Miracle-dz/UniFAR-FTUs huggingface dataset:
Patterns of Recombination in HIV-1M Are Influenced by Selection Disfavouring the Survival of Recombinants with Disrupted Genomic RNA and Protein Structures

Genetic recombination is a major contributor to the ongoing diversification of HIV. It is clearly apparent that across the HIV-genome there are defined recombination hot and cold spots which tend to co-localise both with genomic secondary structures and with either inter-gene boundaries or intra-gene domain boundaries. There is also good evidence that most recombination breakpoints that are detectable within the genes of natural HIV recombinants are likely to be minimally disruptive of intra-protein amino acid contacts and that these breakpoints should therefore have little impact on protein folding. Here we further investigate the impact on patterns of genetic recombination in HIV of selection favouring the maintenance of functional RNA and protein structures. We confirm that chimaeric Gag p24, reverse transcriptase, integrase, gp120 and Nef proteins that are expressed by natural HIV-1 recombinants have significantly lower degrees of predicted folding disruption than randomly generated recombinants. Similarly, we use a novel single-stranded RNA folding disruption test to show that there is significant, albeit weak, evidence that natural HIV recombinants tend to have genomic secondary structures that more closely resemble parental structures than do randomly generated recombinants. These results are consistent with the hypothesis that natural selection has acted both in the short term to purge recombinants with disrupted RNA and protein folds, and in the longer term to modify the genome architecture of HIV to ensure that recombination prone sites correspond with those where recombination will be minimally deleterious.
Handling Discontinuities in Financial Engineering: Good Path Simulation and Smoothing

Discontinuities are common in the pricing and hedging of complex financial derivatives. Quasi-Monte Carlo (QMC) methods for high-dimensional finance problems with discontinuities can be inefficient because of the lack of good smoothness and high dimensionality. Interestingly, path simulation method (PSM) may affect both factors, implying its significance in QMC methods. What defines a “good” PSM for problems with discontinuities? The ability to align the discontinuities with the coordinate axes is a desirable property for a PSM. We show that for an arbitrary PSM, there exists a class of options with discontinuous payoff functions such that the transformed functions have only axis-parallel discontinuities, for which good QMC performance can be expected. In this sense, any PSM can be “good” in QMC methods for a specific class of problems. We analyze the structure of discontinuities for digital options using the new approach and show the superiority and the uniqueness (up to a permutation) of the standard construction. We develop a two-step procedure for pricing and hedging derivatives with discontinuous payoff functions. The first step is to design a good PSM that has the ability to align the discontinuities with the coordinate axes and the second step is to further exploit this nice property to remove the discontinuities completely. We prove that the new estimate is unbiased and has smaller variance. Numerical experiments demonstrate that the two-step procedure is very effective in QMC methods for pricing options and estimating Greeks, leading to a dramatic variance reduction. Both the path simulation step and the smoothing step are crucial and beneficial for QMC methods, with the contribution from each step varying depending on the severity of discontinuity.
Efficient feature weighting methods for ranking

Feature weighting or selection is a crucial process to identify an important subset of features from a data set. Removing irrelevant or redundant features can improve the generalization performance of ranking functions in information retrieval. Due to fundamental differences between classification and ranking, feature weighting methods developed for classification cannot be readily applied to feature weighting for ranking. A state of the art feature selection method for ranking, called GAS, has been recently proposed, which exploits importance of each feature and similarity between every pair of features. However, GAS must compute the similarity scores of all pairs of features, thus it is not scalable for high-dimensional data and its performance degrades on nonlinear ranking functions. This paper proposes novel algorithms, RankWrapper and RankFilter, which is scalable for high-dimensional data and also performs reasonably well on nonlinear ranking functions. RankWrapper and RankFilter are designed based on the key idea of Relief algorithm. Relief is a feature selection algorithm for classification, which exploits the notions of hits (data points within the same class) and misses (data points from different classes) for classification. However, there is no such notion of hits or misses in ranking. The proposed algorithms instead utilize the ranking distances of nearest data points in order to identify the key features for ranking. Our extensive experiments show that RankWrapper and RankFilter generate higher accuracy overall than the GAS and traditional Relief algorithms adapted for ranking, and run substantially faster than the GAS on high dimensional data.
Accelerating the Review of Complex Intellectual Artifacts in Crowdsourced Innovation Challenges

