Miracle-dz/UniFAR-FTUs huggingface dataset:
GSK-3β Homolog Rim11 and the Histone Deacetylase Complex Ume6-Sin3-Rpd3 Are Involved in Replication Stress Response Caused by Defects in Dna2

Lagging strand synthesis is mechanistically far more complicated than leading strand synthesis because it involves multistep processes and requires considerably more enzymes and protein factors. Due to this complexity, multiple fail-safe factors are required to ensure successful replication of the lagging strand DNA. We attempted to identify novel factors that are required in the absence of the helicase activity of Dna2, an essential enzyme in Okazaki-fragment maturation. In this article, we identified Rim11, a GSK-3β-kinase homolog, as a multicopy suppressor of dna2 helicase-dead mutant (dna2-K1080E). Subsequent epistasis analysis revealed that Ume6 (a DNA binding protein, a downstream substrate of Rim11) also acted as a multicopy suppressor of the dna2 allele. We found that the interaction of Ume6 with the conserved histone deacetylase complex Sin3-Rpd3 and the catalytic activity of Rpd3 were indispensable for the observed suppression of the dna2 mutant. Moreover, multicopy suppression by Rim11/Ume6 requires the presence of sister-chromatid recombination mediated by Rad52/Rad59 proteins, but not vice versa. Interestingly, the overexpression of Rim11 or Ume6 also suppressed the MMS sensitivity of rad59Δ. We also showed that the lethality of dna2 helicase-dead mutant was attributed to checkpoint activation and that decreased levels of deoxynucleotide triphosphates (dNTPs) by overexpressing Sml1 (an inhibitor of ribonucleotide reductase) rescued the dna2 mutant. We also present evidence that indicates Rim11/Ume6 works independently but in parallel with that of checkpoint inhibition, dNTP regulation, and sister-chromatid recombination. In conclusion, our results establish Rim11, Ume6, the histone deacetylase complex Sin3-Rpd3 and Sml1 as new factors important in the events of faulty lagging strand synthesis.
Design of Collimation System in Space Laser Communication

In this paper, semiconductor laser beam collimation lenses system which can be used in space laser communication has been optimum simulated and designed. Some new design methods based on the geometrical optical theory have been discussed in details, and an ideal aspheric surface design method has been given. The optical system has been further simulated by optical design software CODE-V. The collimation laser beam divergence angles have been obtained by experimental measure with laser beam analyzer. Experimental test results showed that it can be achieved a good collimation effect. This optimum design laser beam collimation system can be widely used in modern space laser communication
An exact approach to direct aperture optimization in IMRT treatment planning

We consider the problem of intensity-modulated radiation therapy (IMRT) treatment planning using direct aperture optimization. While this problem has been relatively well studied in recent years, most approaches employ a heuristic approach to the generation of apertures. In contrast, we use an exact approach that explicitly formulates the fluence map optimization (FMO) problem as a convex optimization problem in terms of all multileaf collimator (MLC) deliverable apertures and their associated intensities. However, the number of deliverable apertures, and therefore the number of decision variables and constraints in the new problem formulation, is typically enormous. To overcome this, we use an iterative approach that employs a subproblem whose optimal solution either provides a suitable aperture to add to a given pool of allowable apertures or concludes that the current solution is optimal. We are able to handle standard consecutiveness, interdigitation and connectedness constraints that may be imposed by the particular MLC system used, as well as jaws-only delivery. Our approach has the additional advantage that it can explicitly account for transmission of dose through the part of an aperture that is blocked by the MLC system, yielding a more precise assessment of the treatment plan than what is possible using a traditional beamlet-based FMO problem. Finally, we develop and test two stopping rules that can be used to identify treatment plans of high clinical quality that are deliverable very efficiently. Tests on clinical head-and-neck cancer cases showed the efficacy of our approach, yielding treatment plans comparable in quality to plans obtained by the traditional method with a reduction of more than 75% in the number of apertures and a reduction of more than 50% in beam-on time, with only a modest increase in computational effort. The results also show that delivery efficiency is very insensitive to the addition of traditional MLC constraints; however, jaws-only treatment requires about a doubling in beam-on time and number of apertures used. Finally, we showed the importance of accounting for transmission effects when assessing or, preferably, optimizing treatment plan quality.
Factorization of Synchronous Context-Free Grammars in Linear Time

