Miracle-dz/UniFAR-FTUs huggingface dataset:
Acute adaptations and subsequent preservation of strength and speed measures following a Nordic hamstring curl intervention: a randomised controlled trial

ABSTRACT This randomised controlled trial investigated changes in eccentric hamstring strength, 10m sprint speed, and change-of-direction (COD) performance immediately post Nordic hamstring curl (NHC) intervention and following a 3-week detraining period. Fourteen male team sports athletes were randomised to a do-as-usual control group (CG; n = 7) or to a NHC intervention group (NHC; n = 7). Isokinetic dynamometry at 180°/s evaluated eccentric hamstring strength immediately post-intervention as the primary outcome measure. Secondary outcomes included 10 m sprint time and COD. Each outcome was measured, pre, immediately post-intervention and following a 3-week detraining period. Immediately post-intervention significant group differences were observed in the NHC group for eccentric hamstring strength (31.81 Nm−1 vs. 6.44 Nm−1, P = 0.001), COD (−0.12 s vs. 0.20 s; P = 0.003) and sprint (- 0.06 s vs. 0.05 s; P = 0.024) performance. Performance improvements were maintained following a detraining period for COD (−0.11 s vs. 0.20 s; P = 0.014) and sprint (−0.05 s vs. 0.03 s, P = 0.031) but not eccentric hamstring strength (15.67 Nm−1 vs. 6.44 Nm−1, P = 0.145) These findings have important implications for training programmes designed to reduce hamstring injury incidence, whilst enhancing physical qualities critical to sport.
First Principles Calculations Toward Understanding SERS of 2,2′‐Bipyridyl Adsorbed on Au, Ag, and Au–Ag Nanoalloy

First principles electrodyanmics and quantum chemical simulations are performed to gain insights into the underlying mechanisms of the surface enhanced Raman spectra of 22BPY adsorbed on pure Au and Ag as well as on Au–Ag alloy nanodiscs. Experimental SERS spectra from Au and Ag nanodiscs show similar peaks, whereas those from Au–Ag alloy reveal new spectral features. The physical enhancement factors due to surface nano‐texture were considered by numerical FDTD simulations of light intensity distribution for the nano‐textured Au, Ag, and Au–Ag alloy and compared with experimental results. For the chemical insights of the enhancement, the DFT calculations with the dispersion interaction were performed using Au20, Ag20, and Au10Ag10 clusters of a pyramidal structure for SERS modeling. Binding of 22BPY to the clusters was simulated by considering possible arrangements of vertex and planar physical as well as chemical adsorption models. The DFT results indicate that 22BPY prefers a coplanar adsorption on a (111) face with trans‐conformation having close energy difference to cis‐conformation. Binding to pure Au cluster is stronger than to pure Ag or Au–Ag alloy clusters and adsorption onto the alloy surface can deform the surface. The computed Raman spectra are compared with experimental data and assignments for pure Au and Ag models are well matching, indicating the need of dispersion interaction to reproduce strong Raman signal at around 800 cm–1. This work provides insight into 3D character of SERS on nanorough surfaces due to different binding energies and bond length of nanoalloys. © 2018 Wiley Periodicals, Inc.
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

Abstract UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode—the nuclear ribosomal internal transcribed spacer (ITS) region—and offers all ∼1 000 000 public fungal ITS sequences for reference. These are clustered into ∼459 000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275 000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.
NH4OH Wet Etching for Silicon Nano or Sub-Micron Wires

