Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution of nuchal glands, unusual defensive organs of Asian natricine snakes (Serpentes: Colubridae), inferred from a molecular phylogeny

Abstract A large body of evidence indicates that evolutionary innovations of novel organs have facilitated the subsequent diversification of species. Investigation of the evolutionary history of such organs should provide important clues for understanding the basis for species diversification. An Asian natricine snake, Rhabdophis tigrinus, possesses a series of unusual organs, called nuchal glands, which contain cardiotonic steroid toxins known as bufadienolides. Rhabdophis tigrinus sequesters bufadienolides from its toad prey and stores them in the nuchal glands as a defensive mechanism. Among more than 3,500 species of snakes, only 17 Asian natricine species are known to possess nuchal glands or their homologues. These 17 species belong to three nominal genera, Balanophis, Macropisthodon, and Rhabdophis. In Macropisthodon and Rhabdophis, however, species without nuchal glands also exist. To infer the evolutionary history of the nuchal glands, we investigated the molecular phylogenetic relationships among Asian natricine species with and without nuchal glands, based on variations in partial sequences of Mt‐CYB, Cmos, and RAG1 (total 2,767 bp). Results show that all species with nuchal glands belong to a single clade (NGC). Therefore, we infer that the common ancestor of this clade possessed nuchal glands with no independent origins of the glands within the members. Our results also imply that some species have secondarily lost the glands. Given the estimated divergence time of related species, the ancestor of the nuchal gland clade emerged 19.18 mya. Our study shows that nuchal glands are fruitful subjects for exploring the evolution of novel organs. In addition, our analysis indicates that reevaluation of the taxonomic status of the genera Balanophis and Macropisthodon is required. We propose to assign all species belonging to the NGC to the genus Rhabdophis, pending further study.
Recent Developments for Flexible Pressure Sensors: A Review

Flexible pressure sensors are attracting great interest from researchers and are widely applied in various new electronic equipment because of their distinct characteristics with high flexibility, high sensitivity, and light weight; examples include electronic skin (E-skin) and wearable flexible sensing devices. This review summarizes the research progress of flexible pressure sensors, including three kinds of transduction mechanisms and their respective research developments, and applications in the fields of E-skin and wearable devices. Furthermore, the challenges and development trends of E-skin and wearable flexible sensors are also briefly discussed. Challenges of developing high extensibility, high sensitivity, and flexible multi-function equipment still exist at present. Exploring new sensing mechanisms, seeking new functional materials, and developing novel integration technology of flexible devices will be the key directions in the sensors field in future.
Safety of Natural Insecticides: Toxic Effects on Experimental Animals

Long-term application and extensive use of synthetic insecticides have resulted in accumulating their residues in food, milk, water, and soil and cause adverse health effects to human and ecosystems. Therefore, application of natural insecticides in agriculture and public health sectors has been increased as alternative to synthetic insecticides. The question here is, are all natural insecticides safe. Therefore, the review presented here focuses on the safety of natural insecticides. Natural insecticides contain chemical, mineral, and biological materials and some products are available commercially, e.g., pyrethrum, neem, spinosad, rotenone, abamectin, Bacillus thuringiensis (Bt), garlic, cinnamon, pepper, and essential oil products. It can induce hepatotoxicity, renal toxicity, hematotoxicity, reproductive toxicity, neurotoxicity, and oxidative stress. It can induce mutagenicity, genotoxicity, and carcinogenicity in mammals. Some natural insecticides and active compounds from essential oils are classified in categories Ib (Highly hazardous) to U (unlikely toxic). Therefore, the selectivity and safety of natural insecticides not absolute and some natural compounds are toxic and induce adverse effects to experimental animals. In concussion, all natural insecticides are not safe and the term “natural” does not mean that compounds are safe. In this respect, the term “natural” is not synonymous with “organic” and not all-natural insecticide products are acceptable in organic farmers.
A Quadrature Switched-Capacitor RF-DAC Drain Efficiency Model for Back-Off Operation

In this paper a linear, code-dependent model for drain efficiency estimation of radio-frequency switched-capacitor power amplifiers in back-off operation mode is presented. Given a certain modulation scheme this model provides an estimation for output power and drain efficiency in back-off operation, which enables comparison between different modulation schemes and transmitter (TX) architectures like digital intensive quadrature and polar including hybrid polar-I/Q concepts. The model is validated against circuit simulations for a CMOS 28 nm technology.
Two-Layer Localized Sensitive Hashing with Adaptive Re-Ranking