A critical bottleneck in crowdsourced innovation challenges is the process of reviewing and selecting the best submissions. This bottleneck is especially problematic in settings where submissions are complex intellectual artifacts whose evaluation requires expertise. To help reduce the review load from experts, we offer a computational approach that relies on analyzing sociolinguistic and other characteristics of submission text, as well as activities of the crowd and the submission authors, and scores the submissions. We developed and tested models based on data from contests done in a large citizen-science platform - the Climate CoLab - and find that they are able to accurately predict expert decisions about the submissions, and can lead to substantial reduction of review labor, and acceleration of the review process.
A clinical comparison of zirconia, metal and alumina fixed-prosthesis frameworks veneered with layered or pressed ceramic: a three-year report.

BACKGROUND The authors conducted a randomized controlled clinical trial to determine whether performance differed between metal, zirconia and alumina fixed partial denture (FPD) frameworks veneered with pressed or layered ceramics designed for each framework type. METHODS Posterior three-unit FPDs (N = 293) of 10 different framework/veneer ceramic combinations were placed by 115 dentists in 259 patients from their practices according to a masked protocol. Yearly, the clinicians graded the prostheses and the opposing dentition in vivo according to 17 criteria, and two independent scientists graded them in vitro by using gold-sputtered dies, scanning electron micrographs and clinical photographs. RESULTS Three metal and five zirconia frameworks tested were not statistically different, with zero and two fractures, respectively. Alumina frameworks were statistically worse, with 11 fractures. The veneer ceramics CZR Press (Noritake Dental, Aichi, Japan) and Pulse interface (Jensen Dental, North Haven, Conn.) performed best with zirconia and metal frameworks, respectively. Four nonleucite-containing veneer ceramics used with zirconia frameworks had substantially more fractures. CONCLUSIONS Five zirconia framework brands performed equally well and were statistically comparable with metal frameworks at three years. Two leucite-containing veneer ceramics applied by means of pressing techniques had the statistically lowest number of fractures. CLINICAL IMPLICATIONS Dentists can use metal or zirconia frameworks successfully if they are designed properly, but to avoid veneer ceramic surface crumbling and minimize chipping, use of leucite-containing pressed ceramics is indicated.
PEMODELAN INDEKS PEMBANGUNAN MANUSIA KABUPATEN/KOTA DI PROVINSI PAPUA DAN PAPUA BARAT TAHUN 2014

Human Development Index is a measure of human development achievement based on the appropriate dimensions of health, education, and living. Papua is located in eastern Indonesia consisting of 2 provinces of Papua and west Papua. This study conducted a research about modeling of district/city of human development index value using binary logistic regression model, estimation of model parameters using maximum likelihood method. The data used in this study is secondary data obtained from the central statistical agencies of Papua and West Papua provinces. This study involved several factors that predicted to be affected the Human Development Index of district/city in both provinces, namely PDRB/capita, sex ratio, population density, population growth rate and number of mobile health centers. Based on the result of the analysis, it can be seen that the independent variables that significantly influence the value of Human Development Index of district/city in Papua 2014 is income/capita with the probability value of 0.003 and the population of mobile health centers with the probability of 0.034
Characterization of Oilseed Lipids from “DHA-Producing Camelina sativa”: A New Transformed Land Plant Containing Long-Chain Omega-3 Oils

