Large Scale Time-Series Representation Learning via Simultaneous Low-and High-Frequency Feature Bootstrapping.

Learning representations from unlabeled time series data is a challenging problem. Most existing self-supervised and unsupervised approaches in the time-series domain fall short in capturing low-and high-frequency features at the same time. As a result, the generalization ability of the learned representations remains limited. Furthermore, some of these methods employ large-scale models like transformers or rely on computationally expensive techniques such as contrastive learning. To tackle these problems, we propose a noncontrastive self-supervised learning (SSL) approach that efficiently captures low-and high-frequency features in a cost-effective manner. The proposed framework comprises a Siamese configuration of a deep neural network with two weight-sharing branches which are followed by low-and high-frequency feature extraction modules. The two branches of the proposed network allow bootstrapping of the latent representation by taking two different augmented views of raw time series data as input. The augmented views are created by applying random transformations sampled from a single set of augmentations. The low-and high-frequency feature extraction modules of the proposed network contain a combination of multilayer perceptron (MLP) and temporal convolutional network (TCN) heads, respectively, which capture the temporal dependencies from the raw input data at various scales due to the varying receptive fields. To demonstrate the robustness of our model, we performed extensive experiments and ablation studies on five real-world time-series datasets. Our method achieves state-of-art performance on all the considered datasets.

Effect of pulsed electric field treated on quality of curd.

Pulsed electric field (PEF) is a potential pre-treatment technique to improve the quality of milk by reducing its microbial load. The present study aims at addressing this issue with respect to a popular fermented dairy product, that is, curd. Milk was treated with high voltage and frequency (55 kV and 90 Hz) square waves of pulse width 900 µs for 100 s. Curd samples were prepared with conventional heat treatment (CHT), PEF-treated milk subjected to CHT (PT-CHT), and PEF-treated milk (PT). PT samples resulted in curd with higher acidity (0.17 ± 0.005% LA) and microbial load (6.65 ± 0.27 log CFUg-1), while the PT-CHT samples resulted in curd with better whey holding capacity. The firmness recorded for CHT, PT-CHT, and PT was 1.15 ± 0.05, 1.32 ± 0.04, and 0.91 ± 0.03 N, respectively. PT-CHT showed a higher viscosity index, that is, 0.207 ± 0.005 g. Sensorial properties showed the acidic nature of PT-curd with greater syneresis and softer texture resulted in its poorer sensory scores for texture. Shelf-life analysis showed no significant difference between curd prepared using the CH and PT-CHT up to 12 days. The study demonstrated the potential of employing PEF with CHT for improving the texture and shelf life of curd without impacting its quality.

An Outbreak of Fowl Aviadenovirus A-Associated Gizzard Erosion and Ulceration in Captive Bobwhite Quail (Colinus virginianus).

A flock of captive bobwhite quail (Colinus virginianus) experienced loose droppings, depression, and increased mortality starting at 3 wk of age. Necropsy of the affected birds revealed intestines dilated with frothy and tan fluid. Irregular dark brown fissures within the koilin layer of the gizzard were found in 20%-30% of the birds. Histologically, gizzards showed multifocal koilin degeneration or fragmentation, degeneration and necrosis of the subjacent epithelial cells, and infiltration of macrophages, lymphocytes, and heterophils. Necrotic epithelial cells occasionally contained large, smudgy, basophilic intranuclear inclusion bodies with marginated nuclear chromatin. Adenoviral paracrystalline arrays composed of icosahedral virions (60-70 nm diameter) were seen on transmission electron microscopy in the nuclei of epithelial cells in the gizzard mucosa. Adenovirus was isolated from gizzard, liver, intestine, and trachea by inoculation of specific-pathogen-free embryonated chicken eggs. Homogenates of the gizzard, liver, and intestine were positive for the adenovirus hexon gene by PCR. Sequencing of PCR amplicons confirmed the virus as fowl aviadenovirus A. The study isolates showed more than 99% and 97% nucleotide identity with quail bronchitis virus and with aviadenoviruses from gizzard erosion and ulceration (GEU) in broilers, respectively. The viral isolates showed six substitutions (G1T, C174A, A229G, C513A, T579A, and G621C) of which two were nonsynonymous (G1T and A229G), resulting in a change in the translated amino acid as A1S and S77G, respectively. These results indicate that adenoviruses of the same type or species can cause different clinical presentations in quails, e.g., bronchitis or GEU.

