecture using wormhole routing technique for 2D-mesh network by using simple deterministic algorithm, flow control and decoding mechanism. In this router, 2 types of crossbar are used named as multiplexer and tri-state buffer matrix for efficient design. Comparisons of area and power are done for these router designs using ASIC tool flow in Cadence using TSMC 90nm and 180nm process technologies. Simulation results are performed in Cadence NC simulator. It is demonstrated that multiplexer router design is more efficient than a matrix router design as area and power increases for matrix design while using same port-width.
Design of Integrated Triple Band-Notched for Ultra-Wideband Microstrip Antenna

Ultra-wideband (UWB) is one of the recent topics that received a great concern from academia and industry. However, UWB found many difficulties to be standardized due to the overlay working that made UWB an important potential interference source to many licensed and unlicensed spectrum throughout the band 3.1-to-10.6 GHz. This make many industries worried about deploying and standardizing this promising technology. Many techniques have been introduced by academia a friendly UWB design that can mitigate interference. One of these technologies recently proposed is band-notched technique. In this paper we propose a compact ultra-wideband microstrip antenna with triple bandnotched 5.32 GHz, 8.45 GHz and 10.83 GHz. The proposed antenna consists of a rectangular patch with a partial ground plane that is fed by 50 Ω microstrip line. A band-stop function is created by inserting overlapped two u-shape slots on the radiator patch, added additional patch to ground plane side and slit in truncate ground plane. The proposed antenna is simulated in both the frequency domain and time domain. The achieved results show that the antenna performance has good impedance matching and stably performs omni-directional pattern in (x, z) plane over a bandwidth of 3.1 to 10.6 GHz. The proposed antenna could potentially minimize frequency interference from many underlying technologies i.e. WLAN, WiMAX and Aeronautical mobile bands.
Mortality risk score in primary prevention implantable cardioverter defibrillator recipients with non-ischaemic or ischaemic heart disease.

AIMS To assess survival and to construct a baseline mortality risk score in primary prevention implantable cardioverter defibrillator (ICD) patients with non-ischaemic or ischaemic heart disease. METHODS AND RESULTS Since 1996, data of all consecutive patients who received an ICD system in the Leiden University Medical Center were collected and assessed at implantation. For the current study, all 1036 patients [age 63 (SD 11) years, 81% male] with a primary indication for defibrillator implantation were evaluated and followed for 873 (SD 677) days. During follow-up, 138 patients (13%) died. Non-ischaemic and ischaemic patients demonstrated similar survival but exhibited different factors that influence risk for mortality. A risk score, consisting of simple baseline variables could stratify patients in low, intermediate, and high risk for mortality. In non-ischaemic patients, annual mortality was 0.4% (95% CI 0.0-2.2%) in low risk and 9.4% (95% CI 6.6-13.1%) in high risk patients. In ischaemic patients, mortality was 1.0% (95% CI 0.2-3.0%) in low risk and 17.8% (95% CI 13.6-22.9%) in high risk patients. CONCLUSION Utilization of an easily applicable baseline risk score can create an individual patient-tailored estimation on mortality risk to aid clinicians in daily practice.
COMA server for protein distant homology search

SUMMARY Detection of distant homology is a widely used computational approach for studying protein evolution, structure and function. Here, we report a homology search web server based on sequence profile-profile comparison. The user may perform searches in one of several regularly updated profile databases using either a single sequence or a multiple sequence alignment as an input. The same profile databases can also be downloaded for local use. The capabilities of the server are illustrated with the identification of new members of the highly diverse PD-(D/E)XK nuclease superfamily. AVAILABILITY http://www.ibt. lt/bioinformatics/coma/
In response to your inquiry Automatic E-mail Answer Suggestion in a Dutch Contact Centre

In the past years, the number of service requests through e-mail has shown an explosive growth. To cope with the increased numbers of received e-mails, current call centres are “transformed” into so-called contact centres, handling both e-mail and telephone calls. Personal answering (each e-mail is written again by an agent) costs way too much, so most companies use a set of predefined answers that cover most of the e-mail service requests. Incoming e-mails are analysed, where after a set of (maximal) 10 possible answers is presented to the agent. If the selection is successful, writing an answer is replaced by selecting the correct (predefined) answer. Because this selection process works much faster, the number of e-mails that can be handled increases significantly. This is true, as long as the correct answer is presented within the set of suggested answers. If not, the agent has to find the correct answer by typing in those keywords that lead to the right set of suggestions: a time and money consuming process. Therefore, the focus of this study is on the “improvement of relevant answer suggestions”. We try to tackle the answer suggestion problem by transforming the incoming e-mail (the raw question) into a normalized question (uniform way of writing, removal of non-information words, etc.). This normalized question will be classified as belonging to one or more classes (each class has one predefined answer). In this thesis we present two classification techniques (known from regular text classification problems) and apply them to a corpus of 17,000 e-mails collected and classified in a Dutch contact centre. The classification techniques are adjusted in such a way that the implemented application can present a ranked list of relevant categories (representing the answer suggestions) for each incoming e-mail. We will show that both classification techniques are very suitable for automatic answer suggestion in a contact centre: our best method is able to present the correct answer within a ranked list of 5 possible answers, for almost 85% of all incoming e-mails. Moreover, we will show that applying language technology as an advanced text normalization step, may improve the classification accuracy with another 3 percentage points. This brings the final classification accuracy to approximately 88%, which more than doubles the performance of the keyword based system as currently used by the principal of this research: Em@ilco. Finally, we will discuss the possibilities of completely auto-answering incoming e-mails: the ultimate dream of each contact centre manager. Although the results are not “good enough”, for unsupervised auto-answering, our 60%-first-answer-right-result is quite promising. If combined with reliable confidence scores (something out of the scope of this research), the proposed methods can be used to automatically answer incoming e-mails (at least in out-of-office hours).