Miracle-dz/UniFAR-FTUs huggingface dataset:
Reinforcement learning and counterfactual reasoning explain adaptive behavior in a changing environment

Animals routinely adapt to changes in the environment in order to survive. Though reinforcement learning may play a role in such adaptation, it is not clear that it is the only mechanism involved, as it is not well suited to producing rapid, relatively immediate changes in strategies in response to environmental changes. This research proposes that counterfactual reasoning might be an additional mechanism that facilitates change detection. An experiment is conducted in which a task state changes over time and the participants had to detect the changes in order to perform well and gain monetary rewards. A cognitive model is constructed that incorporates reinforcement learning with counterfactual reasoning to help quickly adjust the utility of task strategies in response to changes. The results show that the model can accurately explain human data and that counterfactual reasoning is key to reproducing the various effects observed in this change detection paradigm.
Phase I Trial of Overlapping Long Peptides from a Tumor Self-Antigen and Poly-ICLC Shows Rapid Induction of Integrated Immune Response in Ovarian Cancer Patients

Purpose: Long peptides are efficiently presented to both CD4+ and CD8+ T cells after intracellular processing by antigen-presenting cells. To investigate the safety and in vivo immunogenicity of synthetic overlapping long peptides (OLP) from a human tumor self-antigen, we conducted a phase I clinical trial with OLP from cancer-testis antigen NY-ESO-1 in various adjuvant combinations. Experimental Design: Twenty-eight patients with advanced ovarian cancer in second or third remission were enrolled sequentially in three cohorts and received at least one vaccination. Patients in Cohort 1 (n = 4) received 1.0 mg OLP, Cohort 2 (n = 13) received OLP in Montanide-ISA-51, and Cohort 3 (n = 11) received OLP + 1.4 mg Poly-ICLC in Montanide-ISA-51 on weeks 1, 4, 7, 10, and 13. Humoral and cellular responses were evaluated by standardized immunomonitoring techniques (ELISA, ELISPOT assay, intracellular cytokine staining, and tetramer staining). Results: The vaccine was generally well tolerated with injection site reactions and fatigue that resolved. NY-ESO-1–specific antibody and CD8+ T cells were undetectable after vaccination with OLP alone, but were found in 6 of 13 (46%) and 8 of 13 (62%) patients, respectively, after vaccination with OLP+Montanide, and in 10 of 11 (91%) and 10 of 11 (91%) patients, respectively, after vaccination with OLP+Montanide+Poly-ICLC. NY-ESO-1–specific CD4+ T cells were detected in all patients with greater frequency and polyclonality when Montanide-ISA-51 was used for vaccination. Inclusion of Poly-ICLC as an adjuvant further accelerated the induction of NY-ESO-1–specific immune responses. Conclusions: The current study shows that NY-ESO-1 OLP vaccine is safe and rapidly induces consistent integrated immune responses (antibody, CD8+ and CD4+) in nearly all vaccinated patients when given with appropriate adjuvants. Clin Cancer Res; 18(23); 6497–508. ©2012 AACR.
Searching with expectations

Handling large amounts of data, such as large image databases, requires the use of approximate nearest neighbor search techniques. Recently, Hamming embedding methods such as spectral hashing have addressed the problem of obtaining compact binary codes optimizing the trade-off between the memory usage and the probability of retrieving the true nearest neighbors. In this paper, we formulate the problem of generating compact signatures as a rate-distortion problem. In the spirit of source coding algorithms, we aim at minimizing the reconstruction error on the squared distances with a constraint on the memory usage. The vectors are ranked based on the distance estimates to the query vector. Experiments on image descriptors show a significant improvement over spectral hashing.
Cushing Disease After Treatment of Nonfunctional Pituitary Adenoma