New and sustainable sources of long-chain (LC, ≥C20) omega-3 oils containing DHA (docosahexaenoic acid, 22:6ω3) are required to meet increasing demands. The lipid content of the oilseed of a novel transgenic, DHA-producing land plant, Camelina sativa, containing microalgal genes able to produce LC omega-3 oils, contained 36% lipid by weight with triacylglycerols (TAG) as the major lipid class in hexane extracts (96% of total lipid). Subsequent chloroform-methanol (CM) extraction recovered further lipid (~50% polar lipid, comprising glycolipids and phospholipids) and residual TAG. The main phospholipid species were phosphatidyl choline and phosphatidyl ethanolamine. The % DHA was: 6.8% (of total fatty acids) in the TAG-rich hexane extract and 4.2% in the polar lipid-rich CM extract. The relative level of ALA (α-linolenic acid, 18:3ω3) in DHA-camelina seed was higher than the control. Major sterols in both DHA- and control camelina seeds were: sitosterol, campesterol, cholesterol, brassicasterol and isofucosterol. C16–C22 fatty alcohols, including iso-branched and odd-chain alcohols were present, including high levels of iso-17:0, 17:0 and 19:0. Other alcohols present were: 16:0, iso-18:0, 18:0 and 18:1 and the proportions varied between the hexane and CM extracts. These iso-branched odd-chain fatty alcohols, to our knowledge, have not been previously reported. These components may be derived from wax esters, or free fatty alcohols.
Aberrant expression of human achaete-scute homologue gene 1 in the gastrointestinal neuroendocrine carcinomas.

PURPOSE Gastrointestinal neuroendocrine carcinoma (NEC) is extremely aggressive, but its pathophysiologic features remain poorly understood. There have been no biologically specific markers for this disease. In this study, distinctive up-regulation of human achaete-scute homologue 1 (hASH1) in gastrointestinal NECs was clarified. EXPERIMENTAL DESIGN Expression of hASH1 in NECs (n=10), carcinoid tumors (n = 10), other tumors (10 adenocarcinomas, 2 squamous cell carcinomas and 1 malignant lymphoma), and the corresponding normal mucosa were investigated by in situ hybridization, reverse transcription-PCR (RT-PCR), real-time RT-PCR, and immunohistochemistry. RESULTS By in situ hybridization, mild to intense signals of hASH1 mRNA were detected in 9 of 10 NECs, but not in other tumors or normal mucosa, except for focally weak signals in one carcinoid tumor. RT-PCR showed strong expression of hASH1 in a small cell NEC, followed by a moderately differentiated NEC, and a carcinoid tumor, whereas it is undetectable in adenocarcinomas or normal mucosa. By real-time RT-PCR, the amounts of hASH1 mRNA in a small cell NEC were 16,600 times higher than those in adenocarcinomas and 110 times higher than those in a carcinoid tumor. Immunohistochemically, mammalian homologue of hASH1 was positive in 7 of 10 NECs but was negative in the other tumors. Pan-endocrine markers chromogranin A and synaptophysin were positive in almost all carcinoid tumors, in 4 and 7 of the 10 NECs, respectively. CONCLUSIONS These findings revealed that hASH1 is distinctly up-regulated in gastrointestinal NECs. hASH1 may be used as a more sensitive and specific marker than conventional pan-endocrine markers for clinical diagnosis of gastrointestinal NECs.
The Mammalian Cone Visual Cycle Promotes Rapid M/L-Cone Pigment Regeneration Independently of the Interphotoreceptor Retinoid-Binding Protein

Rapid regeneration of the visual pigment following its photoactivation is critical for the function of cone photoreceptors throughout the day. Though the reactions of the visual cycle in the retinal pigment epithelium (RPE) that recycle chromophore for rod pigment regeneration are well characterized, the corresponding mechanisms that enable rapid regeneration of cone pigment are poorly understood. A key remaining question is the relative contribution of the recently discovered cone-specific retina visual cycle and the classic RPE-dependent visual cycle to mammalian cone pigment regeneration. In addition, it is not clear what role, if any, the abundant interphotoreceptor retinoid-binding protein (IRBP) presumed to facilitate the traffic of chromophore, plays in accelerating mammalian cone pigment regeneration. To address these issues, we used transretinal recordings to evaluate M/L-cone pigment regeneration in isolated retinas and eyecups from control and IRBP-deficient mice. Remarkably, the mouse retina promoted M/L-cone dark adaptation eightfold faster than the RPE. However, complete cone recovery required both visual cycles. We conclude that the retina visual cycle is critical for the initial rapid regeneration of mouse M/L-cone pigment during dark adaptation, whereas the slower RPE visual cycle is required to complete the process. While the deletion of IRBP reduced the amplitude and slowed the kinetics of mouse M/L-cone photoresponses, cone adaptation in bright, steady light and the kinetics of cone dark adaptation were not affected in isolated retina or in intact eyecup. Thus, IRBP does not accelerate cone pigment regeneration and is not critical for the function of mouse M/L-cones in bright light.
Magnetic iron oxide nanoparticles: synthesis, stabilization, vectorization, physicochemical characterizations, and biological applications.

