Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of the Latent Reservoir on the Evolution of HIV at the Within- and Between-Host Levels

The existence of long-lived reservoirs of latently infected CD4+ T cells is the major barrier to curing HIV, and has been extensively studied in this light. However, the effect of these reservoirs on the evolutionary dynamics of the virus has received little attention. Here, we present a within-host quasispecies model that incorporates a long-lived reservoir, which we then nest into an epidemiological model of HIV dynamics. For biologically plausible parameter values, we find that the presence of a latent reservoir can severely delay evolutionary dynamics within a single host, with longer delays associated with larger relative reservoir sizes and/or homeostatic proliferation of cells within the reservoir. These delays can fundamentally change the dynamics of the virus at the epidemiological scale. In particular, the delay in within-host evolutionary dynamics can be sufficient for the virus to evolve intermediate viral loads consistent with maximising transmission, as is observed, and not the very high viral loads that previous models have predicted, an effect that can be further enhanced if viruses similar to those that initiate infection are preferentially transmitted. These results depend strongly on within-host characteristics such as the relative reservoir size, with the evolution of intermediate viral loads observed only when the within-host dynamics are sufficiently delayed. In conclusion, we argue that the latent reservoir has important, and hitherto under-appreciated, roles in both within- and between-host viral evolution.
OLAP Cubes for Social Searches: Standing on the Shoulders of Giants?

The advent of social bookmarking has signaled a new era towards a more “pluralistic” web, where entities of multiple types (e.g., users, resources, tags) can coexist and get interconnected. In this paper, we propose going beyond classical searches for resources based on keywords to exploring social data starting from any type of entity, i.e., user, resource or annotation, and requesting aggregated views of related entities based on the relationships defined between entities. We map this type of social searching to OLAP query processing bridging the gap between OLAP and the social web and we study various ways to support on-the-fly aggregations of social data. We further describe how data cubes can be used for precomputing and materializing the results of all possible aggregate queries over a social dataset. Our experiments show that cubes can efficiently support searches over social data and they particularly fit searches that combine popular entities over large datasets.
The Validity of the Modified Star Excursion Balance Test as a Predictor of Knee Extensor and Hip Abductor Strength

Objectives: To test the construct validity of the modified Star Excursion Balance Test (SEBT) in predicting the strength of knee extensors and hip abductors and to compare performance between dominant and non-dominant legs. Strength, as measured using hand held dynamometry, has been used as one of a variety of measures in order to subgroup patients with patellofemoral pain. This method is not well received in clinical practice due to time constraints and cost. In contrast, the SEBT is a quick and simple functional measure of dynamic stability. This study examined the validity of the SEBT as an alternate strength measure. Design: Within subject correlation. Each participant recorded maximum isometric contractions for hip abduction and knee extension using a HHD and performed the modified SEBT, on both legs, within one test period. Paired t tests were used to compare dominant and non-dominant legs and Pearson’s correlation analyses were used to explore for associations. Setting: Non-clinical environment, Participants: Eighteen healthy male amateur runner’s between 18 and 39 years old (mean age 36.1 years). Main outcome measures: Knee and hip moments normalised for leg length (Nm/m) for the HHD and percent of leg length reach score for each SEBT reach as well as a composite of all three. Results: There was no significant difference between dominant and non-dominant legs for all the tests (knee extension p = 0.72, hip abduction p = 0.90, SEBT composite p = 0.86) therefore data was combined into one set. There was no significant relationship between either hip abduction strength (r = 0.28, p = 0.11), or knee extension strength (r= 0.16, p = 0.17), with any combination of the SEBT. A moderate relationship (r = 0.52, p = 0.38) between hip abduction and SEBT posterolateral reach was seen, however, this was not statistically significant. Conclusion: There was no statistically significant association between either knee extension or hip abduction strength with the modified SEBT. This suggests that strength is unlikely to be a primary construct of the test and the SEBT is not a useful replacement for the HHD when testing strength.
Identification of Amino Acid Residues Responsible for the Selectivity of Tadalafil Binding to Two Closely Related Phosphodiesterases, PDE5 and PDE6*

