Miracle-dz/UniFAR-FTUs huggingface dataset:
Attachment site recognition and regulation of directionality by the serine integrases

Serine integrases catalyze the integration of bacteriophage DNA into a host genome by site-specific recombination between ‘attachment sites’ in the phage (attP) and the host (attB). The reaction is highly directional; the reverse excision reaction between the product attL and attR sites does not occur in the absence of a phage-encoded factor, nor does recombination occur between other pairings of attachment sites. A mechanistic understanding of how these enzymes achieve site-selectivity and directionality has been limited by a lack of structural models. Here, we report the structure of the C-terminal domains of a serine integrase bound to an attP DNA half-site. The structure leads directly to models for understanding how the integrase-bound attP and attB sites differ, why these enzymes preferentially form attP × attB synaptic complexes to initiate recombination, and how attL × attR recombination is prevented. In these models, different domain organizations on attP vs. attB half-sites allow attachment-site specific interactions to form between integrase subunits via an unusual protruding coiled-coil motif. These interactions are used to preferentially synapse integrase-bound attP and attB and inhibit synapsis of integrase-bound attL and attR. The results provide a structural framework for understanding, testing and engineering serine integrase function.
Toward cloud computing QoS architecture: analysis of cloud systems and cloud services

Cloud can be defined as a new computing paradigm that provides scalable, on-demand, and virtualized resources for users. In this style of computing, users can access a shared pool of computing resources which are provisioned with minimal management efforts of users. Yet there are some obstacles and concerns about the use of clouds. Guaranteeing quality of service U+0028 QoS U+0029 by service providers can be regarded as one of the main concerns for companies tending to use it. Service provisioning in clouds is based on service level agreements representing a contract negotiated between users and providers. According to this contract, if a provider cannot satisfy its agreed application requirements, it should pay penalties as compensation. In this paper, we intend to carry out a comprehensive survey on the models proposed in literature with respect to the implementation principles to address the QoS guarantee issue.
Incremental Learning for Fully Unsupervised Word Segmentation Using Penalized Likelihood and Model Selection

We present a novel incremental learning approach for unsupervised word segmentation that combines features from probabilistic modeling and model selection. This includes super-additive penalties for addressing the cognitive burden imposed by long word formation, and new model selection criteria based on higher-order generative assumptions. Our approach is fully unsupervised; it relies on a small number of parameters that permits flexible modeling and a mechanism that automatically learns parameters from the data. Through experimentation, we show that this intricate design has led to top-tier performance in both phonemic and orthographic word segmentation.
Chronic graft‐versus‐host reaction is associated with a decrease in Ig light chain receptor editing in bone marrow self‐reactive B cells

The encounter of developing B cells in the bone marrow with soluble hen egg lysozyme (sHEL) self antigen induces anergy and endogenous κ light chain rearrangements (‘receptor editing’). We have previously shown that induction of chronic graft‐versus‐hostreaction (GVH) in tolerant Ig/sHEL mice results in prevention of B cell anergy in the bone marrow and the spleen. We now report that in chronic GVH, immature self‐reactive B cells also show reduced levels of receptor editing in the bone marrow. This is evidenced by the following observations: (a) a small population of‘receptor‐edited’ B cells, which is found in tolerant mice, is markedly reduced in mice that have lost tolerance in chronic GVH; (b) self‐reactive B cells in GVH mice have reduced levels of endogenous κ chain rearrangements; and (c) recombinase‐activating gene (RAG)‐2 expression is markedly decreased in immature self‐reactive B cells in the bone marrow of chronic GVH mice. These results suggest that in chronic GVH newly emerging B cells escape tolerance, in part because of decreased receptor editing in the bone marrow. Thus, the autoimmunity induced by chronic GVH may ultimately result from the failure of B cell tolerance at multiple checkpoints.
Succession‐induced trait shifts across a wide range of NW European ecosystems are driven by light and modulated by initial abiotic conditions

1. For truly predictive community ecology, it is essential to understand the interplay between species traits, their environment and their impacts on the composition of plant communities. These interactions are increasingly understood for various environmental drivers, but our understanding of how traits, in general, change during succession is still modest. We hypothesize that (initial) abiotic conditions other than light drive the successional dynamics of other traits. The idea that different initial abiotic conditions lead to different trait trajectories during succession was predicted long ago but has never been tested for traits.
Efficacy of common antiseptics against multidrug-resistant Mycobacterium tuberculosis.

