Miracle-dz/UniFAR-FTUs huggingface dataset:
Sup35 methionine oxidation is a trigger for de novo [PSI+] prion formation

ABSTRACT. The molecular basis by which fungal and mammalian prions arise spontaneously is poorly understood. A number of different environmental stress conditions are known to increase the frequency of yeast [PSI+] prion formation in agreement with the idea that conditions which cause protein misfolding may promote the conversion of normally soluble proteins to their amyloid forms. A recent study from our laboratory has shown that the de novo formation of the [PSI+] prion is significantly increased in yeast mutants lacking key antioxidants suggesting that endogenous reactive oxygen species are sufficient to promote prion formation. Our findings strongly implicate oxidative damage of Sup35 as an important trigger for the formation of the heritable [PSI+] prion in yeast. This review discusses the mechanisms by which the direct oxidation of Sup35 might lead to structural transitions favoring conversion to the transmissible amyloid-like form. This is analogous to various environmental factors which have been proposed to trigger misfolding of the mammalian prion protein (PrPC) into the aggregated scrapie form (PrPSc).
Impact of 18F-FDG PET/CT with Retrograde Filling of the Urinary Bladder in Patients with Suspected Pelvic Malignancies

The purpose of this study was to assess the feasibility of selective pelvic PET/CT with retrograde bladder irrigation in evaluating pelvic pathologies. Methods: Thirty-eight patients (22 women and 16 men), with a mean age of 61 y (range, 41–81 y) and a neoplastic background (most of them of pelvic pathology), were assessed with PET/CT. The most prevalent findings were urothelial (14 cases), gynecologic (12 cases), and rectal (7 cases) cancers. All but 3 patients had undergone previous surgical procedures or radio- or chemotherapy. Twenty-two patients had suspected pelvic pathology on a previous diagnostic CT scan. All the patients underwent a standard PET/CT protocol (from head to upper thighs) 60 min after the intravenous injection of 370 MBq of 18F-FDG. Additional delayed pelvic PET/CT images were acquired with a filled-bladder technique. Both series of images were assessed by 2 experienced observers. A lesion was classified as malignant if it showed a standardized uptake value greater than 2.5 or, in the case of subcentimetric lesions, any uptake greater than background activity that persisted or increased on delayed pelvic imaging. All lesions were evaluated histologically or by clinical follow-up. Results: Twenty-seven of 43 studies were categorized as pathologic using PET/CT. Nineteen studies showed abnormalities in the pelvis; the findings of 5 of these studies were false-positive. Ten studies showed pathologic 18F-FDG uptake in the bladder wall; in 7 of these studies the uptake was found to be true-positive on histopathologic examination. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of PET/CT in the pelvic assessment were 100%, 83%, 74%, 100%, and 76%, respectively. The retrograde filling reduced the interference with physiologic urinary accumulation of 18F-FDG in patients with possible pelvic lesions; no false-negative results were documented. Conclusion: In 18F-FDG PET studies, retrograde filling of the urinary bladder is recommended to assess bladder wall lesions and malignancies in other pelvic locations.
Introduction to the Special Issue on Software Architecture

A critical aspect of the design for any large software system is its gross structure represented as a high-level organization of computational elements and interactions between those elements. Broadly speaking, this is the software architectural level of design 11, 22. The structure of software has long been recognized as an important issue of concern e.g., 33, 44. However, recently software architecture has begun to emerge as an explicit eld of study for software engineering practitioners and researchers. Evidence of this trend is apparent in a large body of recent w ork in areas such as module interface languages, domain speciic architectures, architectural description languages, design patterns and handbooks, formal underpinnings for architectural design, and architectural design environments. What exactly do we mean by the term software archi-tecture? " As one might expect of a eld that has only recently emerged as an explicit focus for research and development , there is currently no universally-accepted definition. Moreover, if we look at the common uses of the term architecture" in software, we nd that it is used in quite diierent w a ys, often making it diicult to understand what aspect is being addressed. Among the various uses are a the architecture of a particular system, as in the architecture of this system consists of the following components ," b an architectural style, as in this system adopts a client-server architecture," and c the general study of architecture, as in the papers in this journal are about architecture. " Within software engineering, most uses of the term software architecture" focus on the rst of these interpretations. Typical of these is the following deenition which was developed in a a software architecture discussion group at the SEI in 1994. The structure of the components of a pro-grammsystem, their interrelationships, and principles and guidelines governing their design and evolution over time. As deenitions go, this is not a bad starting point. But deenitions such as this tell only a small part of the story. More important than such explicit deenitions, is the locus of eeort in research and development that implicitly has come to deene the eld of software architecture. To clarify the nature of this eeort it is helpful to observe that the recent emergence of interest in software architecture has been prompted by t w o distinct trends. The rst is the recognition that over the years designers have begun to develop a shared …
A Continuum of Models for Stochastic Estimation 20 June 2000

