Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and characterization of fowl aviadenovirus serotype 11 from chickens with inclusion body hepatitis in Morocco

The present study was conducted in order to isolate, identify and characterize fowl aviadenovirus associated with inclusion body hepatitis (IBH) in three poultry farms (two of broiler chickens and one of breeder broiler chickens) in Morocco during 2015. Liver samples collected from affected three poultry farms were examined by histopathological examination. Tissue samples showing necrosis of hepatocytes associated with basophilic intranuclear inclusion bodies were homogenized and submitted to FAdV isolation in chicken embryo fibroblast (CEF) cell cultures and in SPF embryonated eggs. The cytopathic effect (CPE) was observed in the second passage with swelling and rounding of infected cells. The inoculated embryos were hemorrhagic and showed hepatitis with the presence of basophilic intra-nuclear inclusion bodies within hepatocytes. The presence of the virus was confirmed by conventional polymerase chain reaction based on hexon gene from all investigated samples. Moreover, phylogenetic analysis of the hexon gene revealed that FAdVs isolated from different affected poultry belonged to FAdV 11 serotype of the D genotype group. This work is the first isolation in cell culture and SPF embryonated eggs of FAdV from Moroccan broilers and breeder broiler chickens with IBH.
Serum Adiponectin Levels Do Not Distinguish Primary from Metastatic Liver Tumors

Background/Aim: Adiponectin protects from metabolic disease and cancer. Accordingly, serum adiponectin was reduced in patients with colorectal cancer (CRC). This hepatoprotective factor was definitely increased in hepatocellular carcinoma (HCC). CRC metastases to the liver are common and the aim of the present study was to evaluate whether serum adiponectin discriminates primary from secondary liver cancers. Materials and Methods: Adiponectin was measured by ELISA in the serum of 36 patients with colorectal liver metastases, 32 patients with HCC and 49 patients without cancer. Results: Serum adiponectin levels were higher in cancer than non-tumor patients. Adiponectin was not related to TNM stage in HCC nor to the levels of serum tumor markers. Moreover, hepatic inflammation and liver fibrosis were not correlated with serum adiponectin levels. Metabolic diseases are associated with low adiponectin and a higher risk of cancer. In HCC, but not in CRC serum, adiponectin was increased in patients with hypertension and hyperuricemia. In this cohort, adiponectin positively correlated with chemerin, an adipokine supposed to contribute to metabolic disturbances. Conclusion: Serum adiponectin cannot discriminate primary from secondary liver tumors.
Kyasanur Forest Disease vaccination coverage and its perceived barriers in Goa, India—A mixed methods operational research

Background Kyasanur Forest Disease (KFD) is a highly infectious viral illness transmitted by infected ticks through contact with monkeys and other forest animals. Till date there is no definite treatment available for KFD. Hence, vaccination is considered to be an important public health intervention to control KFD. This study aimed at estimating the vaccination coverage for primary and booster doses of KFD vaccine and exploring the perceived barriers to vaccination in the affected villages of Goa, India during 2015–18. Methodology & principal findings In this explanatory mixed methods study, vaccine coverage was estimated bydata obtained from the KFD vaccination registers maintained at the health centers catering to the KFD affected villages. To understand the barriers to vaccination,key informant interviews were conducted among implementing health officers, medical officers and nurses involved in vaccination. Perceptions of vaccinees and community members were studied through in-depth interviews and focus group discussions. Out of the 35,500 targeted population (6–65 years)for KFD vaccination, 32% received one dose and 13.2% received two doses. The coverage for first booster and annual booster was 4.9% and 0.5% respectively. The drop out from first to second and third doses was 57% and 85% respectively. 69% of doses were delivered during community outreach programmes and remaining at health facilities. Inadequate vaccine stock, inappropriate timing of vaccination campaign, lack of awareness and misconceptions related to indications of vaccines, travel distance for follow up doses given at community health centre and pain due to injection were perceived as reasons for poor vaccination coverage. Conclusions KFD vaccination coverage was poor in the villages affected by KFD in Goa. Both left-out and drop-out phenomena were observed in KFD vaccination. Vaccine implementation plan has to consider suitable time for the local people, maintain adequate vaccine stock and encourage community-based vaccination campaigns instead of facility-based to achieve optimal vaccine coverage.
The Ancient Neapolitan Sweet Lime and the Calabrian Lemoncetta Locrese Belong to the Same Citrus Species