AbstractWe describe a very rare case of nonfunctional pituitary adenoma (NFPA) that exhibited corticotrophic activity after resection and radiotherapy. The possible mechanisms of the transformation from NFPA to Cushing disease (CD) are discussed.A 43-year-old man presented with impaired vision, bilateral frontal headaches, and hyposexuality. He had no symptoms suggestive of hypercortisolism, and 8 am plasma cortisol concentration was 67.88 ng/mL. Brain imaging revealed a 15 × 15 × 21-mm sellar mass suggestive of a macroadenoma. The tumor was resected by transsphenoidal surgery and identified by immunohistochemical analysis as a chromophobic adenoma that did not stain for pituitary hormones. The patient was treated with prednisone and levothyroxine replacement therapy. After a third recurrence, the patient presented with clinical features and physical signs of Cushing syndrome. Plasma adrenocorticotropic hormone (ACTH) and cortisol concentrations were elevated, and there was a loss of circadian rhythms. Inferior petrosal sinus sampling after desmopressin showed the central–peripheral ACTH ratio was greater than 3:1. A repeat transsphenoidal resection was undertaken. Immunohistochemistry revealed ACTH positivity. Three months following surgery, imaging showed little residual tumor, but plasma ACTH remained elevated. He was referred for postoperative Gamma Knife radiotherapy.The immunological activity and biological features of the hormones secreted from a pituitary adenoma vary with time. Because long-term outcomes are unpredictable, postoperative follow-up is essential to detect postoperative transformation from NFPA to CD.
jModelTest: phylogenetic model averaging.

jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" (Guindon and Gascuel 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.). It implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion," the "Bayesian information criterion," and a "decision-theoretic performance-based" approach. This program also calculates the relative importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny. jModelTest is written in Java and runs under Mac OSX, Windows, and Unix systems with a Java Runtime Environment installed. The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo. es.
Orbital order and possible superconductivity in LaNiO3/LaMO3 superlattices.

A hypothetical layered oxide La2NiMO6 where NiO2 and MO2 planes alternate along the c axis of ABO3 perovskite lattice is considered theoretically. Here, M denotes a trivalent cation Al, Ga,. such that MO2 planes are insulating and suppress the c-axis charge transfer. We predict that correlated eg electrons in the NiO2 planes develop a planar x2-y2 orbital order driven by the reduced dimensionality and further supported by epitaxial strain from the substrate. Low-energy electronic states can be mapped to a single-band t - t' - J model, suggesting favorable conditions for high-Tc superconductivity.
Inference in Probabilistic Logic Programs using Weighted CNF's

Probabilistic logic programs are logic programs in which some of the facts are annotated with probabilities. Several classical probabilistic inference tasks (such as MAP and computing marginals) have not yet received a lot of attention for this formalism. The contribution of this paper is that we develop efficient inference algorithms for these tasks. This is based on a conversion of the probabilistic logic program and the query and evidence to a weighted CNF formula. This allows us to reduce the inference tasks to well-studied tasks such as weighted model counting. To solve such tasks, we employ state-of-the-art methods. We consider multiple methods for the conversion of the programs as well as for inference on the weighted CNF. The resulting approach is evaluated experimentally and shown to improve upon the state-of-the-art in probabilistic logic programming.
Hand gesture controlled interface for Intelligent Space applications

Intelligent Space or iSpace is a new kind of computing system aiming at improving the environments of humans, creating a natural and easy to use solution. Its main feature is that the intelligence is not implemented separately in the actors, but it is distributed in the whole space. In this paper, we present a hand gesture and movement recognition system, whose purpose is to be used as an intuitive interface for the iSpace.
Senseye: a multi-tier heterogeneous camera sensor network