Background: Most PDE5-selective inhibitors also potently inhibit photoreceptor PDE6. Results: Evolutionary trace analysis predicted amino acids responsible for the selectivity of tadalafil binding to the PDE6 catalytic site without altering vardenafil binding. Conclusion: A limited number of amino acid residues account for drug selectivity of PDE inhibitors. Significance: This work will help identify more selective PDE5 inhibitors lacking adverse side effects on vision. The 11 families of the Class I cyclic nucleotide phosphodiesterases (PDEs) are critical for regulation of cyclic nucleotide signaling. PDE5 (important in regulating vascular smooth muscle contraction) and PDE6 (responsible for regulating visual transduction in vertebrate photoreceptors) are structurally similar but have several functional differences whose structural basis is poorly understood. Using evolutionary trace analysis and structural homology modeling in conjunction with site-directed mutagenesis, we have tested the hypothesis that class-specific differences between PDE5 and PDE6 account for the biochemical and pharmacological differences in the two enzyme families. Replacing human PDE5 residues in the M-loop region of the binding site for the PDE5-selective inhibitor tadalafil (Cialis®) with the corresponding class-specific cone PDE6 residues (P773E, I778V, E780L, F787W, E796V, D803P, L804M, N806D, I813L, S815K) reduces tadalafil binding affinity to levels characteristic of PDE6. These mutations fail to alter vardenafil (Levitra®) affinity for the active site. Class-specific differences in PDE5 versus cone PDE6 that contribute to the accelerated catalytic efficiency of PDE6 were identified but required heterologous expression of full-length PDE5 constructs. Introduction of PDE6 residues into the background of the PDE5 protein sequence often led to loss of catalytic activity and reduced protein solubility, supporting the idea that multiple structural elements of PDE6 are highly susceptible to misfolding during heterologous expression. This work validates the use of PDE5 as a template to identify functional differences between PDE5 and PDE6 that will accelerate efforts to develop the next generation of PDE5-selective inhibitors with fewer adverse side effects resulting from PDE6 inhibition.
Sugar-induced diarrhoea in children.

In recent years there has been a proliferation of knowledge about normal and abnormal digestion and absorption of carbohydrates. Many of these advances have been made since Anderson's comments about sugar intolerance in her review of intestinal malabsorption in childhood published in this journal in 1966, and since Holzel's review of the problem in 1967. This review is not intended as a comprehensive survey of the vast literature on this topic, but is an attempt to summarize current knowledge of disorders of carbohydrate digestion and absorption in children. Practical rather than theoretical aspects will be emphasized. Application of this knowledge promises to be of great benefit to children throughout the world because these disorders are common and potentially lethal, but eminently treatable. Carbohydrates are of universal dietary importance since they supply about one-half of man's caloric needs. In poorer communities they constitute an even larger proportion of the diet. The major dietary carbohydrates, starch, lactose, and sucrose, are consumed in varying proportions according to custom and age. Lactose is, of course, relatively more important in infants and young children. In health, starch is hydrolysed in the lumen of the gut by amylases to maltose (a disaccharide), maltotriose (a trisaccharide), and limit dextrins (oligosaccharides). As pointed out by Gray (1970) this is contrary to the still widely held notion that disaccharides and monosaccharides are the final products of the hydrolysis of starch. The hydrolytic products of starch digestion are then presented to the small intestinal epithelium where mucosal disaccharidases split them further to the monosaccharides glucose, galactose, and fructose. Glucose and galactose are then transported through the epithelial cell by an energyand sodiumdependent active transport process. This has been reviewed by Crane (1968). It has been
Phytoremediation of aged petroleum sludge: effect of inorganic fertilizer.

