Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimal Estimation of a Large-Dimensional Covariance Matrix Under Stein's Loss

This paper introduces a new method for deriving covariance matrix estimators that are decision-theoretically optimal within a class of nonlinear shrinkage estimators. The key is to employ large-dimensional asymptotics: the matrix dimension and the sample size go to infinity together, with their ratio converging to a finite, nonzero limit. As the main focus, we apply this method to Stein’s loss. Compared to the estimator of Stein (1975, 1986), ours has five theoretical advantages: (1) it asymptotically minimizes the loss itself, instead of an estimator of the expected loss; (2) it does not necessitate post-processing via an ad hoc algorithm (called “isotonization”) to restore the positivity or the ordering of the covariance matrix eigenvalues; (3) it does not ignore any terms in the function to be minimized; (4) it does not require normality; and (5) it is not limited to applications where the sample size exceeds the dimension. In addition to these theoretical advantages, our estimator also improves upon Stein’s estimator in terms of finite-sample performance, as evidenced via extensive Monte Carlo simulations. To further demonstrate the effectiveness of our method, we show that some previously suggested estimators of the covariance matrix and its inverse are decision-theoretically optimal in the large-dimensional asymptotic limit with respect to the Frobenius loss function.
Search-logger analyzing exploratory search tasks

In this paper, we focus on a specific class of search cases: exploratory search tasks. To describe and quantify their complexity, we present a new methodology and corresponding tools to evaluate the user behavior when carrying out exploratory search tasks. These tools consist of a client called Search-Logger, and a server side database with frontend and an analysis environment. The client is a plug-in for Firefox web browsers. The assembly of the Search-Logger tools can be used to carry out user studies for search tasks independent of a laboratory environment. It collects implicit user information by logging a number of significant user events. Explicit information is gathered via user feedback in the form of questionnaires before and after each search task. We also present the results of a pilot user study. Some of our main observations are: When carrying out exploratory search tasks, classic search engines are mainly used as an entrance point to the web. Subsequently users work with several search systems in parallel, they have multiple browser tabs open and frequently use the clipboard to memorize, analyze and synthesize potentially useful data and information. Exploratory search tasks typically consist of various sessions and can span from hours up to weeks.
Effects of Hydration Level and Heat Stress on Thermoregulatory Responses, Hematological and Blood Rheological Properties in Growing Pigs

Heat stress is one of the major limiting factors of production efficiency in the swine industry. The aims of the present study were 1) to observe if hemorheological and hematological parameters could be associated to physiological acclimation during the first days of heat stress exposure and 2) to determine if water restriction could modulate the effect of thermal heat stress on physiological, hematological and hemorheological parameters. Twelve Large White male pigs were divided into an ad libitum and a water restricted group. All pigs were submitted to one week at 24°C (D-7 to D-1). Then, at D0, temperature was progressively increased until 32°C and maintained during one week (D1 to D7). We performed daily measurements of water and feed intake. Physiological (i.e., skin temperature, rectal temperature, respiratory rate), hematological and hemorheological parameters were measured on D-6, D-5, D0, D1, D2 and D7. Water restriction had no effect on physiological, hematological and hemorheological parameters. The first days of heat stress caused an increase in the three physiological parameters followed by a reduction of these parameters suggesting a successful acclimation of pigs to heat stress. We showed an increase in hematocrit, red blood cell aggregation and red blood cell aggregation strength during heat stress. Further, we observed an important release of reticulocytes, an increase of red blood cell deformability and a reduction of feed intake and blood viscosity under heat stress. This study suggests that physiological acute adaptation to heat stress is accompanied by large hematological and hemorheological changes.
A STUDY OF THE DISTRIBUTION OF TIME-DOMAIN SPEECH SAMPLES AND DISCRETE FOURIER COEFFICIENTS