In this work, instead of TMAH (Tetra Methyl Ammonium Hydroxide), ammonium hydroxide (NH4OH) solutions are used to get silicon nano (SiNWs) or sub-micron (SiSMWs) wires, because also these solutions are silicon orientation-dependent wet etching and fully compatible with CMOS (Complementary Metal – Oxide - Semiconductor) technology.These wires were fabricated on Si and SOI (Silicon- On-Insulator) wafers, with (100) crystallographic orientation surfaces. On both wafers, the lateral etch rates under SiO2 of<110> plane Si wire sidewalls between 43 nm/min and 156 nm/min were obtained. Thus,SiNWs and SiSMWs were obtained, indicating that our NH4OH solution is a new alternative to get 3D structures on Si and SOI substrates. To confirm this result, pseudo-MOS (Metal-Oxide-Silicon) transistor on SOI substrate, with conduction channel of n+ Si wire of width of 1.22 μm and height of 100 nm, was fabricated. From drain-source current (IDS) versus back gate – source voltage (VBGS) curve of Pseudo MOS transistor, the threshold voltage (VT) of 1.36 V and the maximum transconductance of $20 \mu \mathrm{S}$ were extracted.
Fluorescence in blue light (FLU) is involved in inactivation and localization of glutamyl‐tRNA reductase during light exposure

Fluorescent in blue light (FLU) is a negative regulator involved in dark repression of 5-aminolevulinic acid (ALA) synthesis and interacts with glutamyl-tRNA reductase (GluTR), the rate-limiting enzyme of tetrapyrrole biosynthesis. In this study, we investigated FLU's regulatory function in light-exposed FLU-overexpressing (FLUOE) Arabidopsis lines and under fluctuating light intensities in wild-type (WT) and flu seedlings. FLUOE lines suppress ALA synthesis in the light, resulting in reduced chlorophyll content, but more strongly in low and high light than in medium growth light. This situation indicates that FLU's impact on chlorophyll biosynthesis depends on light intensity. FLU overexpressors contain strongly increased amounts of mainly membrane-associated GluTR. These findings correlate with FLU-dependent localization of GluTR to plastidic membranes and concomitant inhibition, such that only the soluble GluTR fraction is active. The overaccumulation of membrane-associated GluTR indicates that FLU binding enhances GluTR stability. Interestingly, under fluctuating light, the leaves of flu mutants contain less chlorophyll compared with WT and become necrotic. We propose that FLU is basically required for fine-tuned ALA synthesis. FLU not only mediates dark repression of ALA synthesis, but functions also to control balanced ALA synthesis under variable light intensities to ensure the adequate supply of chlorophyll.
The cellular and molecular mechanism of glutaraldehyde‐didecyldimethylammonium bromide as a disinfectant against Candida albicans

In our previous research, we have developed a new combination disinfectant, glutaraldehyde‐didecyldimethylammonium bromide (GD). It was verified that GD had a strong effect on both Escherichia coli and Staphylococcus aureus. In this work, Candida albicans was selected as an object, and it could be killed by GD. We aimed to investigate the cellular and molecular mechanism of GD effecting on C. albicans.
Vectorial Semantic Spaces Do Not Encode Human Judgments of Intervention Similarity

Despite their practical success and impressive performances, neural-network-based and distributed semantics techniques have often been criticized as they remain fundamentally opaque and difficult to interpret. In a vein similar to recent pieces of work investigating the linguistic abilities of these representations, we study another core, defining property of language: the property of long-distance dependencies. Human languages exhibit the ability to interpret discontinuous elements distant from each other in the string as if they were adjacent. This ability is blocked if a similar, but extraneous, element intervenes between the discontinuous components. We present results that show, under exhaustive and precise conditions, that one kind of word embeddings and the similarity spaces they define do not encode the properties of intervention similarity in long-distance dependencies, and that therefore they fail to represent this core linguistic notion.
EEG Channel Selection Based on Correlation Coefficient for Motor Imagery Classification: A Study on Healthy Subjects and ALS Patient

