Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Dried Distillers Grains With Solubles and Red Osier Dogwood Extract on Fermentation Pattern and Microbial Profiles of a High-Grain Diet in an Artificial Rumen System

The objective of this study was to evaluate the effect of dried distillers grains with solubles (DDGS) and red-osier dogwood (ROD) extract on in vitro fermentation characteristics, nutrient disappearance, and microbial profiles using the rumen simulation technique. The experiment was a completely randomized design with a 2 × 2 factorial arrangement of treatments and four replicates per treatment. A basal diet [10% barley silage, 87% dry-rolled barley grain, and 3% vitamin and mineral supplement, dry matter (DM) basis] and a DDGS diet (as per basal diet with 25% of wheat DDGS replacing an equal portion of barley grain) were supplemented with ROD extract at 0 and 1% (DM basis), respectively. The experimental period was 17 d, consisting 10 days of adaptation and 7 days of data and sample collection. The substitution of wheat DDGS for barley grain did not affect gas production; disappearances of DM, organic matter, and crude protein; total volatile fatty acid (VFA) production; and microbial protein production. However, replacing barley grain with wheat DDGS increased (P = 0.01) fermenter pH and molar proportion of branched-chain VFA, switched (P = 0.06) the fermentation pattern to higher acetate production due to increased (P = 0.01) disappearance of neutral detergent fiber (NDF), and decreased (P = 0.08) methane (CH4) production. In the basal barley diet, the ROD extract increased the acetate to propionate (A:P) ratio (P = 0.08) and reduced the disappearance of starch (P = 0.06) with no effect on any other variables. No effects of ROD in the DDGS diet were observed. The number of operational taxonomic unit (OTUs) and the Shannon diversity index of the microbial community had little variation among treatments. Taxonomic analysis revealed no effect of adding the ROD extract on the relative abundance of bacteria at the phylum level with either the basal diet or DDGS diet, while at the genus level, the microbial community was affected by the addition of both DDGS and the ROD extract. Prevotella and Fibrobacter were the most abundant genera in the basal diet; however, Treponema became the most abundant genus with the addition of the ROD extract. These results indicated that the substitution of wheat DDGS for barley grain may mitigate enteric CH4 emissions. The trend of reduced starch fermentability and increased NDF disappearance with the addition of ROD extract suggests a reduced risk of rumen acidosis and an improvement in the utilization of fiber for cattle-fed high-grain diet.
Comparison of the Ability of High and Low Virulence Strains of Non-cytopathic Bovine Viral Diarrhea Virus-1 to Modulate Expression of Interferon Tau Stimulated Genes in Bovine Endometrium

Bovine Viral Diarrhea virus (BVDV) is a pestivirus with a single-stranded, positive sense RNA genome. It is endemic in many cattle populations, causing major economic losses in part due to reduced fertility. BVDV exhibits great genetic diversity and is classified as type 1 or 2 (BVDV-1, BVDV-2) with either non-cytopathogenic (ncp) or cytopathogenic (cp) biotypes. Differing strains of ncpBVDV differ in virulence, affecting clinical outcome. BVDV replicates in the reproductive tract, affecting host immunity and embryo survival. This study used an in vitro model of primary bovine endometrial cell cultures to compare the effects of two BVDV ncp type 1a strains of differing virulence (termed HO and KY) on endometrial transcription of candidate interferon stimulated genes (ISG) using qPCR. Half the cultures were stimulated with interferon tau (IFNT, the conceptus produced pregnancy recognition factor) in the presence or absence of viral infection. Cultures were replicated on cells from 10 BVDV-free cows. IFNT treatment stimulated transcription of 10 candidate ISGs, whereas both ncpBVDV-1 strains alone inhibited transcription of 8/10 ISGs. In combined BVDV-1+IFNT cultures, the stimulatory effect of IFNT on expression of GBP4, ISG15, HERC5, RSAD2, IFIH1, IFIT3, and MX1 was significantly inhibited by HO, but only ISG15, RSAD2, IFI27, and IFIT3 were decreased by KY. Inhibition by HO was generally greater. The IFNT-induced expression of TRIM56 was, however, increased by HO. These data show that HO, the more virulent ncpBVDV-1 strain, has a greater capacity to inhibit key antiviral pathways. These differences need confirmation at the protein level but may influence immune tolerance of the host. They could also reduce fertility by increasing uterine susceptibility to bacterial infection and disrupting IFNT-mediated pregnancy recognition.
Tracking Rhythms Coherence From Polysomnographic Records: A Time-Frequency Approach

