Miracle-dz/UniFAR-FTUs huggingface dataset:
IS HIV SHORT-SIGHTED? INSIGHTS FROM A MULTISTRAIN NESTED MODEL

An important component of pathogen evolution at the population level is evolution within hosts. Unless evolution within hosts is very slow compared to the duration of infection, the composition of pathogen genotypes within a host is likely to change during the course of an infection, thus altering the composition of genotypes available for transmission as infection progresses. We develop a nested modeling approach that allows us to follow the evolution of pathogens at the epidemiological level by explicitly considering within‐host evolutionary dynamics of multiple competing strains and the timing of transmission. We use the framework to investigate the impact of short‐sighted within‐host evolution on the evolution of virulence of human immunodeficiency virus (HIV), and find that the topology of the within‐host adaptive landscape determines how virulence evolves at the epidemiological level. If viral reproduction rates increase significantly during the course of infection, the viral population will evolve a high level of virulence even though this will reduce the transmission potential of the virus. However, if reproduction rates increase more modestly, as data suggest, our model predicts that HIV virulence will be only marginally higher than the level that maximizes the transmission potential of the virus.
An adaptive switching median filter with anisotropic linking PCNN noise detection for salt and pepper noise reduction

This paper proposes a switching scheme for salt and pepper noise reduction by combining a noise detection algorithm based on a simplified pulse coupled neural network (PCNN) with a simple adaptive median filter. The simplified PCNN utilizes an adaptive synaptic weight matrix created by anisotropic linking mechanism to achieve anisotropic linking model, that is the interconnections between neurons with large absolute difference in intensity will be interrupted. Therefore, the neurons corresponding to noise corrupted pixels will receive smaller feedback signal from the neighborhood and generate smaller internal activities compare with the ones corresponding to noise free pixels. The impulse will be detected by setting an appropriate dynamic threshold. After the PCNN based noise detection scheme, the pixels contaminated by salt and pepper noise will be restored by a simple adaptive median filter. Experimental results prove that the proposed switching median filter outperform over the conventional methods in both noise reduction and detail preserving.
Orderings and Types in Databases

This paper investigates a method to represent database objects as typed expressions in programming languages. A simple typed language supporting non-flat records, higher-order relations, and natural join expressions is defined. A denotational semantics of this language is then presented. Expressions are interpreted into a domain containing Smyth’s powerdomain. In order to give semantics to types, a new model of types, a filter model is proposed. Types are then interpreted as filters in a domain. The type inference system of the language is shown to be sound in this model.
DAP join: Produce massive and immediate result in multi join query using flushing

This paper introduced a method for producing massive and immediate result in multi-join query (DAP Join, for short). Mostly previous research are based on single join operator while DAP join is based on multiple join operators. DAP join distinguishes itself from all previous techniques by concluding benefits of Hash Merge join, Rate Based Progressive Join and State Spilling and its own new approach. DAP join employs a new flushing technique to move N amount of data from memory to disk when memory allotment is exhausted and move N/2 amount of data when data arrival rate is slow in online environment. DAP join moves data to disk which is least useful and use Symmetric Hash Join in in-memory join makes it efficient in order to maximize overall throughput and produce early result.
Predictive Value of Liver Enzymes and Inflammatory Biomarkers for the Severity of Liver Fibrosis Stage in HIV/HCV Co-Infected Patients