Brain-Computer Interface (BCI) provides an alternate channel of interaction for people with severe motor disabilities. The Common Spatial Pattern (CSP) algorithm is effective in extracting discriminative features from EEG data for motor imagery-based Brain-Computer Interface (BCI). CSP yields signal from various locations for better performance. In this study, we selected a subset of EEG channels using correlation coefficient of spectral entropy and compared the classification performance using the Filter Bank Common Spatial Pattern (FBCSP) algorithm. We conducted experiments on 4 healthy subjects and one Amyotrophic Lateral Sclerosis (ALS) patient. The results showed that the proposed channel selection method increased classification accuracy of all subjects from 1.25% to 8.22%. Optimal performance was obtained using between 13 to 24 channels, and channels located over the motor cortex zone possess higher probabilities of being selected. Comparing with the channels manually selected to over the motor cortex area, the correlation coefficient method is able to identify the optimal channel combination and improve the motor imagery decoding accuracy of Healthy and ALS subjects.
Fabrik: An Online Collaborative Neural Network Editor

We present Fabrik, an online neural network editor that provides tools to visualize, edit, and share neural networks from within a browser. Fabrik provides a simple and intuitive GUI to import neural networks written in popular deep learning frameworks such as Caffe, Keras, and TensorFlow, and allows users to interact with, build, and edit models via simple drag and drop. Fabrik is designed to be framework agnostic and support high interoperability, and can be used to export models back to any supported framework. Finally, it provides powerful collaborative features to enable users to iterate over model design remotely and at scale.
Landmark Typology in Applied Morphometrics Studies: What's the Point?

Landmarks are the hallmark of biological shape analysis as discrete anatomical points of correspondence. Various systems have been developed for their classification. In the most widely used system, developed by Bookstein in the 1990s, landmarks are divided into three distinct types based on their anatomical locations and biological significance. As Bookstein and others have argued that different landmark types possess different qualities, e.g., that Type 3 landmarks contain deficient information about shape variation and are less reliably measured, researchers began using landmark types as justification for selecting or avoiding particular landmarks for measurement or analysis. Here, we demonstrate considerable variation in landmark classifications among 17 studies using geometric morphometrics (GM), due to disagreement in the application of both Bookstein's landmark typology and individual landmark definitions. A review of the literature furthermore shows little correlation between landmark type and measurement reproducibility, especially when factors such as differences in measurement tools (calipers, digitizer, or computer software) and data sources (dry crania, 3D models, or 2D images) are considered. Although landmark typology is valuable when teaching biological shape analysis, we find that employing it in research design introduces confusion without providing useful information. Instead, researchers should choose landmark configurations based on their ability to test specific research hypotheses, and research papers should include justifications of landmark choices along with landmark definitions, details on landmark collection methods, and appropriate interobserver and intraobserver analyses. Hence, while the landmarks themselves are crucial for GM, we argue that their typology is of little use in applied studies. Anat Rec, 302:1144–1153, 2019. © 2018 Wiley Periodicals, Inc.
A Simple yet Effective Joint Training Method for Cross-Lingual Universal Dependency Parsing

This paper describes Fudan’s submission to CoNLL 2018’s shared task Universal Dependency Parsing. We jointly train models when two languages are similar according to linguistic typology and then ensemble the models using a simple re-parse algorithm. We outperform the baseline method by 4.4% (2.1%) on average on development (test) set in CoNLL 2018 UD Shared Task.
On-Chip Wireless Channel Propagation: Impact of Antenna Directionality and Placement on Channel Performance

Long range, low latency wireless links in Networks-on-Chip (NoCs) have been shown to be the most promising solution to provide high performance intra/inter-chip communication in many core era. Significant advancements have been made in design of both Wireless NoC (WNoC) topologies and transceiver circuits to support wireless communication at chip level. However, a comprehensive understanding of wireless physical layer and its impact on performance is still lacking. There is still a lot of scope for thorough analysis of the affects of intra-chip wireless channel and antenna characteristics on signal transmission and link reliability in WNoCs. To this end, we analyse signal propagation through wireless channel by accurately modelling the intra-chip environment. We analyse the effects of antenna placement across chip plane and its directionality on the signal loss, delay and dispersion properties. The analysis shows that directional antenna exhibits better delay characteristics, while omnidirectional antennas have low loss for signal transmission in the channel. Furthermore, the placement of antenna shows considerable impact on channel characteristics due to reflections from chip edges and constructive or destructive interference between the multiple signal components. This work provides crucial insights into propagation characteristics of on-chip wireless links for better design of transceiver components and their performance.
Broadband output windows for THz gyro-TWAs