The crosstalk between organs plays a crucial role in physiological processes. This coupling is a dynamical process, it must cope with a huge variety of rhythms with frequencies ranging from milliseconds to hours, days, seasons. The brain is a central hub for this crosstalk. During sleep, automatic rhythmic interrelations are enhanced and provide a direct insight into organ dysfunctions, however their origin remains a difficult issue, in particular in sleep disorders. In this study, we focus on EEG, ECG, and airflow recordings from polysomnography databases. Because these signals are non-stationary, non-linear, noisy, and span wide spectral ranges, a time-frequency analysis, based on wavelet transforms, is more appropriate to handle this complexity. We design a wavelet-based extraction method to identify the characteristic rhythms of these different signals, and their temporal variability. These new constructs are combined in pairs to compute their wavelet-based time-frequency complex coherence. These time-frequency coherence maps highlight the occurrence of a slowly modulated coherence pattern in the frequency range [0.01–0.06] Hz, which appears in both obstructive and central apnea. A preliminary exploration of a large database from the National Sleep Research Resource with respiration disorders, such as apnea provides some clues on its relation with autonomic cardio-respiratory coupling and brain rhythms. We also observe that during sleep apnea episodes (either obstructive or central), the cardiopulmonary coherence (in particular respiratory sinus-arrhythmia) in the frequency range [0.1–0.7] Hz strongly diminishes, suggesting a modification of this coupling. Finally, comparing time-averaged coherence with heart rate variability spectra in different apnea episodes, we discuss their common trait and their differences.
Changes in Cell Vitality, Phenotype, and Function of Dromedary Camel Leukocytes After Whole Blood Exposure to Heat Stress in vitro

The dromedary camel (Camelus dromedarius) is well-adapted to the desert environment with the ability to tolerate increased internal body temperatures rising daily to 41–42°C during extreme hot. This study was undertaken to assess whether in vitro incubation of camel blood at 41°C, simulating conditions of heat stress, differently alters cell vitality, phenotype, and function of leukocytes, compared to incubation at 37°C (normothermia). Using flow cytometry, the cell vitality (necrosis and apoptosis), the expression of several cell markers and adhesion molecules, and the antimicrobial functions of camel leukocytes were analyzed in vitro. The fraction of apoptotic cells within the granulocytes, lymphocytes, and monocytes increased significantly after incubation of camel whole blood at 41°C for 4 h. The higher increase in apoptotic granulocytes and monocytes compared to lymphocytes suggests higher resistance of camel lymphocytes to heat stress. Functionally, incubation of camel blood at 41°C for 4 h enhanced the phagocytosis and ROS production activities of camel neutrophils and monocytes toward S. aureus. Monocytes from camel blood incubated at 41°C for 4 h significantly decreased their expression level of MHC class II molecules with no change in the abundance of CD163, resulting in a CD163high MHC-IIlow M2-like macrophage phenotype. In addition, heat stress treatment showed an inhibitory effect on the LPS-induced changes in camel monocytes phenotype. Furthermore, in vitro incubation of camel blood at 41°C reduced the expression of the cell adhesion molecules CD18 and CD11a on neutrophils and monocytes. Collectively, the present study identified some heat-stress-induced phenotypic and functional alterations in camel blood leukocytes, providing a paradigm for comparative immunology in the large animals. The clinical relevance of the observed changes in camel leukocytes for the adaptation of the camel immune response to heat stress conditions needs further in vitro and in vivo studies.
Editorial: Sensory Processing Across the Lifespan: A 25-Year Initiative to Understand Neurophysiology, Behaviors, and Treatment Effectiveness for Sensory Processing

