Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematics in lensing reconstruction: dark matter rings in the sky?

Context. Non-parametric lensing methods are a useful way of reconstructing the lensing mass of a cluster without making assumptions about the way the mass is distributed in the cluster. These methods are particularly powerful in the case of galaxy clusters with a large number of constraints. The advantage of not assuming implicitly that the luminous matter follows the dark matter is particularly interesting in those cases where the cluster is in a non-relaxed dynamical state. On the other hand, non-parametric methods have several limitations that should be taken into account carefully. Aims. We explore some of these limitations and focus on their implications for the possible ring of dark matter around the galaxy cluster CL0024+17. Methods. We project three background galaxies through a mock cluster of known radial profile density and obtain a map for the arcs (θ map). We also calculate the shear field associated with the mock cluster across the whole field of view (3.3 arcmin). Combining the positions of the arcs and the two-direction shear, we perform an inversion of the lens equation using two separate methods, the biconjugate gradient, and the quadratic programming (QADP) to reconstruct the convergence map of the mock cluster. Results. We explore the space of the solutions of the convergence map and compare the radial density profiles to the density profile of the mock cluster. When the inversion matrix algorithms are forced to find the exact solution, we encounter systematic effects resembling ring structures, that clearly depart from the original convergence map. Conclusions. Overfitting lensing data with a non-parametric method can produce ring-like structures similar to the alleged one in CL0024.
An evaluation of depth perception on volumetric displays

We present an experiment that compares volumetric displays to existing 3D display techniques in three tasks that require users to perceive depth in 3D scenes. Because they generate imagery in true 3D space, volumetric displays allow viewers to use their natural physiological mechanisms for depth perception, without requiring special hardware such as head trackers or shutter glasses. However, it is unclear from the literature as to whether these displays are actually better than the status-quo for enabling the perception of 3D scenes, thus motivating the present study. Our results show that volumetric displays enable significantly better user performance in a simple depth judgment task, and better performance in a collision judgment task, but in its current form does not enhance user comprehension of more complex 3D scenes.
Multi-Label Classification: An Overview

Multi-label classification methods are increasingly required by modern applications, such as protein function classification, music categorization, and semantic scene classification. This article introduces the task of multi-label classification, organizes the sparse related literature into a structured presentation and performs comparative experimental results of certain multilabel classification methods. It also contributes the definition of concepts for the quantification of the multi-label nature of a data set.
Characterising the Mucosal and Systemic Immune Responses to Experimental Human Hookworm Infection

The mucosal cytokine response of healthy humans to parasitic helminths has never been reported. We investigated the systemic and mucosal cytokine responses to hookworm infection in experimentally infected, previously hookworm naive individuals from non-endemic areas. We collected both peripheral blood and duodenal biopsies to assess the systemic immune response, as well as the response at the site of adult worm establishment. Our results show that experimental hookworm infection leads to a strong systemic and mucosal Th2 (IL-4, IL-5, IL-9 and IL-13) and regulatory (IL-10 and TGF-β) response, with some evidence of a Th1 (IFN-γ and IL-2) response. Despite upregulation after patency of both IL-15 and ALDH1A2, a known Th17-inducing combination in inflammatory diseases, we saw no evidence of a Th17 (IL-17) response. Moreover, we observed strong suppression of mucosal IL-23 and upregulation of IL-22 during established hookworm infection, suggesting a potential mechanism by which Th17 responses are suppressed, and highlighting the potential that hookworms and their secreted proteins offer as therapeutics for human inflammatory diseases.
Rhcg1 and NHE3b are involved in ammonium‐dependent sodium uptake by zebrafish larvae acclimated to low‐sodium water