In this paper, we investigate a recursive multiple model tracking approach similar to the Generalized Pseudo–Bayesian 1 (GPB1) [1] approach. However, here we consider a continuum of models rather than the discrete set that is usually implemented in the GPB1 method. By doing so better models are available to improve tracker performance and solve the bias problem inherent in most multiple model approaches.
An Improved Strategy for the Evaluation of Cloud Parameterizations in GCMS

The parameterization schemes used to represent clouds in general circulation models have significantly evolved in their complexity over the last 10 yr. This increases the demand for a thorough evaluation of their performance. Several techniques ranging from the evaluation of the model climate to single column modeling have been proposed for that purpose. This paper aims to provide a strategy for an improved, more coherent use of these techniques. An overview of the different techniques is given using examples from the evaluation of the global model of the European Centre for Medium-Range Weather Forecasts. Advantages and disadvantages of the individual methods are highlighted. The paper closes by proposing a strategy to join the different techniques into a coherent procedure of cloud parameterization evaluation.
Hospital-Based Clinical Implications of the Novel Oral Anticoagulant, Dabigatran Etexilate, in Daily Practice

Abstract Dabigatran etexilate is an oral direct thrombin inhibitor that has been approved by the US Food and Drug Administration for the prevention of stroke and systemic embolization in patients with nonvalvular atrial fibrillation. It has also been studied for the prevention of venous thromboembolism in patients after hip and knee arthroplasty and for treatment of venous thromboembolism. Although routine laboratory monitoring is not needed, there are clinical scenarios in which physicians will need to have a clear understanding of drug pharmacology, laboratory assessment, and reversibility of this drug to make appropriate clinical decisions. We review the pharmacology of dabigatran etexilate, pertinent clinical trials, and the effects of dabigatran etexilate on prothrombin time, activated partial thromboplastin time, thrombin time, and ecarin clotting time. We also provide an approach to patients on dabigatran etexilate who are bleeding, have a suspected therapeutic failure, or require periprocedural management.
Closed loop stability controls for s-aloha satellite communications

S-ALOHA channels are intrinsically unstable and must be equipped with proper controls. The function of the controls is to dynamically adjust the ALOHA channel transmission gates in accordance with the dynamic load fluctuations. The purpose of the controls is to protect the channel from unstable behavior while optimizing channel efficiency and performance during normal operating conditions. Two control algorithms are proposed: the Closed Loop Control-Collision Detect (CLC-CD) algorithm, which assumes the capability of distinguishing collision slots from empty slots at the receiving station; and the Closed Loop Control-Collision Non-Detect (CLC-CND) algorithm, which does not require such capability. The control implementation is distributed among all stations. Channel stability and efficiency is achieved by driving the total transmission and retransmission rate to unity, using a feedback, closed loop control approach. A family of simulation runs was made to evaluate and compare the performance of the CLC schemes with that of other schemes in a variety of traffic conditions. Simulation results show that the controlled systems converge to near optimality at steady state. Futhermore, the performance of the CLC-CND algorithms is about equivalent to that of the CLC-CD algorithm, thus indicating that the requirement of distinguishing collisions from empty slots is not critical for the performance of closed loop controls. The stability properties of the CLC algorithms and their superiority over other schemes for varying load patterns are demonstrated in a series of experiments involving cyclic traffic patterns and pulse patterns. The CLC scheme displays better performance than the uncontrolled schemes as well as the previously proposed control schemes (namely, the Control Limit scheme and the Retransmission Control scheme) even when the latter are specifically tuned to handle the traffic pattern under consideration (the CLC scheme does not require any prior setting of the parameters).
Open Access Research Article Identification of Symptom and Functional Domains That Fibromyalgia Patients Would like to See Improved: a Cluster Analysis