Hashing-based approximated nearest neighbor (ANN) search techniques have been widely studied owing to its compact binary codes and efficient search scheme for large-scale image retrieval. For the most popular existing hashing methods, e.g. the Locality sensitivity Hashing and the Spectral Hashing, the key issue is to choose appropriate binary code length for similarity preserving and computational efficiency. Several extensions have been proposed to address the problem of balancing precision, recall rate and computation efficiency. However, most of existing hashing methods struggle for how to choose appropriate length of hash codes. A bad choice of code length may result in extremely poor performance of retrieval. In this paper, we propose a novel hashing scheme, called the Two-Layer Localized Sensitive Hashing with Adaptive Reranking (TL-LSHAR). This method utilizes a short hash code to generate the weights for a long hash code to further improve the retrieval performance. Moreover, the new scheme can be used by most of the existing hashing methods. The performance is evaluated on two large scale image databases which demonstrates the efficiency of our scheme.
HITS-PR-HHblits: protein remote homology detection by combining PageRank and Hyperlink-Induced Topic Search

As one of the most important fundamental problems in protein sequence analysis, protein remote homology detection is critical for both theoretical research (protein structure and function studies) and real world applications (drug design). Although several computational predictors have been proposed, their detection performance is still limited. In this study, we treat protein remote homology detection as a document retrieval task, where the proteins are considered as documents and its aim is to find the highly related documents with the query documents in a database. A protein similarity network was constructed based on the true labels of proteins in the database, and the query proteins were then connected into the network based on the similarity scores calculated by three ranking methods, including PSI-BLAST, Hmmer and HHblits. The PageRank algorithm and Hyperlink-Induced Topic Search (HITS) algorithm were respectively performed on this network to move the homologous proteins of query proteins to the neighbors of the query proteins in the network. Finally, PageRank and HITS algorithms were combined, and a predictor called HITS-PR-HHblits was proposed to further improve the predictive performance. Tested on the SCOP and SCOPe benchmark datasets, the experimental results showed that the proposed protocols outperformed other state-of-the-art methods. For the convenience of the most experimental scientists, a web server for HITS-PR-HHblits was established at http://bioinformatics.hitsz. edu.cn/HITS-PR-HHblits, by which the users can easily get the results without the need to go through the mathematical details. The HITS-PR-HHblits predictor is a protocol for protein remote homology detection using different sets of programs, which will become a very useful computational tool for proteome analysis.
Online Speech Dereverberation Using RLS-WPE Based on a Full Spatial Correlation Matrix Integrated in a Speech Enhancement System

Reverberation may degrade the performance of automatic speech recognition significantly. Although the weighted prediction error (WPE) provided impressive results, most of the conventional WPE methods were based on batch processing. An efficient WPE method based on frame-by-frame adaptation of the prediction filter in the recursive least squares (RLS) framework was proposed, but the spatial correlation matrix was oversimplified to be a scaled identity matrix. In this paper, we derive a generalized online RLS-WPE method allowing a full spatial correlation matrix. Experimental results showed that the method using a diagonal matrix achieved better performance than that using a scaled identity matrix and employing a full matrix further improved the performance. Furthermore, we also integrated the algorithm into a speech enhancement system, including stereo adaptive echo cancellation and minimum variance distortion response beamforming, implemented onto Xilinx Zynq Ultrascale+ MPSoC.
Online Integration of DNN-Based and Spatial Clustering-Based Mask Estimation for Robust MVDR Beamforming

This paper discusses the online estimation of time- frequency masks, which enables us to perform mask-based beamforming by online processing for robust automatic speech recognition (ASR). Two approaches to online mask estimation have been separately developed for this purpose. One is based on a deep neural network (DNN), which exploits the spectral features of the signal. The other is based on spatial clustering (SC), which exploits the spatial features of the signal. This paper proposes a new method that integrates the two online estimation approaches to further improve online mask estimation by exploiting the advantages of both approaches. Experiments using the real data of the CHiME-3 multichannel noisy speech corpus show that the proposed method greatly outperforms the conventional approaches in terms of improving the word error rate (WER).
Penile doppler ultrasound predicts cardiovascular events in men with erectile dysfunction

Traditional risk factors used to assess cardiovascular risk miss a significant population who are indeed at risk for future cardiac events. Erectile dysfunction (ED) is an emerging marker for future cardiovascular disease (CVD) and major adverse cardiovascular events (MACE), especially in young and middle‐aged men with vasculogenic ED. Cavernous arteries morphological alterations at penile colour doppler ultrasound (P‐CDU) are used to find a vasculogenic ED.
The Status of Pet Rabbit Breeding and Online Sales in the UK: A Glimpse into an Otherwise Elusive Industry