“Neapolitan limmo” is an ancient and rare sweet Mediterranean lime, now almost extinct but used until a few decades ago for the production of a fragrant liqueur called the “four citrus fruits”. The objective of this work was to compare, through the use of chemical (flavonoids, volatile organic compounds, and chiral compounds) and molecular (DNA fingerprint based on RAPD-PCR) markers, the residual population of Neapolitan limmo with other populations of sweet limes, identified in Calabria and known as “lemoncetta Locrese”. We report for the first time specific botanical characteristics of the two fruits and unequivocally show that the ancient sweet Mediterranean limes Neapolitan limmo and lemoncetta Locrese are synonyms of the same Citrus species. Owing to the biodiversity conserved in their places of origin, it will now be possible to recover, enhance and implement the use of this ancient sweet lime for agro-industrial purposes.
Home program practices for supporting and measuring adherence in post-stroke rehabilitation: a scoping review

ABSTRACT Background After stroke, individuals face a variety of impairments that impact function. Increasingly, rehabilitation for these impairments has moved into the community and home settings through the use of home programs. However, adherence to these programs is often low, limiting effectiveness. Objective This scoping review investigated home program implementation and measurement of adherence with persons post-stroke to identify commonly reported practices and determine areas for further research. Methods The electronic databases of PubMed, CINAHL, Scopus, Cochrane Database of Systematic Reviews, and PEDro were searched. Studies focused on post-stroke rehabilitation with an independent home program were selected. Qualitative studies, commentaries, and single-case studies were excluded. Title and abstract screenings were completed by two reviewers with a third for tie-breaking. The full-text review was completed by two reviewers using consensus to resolve any differences. Of the 1,197 articles initially found only 6% (n = 70) met criteria for data extraction. Elements for data extraction included: type of study, area of intervention, description of home program, presence of strategies to support adherence, methods to measure adherence and reported adherence. Results Most commonly reported strategies to support home practice were the use of technology, personalization, and written directions. Only 20 studies reported achieving adherence at or greater than 75% and 18 studies did not report adherence outcomes. Conclusions Future investigations that directly compare and identify the most effective strategies to support adherence to home programs for this population are warranted. The implementation of guidelines for reporting adherence to home programs is recommended.
Molecular and structural characterization of oxidized ribonucleotide insertion into DNA by human DNA polymerase β

During oxidative stress, inflammation, or environmental exposure, ribo- and deoxyribonucleotides are oxidatively modified. 8-Oxo-7,8-dihydro-2′-guanosine (8-oxo-G) is a common oxidized nucleobase whose deoxyribonucleotide form, 8-oxo-dGTP, has been widely studied and demonstrated to be a mutagenic substrate for DNA polymerases. Guanine ribonucleotides are analogously oxidized to r8-oxo-GTP, which can constitute up to 5% of the rGTP pool. Because ribonucleotides are commonly misinserted into DNA, and 8-oxo-G causes replication errors, we were motivated to investigate how the oxidized ribonucleotide is utilized by DNA polymerases. To do this, here we employed human DNA polymerase β (pol β) and characterized r8-oxo-GTP insertion with DNA substrates containing either a templating cytosine (nonmutagenic) or adenine (mutagenic). Our results show that pol β has a diminished catalytic efficiency for r8-oxo-GTP compared with canonical deoxyribonucleotides but that r8-oxo-GTP is inserted mutagenically at a rate similar to those of other common DNA replication errors (i.e. ribonucleotide and mismatch insertions). Using FRET assays to monitor conformational changes of pol β with r8-oxo-GTP, we demonstrate impaired pol β closure that correlates with a reduced insertion efficiency. X-ray crystallographic analyses revealed that, similar to 8-oxo-dGTP, r8-oxo-GTP adopts an anti conformation opposite a templating cytosine and a syn conformation opposite adenine. However, unlike 8-oxo-dGTP, r8-oxo-GTP did not form a planar base pair with either templating base. These results suggest that r8-oxo-GTP is a potential mutagenic substrate for DNA polymerases and provide structural insights into how r8-oxo-GTP is processed by DNA polymerases.
Mapping the Human Exposome to Uncover the Causes of Breast Cancer