Factoring a Synchronous Context-Free Grammar into an equivalent grammar with a smaller number of nonterminals in each rule enables synchronous parsing algorithms of lower complexity. The problem can be formalized as searching for the tree-decomposition of a given permutation with the minimal branching factor. In this paper, by modifying the algorithm of Uno and Yagiura (2000) for the closely related problem of finding all common intervals of two permutations, we achieve a linear time algorithm for the permutation factorization problem. We also use the algorithm to analyze the maximum SCFG rule length needed to cover hand-aligned data from various language pairs.
INEX 2011 Data-Centric Track

We report our experiment results on the INEX 2011 Data-Centric Track. We participated in both the ad hoc and faceted search tasks. On the ad hoc search task, we employ language modeling approaches to do structured object retrieval, trying to capture both the structure in data and structure in query and unify the structured and unstructured information retrieval in a general framework. However, our initial experimental results using INEX test bed show that the unstructured retrieval model performs better than structured retrieval models. On the faceted search task, we propose a simple usersimulation model to evaluate the effectiveness of a faceted search system’s recommending facet-values. We implemented the evaluation system and conducted the evaluations for the track. We also tested basic redundancy and relevance based approaches for recommending facet-values. The results show that our basic approaches of recommending facet-values perform quite well.
Depression and serum interleukin-6 levels in patients on dialysis.

BACKGROUND Depression is a common psychiatric problem in patients undergoing dialysis. Several studies have been performed to validate the association between depression and inflammation in haemodialysis patients. The levels of proinflammatory cytokines are increased in chronic renal failure patients, as in depression. The objective of this study was to compare the incidence of depression in the patients on dialysis (on hemodialysis /HD/ and on continuous ambulatory peritoneal dialysis /CAPD/), and a relationship between depression and the presence of inflammation. SUBJECTS AND METHODS 88 patients (52 on HD and 36 on CAPD) were enrolled in this study. Depressive symptoms were measured with the Beck Depression Inventory (BDI). The BDI is a 21-item self-report instrument, and the elevated symptoms of depression were defined as a BDI score ≥16. HD patients were treated with high-flux polysulphone biocompatible dialyzers and CAPD patients were treated with usual dwell time (4-6 hours during the day and 8-10 hours at night). The presence of an inflammatory state was assesded by determinations of plasma interleukin-6 (IL-6) levels. RESULTS Depression (BDI ≥16) was present in 28.4% of dialysis patients, 35% of patients on hemodialysis (HD) and 18.1% of patients on continous ambulatory peritoneal dialysis (CAPD). The BDI score was significantly lower in CAPD patients comparing to HD patients, as well as the levels of albumin, C-reactive protein (CRP) and interleukin-6 (IL-6). IL-6 serum levels were similar in patients with depression and patients without depression in the whole group, as in HD patients. In CAPD patients without depression IL-6 levels were significantly lower. CONCLUSIONS The prevalence of depression was higher in HD comparing to CAPD patients. Although IL-6 level was higher in HD compared to CAPD patients, the relationship between depression and presence of inflammation parametars were observed in CAPD, but not in HD patients.
COT: Contextual Operating Tensor for Context-Aware Recommender Systems