OBJECTIVES The incidence of infections caused by multidrug-resistant strains of Mycobacterium tuberculosis (MDR-TB) has been increasing. Antiseptics are frequently used to prevent mycobacterial infection. The aim of this study was to determine those antiseptics that are useful against MDR-TB. DESIGN We evaluated bactericidal activity against clinical isolates of MDR-TB in vitro. METHOD Thirteen strains of MDR-TB were tested against povidone-iodine (PVP-I), cresol, akyldiaminoethyl glycine hydrocloride (AEG), and glutaraldehyde. After bacilli were exposed to the antiseptic solution with 2% human serum, the disinfectant was inactivated by addition of neutraliser. RESULTS PVP-1 at a final concentration of 0.2% killed all of the strains within 120 seconds, and PVP-I at 0.1% killed 99.9% or more bacilli within 60 seconds. Most strains were killed after exposure to 0.5% cresol at 300 seconds and to 1.0% cresol at 60 seconds; 3.0% cresol killed all bacilli within 120 seconds, while 0.1%, 0.2%, and 0.5% AEG all required 60 minutes to kill 99.9% or more of the bacilli; 2.0% glutaraldehyde required 10 minutes to kill all bacilli. CONCLUSION The bactericidal activities of antiseptics for MDR-TB were similar to those for drug-sensitive M. tuberculosis strains. PVP-I would be a useful antiseptic against MDR-TB. The bactericidal activities of glutaraldehyde are effective against MDR-TB as an antiseptic for medical equipment.
Performance of routine Helicobacter pylori tests in patients with atrophic gastritis.

BACKGROUND Decreased density of H. pylori in atrophic gastritis may lead to low sensitivity of the routine tests. AIMS To evaluate the accuracy of routinely used H. pylori tests in atrophic gastritis. METHODS We compared 5 H. pylori diagnostic tests in 119 dyspeptic patients (28 males/91 females) with a mean age of 67 years (range 55-84). Patients with gastric cancer, peptic ulcer, previous gastric surgery, or those who have received eradication therapy were excluded. The following tests were performed: histology, rapid urease test (RUT), culture, 13C- urea breath tests (UBT), and H.pylori IgG/IgA antibody test (serology). RESULTS Atrophic gastritis was diagnosed in 26.1% of the patients; H. pylori was present in 87.1%. In the group with atrophy, the sensitivity, specificity, positive predictive value, negative predictive value and overall accuracy were as follows: histology (100% for all parameters); UBT (96; 100; 100; 80; 97%); serology (96; 50; 93; 67; 90%); culture (96; 100; 100; 80; 97%); and RUT (78; 100; 100; 40; 81%), respectively. CONCLUSIONS Histology, UBT and culture were the three best tests for diagnosing H. pylori infection. We cannot recommend using serology as a single test in a case of atrophy, but it would be reasonable to combine serology with one of the above tests.
Optimization of PSAM for diversity 16-QAM

We consider pilot symbol assisted modulation (PSAM) implemented with a sinc interpolator. The sensitivity of the error rate performance to different window functions applied to the sinc interpolator is investigated. The BER's for diversity M-ary quadrature amplitude modulation (MQAM) with different window functions applied to the sinc interpolator are compared. The Kaiser window is found superior to the other windows considered. A thorough discussion of the dependency of the BER performance on the symbol location is also given.
Automated texture registration and stitching for real world models

A system is presented which automatically registers and stitches textures acquired from multiple photographic images onto the surface of a given corresponding 3D model. Within this process the camera position, direction and field of view must be determined for each of the images. For this registration, which aligns a 2D image to a 3D model we present an efficient hardware-accelerated silhouette-based algorithm working on different image resolutions that accurately registers each image without any user interaction. Besides the silhouettes, the given texture information can be used to improve accuracy by comparing one stitched texture to already registered images resulting in a global multi-view optimization. After the 3D-2D registration for each part of the 3D model's surface the view is determined which provides the best available texture. Textures are blended at the borders of regions assigned to different views.
Rapid computation of sodium bioscales using gpu‐accelerated image reconstruction

Quantitative sodium magnetic resonance imaging permits noninvasive measurement of the tissue sodium concentration (TSC) bioscale in the brain. Computing the TSC bioscale requires reconstructing and combining multiple datasets acquired with a non‐Cartesian acquisition that highly oversamples the center of k‐space. Even with an optimized implementation of the algorithm to compute TSC, the overall processing time exceeds the time required to collect data from the human subject. Such a mismatch presents a challenge for sustained sodium imaging to avoid a growing data backlog and provide timely results. The most computationally intensive portions of the TSC calculation have been identified and accelerated using a consumer graphics processing unit (GPU) in addition to a conventional central processing unit (CPU). A recently developed data organization technique called Compact Binning was used along with several existing algorithmic techniques to maximize the scalability and performance of these computationally intensive operations. The resulting GPU+CPU TSC bioscale calculation is more than 15 times faster than a CPU‐only implementation when processing 256 × 256 × 256 data and 2.4 times faster when processing 128 × 128 × 128 data. This eliminates the possibility of a data backlog for quantitative sodium imaging. The accelerated quantification technique is suitable for general three‐dimensional non‐Cartesian acquisitions and may enable more sophisticated imaging techniques that acquire even more data to be used for quantitative sodium imaging. © 2013 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 23, 29–35, 2013.
Autosensitization as a Pathomechanism in Asthma