Background: The purpose of this study was to determine whether some of the clinical features of fibromyalgia (FM) that patients would like to see improved aggregate into definable clusters. Methods: Seven hundred and eighty-eight patients with clinically confirmed FM and baseline pain ≥40 mm on a 100 mm visual analogue scale ranked 5 FM clinical features that the subjects would most like to see improved after treatment (one for each priority quintile) from a list of 20 developed during focus groups. For each subject, clinical features were transformed into vectors with rankings assigned values 1-5 (lowest to highest ranking). Logistic analysis was used to create a distance matrix and hierarchical cluster analysis was applied to identify cluster structure. The frequency of cluster selection was determined, and cluster importance was ranked using cluster scores derived from rankings of the clinical features. Multidimensional scaling was used to visualize and conceptualize cluster relationships. Results: Six clinical features clusters were identified and named based on their key characteristics. In order of selection frequency, the clusters were Pain (90%; 4 clinical features), Fatigue (89%; 4 clinical features), Domestic (42%; 4 clinical features), Impairment (29%; 3 functions), Affective (21%; 3 clinical features), and Social (9%; 2 functional). The "Pain Cluster" was ranked of greatest importance by 54% of subjects, followed by Fatigue, which was given the highest ranking by 28% of subjects. Multidimensional scaling mapped these clusters to two dimensions: Status (bounded by Physical and Emotional domains), and Setting (bounded by Individual and Group interactions). Affective, and Social) based on patient perception of relevance to treatment. Furthermore, these 6 clusters could be charted in the 2 dimensions of Status and Setting, thus providing a unique perspective for interpretation of FM symptomatology. Background Chronic widespread pain is the primary characteristic of FM. Its presence is the essential feature of the current American College of Rheumatology guidelines for the classification of FM [1] and it is the best understood feature of this syndrome [2,3]. In addition to pain, FM patients typically exhibit a number of co-morbidities that limit productivity, personal and family life, and activities of daily living [4-8]. These comorbidities may include fatigue, sleep disturbance, mood disorders, cognitive
The CRFs-Based Chinese Open Entity Relation Extraction

With the rapid development of the Internet, massive Internet text data has brought new opportunities and challenges to the research of entity relation extraction. Open entity relation extraction overcomes the shortage of traditional methods, that relation types need to be predefined and plenty of training data need to be labeled in advance. A lot of work have been done for English Open ERE, and now the Chinese Open ERE is attracting more and more researchers and scholars. This paper presents a novel CRFs-Based Semi-Supervised Chinese Open Entity Relation Extraction method-C-COERE. C-COERE combines the CRFs and the syntax parse tree to extract the entity relation tuples. Then it improves the accuracy of the extracted results through a post-processing filter module. Meanwhile, it enhances the recall of the extracted results by exploiting the duality of patterns and tuples. Experiments on real dataset show that the C-COERE method has achieved good effect.
Using Unmanned Aerial Vehicles (UAV) to Quantify Spatial Gap Patterns in Forests