Phytoremediation is a promising new technology that uses higher plants to enhance biodegradation. Nutrient availability is an important factor governing the success of phytoremediation and can be regulated through the addition of fertilizer. A greenhouse study was conducted to assess the importance of nitrogen and phosphorus for the phytoremediation of petroleum sludge. Degradation of total petroleum hydrocarbons (TPH) was quantified for six fertilization rates and three vegetation treatments: bermuda grass [Cynodon dactylon (L.) Pers. ], tall fescue (Festuca arundinacea Schreb.), and an unvegetated control. During the first 6 mo of the experiment, TPH declined by an average of 49% with no significant differences between treatments. After 1 yr, TPH degradation was significantly greater in both vegetated treatments with a mean TPH reduction of 68% for bermuda, 62% for fescue, and 57% for the unvegetated control. Degradation of TPH in the fescue and bermuda treatments was significantly lower in the treatments in which no fertilizer was added or N and P were added simply to maintain plant growth compared with the higher rates of fertilization. For this short-term, greenhouse experiment, optimal remediation was obtained by fertilization that produced a C to N to P ratio of 100:2:0.2.
Severe bronchospasm after parenteral parecoxib: cyclooxygenase-2 inhibitors: not the answer yet.

IN a subset of patients with asthma, nonsteroidal antiinflammatory drugs (NSAIDs) that inhibit both cyclooxygenase 1 (COX-1) and cyclooxygenase 2 (COX-2) can precipitate dangerous asthmatic attacks. It has been proposed that in these patients, the attacks are triggered by inhibition of COX-1 and not COX-2, and that the use of highly selective COX-2 inhibitors may be safe in asthmatic patients, even those with sensitivity to NSAIDs. We describe two cases of acute, life-threatening bronchospasm after administration of parecoxib, a parenteral COX-2 inhibitor, in patients with a history of asthma but no previous history of aspirin or other NSAID sensitivity.
Development and Initial Validation of the Satisfaction and Recovery Index (SRI) for Measurement of Recovery from Musculoskeletal Trauma

Background: There is a need for a generic patient-reported outcome (PRO) that is patient-centric and offers sound properties for measuring the process and state of recovery from musculoskeletal trauma. This study describes the construction and initial validation of a new tool for this purpose. Methods: A prototype tool was constructed through input of academic and clinical experts and patient representatives. After evaluation of individual items, a 9-item Satisfaction and Recovery Index (SRI) was subject to psychometric evaluation drawn from classical test theory. Subjects were recruited through online and clinical populations, from those reporting pain or disability from musculoskeletal trauma. The full sample (N = 129) completed the prototype tool and a corresponding region-specific disability measure. A subsample (N = 46) also completed the Short-Form 12 version 2 (SF12vs). Of that, a second subsample (N = 29) repeated all measures 3 months later. Results: A single factor ‘health-related satisfaction’ was extracted that explained 71.1% of scale variance, Cronbach’s alpha = 0.95. A priori hypotheses for cross-sectional correlations with region-specific disability measures and the generic Short-form 12 component scores were supported. The SRI tool was equally responsive to change, and able to discriminate between recovered/non-recovered subjects, at a level similar to that of the region-specific measures and generally better than the SF-12 subscales. Conclusion: The new SRI tool, as a measure of health-related satisfaction, shows promise in this initial evaluation of its properties. It is generic, patient-centered, and shows overall measurement properties similar to that of region-specific measures while allowing the potential benefit of comparison between clinical conditions. Despite early promising results, additional properties need to be explored before the tool can be endorsed for routine clinical use.
Necrotizing Enterocolitis: Have We Made Any Progress in Reducing the Risk?

Necrotizing enterocolitis (NEC) is a disease affecting premature infants with potentially devastating complications in the neonatal intensive care unit (NICU). Inadequate knowledge regarding the underlying pathophysiology of this disease has contributed to the minimal progress made in decreasing the incidence and severity of NEC. Because of an improved survival rate of the most immature infants, the number of diagnosed cases of NEC is anticipated to increase. Unfortunately, decades of research have failed to reduce the risk or improve the prognosis of NEC, magnifying the need for risk-reduction strategies for decreasing significant NEC-related morbidity and mortality. Advancements in our understanding of this disease process have facilitated the development of several strategies that have been investigated in the risk reduction of NEC. This article discusses the pathophysiology and causes of NEC and presents strategies investigated regarding risk reduction of this devastating disease.
Are oportunities equal for women in the IT workplace?