1. Introduction 20642. Synthesis of Magnetic Nanoparticles 20662.1. Classical Synthesis by Coprecipitation 20662.2. Reactions in Constrained Environments 20682.3. Hydrothermal and High-TemperatureReactions20692.4. Sol-Gel Reactions 20702.5. Polyol Methods 20712.6. Flow Injection Syntheses 20712.7. Electrochemical Methods 20712.8. Aerosol/Vapor Methods 20712.9. Sonolysis 20723. Stabilization of Magnetic Particles 20723.1. Monomeric Stabilizers 20723.1. 1. Carboxylates 20733.1. 2. Phosphates 20733.2. Inorganic Materials 20733.2. 1. Silica 20733.2. 2. Gold 20743.3. Polymer Stabilizers 20743.3. 1. Dextran 20743.3. 2. Polyethylene Glycol (PEG) 20753.3. 3. Polyvinyl Alcohol (PVA) 20753.3. 4. Alginate 20753.3. 5. Chitosan 20753.3. 6. Other Polymers 20753.4. Other Strategies for Stabilization 20764. Methods of Vectorization of the Particles 20765. Structural and Physicochemical Characterization 20785.1. Size, Polydispersity, Shape, and SurfaceCharacterization20795.2. Structure of Ferro- or FerrimagneticNanoparticles20805.2. 1. Ferro- and Ferrimagnetic Nanoparticles 20805.3. Use of Nanoparticles as Contrast Agents forMRI20825.3. 1. High Anisotropy Model 20845.3. 2. Small Crystal and Low Anisotropy EnergyLimit20855.3. 3. Practical Interests of Magnetic NuclearRelaxation for the Characterization ofSuperparamagnetic Colloid20855.3. 4. Relaxation of Agglomerated Systems 20856. Applications 20866.1. MRI: Cellular Labeling, Molecular Imaging(Inﬂammation, Apoptose, etc.)20866.2.
Cdk5 Is Essential for Amphetamine to Increase Dendritic Spine Density in Hippocampal Pyramidal Neurons

Psychostimulant drugs of abuse increase dendritic spine density in reward centers of the brain. However, little is known about their effects in the hippocampus, where activity-dependent changes in the density of dendritic spine are associated with learning and memory. Recent reports suggest that Cdk5 plays an important role in drug addiction, but its role in psychostimulant’s effects on dendritic spines in hippocampus remain unknown. We used in vivo and in vitro approaches to demonstrate that amphetamine increases dendritic spine density in pyramidal neurons of the hippocampus. Primary cultures and organotypic slice cultures were used for cellular, molecular, pharmacological and biochemical analyses of the role of Cdk5/p25 in amphetamine-induced dendritic spine formation. Amphetamine (two-injection protocol) increased dendritic spine density in hippocampal neurons of thy1-green fluorescent protein (GFP) mice, as well as in hippocampal cultured neurons and organotypic slice cultures. Either genetic or pharmacological inhibition of Cdk5 activity prevented the amphetamine–induced increase in dendritic spine density. Amphetamine also increased spine density in neurons overexpressing the strong Cdk5 activator p25. Finally, inhibition of calpain, the protease necessary for the conversion of p35 to p25, prevented amphetamine’s effect on dendritic spine density. We demonstrate, for the first time, that amphetamine increases the density of dendritic spine in hippocampal pyramidal neurons in vivo and in vitro. Moreover, we show that the Cdk5/p25 signaling and calpain activity are both necessary for the effect of amphetamine on dendritic spine density. The identification of molecular mechanisms underlying psychostimulant effects provides novel and promising therapeutic approaches for the treatment of drug addiction.
The Role of Climate Variability in the Spread of Malaria in Bangladeshi Highlands

