Miracle-dz/UniFAR-FTUs huggingface dataset:
Communications Inspired Linear Discriminant Analysis

We study the problem of supervised linear dimensionality reduction, taking an information-theoretic viewpoint. The linear projection matrix is designed by maximizing the mutual information between the projected signal and the class label. By harnessing a recent theoretical result on the gradient of mutual information, the above optimization problem can be solved directly using gradient descent, without requiring simplification of the objective function. Theoretical analysis and empirical comparison are made between the proposed method and two closely related methods, and comparisons are also made with a method in which Renyi entropy is used to define the mutual information (in this case the gradient may be computed simply, under a special parameter setting). Relative to these alternative approaches, the proposed method achieves promising results on real datasets.
Lactose metabolism in Streptococcus lactis: phosphorylation of galactose and glucose moieties in vivo

Starved cells of Streptococcus lactis ML3 grown previously on lactose, galactose, or maltose were devoid of adenosine 5'-triphosphate contained only three glycolytic intermediates: 3-phosphoglycerate, 2-phosphoglycerate, and phosphoenolpyruvate (PEP). The three metabolites (total concentration, ca 40 mM) served as the intracellular PEP potential for sugar transport via PEP-dependent phosphotransferase systems. When accumulation of [14C]lactose by iodoacetate-inhibited starved cells was abolished within 1 s of commencement of transport, a phosphorylated disaccharide was identified by autoradiography. The compound was isolated by ion-exchange (borate) chromatography, and enzymatic analysis showed that the derivative was 6-phosphoryl-O-beta-D-galactopyranosyl (1 leads to 4')-alpha-D-glucopyranose (lactose 6-phosphate). After maximum lactose uptake (ca. 15 mM in 15 s) the cells were collected by membrane filtration and extracted with trichloroacetic acid. Neither free nor phosphorylated lactose was detected in cell extracts, but enzymatic analysis revealed high levels of galactose 6-phosphate and glucose 6-phosphate. The starved organisms rapidly accumulated glucose, 2-deoxy-D-glucose, methyl-beta-D-thiogalactopyranoside, and o-nitrophenyl-beta-D-galactopyranoside in phosphorylated form to intracellular concentrations of 32, 32, 42, and 38.5 mM, respectively. In contrast, maximum accumulation of lactose (ca. 15 mM) was only 40 to 50% that of the monosaccharides. From the stoichiometry of PEP-dependent lactose transport and the results of enzymatic analysis, it was concluded that (i) ca. 60% of the PEP potential was utilized via the lactose phosphotransferase system for phosphorylation of the galactosyl moiety of the disaccharide, and (ii) the residual potential (ca. 40%) was consumed during phosphorylation of the glucose moiety.
Yips and other movement disorders in golfers

Golf is a sport that requires perfect motor coordination and a balance between mobility and stability. Golfer's “yips,” an intermittent motor disturbance manifested as transient tremor, jerk, or spasm that primarily occurs when the player is trying to chip or make a putt, is a movement disorder frequently encountered in both amateur and professional golfers. In addition, other movement disorders, such as tremors and dystonia, also can interfere with playing golf. Although the pathophysiology of the yips remains poorly understood, recent studies suggest that it may be a form of a task‐specific, focal dystonia involving the hand and arm. Because task‐specific dystonias and tremors are best treated by botulinum toxin injections, this also may be an effective therapy for the yips. The aim of this article is to systematically review the literature and our own experience with the yips and other movement disorders in golfers. © 2013 Movement Disorder Society
Low-budget transient imaging using photonic mixer devices