Citation: Miller LJ, Marco EJ, Chu RC and Camarata S (2021) Editorial: Sensory Processing Across the Lifespan: A 25-Year Initiative to Understand Neurophysiology, Behaviors, and Treatment Effectiveness for Sensory Processing. Front. Integr. Neurosci. 15:652218. doi: 10.3389/fnint.2021. 652218 Editorial: Sensory Processing Across the Lifespan: A 25-Year Initiative to Understand Neurophysiology, Behaviors, and Treatment Effectiveness for Sensory Processing
Editorial: Proceedings of FSTP3 Congress–A Sustainable Durum Wheat Chain for Food Security and Healthy Lives

Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy, Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy, 3 Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Rome, Italy, Department of Agricultural and Environmental Science (DISAAT), University of Bari “Aldo Moro”, Bari, Italy, 5 Lethbridge Research and Development Centre, Lethbridge, AB, Canada, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
Lipid Metabolism Profiles in Rheumatic Diseases

Rheumatic diseases are a group of chronic autoimmune disorders that involve multiple organs or systems and have high mortality. The mechanisms of these diseases are still ill-defined, and targeted therapeutic strategies are still challenging for physicians. Recent research indicates that cell metabolism plays important roles in the pathogenesis of rheumatic diseases. In this review, we mainly focus on lipid metabolism profiles (dyslipidaemia, fatty acid metabolism) and mechanisms in rheumatic diseases and discuss potential clinical applications based on lipid metabolism profiles.
Non-linear Normalization for Non-UMI Single Cell RNA-Seq

Single cell RNA-seq data, like data from other sequencing technology, contain systematic technical noise. Such noise results from a combined effect of unequal efficiencies in the capturing and counting of mRNA molecules, such as extraction/amplification efficiency and sequencing depth. We show that such technical effects are not only cell-specific, but also affect genes differently, thus a simple cell-wise size factor adjustment may not be sufficient. We present a non-linear normalization approach that provides a cell- and gene-specific normalization factor for each gene in each cell. We show that the proposed normalization method (implemented in “SC2P" package) reduces more technical variation than competing methods, without reducing biological variation. When technical effects such as sequencing depths are not balanced between cell populations, SC2P normalization also removes the bias due to uneven technical noise. This method is applicable to scRNA-seq experiments that do not use unique molecular identifier (UMI) thus retain amplification biases.
Fractional Punishment of Free Riders to Improve Cooperation in Optional Public Good Games

Improving and maintaining cooperation are fundamental issues for any project to be time-persistent, and sanctioning free riders may be the most applied method to achieve it. However, the application of sanctions differs from one group (project or institution) to another. We propose an optional, public good game model where a randomly selected set of the free riders is punished. To this end, we introduce a parameter that establishes the portion of free riders sanctioned with the purpose to control the population state evolution in the game. This parameter modifies the phase portrait of the system, and we show that, when the parameter surpasses a threshold, the full cooperation equilibrium point becomes a stable global attractor. Hence, we demonstrate that the fractional approach improves cooperation while reducing the sanctioning cost.
Deleting edges to restrict the size of an epidemic in temporal networks

A variety of potentially disease-spreading contact networks can be naturally modeled with graphs whose structure is subject to discrete changes over time, i.e. with temporal graphs. In such a temporal graph, vertices represent meaningful entities (such as animals or farms) and edges represent potentially infectious contacts between those entities. Furthermore the `availability' of an edge $e$ at time $t$ means that, at time $t$, the entities at the endpoints of $e$ are in contact. In this paper, motivated by network epidemiology applications in the dynamics of disease spreading on a data-derived network, we study the problem of deleting edges and/or edge availabilities from a given temporal graph in order to reduce its (temporal) connectivity. In particular, our aim is to find a temporal subgraph, in which the potential disease of any vertex $u$ can be transferred to only a limited number of other vertices $v$ using a temporal path (i.e. a path from $u$ to $v$, along which the times of the edge availabilities increase). We introduce two natural deletion problems for temporal graphs (for deletion of edges and of edge availabilities, respectively) and we provide positive and negative results on their computational complexity, both in the traditional and the parameterized sense, subject to various natural parameters.
Pathological Alterations Induced by intraneuronal in Alzheimer’s Disease