We study the distribution of time-domain speech samples as well as the distribution of Discrete Fourier Transform (DFT) coefficients obtained from speech segments. We consider four possible pdf model types, namely Gaussian, Laplacian, Gamma, and a Generalized Gaussian density (GGD). Our time-domain results suggest that for segment lengths of 20‐200 ms, the Laplacian density is the better choice, while for shorter segments the Gaussian model is more appropriate. For segments of 20 ms, the Gaussian model is advantageous for broad speech classes of fricatives, nasals and glides, but stop sounds are much better represented with the Laplacian model, making the latter model better on average. Finally, our study supports the often made assumption that DFT coefficients collected within short time intervals can be considered Gaussian distributed, across all types of speech sounds.
Constructing linkage maps in the genomics era with MapDisto 2.0

Motivation: Genotyping by sequencing (GBS) generates datasets that are challenging to handle by current genetic mapping software with graphical interface. Geneticists need new user‐friendly computer programs that can analyze GBS data on desktop computers. This requires improvements in computation efficiency, both in terms of speed and use of random‐access memory (RAM). Results: MapDisto v.2. 0 is a user‐friendly computer program for construction of genetic linkage maps. It includes several new major features: (i) handling of very large genotyping datasets like the ones generated by GBS; (ii) direct importation and conversion of Variant Call Format (VCF) files; (iii) detection of linkage, i.e. construction of linkage groups in case of segregation distortion; (iv) data imputation on VCF files using a new approach, called LB‐Impute. Features i to iv operate through inclusion of new Java modules that are used transparently by MapDisto; (v) QTL detection via a new R/qtl graphical interface. Availability and Implementation: The program is available free of charge at mapdisto.free. fr. Contact: mapdisto@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
People, Places, and Play: A research framework for digital game experience in a socio-spatial context

The invention relates to imaging elements comprising a back surface wherein said back surface has a low frequency roughness component having a roughness average of between 0.30 and 2.00 mu m when measured with a low pass cutoff filter of 500 cycles/mm and a high frequency component having a roughness average of 0.001 to 0.05 mu m when measured with a high pass cutoff filter of 500 cycles/mm.
Determination of Barium,Cadmium,Cobalt,Copper Content in Plastics by ICP-OES after Microwave Ashing

A rapid detection method of the determination of barium,cadmium,cobalt,copper and other harmful elements content in plastics was proved.Microwave ashing was used for the pre-treatment and inductively coupled plasma optical emission spectrometry(ICP-OES) was employed for the further determination.This new method features were simple,rapid and accurate operation,as well as high sensitivity,which can effectively prevent the loss of the test element.
Fighting Dark Silicon: Toward Realizing Efficient Thermal-Aware 3-D Stacked Multiprocessors

This paper investigates the challenges of dark silicon that impede the performance and reliability of 3-D stacked multiprocessors. It presents a multipronged approach toward addressing the thermal issues arising from high-density integration in die stacks, spanning architectural techniques, design methodologies, and runtime temperature management. Importantly, this paper provides novel insights into the causes of hotspot formation in 3-D ICs and details a practical approach toward exploring and mitigating performance-limiting thermal behavior early in the system design flow.
Grammatical Abilities in Young Cochlear Implant Recipients and Children With Normal Hearing Matched by Vocabulary Size.

Purpose This study sought to expand understanding of the impact of cochlear implantation on grammatical acquisition by comparing young children who have vocabularies of comparable size. Two research questions were investigated: (a) Do young cochlear implant (CI) recipients have grammatical skills comparable to those of children with normal hearing (NH) matched by spoken vocabulary size? (b) Do these groups show associations between vocabulary size and grammatical measures? Method The participants included 13 CI recipients at 24 months postactivation (chronological ages = 33-60 months; M = 44.62) and 13 children with NH between 27 and 30 months old (M = 20.69). The 2 groups were matched by their vocabulary size. Four grammatical outcomes were analyzed from the MacArthur Communicative Development Inventory (Fenson, Marchman, Thal, Dale, & Reznick, 2007) and 20-min language samples: (a) grammatical complexity, (b) mean length of utterances, (c) tense marker total, and (d) productivity scores. Results The 2 groups showed comparable grammatical skills across the 4 measures. Consistently significant associations between vocabulary size and grammatical outcomes were found in the CI group, with fewer associations in the NH group. Conclusions The 2 groups showed similar grammatical abilities. The young CI recipients appeared to be following a typical pattern of linguistic development.
Rapid regulation of sialidase activity in response to neural activity and sialic acid removal during memory processing in rat hippocampus