With rapid growth of information on the internet, recommender systems become fundamental for helping users alleviate the problem of information overload. Since contextual information can be used as a significant factor in modeling user behavior, various context-aware recommendation methods are proposed. However, the state-of-the-art context modeling methods treat contexts as other dimensions similar to the dimensions of users and items, and cannot capture the special semantic operation of contexts. On the other hand, some works on multi-domain relation prediction can be used for the context-aware recommendation, but they have problems in generating recommendation under a large amount of contextual information. In this work, we propose Contextual Operating Tensor (COT) model, which represents the common semantic effects of contexts as a contextual operating tensor and represents a context as a latent vector. Then, to model the semantic operation of a context combination, we generate contextual operating matrix from the contextual operating tensor and latent vectors of contexts. Thus latent vectors of users and items can be operated by the contextual operating matrices. Experimental results show that the proposed COT model yields significant improvements over the competitive compared methods on three typical datasets, i.e., Food, Adom and Movielens-1M datasets.
Semantic Segmentation of Urban Environments into Object and Background Categories

Abstract : Advancements in robotic navigation, object search and exploration rest to a large extent on robust, efficient and more advanced semantic understanding of the surrounding environment. Since the choice of most relevant semantic information depends on the task, it is desirable to develop approaches which can be adopted for different tasks at hand and which separate the aspects related to surroundings from object entities. In the proposed work we present an efficient approach for detecting generic objects in urban environments from videos acquired by a moving vehicle by means of semantic segmentation. Compared to traditional approaches for semantic labeling, we strive to detect variety of objects, while avoiding the need for large amounts of training data required for recognizing individual object categories and visual variability within and across the categories. In the proposed approach we exploit the features providing evidence about widely available non-object categories (such as sky, road, buildings) and use informative features which are indicative of the presence of object boundaries to gather the evidence about objects. We formulate the object/non-object semantic segmentation problem in the Conditional Random Field Framework, where the structure of the graph is induced by the minimum spanning tree computed over 3D reconstruction, yielding an efficient algorithm for an exact inference. We carry out extensive experiments on videos of urban environments acquired by a moving vehicle and compare our approach to existing alternatives.
Assessment, Treatment, and Rehabilitation for Interpersonal Violence Victims

Abstract Psychotherapists who have received minimal training in neuropsychology do not consider cognitive rehabilitation among the treatment options for their clients who have mild traumatic brain injury (mTBI). Historical perspectives on mTBI did not acknowledge brain plasticity and/or rehabilitation, yet rehabilitation might provide a necessary foundation for a client to be able to benefit from traditional feminist psychotherapy. This article provides an overview of two treatment modalities, biofeedback and neuropsychologically-informed feminist psychotherapy, for women with mTBI who sought relief from interstitial cystitis and headaches. Assessment for neuropsychological treatment planning and monitoring is illustrated with employment of the Ackerman-Banks Neuropsychological Rehabilitation Battery. Clinical examples are provided to demonstrate a variety of manifestations of mTBI and responses to treatment.
The 5-CNL Front-of-Pack Nutrition Label Appears an Effective Tool to Achieve Food Substitutions towards Healthier Diets across Dietary Profiles

Background Front-of-pack (FOP) nutrition labels are considered helpful tools to help consumers making healthier food choices, thus improving their diet. In France, the implementation of a FOP nutrition label–the 5-Colour Nutrition Label (5-CNL)–is currently under consideration. Our objective was to investigate dietary profiles in a French adult population using the 5-CNL, and to assess its potential impact in improving the diet through substitution of foods. Methods and Findings Subjects included in the NutriNet-Santé cohort, who had completed three 24-h dietary records were included in this cross-sectional analysis. Mutually exclusive clusters of individuals were identified using the percentage of energy derived from foods of each of the 5-CNL colours as input variables. Three scenarios of substitution of foods for healthier alternative using the 5-CNL were tested. Food group and dietary intakes, socio-demographic and lifestyle data were compared across clusters using ANOVAs or Chi-square tests, as appropriate. We identified three mutually exclusive dietary profiles: ‘Healthy’ (N = 28 095, 29.3% of the sample), with high consumption of fruit, vegetables, whole cereals and fish; ‘Western’ (N = 33 386, 34.8%); with high consumption of sweetened beverages, breakfast cereal, cheese, fatty and sugary foods; ‘Traditional’ (N = 34 461, 35.1%), with high consumption of potatoes, bread, meat and dairy desserts. Overall, substitutions strategies led to an increase in the number of subjects reaching the recommended intakes in energy, macro and micronutrients. Increases were particularly high in the ‘Western’ pattern for lipids and saturates intakes: from 16.2% reaching the recommended amount for lipids (13.5% for saturates) to 60.6% and 85.7% respectively. Conclusion The use of the 5-CNL as an indicator of food choice meaningfully characterizes clusters of dietary habits and appears as an effective tool to help improving the nutritional quality of the diet.
Long-Term Effects of Postearthquake Distress on Brain Microstructural Changes