Transient imaging is an exciting a new imaging modality that can be used to understand light propagation in complex environments, and to capture and analyze scene properties such as the shape of hidden objects or the reflectance properties of surfaces. Unfortunately, research in transient imaging has so far been hindered by the high cost of the required instrumentation, as well as the fragility and difficulty to operate and calibrate devices such as femtosecond lasers and streak cameras. In this paper, we explore the use of photonic mixer devices (PMD), commonly used in inexpensive time-of-flight cameras, as alternative instrumentation for transient imaging. We obtain a sequence of differently modulated images with a PMD sensor, impose a model for local light/object interaction, and use an optimization procedure to infer transient images given the measurements and model. The resulting method produces transient images at a cost several orders of magnitude below existing methods, while simultaneously simplifying and speeding up the capture process.
A Randomized Trial of a Computer-Tailored Decision Aid to Improve Prostate Cancer Screening Decisions: Results from the Take the Wheel Trial

Objective: To evaluate a decision aid (DA) designed to promote informed decision making for prostate cancer screening. Methods: Twelve work sites were randomly assigned to an intervention or nonintervention comparison condition. Intervention sites received access to a computer-tailored DA at the workplace. Male employees age 45 years and above (n = 625) completed surveys at baseline and at 3-month follow-up, documenting aspects of informed decision making. Results: Using an intention-to-treat analysis, men in the intervention group were significantly more likely to have made a screening decision and to have improved knowledge without increased decisional conflict, relative to men in the comparison group. These changes were observed despite the fact that only 30% of men in intervention sites used the DA. Among DA users, similar improvements were observed, although the magnitudes of changes were substantially greater, and significant improvements in decision self-efficacy were observed. Conclusions: A DA offered in the workplace promoted decision making, improved knowledge, and increased decision self-efficacy among users, without increasing decisional conflict. However, participation was suboptimal, suggesting that better methods for engaging men in workplace interventions are needed. Impact Statement: This trial shows the efficacy of a computer-tailored DA in promoting informed decisions about prostate cancer screening. The DA was delivered through work sites, thereby providing access to resources required to participate in informed decision making without requiring a medical appointment. However, participation rates were suboptimal, and additional strategies for engaging men are needed. Cancer Epidemiol Biomarkers Prev; 19(9); 2172–86. ©2010 AACR.
A simulation study of the formation of tetrahedral inorganic and hybrid glasses

With modern high performance calculation, computer simulation provides us with a possible way to analyse and visualize the atoms and molecules of materials within nanometre scale and picoseconds which can not be simply achieved in real-life experiments. Therefore it is a great tool to study the nano-structure formation of materials including crystals as well as glasses. In this thesis, alumino-silicates including nepheline and its compositional variations have been studied. Melts of them have been simulated and glasses have been derived by melt-quenching procedures. Static structures and dynamic properties have been studied. Specifically, the distribution of mobile metallic ions, which fundamentally affects the properties of glasses, has been simulated in this study to give a better understanding of the roles mobile ions play. In particular, we are interested in whether micro-segregation of metallic ions occurs as it does in silicates [1]. Molecular dynamics simulations of alumino-silicates nepheline (KX Na4−X Al4Si4O16) have been performed to obtain first the structure of molten nepheline. Five different alkali ratios have been taken to explore the effect of ionic radius and field strength on segregation. Radial Distribution functions, REDOR second moments, Vibrational Densities of States and molecular structure snapshots reveal how alkali ions distribute non-randomly, form channels in between the framework atoms of both molten and glassy nepheline. This nanostructure of nepheline at Tg=1200K is virtually the same as the quenched structure at room temperature, confirmed by the snapshots. When K+ replaces Na+ in the system, it occupies more volume. Both melt viscosity and boson peak intensity in quenched glass showed dramatic increasing due to the percolation channels affected by K+ concentration. To replicate the dynamics properties of melts, three series of molecular dynamics simulations with varied alumino-silicate composition, each containing different ratios of Al/Si, have been performed including nepheline for which Al/Si = 1. Mean square displacements have been calculated from trajectories at 2000K to derive diffusion constant. The Einstein-Stokes equation and the Eyring equation were then used to derive the viscosity and compared. The Eyring results show a better replication of a fitted Adam-Gibbs model with measured viscosity values.
Expert performance: Its structure and acquisition.