Alzheimer’s disease (AD) is pathologically characterized by the deposition of amyloid beta (Aβ) and neurofibrillary tangles (NFT) consisting of hyperphosphorylated tau protein. Since familial mutations in proteins involved in the Aβ generating cascade inevitably lead to AD, the deposition of Aβ is widely believed to be the underlying pathological mechanism of AD. In contrast, mutations in tau lead to frontotemporal dementia. The amyloid hypothesis states that the accumulation of Aβ42 is the underlying cause of AD driving neuron and synapse impairment and loss, eventually leading to behavioral deficits. For many years, the focus of the Aβ hypothesis has been the extracellular deposition of Aβ plaques; however numerous mouse models have been generated based on the familial AD mutations successfully modeling the deposition of Aβ plaques, but with little or no behavioral deficits and only seldom showing a loss of neurons. Furthermore, Aβ plaque deposition does not correlate well with cognitive decline in AD patients and can be found in non-demented controls as well as in AD patients. Recently, a modification of the amyloid hypothesis has been introduced suggesting that intraneuronal accumulation of Aβ rather than extracellular Aβ plaque deposition may be an early pathological hallmark of AD initiating pathological events. However, the presence of intraneuronal Aβ in the human AD brain is currently under debate. The present thesis investigates the presence of intraneuronal Aβ in human AD brain tissue and studies the role of intraneuronal Aβ versus plaques in transgenic mouse models of AD focusing on neuron loss, fiber pathology, and functional deficits concerning immediate early gene (IEG) regulation. Concerning pathological alterations, the present thesis corroborates the intraneuronal Aβ hypothesis, supporting the view of intraneuronal Aβ as an early pathological initiator and showing strong implications for intraneuronal Aβ in the generation of large plaque-independent axonal fiber pathology and neuronal loss. In contrast, plaques are found likely to cause functional disturbances such as deficits in the induction of IEGs upon neuronal activity, but seem not to be involved in the loss of neurons. Optimization of the immunohistochemical staining method for the detection of intraneuronal Aβ peptides provided a strong and robust staining of intraneuronal N-terminal Aβ peptides as well as fibrillar oligomeric Aβ and Aβ fibrils in neurons of the hippocampal formation of AD brain tissue. Finally, a highly significant correlation was identified between the accumulation of intraneuronal N-terminal Aβ peptides and the well-recognized AD risk factor of having one ApoE4 allele, emphasizing an important role of intraneuronal Aβ in AD pathology.
A STUDY ON USING DEEP LEARNING TECHNOLOGIES IN CONVOLUTIONAL NEURAL NETWORKS FOR MULTIPLE OBJECTS IDENTIFICATION

In this paper, the author will use deep learning technology, specifically here to use techniques in convolutional neural networks (CNN) to identify objects, multiple objects and objects’ locations in images. CNN, Region CNN (RCNN), Fast RCNN, Faster RCNN techniques using in convolutional neural networks will be introduced and simulated, citing comparative results to assess the effectiveness of object identification in images. Faster RCNN is considered to be the most appropriate for identifying the objects and their location in the image.
Analysis of Customers’ Reactions to E-Commerce Companies Using Instagram Data

The aim of this study is to develop a web application that supports decision-making processes on subjects—such as customer relations management, marketing, and stock management—with data such as posts, comments, and likes from Instagram to four e-commerce companies. In this context, the data obtained from the Instagram accounts of e-commerce companies were recorded in a database after the pre-processing and classification stages. A web application has been developed that can support managers in their decision-making processes at operational, tactical, and strategic decision-making levels by visualizing the data recorded in the database.
THE RELATIONSHIP OF INDIVIDUAL PSYCHOLOGICAL CHARACTERISTICS AND MOTIVATIONAL COMPONENT WITH THE LEVEL OF ABILITY TO MASTER FOREIGN LANGUAGES