Stressful events can have both short- and long-term effects on the brain. Our recent investigation identified short-term white matter integrity (WMI) changes in 30 subjects soon after the Japanese earthquake. Our findings suggested that lower WMI in the right anterior cingulum (Cg) was a pre-existing vulnerability factor and increased WMI in the left anterior Cg and uncinate fasciculus (Uf) after the earthquake was an acquired sign of postearthquake distress. However, the long-term effects on WMI remained unclear. Here, we examined the 1-year WMI changes in 25 subjects to clarify long-term effects on the WMI. We found differential FAs in the right anterior Cg, bilateral Uf, left superior longitudinal fasciculus (SLF), and left thalamus, suggesting that synaptic enhancement and shrinkage were long-term effects. Additionally, the correlation between psychological measures related to postearthquake distress and the degree of WMI alternation in the right anterior Cg and the left Uf led us to speculate that temporal WMI changes in some subjects with emotional distress occurred soon after the disaster. We hypothesized that dynamic WMI changes predict a better prognosis, whereas persistently lower WMI is a marker of cognitive dysfunction, implying the development of anxiety disorders.
Lipid-mediated release of GLP-1 by mouse taste buds from circumvallate papillae: putative involvement of GPR120 and impact on taste sensitivity

Glucagon-like peptide-1 (GLP-1) signaling modulates sweet-taste sensitivity in the mouse. Because circumvallate papillae (CVPs) express both GLP-1 and its receptor, a local regulation has been suggested. However, whether dietary lipids are involved in this regulation, as shown in the gut, is unknown. By using a combination of biochemical, immunohistochemical, and behavioral approaches, the present data i) confirm the role of GLP-1 signaling in the attraction for sucrose, ii) demonstrate that minute quantities of long-chain FAs (LCFAs) reinforce the attraction for sucrose in a GLP-1 receptor-dependent manner, iii) suggest an involvement of the LCFA receptor GPR120 expressed in taste buds in this system, and iv) support the existence of a regulation by GLP-1 of the lipid sensing mediated by lingual CD36. Therefore, oro-sensory detection of LCFAs may affect sweet and fatty taste responsiveness by controlling the secretion of lingual GLP-1. This regulatory loop, probably triggered by the LCFA-GPR120 interaction, might contribute to the high palatability of foods rich both in fat and sugar.
Contrast enhancement of night images

Night images obtained from a surveillance camera have low visibility compared to daytime images. Images captured at night have low brightness, low contrast and high noise. A modified contrast enhancement (CE) algorithm was proposed and developed in luminance-chrominance space. Only the luminance channel obtained by PCA transform is processed as it contains the most valuable information. Daytime images are simulated with various degrees of contrast and Poisson noise using MATLAB. CE algorithm is applied in three scales to obtain good brightness and contrast of the images. Images are denoised by using bilateral filter that smoothes the noise while preserving edges. The brightness and contrast of the night images have been enhanced significantly and the noise is reduced effectively, preserving the details of the images. Finally, the performance of the proposed algorithm is illustrated by processing images under various lighting conditions without introducing halo and ghosting artifacts. Structural similarity and visual contrast measures demonstrate that the proposed method is more effective over other existing methods.
We'll Meet Again: Revealing Distributional and Temporal Patterns of Social Contact