Artículo regular­Brote de erosiones y ulceraciones de la molleja asociadas con Aviadenovirus A del pollo en codornices de Virginia en cautiverio (Colinus virginianus). Una parvada de codornices de Virginia en cautiverio (Colinus virginianus) mostró heces acuosas, depresión y aumento de la mortalidad a partir de las tres semanas de edad. La necropsia de las aves afectadas reveló intestinos dilatados con líquido espumoso y marrón. Se encontraron fisuras irregulares de color marrón oscuro dentro de la capa de koilin de la molleja en el 20% al 30% de las aves. Histológicamente, las mollejas mostraron degeneración o fragmentación multifocal de la capa de koilin, degeneración y necrosis de las células epiteliales subyacentes e infiltración de macrófagos, linfocitos y heterófilos. Las células epiteliales necróticas contenían ocasionalmente cuerpos de inclusión intranucleares basófilos grandes, con cromatina nuclear marginada. Se observaron matrices paracristalinas adenovirales compuestas de viriones icosaédricos (60-70 nm de diámetro) en el microscopio electrónico de transmisión en los núcleos de las células epiteliales de la mucosa de la molleja. Se aisló adenovirus de molleja, hígado, intestino y tráquea mediante la inoculación de huevos embrionados de pollo libres de patógenos específicos. Los homogeneizados de la molleja, el hígado y el intestino fueron positivos para el gene del hexon del adenovirus por PCR. La secuenciación de amplicones de PCR confirmó la presencia de Aviadenovirus A del pollo. Los aislamientos del estudio mostraron una identidad mayor del 99% y 97% en la secuencia de nucleótidos con el virus de la bronquitis de codorniz y con aviadenovirus asociado con erosión y ulceración de mollejas (con las siglas en inglés GEU) en pollos de engorde, respectivamente. Los aislados virales mostraron seis sustituciones (G1T, C174A, A229G, C513A, T579A y G621C) de las cuales dos eran no-sinónimas (G1T y A229G), lo que resultó en un cambio en el aminoácido traducido como A1S y S77G, respectivamente. Estos resultados indican que los adenovirus del mismo tipo o especie pueden causar diferentes presentaciones clínicas en codornices, por ejemplo, bronquitis o erosión y ulceración de mollejas.

Enteric Viruses Associated with Mid-growth Turkey Enteritis.

Since August 2014, the University of Minnesota Veterinary Diagnostic Laboratory has received cases of turkey enteritis that are clinically different from previously described cases of poult enteritis syndrome and light turkey syndrome. The birds develop dark green and extremely foul-smelling diarrhea starting at 8-10 wk of age, which may last up to 15-16 wk of age. The affected turkey flocks show poor uniformity, and feed conversion and market weights are reduced. Multiple-age farms are affected more often than the single-age farms. Morbidity varies from flock to flock and in some cases reaches 100%. At necropsy, undigested feed with increased mucus is observed in the intestines along with prominent mucosal congestion and/or hemorrhage. Microscopically, lymphocytic infiltrates expand the villi in duodenum and jejunum to form lymphoid follicles, which are often accompanied by heterophils. Next generation sequencing (Illumina Miseq) on a pool of feces from affected birds identified genetic sequences of viruses belonging to Astroviridae, Reoviridae, Picornaviridae, Picobirnaviridae, and Adenoviridae. On testing pools of fecal samples from apparently healthy (16 pools) and affected birds (30 pools), there was a higher viral load in the feces of affected birds. Picobirnavirus was detected only in the affected birds; 20 of 30 pools (66.7%) were positive. These results indicate that a high viral load of turkey picobirnavirus alone, or in association with novel picornaviruses, may be a cause of this new type of turkey enteritis.