Breast cancer is an important cause of morbidity and mortality for women, yet a significant proportion of variation in individual risk is unexplained. It is reasonable to infer that unexplained breast cancer risks are caused by a myriad of exposures and their interactions with genetic factors. Most epidemiological studies investigating environmental contribution to breast cancer risk have focused on a limited set of exposures and outcomes based on a priori knowledge. We hypothesize that by measuring a rich set of molecular information with omics (e.g., metabolomics and adductomics) and comparing these profiles using a case-control design we can pinpoint novel environmental risk factors. Specifically, exposome-wide association study approaches can be used to compare molecular profiles between controls and either breast cancer cases or participants with phenotypic measures associated with breast cancer (e.g., high breast density, chronic inflammation). Current challenges in annotating compound peaks from biological samples can be addressed by creating libraries of environmental chemicals that are breast cancer relevant using publicly available high throughput exposure and toxicity data, and by mass spectra fragmentation. This line of discovery and innovation will extend understanding of how environmental exposures interact with genetics to affect health, and provide evidence to support new breast cancer prevention strategies.
Evolving a Peptide: Library Platforms and Diversification Strategies

Peptides are widely used in pharmaceutical industry as active pharmaceutical ingredients, versatile tools in drug discovery, and for drug delivery. They find themselves at the crossroads of small molecules and proteins, possessing favorable tissue penetration and the capability to engage into specific and high-affinity interactions with endogenous receptors. One of the commonly employed approaches in peptide discovery and design is to screen combinatorial libraries, comprising a myriad of peptide variants of either chemical or biological origin. In this review, we focus mainly on recombinant peptide libraries, discussing different platforms for their display or expression, and various diversification strategies for library design. We take a look at well-established technologies as well as new developments and future directions.
Ectopic Expression of Grapevine Gene VaRGA1 in Arabidopsis Improves Resistance to Downy Mildew and Pseudomonas syringae pv. tomato DC3000 But Increases Susceptibility to Botrytis cinerea

The protein family with nucleotide binding sites and leucine-rich repeat (NBS-LRR) in plants stimulates immune responses caused by effectors and can mediate resistance to hemi-biotrophs and biotrophs. In our previous study, a Toll-interleukin-1(TIR)-NBS-LRR gene cloned from Vitis amurensis “Shuanghong”, VaRGA1, was induced by Plasmopara viticola and could improve the resistance of tobacco to Phytophthora capsici. In this study, VaRGA1 in “Shuanghong” was also induced by salicylic acid (SA), but inhibited by jasmonic acid (JA). To investigate whether VaRGA1 confers broad-spectrum resistance to pathogens, we transferred this gene into Arabidopsis and then treated with Hyaloperonospora arabidopsidis (Hpa), Botrytis cinerea (B. cinerea), and Pseudomonas syringae pv. tomato DC3000 (PstDC3000). Results showed that VaRGA1 improved transgenic Arabidopsis thaliana resistance to the biotrophic Hpa and hemi-biotrophic PstDC3000, but decreased resistance to the necrotrophic B. cinerea. Additionally, qPCR assays showed that VaRGA1 plays an important role in disease resistance by activating SA and inhibiting JA signaling pathways. A 1104 bp promoter fragment of VaRGA1 was cloned and analyzed to further elucidate the mechanism of induction of the gene at the transcriptional level. These results preliminarily confirmed the disease resistance function and signal regulation pathway of VaRGA1, and contributed to the identification of R-genes with broad-spectrum resistance function.
The Human UGT2B7 Nanodisc