Abstract: Recent observations indicate that autoimmune disorders and allergies are more closely connected to each other than traditionally considered. Both diseases are characterized by a break of immunological tolerance and in both Th1‐ and Th2‐driven mechanisms may be involved. Moreover, patients suffering from severe chronic atopic diseases have been shown to develop autoreactive antibodies and vice versa autoreactive IgE antibodies may contribute to the perpetuation of allergic immune responses. However, animal models for the investigation of the underlying mechanisms have not been available so far. Here we demonstrate that allergic sensitization and subsequent airway aerosol challenge of mice to a potential autoantigen leads to an allergic airway inflammation and chronic exposure of sensitized mice to a foreign allergen induces autoreactive antibodies. Thus, autoreactive immune mechanisms may be induced either by molecular mimicry or as a consequence of chronic allergic inflammatory processes and these reactivities may then possibly contribute to the perpetuation of allergic immune responses even in the absence of exogenous allergens and to the development of autoimmune diseases.
Online-rating prediction based on an improved opinion spreading approach

Recommender systems are significantly useful to reduce information explosion nowadays. In order to design an optimized algorithm, we develop an improved opinion spreading approach to predict online rating of recommender systems. The proposed method provides a solution to zero-value problems of similarity results, which is ignored in existing publications. The proposed method could produce a more precise rating prediction for each unrated user-item pair. In our work, the similarity of items is defined as the number of corresponding reviews which a user has given and the differences between those viewpoints spreading in network model. Using Movie-lens data set, experiments confirm that the presented algorithm has better performance than both collaborative filtering algorithm based on Pearson correlation coefficient and the original opinion spreading approach. Our approach produces a mean absolute error (MAE) 2.1% lower and root mean square error (RMSE) 2.5% lower than existing algorithms, which indicates a higher accuracy score.
Is regularization unnecessary for boosting?

Boosting algorithms are often observed to be resistant to over tting, to a degree that one may wonder whether it is harmless to run the algorithms forever, and whether regularization in on way or another is unnecessary [see, e.g., Schapire (1999); Friedman, Hastie and Tibshirani (1999); Grove and Schuurmans (1998); Mason, Baxter, Bartlett and Frean (1999)]. One may also wonder whether it is possible to adapt the boosting ideas to regression, and whether or not it is possible to avoid the need of regularization by just adopting the boosting device.
Direct estimation of regional kinetic rate constant distributions from PET sinograms and correction of statistical estimation error distributions

We present a novel method to estimate the variation of kinetic model parameters directly from sinogram time series data. We determine the kinetic parameters independently for each voxel of the target through mmriimim likelihood estimation. The maximum likelihood estimates in the region of interest are collected into histograms. The histograms contain estimation error, which obeys maximum likelihood theory. We determine the error distribution through repeated estimation with a simulated homogeneous target With simulated sinogram time series data we evaluate the method's performance with the 2K-model and the 3K-model. The results show that after error correction both the mean and the deviation can be obtained with good accuracy from the histograms.
168 GHz dynamic frequency divider in SiGe:C bipolar technology

This paper presents a dynamic frequency divider operating up to a maximum frequency of 168 GHz. The circuit is based on a first regenerative divider stage which is followed by a static divider and an output buffer. With a supply voltage of 4 V the circuit, including both divider stages and the output buffer, consumes 320mW (105mW in the regenerative divider) and operates up to a maximum frequency of 168 GHz. With a reduced supply voltage of 3.3V a maximum operating frequency of 156 GHz is achieved at a power consumption of only 205 mW. The circuit is manufactured in a SiGe:C bipolar process with a cut-off frequency fT of 215 GHz.
Parallel analysis for lightweight network incident detection using nonlinear adaptive systems