Simple Summary Very little is known about where our pet rabbits come from: Who the breeders are, how good/or bad the conditions are that breeding rabbits are kept in, or whether breeders are being monitored by local authorities. This study aimed to bring to light information on breeding rabbits and breeders in the UK. Several methods of data collection were used combining data from online sales adverts, with a breeder survey and a council freedom of information request. From 3446 online rabbit sale adverts we found 94.5% of adverts were from England and only 1% of breeders were licenced. Out of 33 breeders surveyed, 51.5% provided smaller housing than recommended and housed most rabbits singly, against recommendations, and males were most likely to be housed singly, in too small conditions. However, most provided toys and a diet compliant with recommended guidelines. The most commonly sold/bred rabbits were breeds with flat-faces, which can cause significant health and well-being problems. A freedom of information request sent to 10% of UK councils revealed inconsistency in licensing conditions and confusion about eligibility. Without appropriate guidelines for housing and husbandry and regulation, rabbits within the pet rabbit breeding industry are at risk of compromised welfare. Abstract Conditions of pet rabbit breeding colonies and breeder practices are undocumented and very little is known about the pet rabbit sales market. Here, multiple methods were employed to investigate this sector of the UK pet industry. A freedom of information request sent to 10% of councils revealed confusion and inconsistency in licensing conditions. Data from 1-month of online sale adverts (3446) identified 646 self-declared breeders, of which 1.08% were licensed. Further, despite veterinary advice to vaccinate rabbits from five weeks, only 16.7% rabbits were vaccinated and 9.2% of adult rabbits were neutered. Thirty-three breeders completed a questionnaire of which 51.5% provided smaller housing than recommended, the majority housed rabbits singly and bucks were identified as most at risk of compromised welfare. However, most breeders provided enrichment and gave a diet compliant with recommended guidelines. Mini-lops and Netherland dwarfs were the most commonly sold breeds, both of which are brachycephalic, which can compromise their health and wellbeing. From sales data extrapolation, we estimate that 254,804 rabbits are purposefully bred for the UK online pet sales market each year. This data is the first of its kind and highlights welfare concerns within the pet rabbit breeding sector, which is unregulated and difficult to access.
Roles of Smads Family and Alternative Splicing Variants of Smad4 in Different Cancers

Transforming Growth Factor β (TGF-β) is one of the most common secretory proteins which are recognized by membrane receptors joined to transcription regulatory factor. TGF-β signals are transduced by the Smads family that regulate differentiation, proliferation, early growth, apoptosis, homeostasis, and tumor development. Functional study of TGF-β signaling pathway and Smads role is vital for certain diseases such as cancer. Alternative splicing produces a diverse range of protein isoforms with unique function and the ability to react differently with various pharmaceutical products. This review organizes to describe the general study of Smads family, the process of alternative splicing, the general aspect of alternative splicing of Smad4 in cancer and the possible use of spliceoforms for the diagnosis and therapeutic purpose. The main aim and objective of this article are to highlight some particular mechanisms involving in alternatives splicing of cancer and also to demonstrate new evidence about alternative splicing in different steps given cancer initiation and progression.
Digital Audio Tampering Detection Based on ENF Consistency

This paper addresses a method of automatic detection of digital audio signal tampering based on feature fusion. Aiming at the insertion and deletion operations in the digital audio signal tamper chain. In this paper, the Electric Network Frequency (ENF) component of the digital audio signal is extracted and the consistency of the ENF component is analyzed to determine whether the audio signal is tampered with. In this paper, a general framework for passive tamper detection of audio signal based on ENF component consistency and a general framework for ENFC feature extraction are proposed. The feature set is used to quantify the amplitude of the phase and instantaneous frequency variations of the ENF component and to serve as an indicator of the consistency of the ENF component. SVM classifier is used to classify the extracted feature sets. The experimental results show that this method can classify the original signal and the edit signal which is inserted and deleted.
Potential Hazards Not Communicated in Safety Data Sheets of Flavoring Formulations, Including Diacetyl and 2,3-Pentanedione