This paper presents the design, simulation and technical considerations of output windows, based on the multilayer type, for THz gyro- TWAs. Such windows can achieve very low reflection levels over a broadband frequency range when the thickness of the dielectric layers are properly matched. The optimized window, in this design, was numerically calculated to achieve a passband of over 7% with a reflection of less than −30 dB and transmission loss of better than −0.3 dB.
Non uniformity correction in a Long Wave Infrared Focal Plane Array as a function of the higher calibration temperature

It is well known that every detector in a Focal Plane Array (FPA) has a different responsivity and offset. These variations result in a specific kind of noise, the Fixed Pattern Noise (FPN) or spatial noise. During the image processing, those pixels who has a large deviation in responsivity are considered a bad pixel, and has its value removed of FPA. Knowing the answer of all those pixels are the first test procedure in a FPA characterization. However, during the bad pixels analysis it is necessary to choose two reference temperatures, calibration points, and those temperature affects important parameters such as Uniformity, Noise Equivalent Temperature Difference (NETD) and Signal Transfer Function (SiTF). This work will study the influence of higher calibration temperature on the NonUniformity Correction (NUC) quality.
Effect of Gating Charges on Mediating the Dual Activation of BK Channels in Smooth Muscle Cells: A Computational Study

This paper employs a computational model to study the dual gating modalities of BK channels in smooth muscles. These channels are gated by both membrane potential and intracellular calcium concentration. It has been previously reported that the sensors for these two stimuli are located at different regions of the channel. Thus, the two sensing modalities act independent of each other. Yet, they result in a concerted and synergistic opening of the channel pore. In this paper, we investigate the effects of these two gating mechanisms by computing the effective gating charges contributed by the channel’s voltage and calcium sensors. Along with their independent contributions, we study and estimate the interplay and effect of these two modalities on the channel’s activation. The voltage and calcium sensors appear to share the ‘load’ of the gating charges required to activate the channel based on the cytosolic calcium concentration and membrane potential. Thus, through our computational model, we demonstrate how the two independent sensors gate and coordinate the activation of the channel.
Effect of Collapsed Duplications on Diversity Estimates: What to Expect

Abstract The study of segmental duplications (SDs) and copy-number variants (CNVs) is of great importance in the fields of genomics and evolution. However, SDs and CNVs are usually excluded from genome-wide scans for natural selection. Because of high identity between copies, SDs and CNVs that are not included in reference genomes are prone to be collapsed—that is, mistakenly aligned to the same region—when aligning sequence data from single individuals to the reference. Such collapsed duplications are additionally challenging because concerted evolution between duplications alters their site frequency spectrum and linkage disequilibrium patterns. To investigate the potential effect of collapsed duplications upon natural selection scans we obtained expectations for four summary statistics from simulations of duplications evolving under a range of interlocus gene conversion and crossover rates. We confirm that summary statistics traditionally used to detect the action of natural selection on DNA sequences cannot be applied to SDs and CNVs since in some cases values for known duplications mimic selective signatures. As a proof of concept of the pervasiveness of collapsed duplications, we analyzed data from the 1,000 Genomes Project. We find that, within regions identified as variable in copy number, diversity between individuals with the duplication is consistently higher than between individuals without the duplication. Furthermore, the frequency of single nucleotide variants (SNVs) deviating from Hardy–Weinberg Equilibrium is higher in individuals with the duplication, which strongly suggests that higher diversity is a consequence of collapsed duplications and incorrect evaluation of SNVs within these CNV regions.
Co-Sparse Analysis Model Based Image Registration to Compensate Brain Shift by Using Intra-Operative Ultrasound Imaging