Sialidase cleaves sialic acids on the extracellular cell surface as well as inside the cell and is necessary for normal long-term potentiation (LTP) at mossy fiber-CA3 pyramidal cell synapses and for hippocampus-dependent spatial memory. Here, we investigated in detail the role of sialidase in memory processing. Sialidase activity measured with 4-methylumbelliferyl-α-d-N-acetylneuraminic acid (4MU-Neu5Ac) or 5-bromo-4-chloroindol-3-yl-α-d-N-acetylneuraminic acid (X-Neu5Ac) and Fast Red Violet LB was increased by high-K+-induced membrane depolarization. Sialidase activity was also increased by chemical LTP induction with forskolin and activation of BDNF signaling, non-NMDA receptors, or NMDA receptors. The increase in sialidase activity with neural excitation appears to be caused not by secreted sialidase or by an increase in sialidase expression but by a change in the subcellular localization of sialidase. Astrocytes as well as neurons are also involved in the neural activity-dependent increase in sialidase activity. Sialidase activity visualized with a benzothiazolylphenol-based sialic acid derivative (BTP3-Neu5Ac), a highly sensitive histochemical imaging probe for sialidase activity, at the CA3 stratum lucidum of rat acute hippocampal slices was immediately increased in response to LTP-inducible high-frequency stimulation on a time scale of seconds. To obtain direct evidence for sialic acid removal on the extracellular cell surface during neural excitation, the extracellular free sialic acid level in the hippocampus was monitored using in vivo microdialysis. The free sialic acid level was increased by high-K+-induced membrane depolarization. Desialylation also occurred during hippocampus-dependent memory formation in a contextual fear-conditioning paradigm. Our results show that neural activity-dependent desialylation by sialidase may be involved in hippocampal memory processing.
Patterns of Leisure-Time Physical Activity Participation in a British Birth Cohort at Early Old Age

Using data from a nationally representative British birth cohort we characterized the type and diversity of leisure-time physical activity that 2,188 participants (age 60–64 years) engaged in throughout the year by gender and obesity. Participants most commonly reported walking (71%), swimming (33%), floor exercises (24%) and cycling (15%). Sixty-two percent of participants reported ≥2 activities in the past year and 40% reported diversity on a regular basis. Regular engagement in different types of activity (cardio-respiratory, balance/flexibility and strength) was reported by 67%, 19% and 11% of participants, respectively. We found gender differences, as well as differences by obesity status, in the activities reported, the levels of activity diversity and activity type. Non-obese participants had greater activity diversity, and more often reported activities beneficial for cardio-respiratory health and balance/flexibility than obese participants. These findings may be used to inform the development of trials of physical activity interventions targeting older adults, and those older adults with high body mass index.
Signal Quality Improvement Algorithms for MEMS Gyroscope-Based Human Motion Analysis Systems: A Systematic Review

Motion sensors such as MEMS gyroscopes and accelerometers are characterized by a small size, light weight, high sensitivity, and low cost. They are used in an increasing number of applications. However, they are easily influenced by environmental effects such as temperature change, shock, and vibration. Thus, signal processing is essential for minimizing errors and improving signal quality and system stability. The aim of this work is to investigate and present a systematic review of different signal error reduction algorithms that are used for MEMS gyroscope-based motion analysis systems for human motion analysis or have the potential to be used in this area. A systematic search was performed with the search engines/databases of the ACM Digital Library, IEEE Xplore, PubMed, and Scopus. Sixteen papers that focus on MEMS gyroscope-related signal processing and were published in journals or conference proceedings in the past 10 years were found and fully reviewed. Seventeen algorithms were categorized into four main groups: Kalman-filter-based algorithms, adaptive-based algorithms, simple filter algorithms, and compensation-based algorithms. The algorithms were analyzed and presented along with their characteristics such as advantages, disadvantages, and time limitations. A user guide to the most suitable signal processing algorithms within this area is presented.
Towards frequency adaptation for delayed feedback deep brain stimulations

