Miracle-dz/UniFAR-FTUs huggingface dataset:
Dementia in Parkinson disease: a proton magnetic resonance spectroscopy study.

BACKGROUND Magnetic resonance spectroscopy has been shown to be useful in differentiating idiopathic Parkinson disease (PD) from atypical parkinsonian syndromes such as progressive supranuclear palsy, multiple system atrophy, and corticobasal degeneration. OBJECTIVE To systematically investigate the utility of proton magnetic resonance spectroscopy in distinguishing between idiopathic PD with dementia (PDD) and without dementia. DESIGN Group comparisons and correlations of brain metabolites with clinical and neuropsychological variables. PATIENTS AND METHODS Metabolite concentrations were acquired from voxels localized to the basal ganglia and occipital cortex in 14 patients diagnosed as having idiopathic PDD, 12 patients with PD without dementia, and 13 matched control subjects. The 3 groups underwent clinical and neuropsychological assessment. RESULTS In the occipital region, N-acetylaspartate levels were significantly reduced in the PDD group relative to the PD and control groups. N-acetylaspartate values correlated with neuropsychological performance but not with severity of motor impairment. CONCLUSIONS N-acetylaspartate reduction in occipital lobes may be a marker for dementia in PD. The distribution of metabolite reduction differs from that reported in Alzheimer disease. These findings suggest that proton spectroscopy may serve as a metabolic marker of cognitive disturbance in patients with PD.
Postsynaptic density‐95 scaffolding of Shaker‐type K+ channels in smooth muscle cells regulates the diameter of cerebral arteries

Non‐Technical Summary Shaker‐type potassium channels are found on the smooth muscle cells of blood vessels in the brain and are important in keeping the blood vessels open or dilated. We show that a protein called PSD95, previously found in nerve cells, interacts with these potassium channels. PSD95 may act as a scaffold to ensure that the potassium channels are expressed in adequate numbers and in the right location on the smooth muscle cells. When we reduced the number of PSD95 proteins, we saw that the potassium channels were also reduced and the blood vessels were not as dilated compared to blood vessels with normal amounts of PSD95. This research may help us understand how abnormal constriction of blood vessels in the brain occurs in diseases such as high blood pressure and stroke.
Orione, a web-based framework for NGS analysis in microbiology

Summary: End-to-end next-generation sequencing microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that use different software packages is difficult owing to a lack of interoperability, reproducibility and transparency. To overcome these limitations we present Orione, a Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for next-generation sequencing microbiology data analysis. Enabling microbiology researchers to conduct their own custom analysis and data manipulation without software installation or programming, Orione provides new opportunities for data-intensive computational analyses in microbiology and metagenomics. Availability and implementation: Orione is available online at http://orione.crs4.it. Contact: gianmauro.cuccuru@crs4.it Supplementary information: Supplementary data are available at Bioinformatics online.
Random Shuffling and Resets for the Non-stationary Stochastic Bandit Problem

We consider a non-stationary formulation of the stochastic multi-armed bandit where the rewards are no longer assumed to be identically distributed. For the best-arm identification task, we introduce a version of SUCCESSIVE ELIMINATION based on random shuffling of the K arms. We prove that under a novel and mild assumption on the mean gap ∆, this simple but powerful modification achieves the same guarantees in term of sample complexity and cumulative regret than its original version, but in a much wider class of problems, as it is not anymore constrained to stationary distributions. We also show that the original SUCCESSIVE ELIMINATION fails to have controlled regret in this more general scenario, thus showing the benefit of shuffling. We then remove our mild assumption and adapt the algorithm to the best-arm identification task with switching arms. We adapt the definition of the sample complexity for that case and prove that, against an optimal policy with N − 1 switches of the optimal arm, this new algorithm achieves an expected sample complexity of O(∆^{−2} sqrt(N Kdelta^{−1} log(K/delta)), where δ is the probability of failure of the algorithm, and an expected cumulative regret of O(∆^{−1} sqrt(N T K log(T K))) after T time steps.
Amplitude reduction of waviness in elastohydrodynamic lubrication using an Eyring fluid model