What are the dynamics and regularities underlying social contact, and how can contact with the people in one's social network be predicted? In order to characterize distributional and temporal patterns underlying contact probability, we asked 40 participants to keep a diary of their social contacts for 100 consecutive days. Using a memory framework previously used to study environmental regularities, we predicted that the probability of future contact would follow in systematic ways from the frequency, recency, and spacing of previous contact. The distribution of contact probability across the members of a person's social network was highly skewed, following an exponential function. As predicted, it emerged that future contact scaled linearly with frequency of past contact, proportionally to a power function with recency of past contact, and differentially according to the spacing of past contact. These relations emerged across different contact media and irrespective of whether the participant initiated or received contact. We discuss how the identification of these regularities might inspire more realistic analyses of behavior in social networks (e.g., attitude formation, cooperation).
The Value of Foresight: How Prospection Affects Decision-Making

Traditional theories of decision-making assume that utilities are based on the intrinsic value of outcomes; in turn, these values depend on associations between expected outcomes and the current motivational state of the decision-maker. This view disregards the fact that humans (and possibly other animals) have prospection abilities, which permit anticipating future mental processes and motivational and emotional states. For instance, we can evaluate future outcomes in light of the motivational state we expect to have when the outcome is collected, not (only) when we make a decision. Consequently, we can plan for the future and choose to store food to be consumed when we expect to be hungry, not immediately. Furthermore, similarly to any expected outcome, we can assign a value to our anticipated mental processes and emotions. It has been reported that (in some circumstances) human subjects prefer to receive an unavoidable punishment immediately, probably because they are anticipating the dread associated with the time spent waiting for the punishment. This article offers a formal framework to guide neuroeconomic research on how prospection affects decision-making. The model has two characteristics. First, it uses model-based Bayesian inference to describe anticipation of cognitive and motivational processes. Second, the utility-maximization process considers these anticipations in two ways: to evaluate outcomes (e.g., the pleasure of eating a pie is evaluated differently at the beginning of a dinner, when one is hungry, and at the end of the dinner, when one is satiated), and as outcomes having a value themselves (e.g., the case of dread as a cost of waiting for punishment). By explicitly accounting for the relationship between prospection and value, our model provides a framework to reconcile the utility-maximization approach with psychological phenomena such as planning for the future and dread.
Challenges in assessing regional distribution of inhaled drug in the human lungs

Introduction: Both the total amount of drug deposited in the lungs (whole lung deposition) and the amount deposited in different lung regions (regional lung deposition) are potentially important factors that determine the safety and efficacy of inhaled drugs. Radionuclide imaging is well established for quantifying the whole lung deposition of inhaled drugs, but the assessment of regional lung deposition is less straightforward, because of the complex nature of the lung anatomy. Areas covered: This review describes the challenges and problems associated with quantifying regional lung deposition by the two-dimensional (2D) radionuclide imaging method of gamma scintigraphy, and by the three-dimensional (3D) radionuclide imaging methods of single-photon-emission computed tomography (SPECT) and positron-emission tomography (PET). The advantages and disadvantages of each method for assessing regional lung deposition are discussed. Expert opinion: Owing to its 2D nature, gamma scintigraphy provides limited information about regional lung deposition. SPECT provides regional lung deposition data in three dimensions, but usually involves a 99mTc radiolabel. PET enables the regional lung deposition of radiolabeled drug molecules to be quantified in three dimensions, but poses the greatest logistical and technical difficulties. Despite their more challenging nature, 3D imaging methods should be considered as an alternative to gamma scintigraphy whenever the determination of regional lung deposition of pharmaceutical aerosols is a major study objective.