Objective The aim of our study was to assess a possible association between plasma inflammatory biomarkers (CRP, IL-6, soluble CD14) and the extent of fibrosis or cirrhosis using a FibroScan® in HIV/HCV co-infected patients. Methods This cross-sectional study assessed 60 HIV/HCV co-infected patients who had paired plasma samples and FibroScan® values available. All included patients were controlled for HIV infection (HIV-1 RNA <50 copies/mL) and had detectable HCV RNA levels. Levels of three biomarkers were measured in all samples using commercial ELISA kits. Multivariate logistic regression models identified factors associated with the METAVIR stages of fibrosis (F0–F2 vs. F3–F4). Results In univariate logistic regression analyses, in addition to sCD14 (odds ratio [OR] = 3.23, 95% confidence interval [95%CI] = 1.30–7.97, P = 0.01), aspartate aminotransferase (AST), alanine aminotransferase, platelet counts, and CD4 cell counts were associated with the stage of liver fibrosis and, thus, were introduced into the model. However, only AST (OR = 1.06, 95%CI = 1.02–1.10, P = 0.0009) was independently associated with F3–F4 stage liver fibrosis. Conclusions In our study of HIV/HCV co-infected patients, sCD14 plasma level, a biomarker of monocyte activation, was not independently associated with the F3–F4 stage of liver fibrosis. We hypothesize that the higher levels of inflammation markers observed in HIV/HCV co-infected patients, compared to HCV mono-infected patients, prevent this association being observed within this population.
An empirical comparison of dependency issues in OSS packaging ecosystems

Nearly every popular programming language comes with one or more open source software packaging ecosystem(s), containing a large collection of interdependent software packages developed in that programming language. Such packaging ecosystems are extremely useful for their respective software development community. We present an empirical analysis of how the dependency graphs of three large packaging ecosystems (npm, CRAN and RubyGems) evolve over time. We study how the existing package dependencies impact the resilience of the three ecosystems over time and to which extent these ecosystems suffer from issues related to package dependency updates. We analyse specific solutions that each ecosystem has put into place and argue that none of these solutions is perfect, motivating the need for better tools to deal with package dependency update problems.
An iso-sws survey of molecular hydrogen in starburst and seyfert galaxies

We present results from a survey of molecular hydrogen emission from a sample of Starburst and Seyfert galaxies carried out with the Infrared Space Observatory (ISO). Pure rotational H2 emission has been detected in a number of extragalactic objects and a variety of environments. A number of transitions from S(7) to S(0) are detected in both starbursts and Seyferts. Using excitation diagrams we derive temperatures and masses of the \warm" molecular hydrogen. We nd that the temperature of the \warm" gas is similar in starbursts and Seyferts (those Seyferts for which we have rm detections of the S(0) line) with a value of around T 150 K. This \warm" gas accounts for as much as 10% of the total galactic mass (as probed by CO molecular observations) in starbursts. The fraction of \warm" gas is overall higher in Seyferts, ranging between 2{35%. We then investigate the origin of the warm H2 emission. Comparison with published theoretical models and Galactic templates implies that although emission from photodissociation regions (PDR) alone could explain the emission from starbursts and Seyferts, most likely a combination of PDR, shock emission and gas heated by X-rays (mostly for the Seyferts) is responsible for H2 excitation in extragalactic environments. Finally, we nd that although PAH and H2 line emission correlate well in starbursts and the large scale emission in AGN, H2 emission is much stronger compared to PAH emission in cases where a \pure" AGN dominates the energy output.
Evaluation of Improvement in Quality of Life and Physical Activity After Total Knee Arthroplasty in Greek Elderly Women

Background: The aim of this study was to evaluate the changes in quality of life of patients after total knee arthroplasty and to assess the changes in physical activity by using a self-reported questionnaire and by counting the number of steps 3-6 months after post-operatively. Methods: Included were fifty two elderly women (age 72.6±65.9 years, mean±SD) with knee osteoarthritis undergoing primary knee arthroplasty. Health-related quality of life, physical activity, pain and function and the number of steps were assessed before, 3 and 6 months post-operatively. We used the Medical Outcomes Study Short Form (SF-36), the Physical Activity Scale for the Elderly (PASE) and the pedometer SW200 Digiwalker of Yamax. Results: Patients showed a significant improvement (p< 0.01, η2 =0.22) in health–related quality of life, particularly in physical function, (p<0 .001) body pain (p< 0.001) and vitality scale (p< 0.001) of SF-36 at 3 and 6 months after the procedure. Physical activity (PASE score) increased at 3 and 6 months after arthroplasty (p< 0.001, η2 =0.74), and the number of steps increased 6 months after, compared to the assessment that took place 3 months after operation (p< 0.001). Conclusions: Our results suggest that total knee arthroplasty leads to a gradual improvement in quality of life of elderly patients over the first 6 post-operative months.
Impact of Baseline Renal Function on the Efficacy and Safety of Aliskiren Added to Losartan in Patients With Type 2 Diabetes and Nephropathy