Notwithstanding the widespread use of image guided neurosurgery systems in recent years, the accuracy of these systems is strongly limited by the intra-operative deformation of the brain tissue, the so-called brain shift. Intra-operative ultrasound (iUS) imaging as an effective solution to compensate complex brain shift phenomena update patients coordinate during surgery by registration of the intra-operative ultrasound and the pre-operative MRI data that is a challenging problem.In this work a non-rigid multimodal image registration technique based on co-sparse analysis model is proposed. This model captures the interdependency of two image modalities; MRI as an intensity image and iUS as a depth image. Based on this model, the transformation between the two modalities is minimized by using a bimodal pair of analysis operators which are learned by optimizing a joint co-sparsity function using a conjugate gradient.Experimental validation of our algorithm confirms that our registration approach outperforms several of other state-of-the-art registration methods quantitatively. The evaluation was performed using seven patient dataset with the mean registration error of only 1.83 mm. Our intensity-based co-sparse analysis model has improved the accuracy of non-rigid multimodal medical image registration by 15.37% compared to the curvelet based residual complexity as a powerful registration method, in a computational time compatible with clinical use.
A New Method for Facial and Corporal Expression Recognition

Expression recognition via facial and corporal movements plays an important role in our daily lives. In this paper, a new method for expression recognition is proposed. We collected a bi-modal dataset of facial and corporal expressions of 9 subjects performance of six expressions (sadness, surprise, happiness, fear, anger, and neutral) using Kinect (v1) and Kinect (v2). New geometrical features including a combination of angle and distance features are used to train multiple classifiers. This work concentrates on facial and corporal expression and feature extraction. For system performance assessment, we used leave-one-out subject cross-validation. The obtained results show the superior performance of the RGB-D features provided by Kinect (v2).
Spectrogram-channels u-net: a source separation model viewing each channel as the spectrogram of each source

Sound source separation has attracted attention from Music Information Retrieval(MIR) researchers, since it is related to many MIR tasks such as automatic lyric transcription, singer identification, and voice conversion. In this paper, we propose an intuitive spectrogram-based model for source separation by adapting U-Net. We call it Spectrogram-Channels U-Net, which means each channel of the output corresponds to the spectrogram of separated source itself. The proposed model can be used for not only singing voice separation but also multi-instrument separation by changing only the number of output channels. In addition, we propose a loss function that balances volumes between different sources. Finally, we yield performance that is state-of-the-art on both separation tasks.
Qualification of Wrist Functional Performance During Dart Thrower’s Movement

Recently, numerous comprehensive studies have been concentrating on the intricate kinematics of the wrist joint functionality captured with dart thrower’s movement. It is envisaged that the wrist capability in performing daily activities can be more accurately characterized or encapsulated in the dart thrower’s movement. This study examines the characteristic function of wrist movements during dart-throwing motion using only gyroscopic data measured from inertial sensors. A multi-dimensional form of dart throwing trajectory is described using quaternion representation associated with distance metric to quantitatively validate the functional wrist performance between two cohorts; healthy controls and patients. Eight normal subjects and eight patients engaged in a series of clinical trials conducted after undergoing post-surgical reconstructive procedures of the wrist joint. The discriminative results in terms of silhouette clustering evaluation show that the use of distance metric values based quaternion trajectory is well-matched consistently with subjective expert assessments. Our proposed approach captures the relative motions underpinning the wrist joint instead of relying on the traditional measure based on the range of motion measure. Therefore, this paper proposes a reliable approach to dynamically capture the wrist functionality during dart thrower’s movement; a movement envisaged to describe the ability to engage in daily life activities. These quantitative outcomes in terms of measurement consistency will provide insightful information in understanding the significant changes in wrist joint signatures associated with various scenarios.