The article considers the main aspects of the relationship of individual psychological characteristics and motivational component with the level of ability to master foreign languages. It was found that the ability to learn a foreign language affects the level of overall academic performance. The following diagnostic parameters and factors for predicting academic success are identified: the level of language training; dominance of the left or right hemisphere of the brain; level of The Relationship of Individual Psychological Characteristics and Motivational Component with the Level of Ability to Master Foreign Languages http://www.iaeme.com/IJM/index.asp 352 editor@iaeme.com anxiety; properties of higher nervous activity; motivational component. In the course of the analysis it was established that the group of students with a low level of success is a risk group in mastering foreign languages. This group is characterized by a low motivational component, a high level of stress and anxiety. According to the obtained results it is possible to improve the organization of educational process at staffing of educational groups, with an even distribution of students with high and medium levels of projected performance. In addition, risk areas have been identified for the formation of special control groups that need additional pedagogical assistance and an individual approach to learning.
Combining Stage Algorithm for Discovering Causal Models

Many constraint-based algorithms for causal discovery have suﬀered from statistical errors in conditional independence (CI) tests. Those errors are often inevitable in real data because of the limitation of statistical power due to ﬁniteness of data or violations of an assumption called faithfulness or stability condition. We propose a constraint-based al-gorithm that can reduce avoidable CI tests with combining an adjacency identiﬁcation stage with an orientation stage and then provide accurate and fast inference without loss of theoretical correctness, which we call the Combining Stage (CS) algorithm. We also, in the algorithm, introduce unreliable direction , which can reduce orientation errors due to locality of CI tests. Simulations are provided to demonstrate the prominent performance of the algorithm by comparison to often referred algorithms: PC, Three Phase Depen-dency Analysis, Sparse Candidate, and Max-Min Hill-Climbing algorithms.
Real-Time Closed-Loop Feedback in Behavioral Time Scales Using DeepLabCut

Visual Abstract Computer vision approaches have made significant inroads into offline tracking of behavior and estimating animal poses. In particular, because of their versatility, deep-learning approaches have been gaining attention in behavioral tracking without any markers. Here, we developed an approach using DeepLabCut for real-time estimation of movement. We trained a deep-neural network (DNN) offline with high-speed video data of a mouse whisking, then transferred the trained network to work with the same mouse, whisking in real-time. With this approach, we tracked the tips of three whiskers in an arc and converted positions into a TTL output within behavioral time scales, i.e., 10.5 ms. With this approach, it is possible to trigger output based on movement of individual whiskers, or on the distance between adjacent whiskers. Flexible closed-loop systems like the one we have deployed here can complement optogenetic approaches and can be used to directly manipulate the relationship between movement and neural activity.
Stimulation of central b2-adrenoceptors suppresses NFjB activity in rat brain: A role for IjB

In this study we examined the impact of systemic treatment with the long-acting brain penetrant b2adrenoceptor agonist clenbuterol on NFjB activity and IjB expression in rat brain. Clenbuterol decreased NFjB activity (p65 DNA binding) in nuclear extracts prepared from rat cortex and hippocampus for up to 8 h following a single treatment. This was accompanied by increased expression of IjBa mRNA and protein. The temporal increase in IjB protein expression paralleled the suppression of NFjB activity, suggesting that IjBa mediates the suppression NFjB activity observed. These actions of clenbuterol were prevented by pre-treatment with the non-selective b-adrenoceptor antagonist propranolol, the b2-adrenoceptor antagonist ICI-118,551, but not the b1-adrenoceptor antagonist metoprolol, suggesting that the effects of clenbuterol on IjBa expression and NFjB activity are mediated specifically by the b2-adrenoceptor. In addition, the actions of clenbuterol were mimicked by systemic administration of another highly selective long-acting b2-adrenoceptor agonist formoterol. As neurodegenerative diseases are associated with inflammation we determined if clenbuterol could suppress NFjB activation that occurs in response to an inflammatory stimulus. In this regard we demonstrate that clenbuterol inhibited IjB phosphorylation and IjB degradation and inhibited NFjB activity in hippocampus and cortex of rats following a central injection of the inflammagen bacterial lipopolysaccharide (LPS). In tandem, clenbuterol blocked expression of the NFjB-inducible genes TNF-a and ICAM-1 following LPS administration. Our finding that clenbuterol and formoterol inhibit NFjB activity in the CNS further supports the idea that b2-adrenoceptors may be an attractive target for treating neuroinflammation and combating inflammation-related neurodegeneration. 2013 Elsevier Ltd. All rights reserved.