Objectives Workers using flavoring formulations containing diacetyl and 2,3-pentanedione may be at risk of inhalational exposure, as these volatile hazardous chemicals are emitted from the bulk material, especially at elevated temperatures. However, flavoring formulations that contain diacetyl and 2,3-pentanedione might not list these ingredients because they are generally recognized as safe to ingest, may be part of a proprietary mixture deemed a trade secret, or may not be required to be listed if they are present at <1% composition. The objective of this study was to investigate whether potential inhalational hazards present in flavoring samples were reported as chemical ingredients on their corresponding safety data sheets (SDSs). Methods A convenience sample of 26 bulk liquid flavorings obtained from two coffee roasting and packaging facilities in the USA was analyzed for 20 volatile organic chemicals present in the headspaces of vials containing flavoring liquids using gas chromatography-mass spectrometry. Flavoring samples were included in the study if headspace analysis results and SDSs were available. Flavoring samples included hazelnut, French vanilla, amaretto, chocolate, and caramel as well as some flavoring mixtures containing added fruit flavors such as cherry and raspberry. The presence of a chemical in the flavoring formulation was then compared to the ingredient list on the SDSs. Results All the flavoring SDSs contained trade secret designations. None of the SDSs listed diacetyl or 2,3-pentanedione. Headspace analyte concentrations revealed that diacetyl was present in 21 of 26 samples (81%) with a maximum concentration of 5.84 × 104 µg m-3 in flavor 18 (caramel). 2,3-Pentanedione was present in 15 flavors (58%) with a maximum concentration of 3.79 × 105 µg m-3 in flavor 24 (oatmeal cookies). Conclusions A majority of the flavorings tested had diacetyl, 2,3-pentanedione, or both as volatile constituents in the headspace. These chemicals were not listed on the SDSs, but inclusion of diacetyl and 2,3-pentanedione on SDSs would serve to protect downstream users from unrecognized exposure and potential respiratory disease. The headspace technique presented here is a viable tool to rapidly screen for volatile hazardous chemicals that may be present in flavoring formulations. Facilities that use flavorings should be aware that constituents in flavorings may present a potential inhalational hazard even if not identified as such by the SDS. A precautionary approach is warranted when working with flavorings, including exposure monitoring and effective exposure control strategies such as containment and local exhaust ventilation.
Classical Copying versus Quantum Entanglement in Natural Language: The Case of VP-ellipsis

This paper compares classical copying and quantum entanglement in natural language by considering the case of verb phrase (VP) ellipsis. VP ellipsis is a non-linear linguistic phenomenon that requires the reuse of resources, making it the ideal test case for a comparative study of different copying behaviours in compositional models of natural language. Following the line of research in compositional distributional semantics set out by (Coecke et al., 2010) we develop an extension of the Lambek calculus which admits a controlled form of contraction to deal with the copying of linguistic resources. We then develop two different compositional models of distributional meaning for this calculus. In the first model, we follow the categorical approach of (Coecke et al., 2013) in which a functorial passage sends the proofs of the grammar to linear maps on vector spaces and we use Frobenius algebras to allow for copying. In the second case, we follow the more traditional approach that one finds in categorial grammars, whereby an intermediate step interprets proofs as non-linear lambda terms, using multiple variable occurrences that model classical copying. As a case study, we apply the models to derive different readings of ambiguous elliptical phrases and compare the analyses that each model provides.
(Near) Optimal Parallelism Bound for Fully Asynchronous Coordinate Descent with Linear Speedup

When solving massive optimization problems in areas such as machine learning, it is a common practice to seek speedup via massive parallelism. However, especially in an asynchronous environment, there are limits on the possible parallelism. Accordingly, we seek tight bounds on the viable parallelism in asynchronous implementations of coordinate descent. We focus on asynchronous coordinate descent (ACD) algorithms on convex functions $F:\mathbb{R}^n \rightarrow \mathbb{R}$ of the form $$F(x) = f(x) ~+~ \sum_{k=1}^n \Psi_k(x_k),$$ where $f:\mathbb{R}^n \rightarrow \mathbb{R}$ is a smooth convex function, and each $\Psi_k:\mathbb{R} \rightarrow \mathbb{R}$ is a univariate and possibly non-smooth convex function. Our approach is to quantify the shortfall in progress compared to the standard sequential stochastic gradient descent. This leads to a truly simple yet optimal analysis of the standard stochastic ACD in a partially asynchronous environment, which already generalizes and improves on the bounds in prior work. We also give a considerably more involved analysis for general asynchronous environments in which the only constraint is that each update can overlap with at most $q$ others, where $q$ is at most the number of processors times the ratio in the lengths of the longest and shortest updates. The main technical challenge is to demonstrate linear speedup in the latter environment. This stems from the subtle interplay of asynchrony and randomization. This improves Liu and Wright's (SIOPT'15) lower bound on the maximum degree of parallelism almost quadratically, and we show that our new bound is almost optimal.
Quantifying the Reality Gap in Robotic Manipulation Tasks

We quantify the accuracy of various simulators compared to a real world robotic reaching and interaction task. Simulators are used in robotics to design solutions for real world hardware without the need for physical access. The ‘reality gap’ prevents solutions developed or learnt in simulation from performing well, or at all, when transferred to real-world hardware. Making use of a Kinova robotic manipulator and a motion capture system, we record a ground truth enabling comparisons with various simulators, and present quantitative data for various manipulation-oriented robotic tasks. We show the relative strengths and weaknesses of numerous contemporary simulators, highlighting areas of significant discrepancy, and assisting researchers in the field in their selection of appropriate simulators for their use cases.