To investigate whether Na+ uptake by zebrafish is dependent on NH4 + excretion, a scanning ion‐selective electrode technique (SIET) was applied to measure Na+ and NH4 + gradients at the yolk‐sac surface of zebrafish larvae. Low‐Na+ acclimation induced an inward Na+ gradient (uptake), and a combination of low‐Na+ and high‐ NH4 + induced a larger inward Na+ gradient. When measuring the ionic gradients, raising the external NH4 + level (5 mM) simultaneously blocked NH4 + excretion and Na+ uptake; in contrast, raising the external Na+ level (10 mM) simultaneously enhanced Na+ uptake and NH4 + excretion. The addition of MOPS buffer (5 mM) which is known to block NH4 + excretion also suppressed Na+ uptake. These results showed that Na+ uptake and NH4 + excretion by larval skin are associated when ambient Na+ level is low. Knockdown of Rhcg1 translation with morpholino‐oligonucleotides decreased both NH4 + excretion and Na+ uptake by the skin and Na+ content of whole larvae. Knockdown of nhe3b translation or inhibitor (EIPA) treatment also decreased both the NH4 + excretion and Na+ uptake. This study provides loss‐of‐function evidence for the involvement of Rhcg1 and NHE3b in the ammonium‐dependent Na+ uptake mechanism in zebrafish larvae subjected to low‐Na+ water.
Enterprise Resource Planning (ERP) System in Higher Education: A literature Review and Implications

ERP systems are the largest software applications adopted by universities, along with quite significant investments in their implementation. However, unlike other applications little research has been conducted regarding these systems in a university environment. This paper aims at providing a critical review of previous research in ERP system in higher education with a special focus on higher education in Australia. The research not only forms the basis of an evaluation of previous research and research needs, it also makes inroads in identifying the payoff of ERPs in the sector from different perspectives with particular reference to the user. The paper is divided into two parts, the first part focuses on ERP literature in higher education at large, while the second focuses on ERP literature in higher education in Australia.
Summation in Causal Learning: Elemental processing or Configural Generalization?

Results from human causal learning tasks that employ multiple cues are often interpreted in terms of the elemental theory of Rescorla and Wagner (1972). However, most results can also be successfully interpreted by the configural model proposed by Pearce (1987, 1994). One method of discriminating between these alternatives is through an investigation of summation and overexpectation. Indeed, demonstrations of these phenomena are fundamental to an elemental approach but are generally incompatible with an account that involves configural processing. Using a procedure in which the magnitude of the outcome varied, evidence for both summation and overexpectation was obtained in two experiments.
Transmission of MDR and XDR Tuberculosis in Shanghai, China

Background Multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) are global health problems. We sought to determine the characteristics, prevalence, and relative frequency of transmission of MDR and XDR TB in Shanghai, one of the largest cities in Asia. Methods TB is diagnosed in district TB hospitals in Shanghai, China. Drug susceptibility testing for first-line drugs was performed for all culture positive TB cases, and tests for second-line drugs were performed for MDR cases. VNTR-7 and VNTR-16 were used to genotype the strains, and prior treatment history and treatment outcomes were determined for each patient. Results There were 4,379 culture positive TB cases diagnosed with drug susceptibility test results available during March 2004 through November 2007. 247 (5.6%) were infected with a MDR strain of M. tuberculosis and 11 (6.3%) of the 175 MDR patients whose isolate was tested for susceptibility to second-line drugs, were XDR. More than half of the patients with MDR and XDR were newly diagnosed and had no prior history of TB treatment. Nearly 57% of the patients with MDR were successfully treated. Discussion Transmission of MDR and XDR strains is a serious problem in Shanghai. While a history of prior anti-TB treatment indicates which individuals may have acquired MDR or XDR TB, it does not accurately predict which TB patients have disease caused by transmission of MDR and XDR strains. Therefore, universal drug susceptibility testing is recommended for new and retreatment TB cases.
p-i-n Photodiodes for Frequency Mixing in Radio-Over-Fiber Systems

In this paper, the theory of optoelectronic frequency mixing in p-i-n photodiodes is presented. The theory is experimentally approved by measurements of InGaAs/InP p-i-n photodiodes that operate in a frequency range of up to 3 GHz. The design- and operating-regime peculiarities of the InGaAs/InP p-i-n photodiode as an optoelectronic upconverter in a radio-over-fiber system are discussed.
The Efficacy of Paroxetine and Placebo in Treating Anxiety and Depression: A Meta-Analysis of Change on the Hamilton Rating Scales