Abstract This paper presents a first extension of the amplitude reduction approach, where the deformation of harmonic components of the roughness is considered, to non-Newtonian elastohydrodynamic lubrication (EHL) line contact. The amplitude reduction of one-sided waviness is computed as a function of the slide-roll ratio. Non-Newtonian effects result in an increase in the deformation for positive slide-roll ratios. This contrasts with published results using a Newtonian fluid where the deformation decreased for such conditions. Moreover, the amplitude reduction varies significantly throughout the contact, requiring an additional parameter for the characterization of the amplitude reduction. An explanation of these differences based on the velocity profile of the lubricant inside the contact concludes the paper.
Functional Role of Matrix Metalloproteinase-8 in Stem/Progenitor Cell Migration and Their Recruitment Into Atherosclerotic Lesions

Rationale: Accumulating evidence indicates that stem/progenitor cells (SPCs) represent an important source of cells in atheromas and contribute to lesion formation and progression. Objective: We investigated whether matrix metalloproteinase-8 (MMP8) played a role in SPC migration and their recruitment into atheromas. Methods and Results: We found that SPCs in atheromas expressed MMP8 and that MMP8 knockout significantly reduced SPC numbers in atherosclerotic lesions in apolipoprotein E (ApoE)–deficient mice fed a Western diet. Further in vivo experiments showed that ApoE−/−/MMP8−/− mice injected with stem cells isolated from bone marrows of ApoE−/−/MMP8−/− mice had fewer SPCs in atheromas and smaller lesions than ApoE−/−/MMP8−/− mice injected with stem cells isolated from bone marrows of ApoE−/−/MMP8+/+ mice. Ex vivo experiments showed that MMP8 deficiency inhibited the ability of SPCs to migrate from the arterial lumen and the adventitia into atherosclerotic lesions. In vitro assays indicated that MMP8 facilitated SPC migration across endothelial cells and through Matrigel or collagen I. We also found that MMP8 cleaved a-disintegrin-and-metalloproteinase-domain-10 and that MMP8 deficiency reduced mature a-disintegrin-and-metalloproteinase-domain-10 on SPCs. Knockdown of MMP8 or incubation with the a-disintegrin-and-metalloproteinase-domain-10 inhibitor GI254023X decreased E-cadherin shedding on SPCs. The decrease in migratory ability of SPCs with MMP8 knockdown was reduced by incubation of such cells with culture supernatant from SPCs without MMP8 knockdown, and this compensatory effect was abolished by an antibody against soluble E-cadherin. Conclusions: MMP8 plays an important role in SPC migration and their recruitment into atherosclerotic lesions.
Prime Time Light Exposures Do Not Seem to Improve Maximal Physical Performance in Male Elite Athletes, but Enhance End-Spurt Performance

Many sports competitions take place during television prime time, a time of the day when many athletes have already exceeded their time of peak performance. We assessed the effect of different light exposure modalities on physical performance and melatonin levels in athletes during prime time. Seventy-two young, male elite athletes with a median (interquartile range) age of 23 (21; 29) years and maximum oxygen uptake (VO2max) of 63 (58; 66) ml/kg/min were randomly assigned to three different light exposure groups: bright light (BRIGHT), blue monochromatic light (BLUE), and control light (CONTROL). Each light exposure lasted 60 min and was scheduled to start 17 h after each individual's midpoint of sleep (median time: 9:17 pm). Immediately after light exposure, a 12-min time trial was performed on a bicycle ergometer. The test supervisor and participants were blinded to the light condition each participant was exposed to. The median received light intensities and peak wavelengths (photopic lx/nm) measured at eye level were 1319/545 in BRIGHT, 203/469 in BLUE, and 115/545 in CONTROL. In a multivariate analysis adjusted for individual VO2max, total work performed in 12 min did not significantly differ between the three groups. The amount of exposure to non-image forming light was positively associated with the performance gain during the time trial, defined as the ratio of the work performed in the first and last minute of the time trial, and with stronger melatonin suppression. Specifically, a tenfold increase in the exposure to melanopic light was associated with a performance gain of 8.0% (95% confidence interval: 2.6, 13.3; P = 0.004) and a melatonin decrease of −0.9 pg/ml (95% confidence interval: −1.5, −0.3; P = 0.006). Exposure to bright or blue light did not significantly improve maximum cycling performance in a 12-min all-out time trial. However, it is noteworthy that the estimated difference of 4.1 kJ between BRIGHT and CONTROL might represent an important performance advantage justifying further studies. In conclusion, we report novel evidence that evening light exposure, which strongly impacts the human circadian timing system, enables elite athletes to better maintain performance across a 12-min cycling time trial.
The Effect of Bi Concentration on Wettability of Cu Substrate by Sn-Bi Solders