The rapid increasing of security incidents imposes a great burden on Internet users and system administrators. In this paper we discuss a parallel analysis for lightweight network incident detection using nonlinear adaptive systems. We run AID (anomaly intrusion detection) and MID (misuse intrusion detection) systems in parallel. Two detectors generate binary output misuse = {YES/NO} and anomaly = {YES/NO}. Then, we can determine whether we need to perform network or security operation. We apply clustering algorithm for AID and classification algorithm for MID. The nonlinear adaptive system is trained for running MID and AID in parallel. Proposed parallel system is more lightweight and simple to operate even if the number of incident patterns is increased. Experimental results in the case where false positive is frequently caused show that our method is functional with a recognition rate of attacks less than 10%, while finding the anomaly status. Also, performance evaluation show that proposed system can work with reasonable CPU utilization compared with conventional serial search based system.
Starving for Salvation: The Spiritual Dimensions of Eating Problems Among American Girls and Women

In recent years, eating disorders among American girls and women have become a subject of national concern. Conventional explanations of eating problems are usually framed in the language of psychology, medicine, feminism, or sociology. Although they differ in theory and approach, these interpretations are linked by one common assumption-that female preoccupation with food and body is an essentially secular phenomenon. In Starving for Salvation, Michelle Lelwica challenges traditional theories by introducing and exploring the spiritual dimensions of anorexia, bulimia, and related problems. Drawing on a range of sources that include previously published interviews with sufferers of eating disorders, Lelwica claims that girls and women starve, binge, and purge their bodies as a means of coping with the pain and injustice of their daily lives. She provides an incisive analysis of contemporary American culture, arguing that our dominant social values and religious legacies produce feelings of emptiness and dissatisfaction in girls and women. Trapped in a society that ignores and denies their spiritual needs, girls and women construct a network of symbols, beliefs, and rituals around food and their bodies. Lelwica draws a parallel between the patriarchal legacy of Christianity, which associates women with sin and bodily cravings, and the cultural preference for a thin female body. According to Lelwica, these complimentary forces form a popular salvation myth that encourages girls and women to fixate on their bodies and engage in disordered eating patterns. While this myth provides a sense of meaning and purpose in the face of uncertainty and injustice, Lelwica demonstrates that such rigid and unhealthy devotion to the body only deepens the spiritual void that women long to fill. Although Lelwica presents many disturbing facts about the origins of eating disorders, she also suggests positive ways that our society can nourish the creative and spiritual needs of girls and women. The first step, however, is to acknowledge that female preoccupation with thinness and food signifies a strong desire for fulfillment. Until we recognize and contest the religious legacies and cultural values that perpetuate eating disorders, many women will continue to turn to the most accessible symbolic and ritual resources available to them-food and their bodies-in an attempt to satiate their profound spiritual hunger.
EFFECTS OF ENDOTOXIN ON THE GUINEA PIG HEART RESPONSE TO ISCHEMIA REPERFUSION INJURY

ABSTRACT Ischemia causes significant damage to the heart as manifested by decreases in ventricular performance. Several different methods have been shown to protect the heart from ischemic injury–one is operative over a short period (an hour) and the other over longer periods (a day). The latter form of protection has been demonstrated in rats after induction of Gram-negative sepsis or administration of endotoxin or cytokines. In the present study we determined whether guinea pigs would also show induction of cardiac protection subsequent to a dose of endotoxin. Male guinea pigs were injected with 1 mg of endotoxin and studied the following day. Hearts were perfused at a constant perfusion pressure and studied in an isovolumic mode. Left ventricular developed pressure was significantly lower in the endotoxin-treated group than in the control group. After 35 min of total ischemia and 25 min of reperfusion, recovery of left ventricular developed pressure was complete in the endotoxin group but significantly decreased in the control group such that after ischemia and reperfusion, there was no significant difference in left ventricular performance between the two groups. Coronary flow was significantly greater in the endotoxin group than in the control group both prior to and after ischemia. Hearts from endotoxin-treated guinea pigs resumed spontaneous contractile activity sooner and released less lactate upon reperfusion than did the control group. Thus prior treatment of guinea pigs with endotoxin resulted in depression of the isolated heart but also resulted in protection of the isolated heart from further damage due to ischemia/reperfusion injury.
Somatic and autonomic regulation in sleep : physiological and clinical aspects

Indice. - I Biochemistry, Metabolism and Physiology of Sleep. - 1 Biochemical Approach to the Wake-Sleep Cycle. - 2 Regulation of Cerebral and Extracerebral Circulation During the Wake-Sleep Cycle. - 3 Effects of Systemic Circulation on Hypothalamic Temperature in the Behavioural States of Sleep. - II Pathophysiological Aspects of Human Sleep. - 4 Circadian Rhythm of Body Core Temperature in Neurodegenerative Diseases. - 5 Descriptive Epidemiology of Excessive Daytime Sleepiness. - 6 Breathing Disorders and Sleep. - 7 Disorders of Motor Control and Sleep. - 8 The Syndrome of Nocturnal Frontal Lobe Epilepsy.