Background Previous meta-analyses of published and unpublished trials indicate that antidepressants provide modest benefits compared to placebo in the treatment of depression; some have argued that these benefits are not clinically significant. However, these meta-analyses were based only on trials submitted for the initial FDA approval of the medication and were limited to those aimed at treating depression. Here, for the first time, we assess the efficacy of a selective serotonin reuptake inhibitor (SSRI) in the treatment of both anxiety and depression, using a complete data set of all published and unpublished trials sponsored by the manufacturer. Methods and Findings GlaxoSmithKline has been required to post the results for all sponsored clinical trials online, providing an opportunity to assess the efficacy of an SSRI (paroxetine) with a complete data set of all trials conducted. We examined the data from all placebo-controlled, double-blind trials of paroxetine that included change scores on the Hamilton Rating Scale for Anxiety (HRSA) and/or the Hamilton Rating Scale for Depression (HRSD). For the treatment of anxiety (k = 12), the efficacy difference between paroxetine and placebo was modest (d = 0.27), and independent of baseline severity of anxiety. Overall change in placebo-treated individuals replicated 79% of the magnitude of paroxetine response. Efficacy was superior for the treatment of panic disorder (d = 0.36) than for generalized anxiety disorder (d = 0.20). Published trials showed significantly larger drug-placebo differences than unpublished trials (d’s = 0.32 and 0.17, respectively). In depression trials (k = 27), the benefit of paroxetine over placebo was consistent with previous meta-analyses of antidepressant efficacy (d = 0.32). Conclusions The available empirical evidence indicates that paroxetine provides only a modest advantage over placebo in treatment of anxiety and depression. Treatment implications are discussed.
Predictive risk factors for lymph node metastasis in patients with small size non-small cell lung cancer.

BACKGROUND Accurate clinical staging of non-small cell lung cancer (NSCLC) is essential for developing an optimal treatment strategy. This study aimed to determine the predictive risk factors for lymph node metastasis, including both N1 and N2 metastases, in clinical T1aN0 NSCLC patients. METHODS We retrospectively evaluated clinical T1aN0M0 NSCLC patients who showed no radiologic evidence of lymph node metastasis, and who had undergone surgical pulmonary resection with systematic mediastinal node dissection or sampling at the First Affiliated Hospital of Zhejiang University between January 2011 and June 2013. Univariate and multivariate logistic regression analyses were performed to identify predictive factors for node metastasis. RESULTS Pathologically positive lymph nodes were found in 16.2% (51/315) of the patients. Positive N1 nodes were found in 12.4% (39/315) of the patients, and positive N2 nodes were identified in 13.0% (41/315) of the patients. Some 9.2% (29/315) of the patients had both positive N1 and N2 nodes, and 3.8% (12/315) of the patients had nodal skip metastasis. Variables of preoperative radiographic tumor size, non-upper lobe located tumors, high carcinoembryonic antigen (CEA) levels and micropapillary predominant adenocarcinoma (AC) were identified as predictors for positive N1 or N2 node multivariate analysis. CONCLUSIONS Pathologically positive lymph nodes were common in small size NSCLC patients with clinical negative lymph nodes. Therefore, preoperative staging should be performed more thoroughly to increase accuracy, especially for patients who have the larger size, non-upper lobe located, high CEA level or micropapillary predominant ACs.
Is the Rapid Virologic Response a Positive Predictive Factor of Sustained Virologic Response in all Pretreatment Status Genotype 1 Hepatitis C Patients Treated With Peginterferon-α2b and Ribavirin?