Newborn Screening for Congenital Hypothyroidism, Congenital Adrenal Hyperplasia, and Glucose-6-Phosphate Dehydrogenase Deficiency for Improving Health Care in India.

Newborn screening (NBS) aims toward early detection of treatable congenital disorders. From January 2008 through December 2017, 13,376 newborns were screened for congenital hypothyroidism (CH), congenital adrenal hyperplasia (CAH), and glucose-6-phosphate dehydrogenase (G6PD) deficiency at Sir Ganga Ram Hospital, India, by measuring G6PD activity, thyroid-stimulating hormone, and 17-hydroxyprogesterone on dried blood specimens. The birth prevalence of 1:2,000 for CH, 1:2,500 for CAH, and 1:125 for G6PD deficiency indicates the latter as the most prevalent. Performance evaluation of testing reveals a robust screening program with 100% sensitivity and >99% specificity. Hence, we recommend NBS for early diagnosis and treatment to prevent adverse outcomes.

Molecular characterization of quail bronchitis virus isolated from bobwhite quail in Minnesota.

From 2008 to 2012, 4 separate cases of quail bronchitis virus infection were seen in bobwhite quail (Colinus virginianus) raised in Minnesota. The quail chicks ranged in age from 5 d to 8 wk and suffered from respiratory distress and elevated mortality. On necropsy, gross lesions consisted of mucus in trachea, congested lungs, caseous air sacculitis, accumulation of chalky white urates on internal organs, necrotic foci in liver, and enlarged spleen. Histologic examination revealed fibrinoheterophilic rhinitis, heterophilic bronchitis, heterophilic tracheitis, and interstitial pneumonia in addition to deciliation, desquamation, and necrosis of bronchial respiratory epithelium. Karyomegaly with basophilic intranuclear inclusions was also seen in affected epithelium. Severe epicarditis, pericarditis, myocarditis, multifocal necrotizing hepatitis, and splenitis were additional pathological findings. Quail bronchitis virus (QBV) was isolated from all four samples when inoculated in specific-pathogen-free (SPF) embryonated chicken eggs. The virus was confirmed by electron microscopy and polymerase chain reaction using fowl adenovirus (FAdV) hexon gene-specific primers. Nucleotide sequences of the four isolates showed 99.0% identity with CELO strain of fowl adenovirus A. Nine nucleotide substitutions were observed; 3 of these were nonsynonymous (A281G, C314T and G565C), leading to changes in deduced amino acid sequences (S94G, T105M and A189P, respectively). Based on partial sequence of the hexon gene, QBV isolates of this study clustered closely with fowl adenovirus A and were different from FAdV groups B through E and from adenoviruses of goose, duck, turkey, and pigeon. Further studies are indicated to determine the impact of nonsynonymous substitutions on host specific pathogenicity of these viruses.

Detection and molecular characterization of astroviruses in turkeys.

This study was conducted to determine the prevalence and molecular characteristics of turkey astrovirus 1 (TAstV-1) and avian nephritis virus (ANV) in turkeys with light turkey syndrome (LTS), which is characterized by lower body weight in market-age turkeys than their standard breed character. We collected pools of fecal samples from four LTS and two non-LTS turkey flocks in Minnesota at 2, 3, 5 and 8 weeks of age. Of the 80 LTS pools tested, 16 (20.0 %) and 11 (13.8 %) were positive for TAstV-1 and ANV, respectively. For non-LTS flocks, these numbers were 8 (20.0 %) and 5 (12.5 %), respectively. The maximum number of birds was positive at five weeks of age. We also tested 130 fecal samples of poult enteritis syndrome (PES) cases submitted to the Minnesota Veterinary Diagnostic Laboratory and found 19 and 11 positive for TAstV-1 and ANV, respectively. RdRp gene sequences were determined for a total of 29 TAstV-1 and 22 ANV samples. Phylogenetic analysis of the RdRp gene revealed 92-100 % and 88-100 % nucleotide sequence identity among TAstV-1 and ANV sequences, respectively. A large number of nucleotide and amino acid substitutions were observed in LTS and PES flocks than in non-LTS flocks. One of the PES sequences grouped with ANV-like sequences detected in chickens, indicating that regular screening of birds should be continued. Further, complete genome analysis should be conducted to determine whether this virus is a novel divergent strain or a recombinant of chicken and turkey ANV-like viruses. The detection of TAstV-1 and ANV in a considerable number of non-LTS cases emphasizes the need for further studies on the transmission pattern and pathogenesis of these viruses to determine their role as pathogens of turkeys.