In neurodegenerative disorders such as Parkinson’s disease (PD), deep brain stimulation (DBS) is a desirable approach when the medication is less effective for treating the symptoms. DBS incorporates transferring electrical pulses to a specific tissue of the central nervous system, obtaining therapeutic results by modulating the neuronal activity of that region. DBS has certain advantages such as reversibility and adjustability features over medication, since the neuronal firing patterns can be recorded and used to alter the parameters of the DBS signal (Benabid et al., 2009). One of the DBS indications is its ability to suppress the abnormal neuronal activity to treat symptoms like tremor, akinesia and dystonia. Although the mechanism of DBS is not fully understood, the inhibition of neurons, entrainment of bursting neurons and activation of axons has been associated with DBS therapy (Chiken and Nambu, 2016). Electric fields induced by DBS generally disrupt any abnormal information flow coming from the cortex to the basal ganglia neurons. DBS signals also increase and regularize the neuronal firing rates by direct activation of the axons of the stimulated neuron. This regularization of neuronal firing rate prohibits the oscillatory and bursting abnormalities of the basal ganglia neurons, leading to highly therapeutic results in PD. The therapeutic effects of DBS are enhanced once it is used in a closed loop paradigm. The cortical and pallidal discharge patterns of neurons are more improved by closed loop DBS rather than traditional open loop stimulations (Rosin et al., 2011). DBS is mainly targeted at subthalamic nucleus (STN) or globus pallidus externa (GPe) cells to disrupt the thalamo-cortical synchronizations seen in PD. Therefore, the local field potential (LFP) recorded from a population of the STN cells is often used as the feedback variable for DBS parametrization. Retrospective studies mainly focused on adjusting the stimulation amplitude based on the recorded LFP (Popovych et al., 2017). However, adapting the frequency of stimulation might provide superior results in desynchronizing the coupling patterns of STN-GPe. In addition, high frequency stimulation (HFS) typically used in DBS, significantly increases the device battery usage. In contrast, adapting the frequency of stimulation to a protocol where HFS is only used when high desynchronization is needed, can expand the battery lifespan and reduces the necessity of costly battery replacement surgeries (Lyons et al., 2004).
The caudal infrasylvian surface in dyslexia

Objective: To detect anatomic abnormalities of auditory association cortex in dyslexia by measuring the area of the perisylvian region known as the caudal infrasylvian surface(s) (cIS) in dyslexic and control subjects. Background: Several quantitative morphometric investigations of cortical areas in dyslexia have focused on the cIS, which encompasses the supratemporal plane and the inferior bank of the posterior ascending ramus of the sylvian fissure. Inconsistencies in the results of these studies may be attributable in part to the use of measurement methods that do not account fully for surface undulations of the cIS. Methods: The authors used an MRI-based surface reconstruction technique that models the curvature of the cerebral cortex in three dimensions to obtain whole-hemisphere and regional surface area estimates. Measurements were obtained in both hemispheres of eight right-handed male dyslexic subjects and eight right-handed male control subjects. Results: The cIS area of dyslexic subjects was significantly larger than that of control subjects, and this result was not attributable to a difference in whole-hemisphere surface area. Neither the dyslexic nor control subjects showed a left or right asymmetry in this region, although there was a trend toward less variance of the asymmetry scores in dyslexic subjects. Conclusions: The gross anatomic organization of this region is different in dyslexic subjects, and elucidation of the precise nature of these differences may be aided by surface modeling techniques.
A New Experimental Technique for Applying Impulse Tension Loading