Despite the growing literature on women in the information technology (IT) industry, knowledge about gender discrimination within employing organizations is inadequate. This article fills the gap by testing four hypotheses that explore whether work opportunities are equal for women in India. The study did not find any support for the delineated hypotheses and concluded the following: women software workers do not perform low-skilled activities; they experience the same as men on core job characteristics, they do not feel marginalized in work teams; and work hours do not differ for men and women. Conclusions support the view that structural constraints outside the IT organizations need to be removed to increase the participation of women in IT
Gesturing and Naming

Studies using functional imaging show reliable activation of premotor cortex when observers view manipulable objects. This result has led to the view that knowledge of object function, particularly the actions associated with the typical use of objects, may play a causal role in object identification. To obtain relevant evidence regarding this causal role, we asked subjects to learn gesture-color associations and then attempt to identify objects presented in colors denoting functional gestures that were congruent or incongruent with the objects' use. A strong congruency effect was observed when subjects gestured the use of an object, but not when they named an object. We conclude that our procedure constitutes a sensitive measure of the recruitment and causal role of functional knowledge and that this recruitment is not present during object naming. Preliminary evidence, however, indicates that gestures evoked by the volumetric shape of an object do contribute to object naming.
Amplification Mechanisms in Liquidity Crises

I describe two amplifications mechanisms that operate during liquidity crises and discuss the scope for central bank policies during crises as well as preventive policies in advance of crises. The first mechanism works through asset prices and balance sheets. A negative shock to the balance sheets of asset-holders causes them to liquidate assets, lowering prices, further deteriorating balance sheets, culminating in a crisis. The second mechanism involves investors' Knightian uncertainty. Unusual shocks to untested financial innovations lead agents to become uncertain about their investments causing them to disengage from markets and increase their demand for liquidity. This behavior leads to a loss of liquidity and a crisis.
Marcus from single molecule studies of nanoparticles Interaction of theory and experiment : examples

References l.html#ref-list-1 http://rsta.royalsocietypublishing. org/content/368/1914/1109.ful This article cites 28 articles, 2 of which can be accessed free This article is free to access Rapid response 1914/1109 http://rsta.royalsocietypublishing. org/letters/submit/roypta;368/ Respond to this article Subject collections (10 articles) computational chemistry  (4 articles) physical chemistry  (91 articles) nanotechnology  (17 articles) inorganic chemistry  collections Articles on similar topics can be found in the following
Evaluation of the Sysmex XN‐550, a Novel Compact Haematology analyser from the XN‐L® series, compared to the XN‐20 system

The XN‐550 is a new, automated, compact, haematology analyser designed to generate a full blood count with a standard five‐part white blood cell differential and an immature granulocyte count, as well as an optional reticulocyte and optical platelet (PLT) counts. The aim of the study was to evaluate the performance of the XN‐550 and compare it to the established XN‐20 system.
Toxoplasma gondii sporozoites form a transient parasitophorous vacuole that is impermeable and contains only a subset of dense-granule proteins

Toxoplasma gondii sporozoites form two parasitophorous vacuoles during development within host cells, the first (PV1) during host cell invasion and the second (PV2) 18 to 24 h postinoculation. PV1 is structurally distinctive due to its large size, yet it lacks a tubulovesicular network (C. A. Speer, M. Tilley, M. Temple, J. A. Blixt, J. P. Dubey, and M. W. White, Mol. Biochem. Parasitol. 75:75-86, 1995). Confirming the finding that sporozoites have a different electron-dense-granule composition, we have now found that sporozoites within oocysts lack the mRNAs encoding the 5' nucleoside triphosphate hydrolases (NTPase). NTPase first appears 12 h postinfection. Other tachyzoite dense-granule proteins, GRA1, GRA2, GRA4, GRA5, and GRA6, were detected in oocyst extracts, and antibodies against these proteins stained granules in the sporozoite cytoplasm. In contrast to tachyzoite invasion of host cells, however, sporozoites did not exocytose the dense-granule proteins GRA1, GRA2, or GRA4 during PV1 formation. Even after NTPase induction, these proteins were retained within cytoplasmic granules rather than being secreted into PV1. Only GRA5 was secreted by the sporozoite during host cell invasion, becoming associated with the membrane surrounding PV1. Microinjection of sporozoite-infected cells with fluorescent dyes showed that PV1 is impermeable to fluorescent dyes with molecular masses as small as 330 Da, indicating that PV1 lacks channels through which molecules can pass from the host cytoplasm into the vacuole. By contrast, lucifer yellow rapidly diffused into PV2, demonstrating the presence of molecular channels. These studies indicate that PV1 and PV2 are morphologically, immunologically, and functionally distinct, and that PV2 appears to be identical to the tachyzoite vacuole. The inaccessibility of PV1 to host cell nutrients may explain why parasite replication does not occur in this vacuole.
From Meehl (1954) to fast and frugal heuristics (and back): new insights into how to bridge the clinical–actuarial divide.