OBJECTIVE Proteinuric diabetic patients with reduced glomerular filtration rate (GFR) are at high risk of renal and cardiovascular disease progression and treatment-related adverse events. This post hoc analysis assessed the efficacy and safety of aliskiren added to the maximal recommended dose of losartan according to baseline estimated GFR (eGFR) (stage 1–3 chronic kidney disease [CKD]). RESEARCH DESIGN AND METHODS In the Aliskiren in the Evaluation of Proteinuria in Diabetes (AVOID) study, 599 hypertensive patients with type 2 diabetes and nephropathy received 6 months of aliskiren (150 mg daily titrated to 300 mg daily after 3 months) or placebo added to 100 mg losartan and optimal antihypertensive therapy. Exclusion criteria included eGFR <30 ml/min per 1.73 m2 and serum potassium >5.1 mmol/l. RESULTS Baseline characteristics were similar between treatment groups in all CKD stages. The antiproteinuric effects of aliskiren were consistent across CKD stages (19, 22, and 18% reduction). In the stage 3 CKD group, baseline serum creatinine levels were equal, but renal dysfunction, prespecified as a postrandomization serum creatinine elevation >176.8 μmol/l (2.0 mg/dl) occurred more frequently in the placebo group (29.2 vs. 13.6%, P = 0.032). Serum potassium elevations >5.5 mmol/l (based on a single measurement) were more frequent with aliskiren (22.5 vs. 13.6%) in stage 3 CKD. Adverse event rates were similar between treatments, irrespective of CKD stage. CONCLUSIONS Aliskiren added to losartan reduced albuminuria and renal dysfunction and was well tolerated, except for hyperkalemia (stage 3), independent of baseline CKD stage in patients with type 2 diabetes, hypertension, and nephropathy.
Cypriot Urban Elementary Students’ Attitude Toward Physical Education

Purpose: This study examined the attitudes of Cypriot elementary school students toward physical education. Fourth, fifth and sixth grade students (N = 763) from six urban Cypriot elementary schools completed an attitude instrument. Methods: Adapting the attitude instrument for Greek-speaking students an extensive two-step pilot study showed the instrument scores were valid for a two factor model (affect and cognition) of attitude. Results: The authors found that Cypriot upper elementary school students have an overall moderate to high attitude toward physical education. Comparisons indicated there was a grade level effect with sixth grade students having lower attitudes for the usefulness-curriculum sub-factor, the perceived usefulness factor, and for total attitude. There were no differences for other attitude variables and no gender effects. Discussion/Conclusion: The results suggest that Cypriot students perceive the curriculum less useful as they get older.
The Bereavement Exclusion Debate in the DSM-5: A History

Beginning with the Diagnostic and Statistical Manual of Mental Disorders (3rd ed.; DSM-III), depressive episodes following the loss of a loved one were considered to represent normal grief if they did not include certain severe symptoms or if they lasted less than 2 months. This was called the bereavement exclusion rule. A debate about whether to eliminate the bereavement exclusion became a hotly contested issue during the DSM-5 revision process. The debate involved disagreements about which research studies were most relevant to assessing the validity of the bereavement exclusion rule, different value commitments regarding the distinction between normal and abnormal, and contrasting philosophical assumptions about the nature of psychiatric disorder. Based on a review of the arguments offered in academic journals, the blogosphere, and in the mass media, and on interviews with active participants in the debate, this article narrates a consensus history that reflects the diversity of viewpoints promoted during the debate and the diversity of views on the outcome.
On TDMA Optimality in Locally Connected Networks with no CSIT