Counter to the common belief that expert performance reflects innate abilities and capacities, recent research in different domains of expertise has shown that expert performance is predominantly mediated by acquired complex skills and physiological adaptations. For elite performers, supervised practice starts at very young ages and is maintained at high daily levels for more than a decade. The effects of extended deliberate practice are more far-reaching than is commonly believed. Performers can acquire skills that circumvent basic limits on working memory capacity and sequential processing. Deliberate practice can also lead to anatomical changes resulting from adaptations to intense physical activity. The study of expert performance has important implications for our understanding of the structure and limits of human adaptation and optimal learning.
Matrix metalloproteinase‐3 expression profile differentiates adaptive and maladaptive synaptic plasticity induced by traumatic brain injury

The interaction between extracellular matrix (ECM) and regulatory matrix metalloproteinases (MMPs) is important in establishing and maintaining synaptic connectivity. By using fluid percussion traumatic brain injury (TBI) and combined TBI and bilateral entorhinal cortical lesion (TBI + BEC), we previously demonstrated that hippocampal stromelysin‐1 (MMP‐3) expression and activity increased during synaptic plasticity. We now report a temporal analysis of MMP‐3 protein and mRNA response to TBI during both degenerative (2 day) and regenerative (7, 15 day) phases of reactive synaptogenesis. MMP‐3 expression during successful synaptic reorganization (following unilateral entorhinal cortical lesion; UEC) was compared with MMP‐3 expression when normal synaptogenesis fails (after combined TBI + BEC insult). Increased expression of MMP‐3 protein and message was observed in both models at 2 days postinjury, and immuohistochemical (IHC) colocalization suggested that reactive astrocytes contribute to that increase. By 7 days postinjury, model differences in MMP‐3 were observed. UEC MMP‐3 mRNA was equivalent to control, and MMP‐3 protein was reduced within the deafferented region. In contrast, enzyme mRNA remained elevated in the maladaptive TBI + BEC model, accompanied by persistent cellular labeling of MMP‐3 protein. At 15 days survival, MMP‐3 mRNA was normalized in each model, but enzyme protein remained higher than paired controls. When TBI + BEC recovery was enhanced by the N‐methyl‐D‐aspartate antagonist MK‐801, 7‐day MMP‐3 mRNA was significantly reduced. Similarly, MMP inhibition with FN‐439 reduced the persistent spatial learning deficits associated with TBI + BEC insult. These results suggest that MMP‐3 might differentially affect the sequential phases of reactive synaptogenesis and exhibit an altered pattern when recovery is perturbed. © 2006 Wiley‐Liss, Inc.
Early and short-term acenocumarine or dalteparin for the prevention of central vein catheter-related thrombosis in cancer patients: a randomized controlled study based on serial venographies.

BACKGROUND We evaluated efficacy and safety of early and short-term prophylaxis with acenocumarine or dalteparin in the prevention of non-occlusive or occlusive central vein catheter-related thrombosis (CVCrT). PATIENTS AND METHODS Consecutive cancer patients scheduled for chemotherapy randomly received: acenocumarine 1 mg/day for 3 days before and 8 days after central vein catheter (CVC) insertion; dalteparin 5000 IU 2 h before and daily for 8 days after CVC insertion; no anticoagulant treatment (NT). All patients underwent venography on days 8 and 30, some of them on days 90, 150 and 210 after CVC. RESULTS A total of 450 patients were randomized, 348 underwent at least two venography. Both acenocumarine and dalteparin reduced venography-detected CVCrT rate [21.9% acenocumarine versus 52.6% NT, odds ratio (OR) 0.3, P < 0.01; 40% dalteparin versus 52.6% NT, OR 0.6, P = 0.05]. Acenocumarine was more effective than dalteparin (OR 0.4, P = 0.01). The rate of occlusive CVCrT was not different in the three groups (0.9% acenocumarine, 3.3% dalteparin, 1.8% NT; P = 0.40). Most CVCrTs (95.6%) were observed on day 8 after CVC insertion and were non-occlusive. CONCLUSIONS In this study of early and short-term prophylaxis, acenocumarine was more effective than dalteparin on non-occlusive and asymptomatic CVCrT events. The first days following CVC insertion represent the highest risk for CVCrT.
Cells previously identified as retinal stem cells are pigmented ciliary epithelial cells