Gap distributions in forests reflect the spatial impact of man-made tree harvesting or naturally-induced patterns of tree death being caused by windthrow, inter-tree competition, disease or senescence. Gap sizes can vary from large (>100 m2) to small (<10 m2), and they may have contrasting spatial patterns, such as being aggregated or regularly distributed. However, very small gaps cannot easily be recorded with conventional aerial or satellite images, which calls for new and cost-effective methodologies of forest monitoring. Here, we used an unmanned aerial vehicle (UAV) and very high-resolution images to record the gaps in 10 temperate managed and unmanaged forests in two regions of Germany. All gaps were extracted for 1-ha study plots and subsequently analyzed with spatially-explicit statistics, such as the conventional pair correlation function (PCF), the polygon-based PCF and the mark correlation function. Gap-size frequency was dominated by small gaps of an area <5 m2, which were particularly frequent in unmanaged forests. We found that gap distances showed a variety of patterns. However, the polygon-based PCF was a better descriptor of patterns than the conventional PCF, because it showed randomness or aggregation for cases when the conventional PCF showed small-scale regularity; albeit, the latter was only a mathematical artifact. The mark correlation function revealed that gap areas were in half of the cases negatively correlated and in the other half independent. Negative size correlations may likely be the result of single-tree harvesting or of repeated gap formation, which both lead to nearby small gaps. Here, we emphasize the usefulness of UAV to record forest gaps of a very small size. These small gaps may originate from repeated gap-creating disturbances, and their spatial patterns should be monitored with spatially-explicit statistics at recurring intervals in order to further insights into forest dynamics.
Heterogeneous feature machines for visual recognition

With the recent efforts made by computer vision researchers, more and more types of features have been designed to describe various aspects of visual characteristics. Modeling such heterogeneous features has become an increasingly critical issue. In this paper, we propose a machinery called the Heterogeneous Feature Machine (HFM) to effectively solve visual recognition tasks in need of multiple types of features. Our HFM builds a kernel logistic regression model based on similarities that combine different features and distance metrics. Different from existing approaches that use a linear weighting scheme to combine different features, HFM does not require the weights to remain the same across different samples, and therefore can effectively handle features of different types with different metrics. To prevent the model from overfitting, we employ the so-called group LASSO constraints to reduce model complexity. In addition, we propose a fast algorithm based on co-ordinate gradient descent to efficiently train a HFM. The power of the proposed scheme is demonstrated across a wide variety of visual recognition tasks including scene, event and action recognition.
Efficient FPGA implementation of probabilistic gallager B LDPC decoder

This paper presents the performance evaluation of the Probabilistic Gallager B (PGaB), a hard decision message passing Low Density Parity Check (LDPC) Decoder, with respect to the soft decision based decoders MinSum (MS) and Offset-MinSum (OMS). PGaB algorithm relies on introducing deliberate and controlled randomness to some of the exchanged messages of the GaB decoder such that it is able to escape from local minima associated with dominant trapping sets. We show that PGaB delivers higher decoding throughput than soft decision based decoders MS and OMS while using much fewer amount of Field Programmable Gate Array (FPGA) resources. Our Monte-Carlo simulation results show that the decoding performance of the PGaB on Binary Symmetric Channel (BSC) is far better than the deterministic GaB and very close to MS and OMS performances especially in error floor region.
Long-term colorectal-cancer incidence and mortality after lower endoscopy.