In this work, we study scenarios of wireless networks where using simple Time-Division-Multiple-Access (TDMA) is optimal if no channel state information is available at the transmitters (no CSIT). We consider single-hop locally connected interference networks where each transmitter is connected to the receiver that has the same index as well as L succeeding receivers. The considered rate criterion is the per user Degrees of Freedom as the number of transmitter-receiver pairs goes to infinity. For the case when L=1, it was shown in previous work that TDMA is optimal, even if each message can be available at multiple transmitters and linear cooperation schemes are allowed. Here, we extend this conclusion to the case where L=2, by proving optimality of TDMA in this case as well. We then study the problem for general values of L without allowing for cooperative transmission. We prove optimality of TDMA when each transmitter is serving the receiver with the same index, and finally conjecture - based on an example - that the same conclusion applies even if each receiver can be served by any single transmitter connected to it.
An Integrated Hardware-Software Approach to Task Graph Management

Task-based parallel programming models with explicit data dependencies, such as OmpSs, are gaining popularity, due to the ease of describing parallel algorithms with complex and irregular dependency patterns. These advantages, however, come at a steep cost of runtime overhead incurred by dynamic dependency resolution. Hardware support for task management has been proposed in previous work as a possible solution. We present VSs, a runtime library for the OmpSs programming model that integrates the Nexus++ hardware task manager, and evaluate the performance of the VSs-Nexus++ system. Experimental results show that applications with fine-grain tasks can achieve speedups of up to 3.4×, while applications optimized for current runtimes attain 1.3×. Providing support for hardware task managers in runtime libraries is therefore a viable approach to improve the performance of OmpSs applications.
Thinking Outside the Box

Rigid thinking is associated with less creativity, suggesting that priming a flexible mind-set should boost creative thought. In three studies, we investigate whether priming multiple social identities predicts more creativity in domains unrelated to social identity. Study 1 asked monoracial and multiracial participants to write about their racial identities before assessing creativity. Priming a multiracial’s racial identity led to greater creativity compared to a no-prime control. Priming a monoracial’s racial identity did not affect creativity. Study 2 showed that reminding monoracials that they, too, have multiple identities increased creativity. Study 3 replicated this effect and demonstrated that priming a multiracial identity for monoracials did not affect creativity. These results are the first to investigate the association between flexible identities and flexible thinking, highlighting the potential for identity versatility to predict cognitive differences between individuals who have singular versus multifaceted views of their social selves.
Northern gannets anticipate the spatio–temporal occurrence of their prey

SUMMARY Seabirds, as other marine top predators, are often assumed to forage in an unpredictable environment. We challenge this concept and test the hypothesis that breeding Northern gannets (Morus bassanus) anticipate the spatio–temporal occurrence of their prey in the English Channel. We analyzed 23 foraging tracks of Northern gannets breeding on Rouzic Island (Brittany) that were recorded using GPS loggers during 2 consecutive years. All birds commuted between the breeding colony and foraging areas located at a mean distance of 85 km and 72 km (in 2005 and 2006, respectively) from the colony. Mean linearity indices of the outbound and inbound trips were between 0.83 and 0.87, approaching a beeline path to and from the foraging area. Additional parameters (flight speed, and number and duration of stopovers at sea) for the outbound and inbound trip were not statistically different, indicating that birds are capable of locating these feeding areas in the absence of visual clues, and to pin-point their breeding site when returning from the sea. Our bearing choice analysis also revealed that gannets anticipate the general direction of their foraging area during the first 30 min and the first 10 km of the trip. These results strongly suggest that birds anticipate prey location, rather than head into a random direction until encountering a profitable area. Further investigations are necessary to identify the mechanisms involved in seabird resource localization, such as sensorial abilities, memory effects, public information or a combination of these factors.
Markers for Risk of Type 1 Diabetes in Relatives of Alsacian Patients With Type 1 Diabetes