Introduction Currently it is not yet defined if the rapid virologic response (RVR) can predict a sustained virologic response (SVR) in relapsers and nonresponders. Objective To evaluate treatment-RVR as a predictive factor of SVR in genotype 1 hepatitis C treatment naive, relapsers, and nonresponder patients treated with pegylated interferon-alpha (PEG-IFN-α2b) and ribavirin. Methods One hundred sixty-seven genotype 1 hepatitis C patients who were treated with PEG-IFN-α2b and ribavirin and had SVR assessed were included. Hepatitis C virus RNA analysis at the fourth week of treatment was performed in all patients. The exclusion criteria were hepatitis B virus and/or HIV co-infection. A comparative analysis was performed between the groups with and without RVR and a logistic regression model was applied. Results One hundred sixty-seven patients were analyzed, 103 (62%) were naives, 22 (13%) relapsers, and 42 (25%) nonresponders. The SVR rates were 44% in naives, 68% in relapsers, and 12% in nonresponders. RVR was attained in 51/167 (31%) patients and in this group the SVR was higher than in those without RVR (75% vs. 23%; P<0.001). This difference was also observed in all subgroups: naives (71% vs. 29%; P=0.001), relapsers (92% vs. 40%; P=0.02), and nonresponders (50% vs. 8%; P=0.06). A stepwise logistic regression model identified RVR and absence of cirrhosis as the factors independently associated to SVR. Conclusions RVR and absence of cirrhosis are the strongest predictive factors of SVR in HCV genotype 1 patients. Assessment of RVR is very useful in all pretreatment status patients in predicting SVR and provides information for individualizing therapy.
Next‐generation small RNA sequencing for microRNAs profiling in the honey bee Apis mellifera

MicroRNAs (miRNAs) are key regulators in various physiological and pathological processes via post‐transcriptional regulation of gene expression. The honey bee (Apis mellifera) is a key model for highly social species, and its complex social behaviour can be interpreted theoretically as changes in gene regulation, in which miRNAs are thought to be involved. We used the SOLiD sequencing system to identify the repertoire of miRNAs in the honey bee by sequencing a mixed small RNA library from different developmental stages. We obtained a total of 36 796 459 raw sequences; of which 5 491 100 short sequences were fragments of mRNA and other noncoding RNAs (ncRNA), and 1 759 346 reads mapped to the known miRNAs. We predicted 267 novel honey bee miRNAs representing 380 182 short reads, including eight miRNAs of other insects in 14 107 583 genome‐mapped sequences. We verified 50 of them using stem‐loop reverse‐transcription PCR (RT‐PCR), in which 35 yielded PCR products. Cross‐species analyses showed 81 novel miRNAs with homologues in other insects, suggesting that they were authentic miRNAs and have similar functions. The results of this study provide a basis for studies of the miRNA‐modulating networks in development and some intriguing phenomena such as caste differentiation in A. mellifera.
Septic plasma suppresses superoxide anion synthesis by normal homologous polymorphonuclear leukocytes

In vitro exposure of normal ORh− PMN to plasma obtained from patients with septic shock results in inhibition of formyl-methionyl-leucyl-phenylalanine stimulated superoxide anion (O2−) production by 40%. Although all reaction velocities and extent of reaction at 5 min were suppressed, neither lag time preceding O2− production nor duration of initial velocity linearity was affected. No such inhibition was noted when plasma from healthy controls or nonseptic critically ill patients was utilized in the reaction. These results demonstrate that neutrophils are not only a cause, but also a target of the septic shock host inflammatory response. (Crit Care Med 1989; 17:1241)
Deep Belief Network Training Improvement Using Elite Samples Minimizing Free Energy

Nowadays this is very popular to use deep architectures in machine learning. Deep Belief Networks (DBNs) are deep architectures that use stack of Restricted Boltzmann Machines (RBM) to create a powerful generative model using training data. In this paper we present an improvement in a common method that is usually used in training of RBMs. The new method uses free energy as a criterion to obtain elite samples from generative model. We argue that these samples can more accurately compute gradient of log probability of training data. According to the results, an error rate of 0.99% was achieved on MNIST test set. This result shows that the proposed method outperforms the method presented in the first paper introducing DBN (1.25% error rate) and general classification methods such as SVM (1.4% error rate) and KNN (with 1.6% error rate). In another test using ISOLET dataset, letter classification error dropped to 3.59% compared to 5.59% error rate achieved in those papers using this dataset. The implemented method is available online at "this http URL Toolbox.html".
Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns

MOTIVATION Multiple sequence alignments (MSAs) are widely used approaches in bioinformatics to carry out other tasks such as structure predictions, biological function analyses or phylogenetic modeling. However, current tools usually provide partially optimal alignments, as each one is focused on specific biological features. Thus, the same set of sequences can produce different alignments, above all when sequences are less similar. Consequently, researchers and biologists do not agree about which is the most suitable way to evaluate MSAs. Recent evaluations tend to use more complex scores including further biological features. Among them, 3D structures are increasingly being used to evaluate alignments. Because structures are more conserved in proteins than sequences, scores with structural information are better suited to evaluate more distant relationships between sequences. RESULTS The proposed multiobjective algorithm, based on the non-dominated sorting genetic algorithm, aims to jointly optimize three objectives: STRIKE score, non-gaps percentage and totally conserved columns. It was significantly assessed on the BAliBASE benchmark according to the Kruskal-Wallis test (P < 0.01). This algorithm also outperforms other aligners, such as ClustalW, Multiple Sequence Alignment Genetic Algorithm (MSA-GA), PRRP, DIALIGN, Hidden Markov Model Training (HMMT), Pattern-Induced Multi-sequence Alignment (PIMA), MULTIALIGN, Sequence Alignment Genetic Algorithm (SAGA), PILEUP, Rubber Band Technique Genetic Algorithm (RBT-GA) and Vertical Decomposition Genetic Algorithm (VDGA), according to the Wilcoxon signed-rank test (P < 0.05), whereas it shows results not significantly different to 3D-COFFEE (P > 0.05) with the advantage of being able to use less structures. Structural information is included within the objective function to evaluate more accurately the obtained alignments. AVAILABILITY The source code is available at http://www.ugr. es/~fortuno/MOSAStrE/MO-SAStrE.zip.
Dopaminergic Modulation of Visual-Spatial Working Memory in Parkinson’s Disease

Visual-spatial working memory (WM) impairment is frequently associated with the early stage of Parkinson’s disease (PD). The aim of this study was to evaluate the performance of a group of PD patients in visual-spatial and visual-object WM tasks and to investigate the effect of administering the dopaminergic agonist apomorphine (experiment 1) or the dopamine precursor L-dopa (experiment 2) on the performance of tests assessing these functions. To study WM processes, the PD patients and age-matched normal controls were given an n-back task paradigm. In both experiments, the PD patients were submitted to two evaluations: one after a 12-hour therapy washout and the other 15 min after a subcutaneous infusion of apomorphine (average 0.04 mg/kg) or 20/30 min after L-dopa intake (200 mg p.o.). The apomorphine infusion had a worsening effect on reaction times in both visual-spatial and visual-object WM tasks, but it did not influence performance accuracy. Instead, L-dopa administration had a ameliorative effect on accuracy and reaction times in both visual-spatial and visual-object tasks. These results highlight the role of dopamine in the modulation of the WM function in PD patients.
Synthetic edge and scrape-off layer diagnostics—a bridge between experiments and theory

The scrape off layer (SOL) plasma in a Tokamak device and its coupling with the edge dictate the performance of a discharge to a high degree—especially as all plasma has to go through the SOL, which is the main exhaust channel for the hot plasma. This contribution provides an introduction to the modelling efforts of the plasma dynamics in the SOL and the edge regions. We employ a fully dynamical fluid model, the HESEL code. HESEL is equipped with synthetic diagnostic tools as probe arrays, Li-beam spectroscopy, and Gas Puff Imaging. Using the synthetic probe arrays to measure the electron and ion heat advection and conduction we obtain the upstream power fall-off length for a broad range of plasma parameters and by applying non-linear fitting procedures we derive the scaling of the fall-off length. The obtained results are in agreement with recent experimental observations from L-mode ASDEX Upgrade data. A workflow for generating synthetic Lithium beam data, where the fluctuation data from HESEL are passed to the RENATE code are discussed using experimental results from ASDEX Upgrade.
Receding horizon control of multi-vehicle formations: a distributed implementation

We consider the control of interacting subsystems whose dynamics and constraints are decoupled, but whose state vectors are coupled non-separably in a single cost function of a finite horizon optimal control problem. For a given cost structure, we generate distributed optimal control problems for each subsystem and establish that a distributed receding horizon control implementation is stabilizing. The implementation requires synchronous updates and the exchange of the most recent optimal control trajectory between coupled subsystems prior to each update. Key requirements for stability are that each subsystem not deviates too far from the previous open-loop state trajectory, and that the receding horizon updates happen sufficiently fast. The venue of multi-vehicle formation stabilization is used to demonstrate the distributed implementation and simulations are provided.