It is difficult to overestimate Paul Meehl's influence on judgment and decision-making research. His 'disturbing little book' (Meehl, 1986, p. 370) Clinical versus Statistical Prediction: A Theoretical Analysis and a Review of the Evidence (1954) is known as an attack on human judgment and a call for replacing clinicians with actuarial methods. More than 40 years later, fast and frugal heuristics - proposed as models of human judgment - were formalized, tested, and found to be surprisingly accurate, often more so than the actuarial models that Meehl advocated. We ask three questions: Do the findings of the two programs contradict each other? More generally, how are the programs conceptually connected? Is there anything they can learn from each other? After demonstrating that there need not be a contradiction, we show that both programs converge in their concern to develop (a) domain-specific models of judgment and (b) nonlinear process models that arise from the bounded nature of judgment. We then elaborate the differences between the programs and discuss how these differences can be viewed as mutually instructive: First, we show that the fast and frugal heuristic models can help bridge the clinical - actuarial divide, that is, they can be developed into actuarial methods that are both accurate and easy to implement by the unaided clinical judge. We then argue that Meehl's insistence on improving judgment makes clear the importance of examining the degree to which heuristics are used in the clinical domain and how acceptable they would be as actuarial tools.
On the equivariant Tamagawa number conjecture in tame CM-extensions, II

Abstract We use the notion of non-commutative Fitting invariants to give a reformulation of the equivariant Iwasawa main conjecture (EIMC) attached to an extension F/K of totally real fields with Galois group 𝒢, where K is a global number field and 𝒢 is a p-adic Lie group of dimension one for an odd prime p. We attach to each finite Galois CM-extension L/K with Galois group G a module SKu(L/K) over the center of the group ring ℤG which coincides with the Sinnott–Kurihara ideal if G is abelian. We state a conjecture on the integrality of SKu (L/K) which follows from the equivariant Tamagawa number conjecture (ETNC) in many cases, and is a theorem for abelian G. Assuming the vanishing of the Iwasawa μ-invariant, we compute Fitting invariants of certain Iwasawa modules via the EIMC, and we show that this implies the minus part of the ETNC at p for an infinite class of (non-abelian) Galois CM-extensions of number fields which are at most tamely ramified above p, provided that (an appropriate p-part of) the integrality conjecture holds.
A Hybrid Japanese Parser with Hand-crafted Grammar and Statistics

This paper describes a hybrid parsing method for Japanese which uses both a hand-crafted grammar and a statistical technique. The key feature of our system is that in order to estimate likelihood for a parse tree, the system uses information taken from alternative partial parse trees generated by the grammar. This utilization of alternative trees enables us to construct a new statistical model called Triplet/Quadruplet Model. We show that this model can capture a certain tendency in Japanese syntactic structures and this point contributes to improvement of parsing accuracy on a shallow level. We report that, with an underspecified HPSG-based grammar and a maximum entropy estimation, our parser achieved high accuracy: 88.6% accuracy in dependency analysis of the EDR annotated corpus, and that it outperformed other purely statistical parsing methods on the same corpus. This result suggests that proper treatment of hand-crafted grammars can contribute to parsing accuracy on a shallow level.