Rapid technological developments in sensing devices, embedded platforms and wireless communication technologies, have enabled and led to a large research focus in sensor networks. Traditional sensor networks have been designed as networks of homogeneous sensor nodes. Single-tier networks consisting of homogeneous nodes achieve only a subset of application requirements and often sacrifice others. In this thesis, I propose the notion of multi-tier heterogeneous sensor networks, sensors organized hierarchically into multiple tiers. With intelligent use of resources across tiers, multi-tier heterogeneous sensor networks have the potential to simultaneously achieve the conflicting goals of network lifetime, sensing reliability and functionality. I consider a class of sensor networks---camera sensor networks---wireless networks with image sensors. I address the issues of automatic configuration and initialization and design of camera sensor networks. Like any sensor network, initialization of cameras is an important pre-requisite for camera sensor networks applications. Since, camera sensor networks have varying degrees of infrastructure support and resource constraints a single initialization procedure is not appropriate. I have proposed the notions of accurate and approximate initialization to initialize cameras with varying capabilities and resource constraints. I have developed and empirically evaluated Snapshot, an accurate calibration protocol tailored for sensor network deployments. I have also developed approximate initialization techniques that estimate the degree of overlap and region of overlap estimates at each camera. Further, I demonstrate usage of these estimates to instantiate camera sensor network applications. As compared to manual calibration, which can take a long time (order of hours) to calibrate several cameras, is inefficient and error prone, the automated calibration protocol is accurate and greatly reduces the time for accurate calibration---tens of seconds to calibrate a single camera and can easily scale to calibrate several cameras in order of minutes. The approximate techniques demonstrate feasibility of initializing low-power resource constrained cameras with no or limited infrastructure support. With regards to design of camera sensor networks, I present the design and implementation of SensEye, a multi-tier heterogeneous camera sensor network and address the issue of energy-reliability tradeoff. Multi-tier networks provide several levels of reliability and energy usage based on the type of sensor used for application tasks. Using SensEye I demonstrate how multi-tier networks can achieve simultaneous system goals of energy efficiency and reliability.
Borrelia carolinensis sp. nov., a novel species of the Borrelia burgdorferi sensu lato complex isolated from rodents and a tick from the south-eastern USA

A group of 16 isolates with genotypic characteristics different from those of known species of the Borrelia burgdorferi sensu lato complex were cultured from ear biopsies of the rodents Peromyscus gossypinus and Neotoma floridana trapped at five localities in South Carolina, USA, and from the tick Ixodes minor feeding on N. floridana. Multilocus sequence analysis of members of the novel species, involving the 16S rRNA gene, the 5S–23S (rrf–rrl) intergenic spacer region and the flagellin, ospA and p66 genes, was conducted and published previously and was used to clarify the taxonomic status of the novel group of B. burgdorferi sensu lato isolates. Phylogenetic analysis based on concatenated sequences of the five analysed genomic loci showed that the 16 isolates clustered together but separately from other species in the B. burgdorferi sensu lato complex. The analysed group therefore represents a novel species, formally described here as Borrelia carolinensis sp. nov., with the type strain SCW-22T (=ATCC BAA-1773T =DSM 22119T).
Prediction of river hydraulic conditions via satellite multi-spectral imagery and statistical learners

The hydrologic regimes and ecology of many rivers have been altered through human action. Understanding the natural processes and the extent of alteration is a crucial component of management and restoration of these systems. River and floodplain systems are often highly dynamic, requiring data sets that cover a large spatial extent to fully assess ecological structure and function. However, in situ data collection is extremely challenging in these environments, particularly in localities of high river velocity. This article discusses an approach that exploits high resolution remotely sensed images for expanding data coverage, and thereby enhancing the quantification of important hydraulic parameters, specifically water depth, flow velocity and energetic state through Froude number. The primary elements of this approach are (i) acoustic Doppler profilers coupled with GPS for in situ data collection of water depth and velocity (ii) satellite multispectral imagery, (iii) modern distribution-free statistical learners, and (iv) error analysis. Herein, we provide motivation and background for the study of riverine landscapes via remote sensing, though the article concentrates on the third and fourth elements of the approach. An analysis of a 12 km reach of the Tagliamento River located in Northern Italy provides an example of our approach.
The Drosophila Receptor Guanylyl Cyclase Gyc76C Is Required for Semaphorin-1a-Plexin A-Mediated Axonal Repulsion