The 20 uridine diphosphate glycosyl-transferases (UGTs) encoded in the human genome form an essential homeostatic network of overlapping catalytic functions that surveil and regulate the activity and clearance of scores of small molecule metabolites. Biochemical and biophysical UGT studies have been hampered by the inability to purify these membrane-bound proteins. Here, using cell-free expression and nanodisc technology, we assemble and purify to homogeneity the first UGT nanodisc—the human UGT2B7•nanodisc. The complex is readily isolated in milligram quantities. It is stable and its initial-rate parameters are identical within error to those associated with UGT2B7 in microsomal preparations (i.e., Supersomes). The high purity of the nanodisc preparation simplifies UGT assays, which allows complexities traditionally associated with microsomal assays (latency and the albumin effect) to be circumvented. Each nanodisc is shown to harbor a single UGT2B7 monomer. The methods described herein should be widely applicable to UGTs, and these findings are expected to set the stage for experimentalists to more freely explore the structure, function, and biology of this important area of phase II metabolism. SIGNIFICANCE STATEMENT Lack of access to pure, catalytically competent human uridine diphosphate glucuronosyl-transferases (UGTs) has long been an impediment to biochemical and biophysical studies of this disease-relevant enzyme family. Here, we demonstrate this barrier can be removed using nanodisc technology—a human UGT2B7•nanodisc is assembled, purified to homogeneity, and shown to have activity comparable to microsomal UGT2B7.
Genome-Wide Tiling Array Analysis of HPV-Induced Warts Reveals Aberrant Methylation of Protein-Coding and Non-Coding Regions

The human papillomaviruses (HPV) are a group of double-stranded DNA viruses that exhibit an exclusive tropism for squamous epithelia. HPV can either be low- or high-risk depending on its ability to cause benign lesions or cancer, respectively. Unsurprisingly, the majority of epigenetic research has focused on the high-risk HPV types, neglecting the low-risk types in the process. Therefore, the main objective of this study is to better understand the epigenetics of wart formation by investigating the differences in methylation between HPV-induced cutaneous warts and normal skin. A number of clear and very significant differences in methylation patterns were found between cutaneous warts and normal skin. Around 55% of the top-ranking 100 differentially methylated genes in warts were protein coding, including the EXOC4, KCNU, RTN1, LGI1, IRF2, and NRG1 genes. Additionally, non-coding RNA genes, such as the AZIN1-AS1, LINC02008, and MGC27382 genes, constituted 11% of the top-ranking 100 differentially methylated genes. Warts exhibited a unique pattern of methylation that is a possible explanation for their transient nature. Since the genetics of cutaneous wart formation are not completely known, the findings of the present study could contribute to a better understanding of how HPV infection modulates host methylation to give rise to warts in the skin.
Monitoring hunted species of cultural significance: Estimates of trends, population sizes and harvesting rates of flying-fox (Pteropus sp.) in New Caledonia

Assessing population trends and their underlying factors is critical to propose efficient conservation actions. This assessment can be particularly challenging when dealing with highly mobile, shy and nocturnal animals such as flying-foxes. Here we investigated the dynamics of hunted populations of Pteropus ornatus and P. tonganus in the Northern Province of New Caledonia. First, an ethno-ecological survey involving 219 local experts identified 494 flying-fox roosts. Current status was assessed for 379 of them, among which 125 were no longer occupied, representing a loss of 33% over ca. 40 years. Second, species-specific counts conducted at 35 roosts, and a sample of animals killed by hunters, revealed that the endemic species, P. ornatus, was dominant (68.5%). Between 2010 and 2016, 30 roosts were counted annually during the pre-parturition period. Roosts size averaged 1,425 ± 2,151 individuals (N = 180 counts) and showed high among-year variations (roost-specific CV = 37–162%). If we recorded significant inter-annual variation, we did not detect a significant decline over the 7-yr period, although one roost went possibly extinct. Population size of the two species combined was estimated at 338,000−859,000 individuals distributed over ca. 400 roosts in the Northern Province. Flying-foxes are popular game species and constitute traditional food for all communities of New Caledonia. Annual bags derived from a food survey allowed us to estimate harvesting rates at 5–14%. Such a level of harvesting for species with a ‘slow’ demography, the occurrence of poaching and illegal trade, suggest the current species use might not be sustainable and further investigations are critically needed.
The Effect of Various Doses of Oral Vitamin D3 Supplementation on Gut Microbiota in Healthy Adults: A Randomized, Double-blinded, Dose-response Study

