Here, we present the draft genome sequence of Bacillus sp. strain MHSD28 which was sequenced, and assembled with a total length of 5,571,729 bp. The genome has 43 contigs, the largest contig with 1,785,042 bp, N50 of 1,474,247 bp, G + C% content of 35.23%. The strain was isolated from surface sterilized leaves of Dicoma anomala, obtained in Limpopo province, South Africa. The genome has 5792 total genes which include 5701 protein coding sequences (CDS), 192 pseudogenes, 7 rRNA genes with 3 operons (5S, 16S and 23S), 79 tRNA genes and 5 noncoding RNA (ncRNA) genes. This whole genome shotgun project has been deposited in DDBJ/ENA/GenBank under accession number VHIV00000000. The version described in this paper is version VHIV01000000.

Di (2-ethylhexyl) phthalate (DEHP) is used as plasticizer in the industry and belongs to the phthalate family which can induce tissue damage including kidney, liver, and testis as a result of elevated oxidative stress levels. Glutathione reductase (GR), Glucose-6-phosphate dehydrogenase (G6PD), glutathione S-transferase (GST), 6-phosphogluconate dehydrogenase (6PGD), enzyme activities, trace element and mineral levels were evaluated in the brain and testis tissue samples. Our data revealed that, antioxidant enzyme activities in the brain and testis samples were statistically insignificant in the DEHP administered groups compared to the control group except 400 mg/kg/day DEHP dose group in the testis samples. DEHP can disrupt trace element and mineral levels unlike antioxidant enzyme levels that may due to blood-brain and testis-blood barrier and/or short-term exposure to the DEHP. For more detailed information than the data presented in this article, please see the research article "Impact of the Di (2-Ethylhexyl) Phthalate Administration on Trace Element and Mineral Levels in Relation of Kidney and Liver Damage in Rats" [1].

This article contains raw and processed data related to research published by Takiya et al. [1]. Literature have shown that treatment with the nonsteroidal anti-inflammatory agent sodium salicylate (SS) during the first days postpartum in dairy cows increased lactation performance [2], and tended to alter glucose metabolism [3]. Yet, the specific effects of systemic SS treatment on the proteome of the adipose tissue (AT) and on the inflammatory process in AT of postpartum cows is unknown. Subcutaneous AT samples were collected at 7 d of lactation from control cows (n = 5) and from cows treated with 2.3 g/L SS (n = 5) via drinking water during the first 7 d of lactation. Protein extraction and liquid chromatography-mass spectrometry were performed to obtain proteomics data. Differential abundance of proteins was determined through MS1 intensity based label-free method. Proteomics analysis generated a novel dataset consisted of 1422 proteins, 80 (5.6%) of which were differentially abundant [fold change ± 1.5, P < 0.05 2-way ANOVA] when comparing control and SS-treated cows. The present dataset of subcutaneous AT proteome from postpartum dairy cows treated with SS can be used as a reference for any research involving nonsteroidal anti-inflammatory agent treatment in dairy cows or in comparative research between species.

This data article describes the complete draft genome sequence of Salmonella specific bacteriophage ΦSP3 isolated from chicken intestinal contents. The ΦSP3 genome was sequenced by paired end runs using Illumina HiSeq 2500 with 100X coverage. Phylogenetic analysis using major capsid gene and genome wide comparison were performed to understand bacteriophage evolutionary relationship. Genome sequence of bacteriophage ΦSP3 was deposited in GenBank under the accession number MG387042.

The data contain information related to the research article entitled "Profiling of promoter occupancy by the SND1 transcriptional coactivator identifies downstream glycerolipid metabolic genes involved in TNFα response in human hepatoma cells" (DOI: 10.1093/nar/gkv858). In the article alluded to, we reported that tumor necrosis factor alpha (TNFα) increases notably the cellular content of the major glycerolipid phosphatidylcholine (PC). Here, accompanying lipidomic data determine the PC structural variants that have been identified in human hepatoma HepG2 cells and those whose relative abundance is modified by TNFα. We used ultrahigh performance liquid chromatography (UHPLC) coupled to electrospray ionization (ESI) tandem mass spectrometry (MS/MS)-based lipidomic profiling to analyze lipid extracts of control and TNFα-treated HepG2 cells. The identity of PC individual species was elucidated using the values of the retention time and molecular weight in addition to the fragmentation patterns. MS data were then processed and analyzed for the characterization of statistically significant differences in detected structural variants. We have annotated the dataset of PC species that characterize HepG2 cells' phenotype, both under normal and pro-inflammatory conditions.