Cyclic nucleotide levels within extending growth cones influence how navigating axons respond to guidance cues. Pharmacological alteration of cAMP or cGMP signaling in vitro dramatically modulates how growth cones respond to attractants and repellents, although how these second messengers function in the context of guidance cue signaling cascades in vivo is poorly understood. We report here that the Drosophila receptor-type guanylyl cyclase Gyc76C is required for semaphorin-1a (Sema-1a)-plexin A repulsive axon guidance of motor axons in vivo. Our genetic analyses define a neuronal requirement for Gyc76C in axonal repulsion. Additionally, we find that the integrity of the Gyc76C catalytic cyclase domain is critical for Gyc76C function in Sema-1a axon repulsion. Our results support a model in which cGMP production by Gyc76C facilitates Sema-1a-plexin A-mediated defasciculation of motor axons, allowing for the generation of neuromuscular connectivity in the developing Drosophila embryo.
Carbohydrate Mouth Rinse Improves 1.5 h Run Performance: Is There A Dose-Effect?

There is a substantial body of recent evidence showing ergogenic effects of carbohydrate (CHO) mouth rinsing on endurance performance. However, there is a lack of research on the dose-effect and the aim of this study was to investigate the effect of two different concentrations (6% and 12% weight/volume, w/v) on 90 minute treadmill running performance. Seven active males took part in one familiarization trial and three experimental trials (90-minute self-paced performance trials). Solutions (placebo, 6% or 12% CHO-electrolyte solution, CHO-E) were rinsed in the mouth at the beginning, and at 15, 30 and 45 minutes during the run. The total distance covered was greater during the CHO-E trials (6%, 14.6 ± 1.7 km; 12%, 14.9 ± 1.6 km) compared to the placebo trial (13.9 ± 1.7 km, P < 0.05). There was no significant difference between the 6% and 12% trials (P > 0.05). There were no between trial differences (P > 0.05) in ratings of perceived exertion (RPE) and feeling or arousal ratings suggesting that the same subjective ratings were associated with higher speeds in the CHO-E trials. Enhanced performance in the CHO-E trials was due to higher speeds in the last 30 minutes even though rinses were not provided during the final 45 minutes, suggesting the effects persist for at least 20–45 minutes after rinsing. In conclusion, mouth rinsing with a CHO-E solution enhanced endurance running performance but there does not appear to be a dose-response effect with the higher concentration (12%) compared to a standard 6% solution.
Road Scene Analysis by Stereovision: a Robust and Quasi-Dense Approach

A stereovision method is presented in this paper, to compute reliable and quasi-dense disparity maps of road scenes using in-vehicle cameras. It combines the advantages of the "v-disparity" approach and a quasi-dense matching algorithm. In this aim, road surface and vertical planes of the scene are first extracted using the sparse "v-disparity" approach. The knowledge of these global surfaces of the scene is then used to guide a quasi-dense matching algorithm and to propagate disparity information on horizontal edges. Both algorithms are presented and compared. Then, our approach is presented and examples of quasi-dense disparity maps are given. Finally, the efficiency of the method is illustrated by the accurate positioning of a bounding box around a vehicle in a bad contrasted video sequence
Aliskiren Effect on Plaque Progression in Established Atherosclerosis Using High Resolution 3D MRI (ALPINE): A Double-Blind Placebo-Controlled Trial

Background The renin–angiotensin system is well recognized as a mediator of pathophysiological events in atherosclerosis. The benefits of renin inhibition in atherosclerosis, especially when used in combination with angiotensin-converting enzyme inhibitors/angiotensin receptor blockers (ACEIs/ARBs) are currently not known. We hypothesized that treatment with the renin inhibitor aliskiren in patients with established cardiovascular disease will prevent the progression of atherosclerosis as determined by high-resolution magnetic resonance imaging (MRI) measurements of arterial wall volume in the thoracic and abdominal aortas of high-risk patients with preexisting cardiovascular disease. Methods and Results This was a single-center, randomized, double-blind, placebo-controlled trial in patients with established cardiovascular disease. After a 2-week single-blind placebo phase, patients were randomized to receive either placebo (n=37, mean±SD age 64.5±8.9 years, 3 women) or 150 mg of aliskiren (n=34, mean±SD age 63.9±11.5 years, 9 women). Treatment dose was escalated to 300 mg at 2 weeks and maintained during the remainder of the study. Patients underwent dark-blood, 3-dimensional MRI assessment of atherosclerotic plaque in the thoracic and abdominal segments at baseline and on study completion or termination (up to 36 weeks of drug or matching placebo). Aliskiren use resulted in significant progression of aortic wall volume (normalized total wall volume 5.31±6.57 vs 0.15±4.39 mm3, P=0.03, and percentage wall volume 3.37±2.96% vs 0.97±2.02%, P=0.04) compared with placebo. In a subgroup analysis of subjects receiving ACEI/ARB therapy, atherosclerosis progression was observed only in the aliskiren group, not in the placebo group. Conclusions MRI quantification of atheroma plaque burden demonstrated that aliskiren use in patients with preexisting cardiovascular disease resulted in an unexpected increase in aortic atherosclerosis compared with placebo. Although preliminary, these results may have implications for the use of renin inhibition as a therapeutic strategy in patients with cardiovascular disease, especially in those receiving ACEI/ARB therapy. Clinical Trial Registration URL: http://ClinicalTrials.gov Unique identifier: NCT01417104.
Beyond Genetics—Stratified and Personalised Medicines Using Multiple Parameters