This paper deals with a new experimental technique for applying impulse tension loads. Briefly, the technique is based on the use of pulsed-magnetic-driven tension loading. Electromagnetic forming (EMF) can be quite effective in increasing the forming limits of metal sheets, such as aluminium and magnesium alloys. Yet, why the forming limit is increased is still an open question. One reason for this is the difficulty to let forming proceed on a certain influence monotonically: the main phenomena causing this increase in formability are considered to due to “body force” effect, inertia effect, changes in strain rate sensitivity. In this study, an impulse tension loading setup is presented. “Body force” effect and strain rate, which are known to be the two key factors leading to higher formability, can now be separated freely by our designed device. Reproducible and adjustable loading rate (80s-1~3267s-1) can be achieved by adjusting the discharge voltage and capacitance. The relation between the discharge voltage and strain rate was obtained with the help of finite element calculations and high-camera measurement results. The results of an exploratory experiment carried out on the designed device are presented for aluminum alloy AA5052 sheet. It shows that this technique could be used to study the dynamic response of sheets.
Signaling adaptor ShcD suppresses extracellular signal-regulated kinase (Erk) phosphorylation distal to the Ret and Trk neurotrophic receptors

Proteins of the Src homology and collagen (Shc) family are typically involved in signal transduction events involving Ras/MAPK and PI3K/Akt pathways. In the nervous system, they function proximal to the neurotrophic factors that regulate cell survival, differentiation, and neuron-specific characteristics. The least characterized homolog, ShcD, is robustly expressed in the developing and mature nervous system, but its contributions to neural cell circuitry are largely uncharted. We now report that ShcD binds to active Ret, TrkA, and TrkB neurotrophic factor receptors predominantly via its phosphotyrosine-binding (PTB) domain. However, in contrast to the conventional Shc adaptors, ShcD suppresses distal phosphorylation of the Erk MAPK. Accordingly, genetic knock-out of mouse ShcD enhances Erk phosphorylation in the brain. In cultured cells, this capacity is tightly aligned to phosphorylation of ShcD CH1 region tyrosine motifs, which serve as docking platforms for signal transducers, such as Grb2. Erk suppression is relieved through independent mutagenesis of the PTB domain and the CH1 tyrosine residues, and successive substitution of these tyrosines breaks the interaction between ShcD and Grb2, thereby promoting TrkB-Grb2 association. Erk phosphorylation can also be restored in the presence of wild type ShcD through Grb2 overexpression. Conversely, mutation of the ShcD SH2 domain results in enhanced repression of Erk. Although the SH2 domain is a less common binding interface in Shc proteins, we demonstrate that it associates with the Ptpn11 (Shp2) phosphatase, which in turn regulates ShcD tyrosine phosphorylation. We therefore propose a model whereby ShcD competes with neurotrophic receptors for Grb2 binding and opposes activation of the MAPK cascade.
Lipid packing defects and membrane charge control RAB GTPase recruitment

Specific intracellular localization of RAB GTPases has been reported to be dependent on protein factors, but the contribution of the membrane physicochemical properties to this process has been poorly described. Here, we show that three RAB proteins (RAB1/RAB5/RAB6) preferentially bind in vitro to disordered and curved membranes, and that this feature is uniquely dependent on their prenyl group. Our results imply that the addition of a prenyl group confers to RAB proteins, and most probably also to other prenylated proteins, the ability to sense lipid packing defects induced by unsaturated conical‐shaped lipids and curvature. Consistently, RAB recruitment increases with the amount of lipid packing defects, further indicating that these defects drive RAB membrane targeting. Membrane binding of RAB35 is also modulated by lipid packing defects but primarily dependent on negatively charged lipids. Our results suggest that a balance between hydrophobic insertion of the prenyl group into lipid packing defects and electrostatic interactions of the RAB C‐terminal region with charged membranes tunes the specific intracellular localization of RAB proteins.