Background Malaria is a major public health problem in Bangladesh, frequently occurring as epidemics since the 1990s. Many factors affect increases in malaria cases, including changes in land use, drug resistance, malaria control programs, socioeconomic issues, and climatic factors. No study has examined the relationship between malaria epidemics and climatic factors in Bangladesh. Here, we investigate the relationship between climatic parameters [rainfall, temperature, humidity, sea surface temperature (SST), El Niño-Southern Oscillation (ENSO), the normalized difference vegetation index (NDVI)], and malaria cases over the last 20 years in the malaria endemic district of Chittagong Hill Tracts (CHT). Methods and Principal Findings Monthly malaria case data from January 1989 to December 2008, monthly rainfall, temperature, humidity sea surface temperature in the Bay of Bengal and ENSO index at the Niño Region 3 (NIÑO3) were used. A generalized linear negative binomial regression model was developed using the number of monthly malaria cases and each of the climatic parameters. After adjusting for potential mutual confounding between climatic factors there was no evidence for any association between the number of malaria cases and temperature, rainfall and humidity. Only a low NDVI was associated with an increase in the number of malaria cases. There was no evidence of an association between malaria cases and SST in the Bay of Bengal and NIÑO3. Conclusion and Significance It seems counterintuitive that a low NDVI, an indicator of low vegetation greenness, is associated with increases in malaria cases, since the primary vectors in Bangladesh, such as An. dirus, are associated with forests. This relationship can be explained by the drying up of rivers and streams creating suitable breeding sites for the vector fauna. Bangladesh has very high vector species diversity and vectors suited to these habitats may be responsible for the observed results.
High Trait Anxiety: A Challenge for Disrupting Fear Memory Reconsolidation

Disrupting reconsolidation may be promising in the treatment of anxiety disorders but the fear-reducing effects are thus far solely demonstrated in the average organism. A relevant question is whether disrupting fear memory reconsolidation is less effective in individuals who are vulnerable to develop an anxiety disorder. By collapsing data from six previous human fear conditioning studies we tested whether trait anxiety was related to the fear-reducing effects of a pharmacological agent targeting the process of memory reconsolidation - n = 107. Testing included different phases across three consecutive days each separated by 24 h. Fear responding was measured by the eye-blink startle reflex. Disrupting the process of fear memory reconsolidation was manipulated by administering the β-adrenergic receptor antagonist propranolol HCl either before or after memory retrieval. Trait anxiety uniquely predicted the fear-reducing effects of disrupting memory reconsolidation: the higher the trait anxiety, the less fear reduction. Vulnerable individuals with the propensity to develop anxiety disorders may need higher dosages of propranolol HCl or more retrieval trials for targeting and changing fear memory. Our finding clearly demonstrates that we cannot simply translate observations from fundamental research on fear reduction in the average organism to clinical practice.
Understanding Perceptions of Economic Status among Centenarians

Centenarians are often concerned with outliving their accumulated resources. Yet, research consistently finds that older adults, despite low incomes, are more financially satisfied than younger adults. This “satisfaction paradox” has been attributed to psychological accommodation to poor financial circumstances and lower expectations. As a result, scholars differentiate between objective levels of need and subjective perceptions. Missing is an understanding of whether feeling economically secure is associated with physical, mental, and/or psychological well-being and whether it varies by institutionalization status. This study examined data from 152 centenarians who participated in the first wave of the Iowa Centenarian Study. Analyses examined six perceived economic status variables (sufficiency of financial resources, ability to meet expenses, finances compared to others, meeting needs, ability to purchase extras, and having enough money for the future) and measures derived from activities of daily living, the Short Portable Mental Status Questionnaire (Pfeiffer, 1975) and the Geriatric Depression Scale (Yesavage, Brink, Rose, Lum, Huang, Adey, et al., 1983). Findings indicated that most centenarians do not feel able to handle their finances, yet believe that they are doing relatively well financially. Perceived economic status was positively associated with ability to complete daily living activities, cognitive ability, and psychological well-being with results differing by institutional status. In the end, we agree with other scholars that these relationships are rarely simple and require future exploration.