The data article refers to the paper "Nutritional, physico-chemical and functional characterization of a global chickpea collection" [1]. The data are referred to a germplasm collection of 57 chickpea accessions from the ex situ repositories of the United States Department of Agriculture (USDA), the Department of Plant, Soil and Food Science of the University of Bari, Italy (DiSSPA), and the Institute of Biosciences and Bioresources of the Italian National Research Council (CNR-IBBR). Thirty-six accessions, belonging to desi and kabuli types, were representative of the geographic distribution of chickpea global cultivation, whereas twenty-one accessions, referable to the Apulian black type, derived from different area of the Apulian region, south of Italy. All the accessions were grown at the experimental farm "P. Martucci" of the University of Bari "Aldo Moro" (41°01'22.1″ N 16°54'21.0″ E) during the growing season 2017-2018, according to a randomized block design with two replicates, each replicate formed by 30 individual plants. This article reports the data of the proximate composition, the total bioactive compounds content, the fatty acid composition and the physico-chemical and functional properties of chickpea flour. Information provided in this article can be used by food industry to develop chickpea-based foods and by geneticists for studies of association mapping aimed at the identification of genomic regions controlling the nutritional and technological traits.

Although widespread cortical asymmetries have been identified in Alzheimer's disease (AD), thalamic asymmetries and their relevance to clinical severity in AD remain unclear.

Lymphoma patients are frequently treated with cancer therapies that may increase the risk of adverse health outcomes later in life, including cardiovascular disease (CVD) mortality. We sought to investigate the long-term risk of CVD incidence in this survivor population relative to the general population to quantify this health burden.

Adolescent idiopathic scoliosis is the most common spinal disorder in adolescents with a prevalence of 0.5-5.2% worldwide. The traditional methods for scoliosis screening are easily accessible but require unnecessary referrals and radiography exposure due to their low positive predictive values. The application of deep learning algorithms has the potential to reduce unnecessary referrals and costs in scoliosis screening. Here, we developed and validated deep learning algorithms for automated scoliosis screening using unclothed back images. The accuracies of the algorithms were superior to those of human specialists in detecting scoliosis, detecting cases with a curve ≥20°, and severity grading for both binary classifications and the four-class classification. Our approach can be potentially applied in routine scoliosis screening and periodic follow-ups of pretreatment cases without radiation exposure.

The neural underpinnings of subjective experience during resting state remain elusive. Dynamic features of EEG oscillations may provide more understanding of the relationship between the content of inner conscious experience and electrical brain activity. We tested a correlation of rating on the Amsterdam Resting-State Questionnaire (ARSQ) with dynamic parameters of EEG recorded in 49 healthy volunteers during the 10-min resting session. The participants filled ARSQ immediately after the rest. We investigated both linear (1 Hz-band power spectral density - PSD) and dynamic features (standard deviation and frequency of Hilbert envelope) of EEG averaged for the whole resting-state segment. Besides, we conducted a procedure of k-mean clustering based on PSD, localization of components retrieved by independent component analysis for 10-sec EEG epochs to assess spectral and temporal variability of EEG. The correlation analysis showed that the increase of PSD and cluster duration of the high-frequency alpha rhythm (12-13 Hz) in central and frontal areas was positively associated with the rating of experienced thoughts related to Planning (r = 0.44). The time of the presence of low amplitude delta oscillations correlated negatively with Planning (r = -0.52). The participants with higher ARSQ scores of Visual Thoughts had a higher standard deviation of the wideband (1-30 Hz) Hilbert envelope. Our data suggest that the dynamic properties of EEG reflect cognitive states assessed by ARSQ.

The ability of Staphylococcus aureus to form biofilms is an important virulence factor because this has been associated with persistent bovine intramammary infections. Different mechanisms of biofilm formation have been described in S. aureus; however, the process has been found to be mainly driven by the ica and bap genes. The presence of the ica and bap genes, as well as the biofilm formation in vitro were evaluated in 229 S. aureus strains isolated from bovine milk collected from different regions of Department of Antioquia, Colombia. Three different genotypes grouped into three separate clusters were identified from in vitro assays. Genotype 1 (ica positive and bap negative) was the most prevalent (78.17%), followed by genotype 2 (ica and bap positive) (12.66%) and genotype 0 (ica and bap negative) (9.17%). Biofilm formation was observed in 81.26% of the strains from which 100% of genotype 2 isolates showed biofilm formation. The biofilms formed by genotype 2 isolates were also found to have the highest optical density (>2.4). These results showed that most of the S. aureus strains were capable of biofilm formation, suggesting the virulence potential particularly in bap-positive strains.