Prescribers have been practicing stratified medicine for many years. Patient characteristics, usually non-genetic, including age, comorbidities and concomitant medications are taken into account when deciding which drug to prescribe. In addition, the majority of drugs require dose adjustments across patient subgroups, usually determined by non-genetic differences between the subgroups. Whilst pharmacogenetics hold promise for enhancing treatment stratification and even treatment individualisation, non-genetic factors will continue to be very important. Both non-genetic and genetic factors must be considered to improve understanding and quantification of the variability in treatment outcomes and to guide stratification and targeting of patient subgroups to the right drug and also to the right range of doses within that subgroup. Development of stratified medicines must consider non-genetic as well as genetic factors and, where appropriate, include stratification through optimising the dose for each patient or subgroup as well as by choosing the drug most likely to deliver efficacy to that patient or group.
Improved Boussinesq-type equations for highly variable depth

Intermediate-depth, Boussinesq-type modelling is used to generalize previously known results for surface water waves propagating over arbitrarily shaped topographies. The improved reduced wave model is obtained after studying how small changes in the linear dispersion relation (over a flat bottom) can become dramatically important in the presence of a highly fluctuating topography. Numerical validation of the dispersive properties, regarding several possible truncations for the reduced models, are compared with the complete (non-truncated) linear potential theory model. Moreover, linear L 2 -estimates are extended from the analysis of KdV-type models to include the improved Boussinesq systems in contrast with potential theory. Discrepancies observed among the different possible reduced models become even more important in the wave-form inversion problem. The time reversal technique is used for recompressing a long fluctuating signal, representing a highly scattered wave that has propagated for very long distances. When properly back-propagated (through a numerical model), the scattered signal refocuses into a smooth profile representing the onset of the ocean's surface disturbance. Previous Boussinesq models underestimate the original disturbance's amplitude. The improved Boussinesq system agrees very well with the full potential theory predictions.
The Correlational Study of the Personality Traits, Organizational Commitment and Self-Efficacy of Saving and Credit Co-Operative Societies (SACCOS) Employees of Kathmandu

This research is about the study of the Saving and Credit Co-operative Societies (SACCOS) employees’ personality traits, self-efficacy, and organizational commitment of Kathmandu district. The researchers have used Mini-IPIP five-factor model personality. The scale consists of 20-items short form of the 50-items IPIP-FFM. The Big Five personality traits have measured employee’s agreeableness, conscientiousness, emotional stability, extraversion and intellect. The Organizational commitment scale is used to measure the employee’s affective, normative and continuance commitment. The employees are human capital and without their contribution, no one can imagine of this present digital world. The Self-efficacy scale is used to find the optimistic beliefs of employees’ competence to deal efficiently with a variety of stressful situations. The total sample size consists of 260 employees (Male = 127 & Female = 133). The samples are drawn from Sixty Three SACCOS of Kathmandu district only. This study finds the relationships among the SACCOS employees’ personality traits, commitment and self-efficacy to handle the employees’ behavior efficiently for the overall productivity of an organization.