BACKGROUND Colonoscopy and sigmoidoscopy provide protection against colorectal cancer, but the magnitude and duration of protection, particularly against cancer of the proximal colon, remain uncertain. METHODS We examined the association of the use of lower endoscopy (updated biennially from 1988 through 2008) with colorectal-cancer incidence (through June 2010) and colorectal-cancer mortality (through June 2012) among participants in the Nurses' Health Study and the Health Professionals Follow-up Study. RESULTS Among 88,902 participants followed over a period of 22 years, we documented 1815 incident colorectal cancers and 474 deaths from colorectal cancer. With endoscopy as compared with no endoscopy, multivariate hazard ratios for colorectal cancer were 0.57 (95% confidence interval [CI], 0.45 to 0.72) after polypectomy, 0.60 (95% CI, 0.53 to 0.68) after negative sigmoidoscopy, and 0.44 (95% CI, 0.38 to 0.52) after negative colonoscopy. Negative colonoscopy was associated with a reduced incidence of proximal colon cancer (multivariate hazard ratio, 0.73; 95% CI, 0.57 to 0.92). Multivariate hazard ratios for death from colorectal cancer were 0.59 (95% CI, 0.45 to 0.76) after screening sigmoidoscopy and 0.32 (95% CI, 0.24 to 0.45) after screening colonoscopy. Reduced mortality from proximal colon cancer was observed after screening colonoscopy (multivariate hazard ratio, 0.47; 95% CI, 0.29 to 0.76) but not after sigmoidoscopy. As compared with colorectal cancers diagnosed in patients more than 5 years after colonoscopy or without any prior endoscopy, those diagnosed in patients within 5 years after colonoscopy were more likely to be characterized by the CpG island methylator phenotype (CIMP) (multivariate odds ratio, 2.19; 95% CI, 1.14 to 4.21) and microsatellite instability (multivariate odds ratio, 2.10; 95% CI, 1.10 to 4.02). CONCLUSIONS Colonoscopy and sigmoidoscopy were associated with a reduced incidence of cancer of the distal colorectum; colonoscopy was also associated with a modest reduction in the incidence of proximal colon cancer. Screening colonoscopy and sigmoidoscopy were associated with reduced colorectal-cancer mortality; only colonoscopy was associated with reduced mortality from proximal colon cancer. Colorectal cancer diagnosed within 5 years after colonoscopy was more likely than cancer diagnosed after that period or without prior endoscopy to have CIMP and microsatellite instability. (Funded by the National Institutes of Health and others.).
The Reconfigurable Instruction Cell Array

This paper presents a novel instruction cell-based reconfigurable computing architecture for low-power applications, thereafter referred to as the reconfigurable instruction cell array (RICA). For the development of the RICA, a top-down software driven approach was taken and revealed as one of the key design decisions for a flexible, easy to program, low-power architecture. These features make RICA an architecture that inherently solves the main design requirements of modern low-power devices. Results show that it delivers considerably less power consumption when compared to leading VLIW and low-power digital signal processors, but still maintaining their throughput performance.
Verification of low-level crypto-protocol implementations using automated theorem proving

Designing and implementing cryptographic protocols is known to be difficult. A lot of research has been devoted to developing formal techniques to analyze abstract designs of cryptographic protocols. Less attention has been paid to the verification of implementation-relevant aspects of cryptographic protocols. This is an important challenge since it is non-trivial to securely implement secure designs, because a specification by its nature is more abstract than the corresponding implementation, and the additional information may introduce attacks not present on the design level. In this paper, we address aspects of crypto protocol implementations close to the hardware level. More concretely, we consider the industrial cryptographic token interface standard PKCS 11 which defines how software on untrustworthy hardware can make use of tamper-proof hardware such as smart-cards to perform cryptographic operations on sensitive data. We propose an approach for automated security analysis with first-order logic theorem provers of crypto protocol implementations making use of this standard.
A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria

We describe a nitrogenase gene sequence database that facilitates analysis of the evolution and ecology of nitrogen-fixing organisms. The database contains 32 954 aligned nitrogenase nifH sequences linked to phylogenetic trees and associated sequence metadata. The database includes 185 linked multigene entries including full-length nifH, nifD, nifK and 16S ribosomal RNA (rRNA) gene sequences. Evolutionary analyses enabled by the multigene entries support an ancient horizontal transfer of nitrogenase genes between Archaea and Bacteria and provide evidence that nifH has a different history of horizontal gene transfer from the nifDK enzyme core. Further analyses show that lineages in nitrogenase cluster I and cluster III have different rates of substitution within nifD, suggesting that nifD is under different selection pressure in these two lineages. Finally, we find that that the genetic divergence of nifH and 16S rRNA genes does not correlate well at sequence dissimilarity values used commonly to define microbial species, as stains having <3% sequence dissimilarity in their 16S rRNA genes can have up to 23% dissimilarity in nifH. The nifH database has a number of uses including phylogenetic and evolutionary analyses, the design and assessment of primers/probes and the evaluation of nitrogenase sequence diversity. Database URL: http://www.css. cornell.edu/faculty/buckley/nifh.htm