Background: The cytotoxic T lymphocyteassociated antigen 4 gene (CTLA-4) encode the T cell receptor involved in the control of T cell proliferation and mediates T cell apoptosis. The receptor protein is a specific T lymphocyte surface antigen that is detected on cells only after antigen presentation. Thus, CTLA-4 is directly involved in both immune and autoimmune responses and may be involved in the pathogenesis of multiple T cell-mediated autoimmune disorders. There is polymorphism at position 49 in exon 1 of the CTLA-4 gene, providing an A-G exchange. Moreover, we assessed the CTLA-4 49 (Thr/Ala) polymorphism in diabetic patients and first-degree relatives as compared to control subjects. Research design and methods: Three loci (HLA-DQB1, DQA1 and CTLA-4) were analysed in 62 type 1 diabetic patients, 72 firstdegree relatives and 84 nondiabetic control subjects by means of PCR-RFLP. Results: A significant enrichment in DQB1 alleles encoding for an amino acid different from Asp in position 57 (NA) and DQA1 alleles encoding for Arg in position 52 was observed in diabetic subjects and first-degree relatives as compared to controls. The genotype and allele frequencies of these polymorphisms in type 1 diabetic patients and firstdegree relatives differed significantly from those of controls (p< 0.001 and 0.05 respectively). CTLA-49 Ala alleles frequencies were 75.8% in type 1 diabetic patients and 68.1% in first-degree relatives in comparison to 35.7% in control subjects. The Ala/Ala genotype conferred a relative risk of 18.8 (p < 0.001). Conclusion: The CTLA-4 49 Ala allele confers an increased risk of type 1 diabetes, independent of age and HLA-DQ genetic markers.
The Role of Acceptance in Reducing Anxiety in Stuttering: A Theoretical Framework

1 CHAPTER 1: INTRODUCTION: DEVELOPMENT OF STUTTERING.2 Childhood Onset Stuttering Causes of Stuttering The Significance of “Nurture” and the Role of Anxiety CHAPTER 2: MEMORY PROCESSING . 6 MEMORY’S ROLE IN STUTTERING REACTIVITY AND ITS INFLUENCE ON ENCODING ENCODING & STORAGE RETRIEVAL AS AN AUTOMATIC PROCESS CHAPTER 3: FORMATION OF AUTOMATIC THOUGHT PROCESSING . 12 MEMORY CONSOLIDATION SYNAPTIC CONSOLIDATION Synaptic Consolidation & Emotions SYSTEMATIC CONSOLIDATION Systematic Consolidation & Emotions CHAPTER 4: ANXIETY & BELIEF SYSTEMS . 18 EMOTIONAL RESPONSES: ANXIETY ESTABLISHMENT OF BELIEF SYSTEMS CHAPTER 5: MEMORY RECONSOLIDATION: THE MECHANISM OF FUNCTIONAL CHANGE IN AUTOMATIC THOUGHT PROCESSING . 22 THE CORE PROCESS Defusion of the Target Schema: Acceptance Guiding A Contradictory Experience: Being Present Repeating the Contradictory Experience: Committed Action COMMON MISCONCEPTIONS CHAPTER 6: ACCEPTANCE AND COMMITMENT THERAPY (ACT) . 29 ACCEPTANCE & STUTTERING THE 6 CORE PRINCIPLES OF ACT Acceptance Being Present Cognitive Defusion Self as Context Defining Values Committed Action CHAPTER 7: CBT VS. ACT . 35 COGNITIVE BEHAVIORAL THERAPY (CBT) RECOGNITION OF COGNITION IN CBT AND ACT ADAPTATION VS. RESTRUCTURING References.41
Multi-flux warped throats and cascading gauge theories

We describe duality cascades and their infrared behavior for systems of D3-branes at singularities given by complex cones over del Pezzo surfaces (and related examples), in the presence of fractional branes. From the gauge field theory viewpoint, we show that D3-branes probing the infrared theory have a quantum deformed moduli space, given by a complex deformation of the initial geometry to a simpler one. This implies that for the dual supergravity viewpoint, the gauge theory strong infrared dynamics smoothes out the naked singularities of the recently constructed warped throat solutions with 3-form fluxes, describing the cascading RG flow of the gauge theory. This behavior thus generalizes the Klebanov-Strassler deformation of the conifold. We describe several explicit examples, including models with several scales of strong gauge dynamics. In the regime of widely separated scales, the dual supergravity solutions should correspond to throats with several radial regions with different exponential warp factors. These rich throat geometries are expected to have interesting applications in compactification and model building. Along our studies, we also construct explicit duality cascades for gauge theories with irrational R-charges, obtained from D-branes probing complex cones over dP1 and dP2.