The terciopelo (Bothrops asper) inhabits human-modified environments such as agricultural areas, becoming more prone to be exposed to organophosphate insecticides. These chemicals can inhibit plasmatic butyrylcholinesterases (BChE) activity in B. asper. Caribbean and Pacific populations of B. asper belong to two divergent lineages that exhibit robust genetic partitioning; however, differences across versants in biochemistry and hematology have not yet been examined, especially in BChE variations. This study aims to evaluate the differences of BChE plasmatic values, hematology parameters, and some biochemical analytes as biomarkers in the presence of organophosphates between the Pacific and Caribbean population of B. asper in Costa Rica. A total of 89 snakes (41 Pacific and 48 Caribbean) were used, and hematology parameter, albumin, aspartate aminotransferase (AST), total protein and BChEs were evaluated. Differences in hemoglobin content, thrombocytes, white cell count, AST, and BChE values were found between both versants. Intrinsic genetic factors might influence the variation found in BChE and AST values in the snakes sampled from both versants; moreover, understanding this variation in BChE and AST values across the B. asper's distribution can be useful in future ecotoxicology, biomonitoring, genetic and other clinical/health studies.

Despite the high burden of tuberculosis (TB) worldwide, specific factors influencing disease transmission remain elusive. Long term epidemiological studies and in vitro experimental models provide evidence of variable relative fitness of Mycobacterium tuberculosis (Mtb) strains but few such studies are available. Large sequence polymorphisms (LSP) are a robust molecular marker and are feasible as an epidemiological investigative tool. Few Mtb molecular epidemiological studies have been reported in Malawi owing to lack of laboratories with molecular tools. We characterized the genetic diversity of Mtb clinical isolates amongst TB patients in Blantyre, Malawi. We genotyped 64 Mtb clinical isolates using LSP-PCR, assigned specific lineages and confirmed 18 of the isolates using SMRT sequencing. The 64 isolates clustered into 4 lineages (L1-L4) with L4 predominating. There were 10/64 (16%) isolates belonging to L1, 6/64 (9%) belonging to L2, 2/64 (3%) belonging to L3 and 46/64 (72%) belonging to L4. Comparison with a previous study done in Karonga revealed concordance in L1 and L4 but discodance in L2 and L3. The phylogenetic tree constructed, comprised of 3/4 lineages present in Blantyre with 3/18 belonging to L1, 3/18 belonging to L2 and 12/18 belonging to L4. Four Mtb lineages were present in Blantyre with L4 predominating. Larger studies are needed to understand the molecular epidemiology of TB in Blantyre in light of increased bi-directional migration with South Africa.

Epidemic of flu is highly contagious and it spreads through air. In 2009 H1N1 influenza virus emerged after reassortment of North American TRIG and Eurasia Avian like virus of swine and started epidemic in Mexico. The first cases were reported from Hyderabad city on 16th May 2009 in India that spread rapidly within a short span of time. During this period large population of Odisha situated at the eastern side of India was also affected and incidences of H1N1 cases were recorded through state Government surveillance system. In this study real time RT-PCR based diagnosis was conducted for the throat swabs collected from suspected H1N1 cases in Odisha during 2009-2017. A total of 2872 throat swabs were received from 23 different Government and private hospitals and 21.1% positivity was confirmed. The disease affected mostly 46-60 years age group, males (50.6%) being more affected. The clinical features had shown that fever with cough (89.6%) was the most common symptom followed by shortness of breath (72.7%). Post monsoon was the peak season in which most of the cases were reported. Neurological signs, pregnancy, diabetes and hypertension were found to be risk factors for H1N1. The case fatality rate (CFR) was 15%.

3D printing/bioprinting are promising techniques to fabricate scaffolds with well controlled and patient-specific structures and architectures for bone tissue engineering. In this study, we developed a composite bioink consisting of silk fibroin (SF), gelatin (GEL), hyaluronic acid (HA), and tricalcium phosphate (TCP) and 3D bioprinted the silk fibroin-based hybrid scaffolds. The 3D bioprinted scaffolds with dual crosslinking were further treated with human platelet-rich plasma (PRP) to generate PRP coated scaffolds. Live/Dead and MTT assays demonstrated that PRP treatment could obviously promote the cell growth and proliferation of human adipose derived mesenchymal stem cells (HADMSC). In addition, the treatment of PRP did not significantly affect alkaline phosphatase (ALP) activity and expression, but significantly upregulated the gene expression levels of late osteogenic markers. This study demonstrated that the 3D printing of silk fibroin-based hybrid scaffolds, in combination with PRP post-treatment, might be a more efficient strategy to promote osteogenic differentiation of adult stem cells and has significant potential to be used for bone tissue engineering.