In the present work, the wettability and interfacial tension between Cu-substrate and Sn–Bi solder were examined. The variables of this experiment used the content of Bi, types of flux and soldering temperature. Through analyzing the experimental result concerning wettability, it was found that the role of Bi was diminishing wettability of Cu substrate during soldering. The increasing Bi contents made liquid solder-Cu substrate interfacial tension (γsl) go up. Consequently, the increasing liquid solder-Cu substrate interfacial tension (γsl) led to the degradation of wettability in solder. The rates of wetting can be controlled by the interfacial energy between liquid solder and substrate. This paper describes the effect of Bi element on the wettability of Sn–Bi solders.
Chromatin alterations associated with down-regulated metabolic gene expression in the prefrontal cortex of subjects with schizophrenia.

BACKGROUND Schizophrenia is frequently accompanied by hypometabolism and altered gene expression in the prefrontal cortex. Cellular metabolism regulates chromatin structure, including covalent histone modifications, which are epigenetic regulators of gene expression. OBJECTIVE To test the hypothesis that down-regulated metabolic gene expression is associated with histone modification changes in the prefrontal cortex of subjects with schizophrenia. DESIGN AND SUBJECTS Histones and gene transcripts were profiled in the postmortem prefrontal cortex of 41 subjects with schizophrenia and 41 matched controls. The phosphorylation, acetylation, and methylation of 6 lysine, serine, and arginine residues of histones H3 and H4 were examined together with 16 metabolic gene transcripts using serial immunoblotting, immunohistochemical analysis, custom-made complementary DNA arrays, and quantitative real-time reverse transcriptase-polymerase chain reaction. RESULTS Subjects with schizophrenia, as a group, showed no significant alterations in histone profiles or gene expression. In a subgroup of 8 patients with schizophrenia, levels of H3-(methyl)arginine 17, H3meR17, exceeded control values by 30%, and this was associated with the decreased expression of 4 metabolic transcripts. CONCLUSIONS High levels of H3-(methyl)arginine 17 are associated with down-regulated metabolic gene expression in the prefrontal cortex of a subset of subjects with schizophrenia. Histone modifications may contribute to the pathogenesis of prefrontal dysfunction in schizophrenia.
Molecular Recognition‐Mediated Transformation of Single‐Chain Polymer Nanoparticles into Crosslinked Polymer Films

Abstract We describe single‐chain polymer nanoparticles (SCNPs) possessing intramolecular dynamic covalent crosslinks that can transform into polymer films through a molecular recognition‐mediated crosslinking process. The SCNPs utilise molecular recognition with surface‐immobilised proteins to concentrate upon a substrate, bringing the SCNPs into close spatial proximity with one another and allowing their dynamic covalent crosslinkers to undergo intra‐ to interpolymer chain crosslinking leading to the formation of polymeric film. SCNPs must possess both the capacity for specific molecular recognition and a dynamic nature to their intramolecular crosslinkers to form polymer films, and an investigation of the initial phase of film formation indicates it proceeds from features which form upon the surface then grow predominantly in the xy directions. This approach to polymer film formation presents a potential method to “wrap” surfaces displaying molecular recognition motifs—which could potentially include viral, cellular and bacterial surfaces or artificial surfaces displaying multivalent recognition motifs—within a layer of polymer film.
Approaches to fault-tolerant and transactional mobile agent execution---an algorithmic view