It was previously reported that the ciliary epithelium (CE) of the mammalian eye contains a rare population of cells that could produce clonogenic self-renewing pigmented spheres in culture. Based on their ability to up-regulate genes found in retinal neurons, it was concluded that these sphere-forming cells were retinal stem cells. This conclusion raised the possibility that CE-derived retinal stem cells could help to restore vision in the millions of people worldwide who suffer from blindness associated with retinal degeneration. We report here that human and mouse CE-derived spheres are made up of proliferating pigmented ciliary epithelial cells rather than retinal stem cells. All of the cells in the CE-derived spheres, including the proliferating cells, had molecular, cellular, and morphological features of differentiated pigmented CE cells. These differentiated cells ectopically expressed nestin when exposed to growth factors and low levels of pan-neuronal markers such as beta-III-tubulin. Although the cells aberrantly expressed neuronal markers, they retained their pigmented CE cell morphology and failed to differentiate into retinal neurons in vitro or in vivo. Our results provide an example of a differentiated cell type that can form clonogenic spheres in culture, self-renew, express progenitor cell markers, and initiate neuronal differentiation that is not a stem or progenitor cell. More importantly, our findings highlight the importance of shifting the focus away from studies on CE-derived spheres for cell-based therapies to restore vision in the degenerating retina and improving techniques for using ES cells or retinal precursor cells.
Immunopharmacology and in fl ammation CARD 15 gene overexpression reduces effect of etanercept , in fl iximab , and adalimumab on cytokine secretion from PMA activated U 937 cells

Crohn's disease (CD), a subcategory of inflammatory bowel disease, is an immune-related disorder characterized by inflammation of the gastrointestinal mucosa, which can take place in any region along the alimentary tract. The most important gene involved in the etiology of CD is NOD2/CARD15 located on chromosome 16. It has been shown that CARD15 is overexpressed in monocytes of CD patients. The common treatment for the disease is anti-TNF-alpha drugs, the most hopeful of which are probably infliximab and etanercept. Infliximab rapidly reduces signs and symptoms of active Crohn’s disease. In contrast, etanercept shows no such effect. In the present study, we evaluated the effects of the CARD15 gene overexpression in monocytic cell line U937 in the production of anti-inflammatory cytokine, IL-10, and proinflammatory cytokine, Il-1 beta, produced after incubation with infliximab, adalimumab, and etanercept separately. Our results show that infliximab and adalimumab significantly decreased IL-10 and IL-1beta secretion levels. However, etanercept inhibition of secretion was less compared with infliximab or adalimumab. In all three cases, suppression of cytokine production is reduced by CARD15 overexpression. & 2015 Elsevier B.V. All rights reserved.
Overlapping and Distinct Neural Systems Code for Subjective Value during Intertemporal and Risky Decision Making

During decision making, valuation of different types of rewards may involve partially distinct neural systems, but efficient choice behavior requires a common neural coding of stimulus value. We addressed this issue by measuring neural activity with functional magnetic resonance imaging while volunteers processed delayed and probabilistic decision options. Behaviorally, participants discounted both types of rewards in a hyperbolic manner, and discount rates, reflecting individual preferences, varied considerably between participants. Ventral striatum and orbitofrontal cortex showed a domain-general coding of subjective value regardless of whether rewards were delayed or probabilistic, strongly implicating these regions in the implementation of a common neural currency of value. In contrast, fronto-polar and lateral parietal cortex, as well as a region in the posterior cingulate cortex only correlated with the value of delayed rewards, whereas superior parietal cortex and middle occipital areas only represented the value of probabilistic rewards. These results suggest a mechanism for the neural coding of subjective value in the human brain that is based on the combination of domain-general and domain-specific valuation networks.
Fish and robots swimming together: attraction towards the robot demands biomimetic locomotion