Aging is associated with significant bone loss and increased fracture risk, which has been attributed to a diminished response to anabolic mechanical loading. In adults, skeletal progenitors proliferate and differentiate into bone-forming osteoblasts in response to increasing mechanical stimuli, though the effects of aging on this response are not well-understood. Here we show that both adult and aged mice exhibit load-induced periosteal bone formation, though the response is significantly attenuated with age. We also show that the acute response of adult bone to loading involves expansion of Sca-1+Prrx1+ and Sca-1-Prrx1+ cells in the periosteum. On the endosteal surface, loading enhances proliferation of both these cell populations, though the response is delayed by 2 days relative to the periosteal surface. In contrast to the periosteum and endosteum, the marrow does not exhibit increased proliferation of Sca-1+Prrx1+ cells, but only of Sca-1-Prrx1+ cells, underscoring fundamental differences in how the stem cell niche in distinct bone envelopes respond to mechanical stimuli. Notably, the proliferative response to loading is absent in aged bone even though there are similar baseline numbers of Prrx1 + cells in the periosteum and endosteum, suggesting that the proliferative capacity of progenitors is attenuated with age, and proliferation of the Sca-1+Prrx1+ population is critical for load-induced periosteal bone formation. These findings provide a basis for the development of novel therapeutics targeting these cell populations to enhance osteogenesis for overcoming age-related bone loss. © 2019 The Authors. JBMR Plus published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research.

Extraordinary advances in medicine and public health have contributed to increasing life expectancy worldwide. However, health span-"healthy aging"-has paradoxically lagged to parallel this increase. Consequently, aging-associated illnesses, such as Alzheimer's disease and aging frailty, are having a growing impact on patients, their families, and entire health-care systems. Typically, such disorders have been treated as isolated disease entities. However, the inextricable links between aging-associated disorders and the aging process itself have become increasingly recognized, leading to formation of the field of geroscience. The geroscience concept is that treating the aging process itself should lead to treatment and prevention of aging-related disorders. However, the aging process is complex, dictated by highly interrelated pleiotropic processes. As such, therapeutics with pleiotropic mechanisms of action (either alone, or as part of combinatorial strategies) will be required for preventing and treating both aging and related disorders. Mesenchymal stem cells (MSCs) have multiple mechanisms of action that make these highly promising geroscience therapeutic candidates. These cells have a high safety profile for clinical use, are amenable to allogeneic use since tissue-type matching is not required, and can have sustained activity after transplantation. Herein, we review preclinical and clinical data supporting the utility of allogeneic MSCs as a geroscience therapeutic candidate.

The PTEN-induced putative kinase 1 knockout rat (Pink1-/-) is marketed as an established model for Parkinson's disease, characterized by development of motor deficits and progressive degeneration of half the dopaminergic neurons in the substantia nigra pars compacta by 8 months of age. In this study, we address our concerns about the reproducibility of the Pink1-/- rat model. We evaluated behavioural function, number of substantia nigra dopaminergic neurons and extracellular striatal dopamine concentrations by in vivo microdialysis. Strikingly, we and others failed to observe any loss of dopaminergic neurons in 8-month-old male Pink1-/- rats. To understand this variability, we compared key experimental parameters from the different studies and provide explanations for contradictory findings. Although Pink1-/- rats developed behavioural deficits, these could not be attributed to nigrostriatal degeneration as there was no loss of dopaminergic neurons in the substantia nigra and no changes in neurotransmitter levels in the striatum. To maximize the benefit of Parkinson's disease research and limit the unnecessary use of laboratory animals, it is essential that the research community is aware of the limits of this animal model. Additional research is needed to identify reasons for inconsistency between Pink1-/- rat colonies and why degeneration in the substantia nigra is not consistent.

Reelin is an extracellular matrix protein, known for its dual role in neuronal migration during brain development and in synaptic plasticity at adult stages. During the perinatal phase, Reelin expression switches from Cajal-Retzius (CR) cells, its main source before birth, to inhibitory interneurons (IN), the main source of Reelin in the adult forebrain. IN-derived Reelin has been associated with schizophrenia and temporal lobe epilepsy; however, the functional role of Reelin from INs is presently unclear. In this study, we used conditional knockout mice, which lack Reelin expression specifically in inhibitory INs, leading to a substantial reduction in total Reelin expression in the neocortex and dentate gyrus. Our results show that IN-specific Reelin knockout mice exhibit normal neuronal layering and normal behavior, including spatial reference memory. Although INs are the major source of Reelin within the adult stem cell niche, Reelin from INs does not contribute substantially to normal adult neurogenesis. While a closer look at the dentate gyrus revealed some unexpected alterations at the cellular level, including an increase in the number of Reelin expressing CR cells, overall our data suggest that Reelin derived from INs is less critical for cortex development and function than Reelin expressed by CR cells.

Epidemiological studies have shown that increased circulating branched-chain amino acids (BCAAs) are associated with insulin resistance and type 2 diabetes (T2D). This may result from altered energy metabolism or dietary habits.