Over the past years, mobile agent technology has attracted considerable attention, and a significant body of literature has been published. To further develop mobile agent technology, reliability mechanisms such as fault tolerance and transaction support are required. This article aims at structuring the field of fault-tolerant and transactional mobile agent execution and thus at guiding the reader to understand the basic strengths and weaknesses of existing approaches. It starts with a discussion on providing fault tolerance in a system in which processes simply fail. For this purpose, we first identify two basic requirements for fault-tolerant mobile agent execution: (1) non-blocking (i.e., a single failure does not prevent progress of the mobile agent execution) and (2) exactly-once (i.e., multiple executions of the agent are prevented). This leads us to introduce the notion of a <i>local transaction</i> as the basic building block for fault-tolerant mobile agent execution and to classify existing approaches according to when and by whom the local transactions are committed. In a second part, we show that transactional mobile agent execution additionally ensures execution atomicity and present a survey of existing approaches. In the last part of the survey, we extend the notion of fault tolerance to arbitrary Byzantine failures and security-related issues of the mobile agent execution.
Avoiding Communication in Nonsymmetric Lanczos-Based Krylov Subspace Methods

Krylov subspace methods are iterative methods for solving large, sparse linear systems and eigenvalue problems in a variety of scientific domains. On modern computer architectures, communication, or movement of data, takes much longer than the equivalent amount of computation. Classical formulations of Krylov subspace methods require data movement in each iteration, creating a performance bottleneck, and thus increasing runtime. This motivated $s$-step, or communication-avoiding, Krylov subspace methods, which only perform data movement every $O(s)$ iterations. We present new communication-avoiding Krylov subspace methods, CA-BICG and CA-BICGSTAB. We are the first to provide derivations of these methods. For both sequential and parallel implementations, our methods reduce data movement by a factor of $O(s)$ versus the classical algorithms. We implement various polynomial bases and perform convergence experiments to enable comparison with the classical algorithm. We discuss recent results in improving both.
A beam-matching concept for medical linear accelerators

The flexibility in radiotherapy can be improved if a patient can be moved between any one of the department's medical linear accelerators without the need to change anything in the patient's treatment plan. For this to be possible, the dosimetric characteristics of the various accelerators must be the same, or nearly the same i.e. the accelerators must be beam-matched. During a period of nine months, eight Varian iX accelerators with 6 and 15 MV photon beams and 6–18 MeV electron beams (only four of the eight) were installed at our clinic. All accelerators fulfilled the vendor-defined “fine beam-match” criteria, and a more extensive set of measurements was carried out during commissioning. The measured absorbed dose data for each accelerator were compared with the first accelerator, chosen as reference, and the TPS calculations. Two of the eight accelerators showed a larger discrepancy for the 15 MV beam not revealed by the vendor-defined acceptance criteria, whereas the other six accelerators were satisfactorily matched. The beam-matching acceptance criteria defined by the vendor are not strict enough to guarantee optimal beam-match. Deviations related to dose calculations and to beam-matched accelerators may add up. The safest and most practical way to ensure that all accelerators are within clinical acceptable accuracy is to include TPS calculations in the evaluation. Further, comparisons between measurements and calculations should be done in absolute dose terms.
How the agent's gender influence users' evaluation of a QA system

In this paper we present the results of a pilot study investigating the effects of agents' gender-ambiguous vs. gender-marked look on the perceived interaction quality of a multimodal question answering system. Eight test subjects interacted with three system agents, each having a feminine, masculine or gender-ambiguous look. The subjects were told each agent was representing a differently configured system. In fact, they were interacting with the same system. In the end, the subjects filled in an evaluation questionnaire and participated in an in-depth qualitative interview. The results showed that the user evaluation seemed to be influenced by the agent's gender look: the system represented by the feminine agent achieved on average the highest evaluation scores. On the other hand, the system represented by the gender-ambiguous agent was systematically lower rated. This outcome might be relevant for an appropriate agent look, especially since many designers tend to develop gender-ambiguous characters for interactive interfaces to match various users' preferences. However, additional empirical evidence is needed in the future to confirm our findings.
Extrusion Freeform Fabrication of Chopped-Fibre Reinforced Composites