The integration of biomimetic robots in a fish school may enable a better understanding of collective behaviour, offering a new experimental method to test group feedback in response to behavioural modulations of its ‘engineered’ member. Here, we analyse a robotic fish and individual golden shiners (Notemigonus crysoleucas) swimming together in a water tunnel at different flow velocities. We determine the positional preference of fish with respect to the robot, and we study the flow structure using a digital particle image velocimetry system. We find that biomimetic locomotion is a determinant of fish preference as fish are more attracted towards the robot when its tail is beating rather than when it is statically immersed in the water as a ‘dummy’. At specific conditions, the fish hold station behind the robot, which may be due to the hydrodynamic advantage obtained by swimming in the robot's wake. This work makes a compelling case for the need of biomimetic locomotion in promoting robot–animal interactions and it strengthens the hypothesis that biomimetic robots can be used to study and modulate collective animal behaviour.
Identification of Bradyrhizobium elkanii Genes Involved in Incompatibility with Vigna radiata

The establishment of a root nodule symbiosis between a leguminous plant and a rhizobium requires complex molecular interactions between the two partners. Compatible interactions lead to the formation of nitrogen-fixing nodules, however, some legumes exhibit incompatibility with specific rhizobial strains and restrict nodulation by the strains. Bradyrhizobium elkanii USDA61 is incompatible with mung bean (Vigna radiata cv. KPS1) and soybean cultivars carrying the Rj4 allele. Here, we explored genetic loci in USDA61 that determine incompatibility with V. radiata KPS1. We identified five novel B. elkanii genes that contribute to this incompatibility. Four of these genes also control incompatibility with soybean cultivars carrying the Rj4 allele, suggesting that a common mechanism underlies nodulation restriction in both legumes. The fifth gene encodes a hypothetical protein that contains a tts box in its promoter region. The tts box is conserved in genes encoding the type III secretion system (T3SS), which is known for its delivery of virulence effectors by pathogenic bacteria. These findings revealed both common and unique genes that are involved in the incompatibility of B. elkanii with mung bean and soybean. Of particular interest is the novel T3SS-related gene, which causes incompatibility specifically with mung bean cv. KPS1.
QuadCover ‐ Surface Parameterization using Branched Coverings

We introduce an algorithm for the automatic computation of global parameterizations on arbitrary simplicial 2‐manifolds, whose parameter lines are guided by a given frame field, for example, by principal curvature frames. The parameter lines are globally continuous and allow a remeshing of the surface into quadrilaterals. The algorithm converts a given frame field into a single vector field on a branched covering of the 2‐manifold and generates an integrable vector field by a Hodge decomposition on the covering space. Except for an optional smoothing and alignment of the initial frame field, the algorithm is fully automatic and generates high quality quadrilateral meshes.
Silencing of DNase Colicin E8 Gene Expression by a Complex Nucleoprotein Assembly Ensures Timely Colicin Induction

Colicins are plasmid-encoded narrow spectrum antibiotics that are synthesized by strains of Escherichia coli and govern intraspecies competition. In a previous report, we demonstrated that the global transcriptional factor IscR, co dependently with the master regulator of the DNA damage response, LexA, delays induction of the pore forming colicin genes after SOS induction. Here we show that IscR is not involved in the regulation of nuclease colicins, but that the AsnC protein is. We report that AsnC, in concert with LexA, is the key controller of the temporal induction of the DNA degrading colicin E8 gene (cea8), after DNA damage. We demonstrate that a large AsnC nucleosome-like structure, in conjunction with two LexA molecules, prevent cea8 transcription initiation and that AsnC binding activity is directly modulated by L asparagine. We show that L-asparagine is an environmental factor that has a marked impact on cea8 promoter regulation. Our results show that AsnC also modulates the expression of several other DNase and RNase colicin genes but does not substantially affect pore-forming colicin K gene expression. We propose that selection pressure has “chosen” highly conserved regulators to control colicin expression in E. coli strains, enabling similar colicin gene silencing among bacteria upon exchange of colicinogenic plasmids.