Inherited metabolic disorders: Quality management for laboratory diagnosis.

BACKGROUND: The advancements in laboratory technology and knowledge of the mechanisms behind metabolic disorders have facilitated accurate and reliable laboratory testing in screening, diagnosis and treatment of inherited metabolic disorders. Therefore, quality assurance and improvement in diagnostic proficiency have become essential in this area. In most developing countries, standard practices for quality assurance in testing of enzymes, hormones and metabolites involved in these genetic disorders have not been fully implemented. We highlight the benefits of quality assurance and aim to create awareness for greater compliance with the criteria established for quality control to ensure accuracy in biochemical genetic testing. METHODS: Establishing the limit of detection and testing range for each analyte and enzyme are useful as a reference while setting up new assays. To minimize error, %CV should be monitored regularly. Evaluation of proficiency testing performance provides scope to the laboratory for improving testing quality. RESULTS: Low precision seen in lysosomal enzyme assays does not undermine their diagnostic efficacy as differentiation between patients and normal subjects is possible by setting % coefficient of variation cutoffs. CONCLUSIONS: The study will facilitate the collaboration with other screening and diagnostic systems and help in development of new laboratory standards.

Inhibition of infectious bursal disease virus by vector delivered SiRNA in cell culture.

Infectious Bursal Disease (IBD) is major threat to poultry industry. It causes severe immunosuppression and mortality in chicken generally at 3 to 6 weeks of age. RNA intereference (RNAi) emerges as a potent gene regulatory tool in last few years. The present study was conducted to evaluate the efficiency of RNAi to inhibit the IBD virus (IDBV) replication in-vitro. VP2 gene of virus encodes protein involved in capsid formation, cell entry and induction of protective immune responses against it. Thus, VP2 gene of IBDV is the candidate target for the molecular techniques applied for IBDV detection and inhibition assay. In this study, IBDV was isolated from field cases and confirmed by RT-PCR. The virus was then adapted on chicken embryo fibroblast cells (CEF) in which it showed severe cytopathic effects (CPE). The short hairpin RNA (shRNAs) constructs homologous to the VP2 gene were designed and one, having maximum score and fulfilling maximum Reynolds criteria, was selected for evaluation of effective inhibition. Selected shRNA construct (i.e., VP2-shRNA) was observed to be the most effective for inhibiting VP2 gene expression. Real time PCR analysis was performed to measure the relative expression of VP2 gene in different experimental groups. The VP2 gene was less expressed in virus infected cells co-transfected with VP2-shRNA as compared to mock transfected cells and IBDV+ cells (control) at dose 1.6 µ g. The result showed ∼95% efficient down regulation of VP2 gene mRNA in VP2-shRNA treated cells. These findings suggested that designed shRNA construct achieved high level of inhibition of VP2 gene expression in-vitro.

Detection of very virulent infectious bursal disease virus from a field outbreak in Central India.

In order to detect infectious bursal disease virus (IBDV), bursal tissue was collected from 10 IBD-suspected birds from a 30-day-old, IBDV-vaccinated commercial broiler chicken flock of 2000 birds exhibiting clinical signs suggestive of infectious bursal disease (IBD). The presence of IBDV was confirmed by partial amplification of the VP2 gene by reverse transcription and polymerase chain reaction. Isolates were identified as very virulent strains of IBDV (vvIBDV) by nucleotide sequence analysis. The comparison of the VP2 nucleotide sequences among the isolates revealed the presence of single-nucleotide polymorphisms in the VP2 gene of IBDV in the same flock. The comparative analysis indicated that these viruses were genetically close to the vvIBDVs previously detected in India. Our analysis provided information about the existence of vvIBDV in Central India.