Extrusion freeform fabrication is a process whereby three-dimensional parts are built by writing successive layers of material onto a support. In this case, two types of epoxy resin have been formed into test bars containing varying fractions of chopped carbon fibre of various lengths. It is shown that the fibre orientation follows the writing direction and has a large influence on the directional elastic properties of the composite. Test bars have also been formed containing multiple layers of reinforced and unreinforced resin to demonstrate the flexibility of this method.
Touch Screen as Input Device: Does it Influence Memory Retrieval?

The main objective of this research is to investigate how input device type influences users’ memory retrieval (i.e., stimulus recognition). We build upon prior research on the somatosensory (tactile) system to argue that the use of a direct input device (i.e., touch screen) involves a multisensory experience and more cerebral activities than an indirect input device (i.e., mouse), leading to richer information encoding, and consequently to better information retrieval from memory. A one-factor between-subject experimental design was used to test our hypotheses. Thirty participants were randomly assigned to either a mouse or touch screen input device condition. Our results indicate that for individuals with higher need for touch, input device influences activity in the posterior parietal cortex (PPC), a brain region associated with multisensory experience, during memory retrieval and stimulus recognition.
Underwater Localization in Sparse 3D Acoustic Sensor Networks

We study the localization problem in sparse 3D underwater sensor networks. Considering the fact that depth information is typically available for underwater sensors, we transform the 3D underwater positioning problem into its two- dimensional counterpart via a projection technique and prove that a non-degenerative projection preserves network localizability. We further prove that given a network and a constant k, all of the geometric k-lateration localization methods are equivalent. Based on these results, we design a purely distributed localization framework termed USP. This framework can be applied with any ranging method proposed for 2D terrestrial sensor networks. Through theoretical analysis and extensive simulation, we show that USP preserves the localizability of the original 3D network via a simple projection and improves localization capabilities when bilateration is employed. USP has low storage and computation requirements, and predictable and balanced communication overhead.
Developmental Assembly of Transduction Apparatus in Chick Basilar Papilla

Hair cells, the sensory receptors of auditory and vestibular systems, use a transducer apparatus that renders them remarkably sensitive to mechanical displacement as minute as 1 nm. To study the embryonic development of the transducer apparatus in hair cells of the chick auditory papilla, we examined hair cells that have been labeled with N-(3-triethylammoniumpropyl)-4-(4-(dibutylamino)styryl) pyridiniumdibromide, which has been shown to permeate the transducer channels. In addition, mechanotransduction currents were recorded directly using whole-cell patch-clamp techniques. The structure of the hair bundle was examined using scanning electron microscopy, and immunofluorescence labeling for myosin 1c, myosin 7a, and plasma membrane Ca2+ ATPase 2 was studied to determine the developmental expression of these proteins in embryonic chick papillas. We demonstrate that the transducer apparatus is assembled jointly at embryonic day 11 (E11) of the developing chick basilar papilla. The resting open probability of the transducer channels was high at E12 (∼0.5) and remained substantially elevated at E14-16; it then declined to the mature value of ∼0.15 at E21. The displacement sensitivity of the transduction apparatus, the gating force, increased from E12 to E21. Although the expression of different components of the transducer apparatus and the transduction current peaked at ∼E14-16, marked refinement occurred beyond E16. For example, myosin 1c appeared diffusely localized in hair bundles from E12 to E16, but subsequently consolidated into punctate pattern. The fine temporal and precise spatial assembly of the transducer apparatus likely contributes toward the exquisite sensitivity of the transduction ensemble.