Background/Aim: To investigate the effects of vitamin D3 supplementation on gut microbiota. Patients and Methods: Twenty adults with vitamin D insufficiency/deficiency [25(OH)D <30 ng/ml] were enrolled and given 600, 4,000 or 10,000 IUs/day of oral vitamin D3. Stool samples were collected at baseline and 8 weeks for identifying gut microbiota using 16S rRNA gene amplification and sequencing. Results: Baseline serum 25(OH)D was associated with increased relative abundance of Akkermansia and decreased relative abundance of Porphyromonas (p<0.05). After the intervention, we observed a dose-dependent increase in relative abundance of Bacteroides with a significant difference between the 600 IUs and the 10,000 IUs groups (p=0.027), and Parabacteroides with a significant difference between the 600 IUs and the 4,000 IUs groups (p=0.039). Conclusion: Increased serum 25(OH)D was associated with increased beneficial bacteria and decreased pathogenic bacteria. A dose-dependent increase in bacteria associated with decreased inflammatory bowel disease activity was observed after vitamin D3 supplementation.
Sensor Classification Using Convolutional Neural Network by Encoding Multivariate Time Series as Two-Dimensional Colored Images

This paper proposes a framework to perform the sensor classification by using multivariate time series sensors data as inputs. The framework encodes multivariate time series data into two-dimensional colored images, and concatenate the images into one bigger image for classification through a Convolutional Neural Network (ConvNet). This study applied three transformation methods to encode time series into images: Gramian Angular Summation Field (GASF), Gramian Angular Difference Field (GADF), and Markov Transition Field (MTF). Two open multivariate datasets were used to evaluate the impact of using different transformation methods, the sequences of concatenating images, and the complexity of ConvNet architectures on classification accuracy. The results show that the selection of transformation methods and the sequence of concatenation do not affect the prediction outcome significantly. Surprisingly, the simple structure of ConvNet is sufficient enough for classification as it performed equally well with the complex structure of VGGNet. The results were also compared with other classification methods and found that the proposed framework outperformed other methods in terms of classification accuracy.
Enhanced Heavy Metal Removal from Acid Mine Drainage Wastewater Using Double-Oxidized Multiwalled Carbon Nanotubes

Due to the unique properties of carbon nanotubes (CNTs), they have attracted great research attention as an emergent technology in many applications including water and wastewater treatment. However, raw CNTs have few functional groups, which limits their use in heavy metal removal. Nevertheless, their removal properties can be improved by oxidation processes that modify its surface. In this study, we assessed the capacity of oxidized and double-oxidized multiwalled carbon nanotubes (MWCNTs) to remove heavy metals ions from acidic solutions. The MWCNTs were tested for copper (Cu), manganese (Mn), and zinc (Zn) removal, which showed an increment of 79%, 78%, and 48%, respectively, with double-oxidized MWCNTs compared to oxidized MWCNTs. Moreover, the increase in pH improved the sorption capacity for all the tested metals, which indicates that the sorption potential is strongly dependent on the pH. The kinetic adsorption process for three metals can be described well with a pseudo-second-order kinetic model. Additionally, in multimetallic waters, the sorption capacity decreases due to the competition between metals, and it was more evident in the removal of Zn, while Cu was less affected. Besides, XPS analysis showed an increase in oxygen-containing groups on the MWCNTs surface after oxidation. Finally, these analyses showed that the chemical interactions between heavy metals and oxygen-containing groups are the main removal mechanism. Overall, these results contribute to a better understanding of the potential use of CNTs for water treatment.