Miracle-dz/UniFAR-FTUs huggingface dataset:
Pathomorphology of Concurrent Peste des Petits Ruminants (PPR) and Contagious Caprine Pleuropneumonia (CCPP) in a Cross Breed Goat Flock

Background: Respiratory diseases are very common in goats and cause severe economic loss to the rural poor farmers. Proper identification of the actual pathogen(s) responsible for the respiratory infections is critical for timely and proper management of those diseases. The present communication describes the spontaneous occurrence of concurrent Peste des petits ruminants (PPR) and contagious caprine pleuro-pneumonia (CCPP) in a goat flock.Methods: An outbreak of respiratory disease in a goat flock consisting of 45 Tellicherry cross bred animals in varying age groups was investigated during the month of February 2019 in Namakkal district of Tamil Nadu. Information of disease outbreak and flock details were collected. Samples from live (nasal, ocular and rectal swabs) and dead (lung, spleen and mesenteric lymph nodes) were collected for detection of Peste des petits ruminants virus (PPRV) and Mycoplasma capricolum subsp.capripneumoniae (MCCP) antigen by polymerase chain reaction. Tissues from heart, lung, liver, kidney, intestine, spleen and lymph node were collected in 10% neutral buffered formalin for histopathological examination.Result: Out of 45 goats at risk, 23 showed clinical signs and 17 died of disease conditions with morbidity, mortality and case fatality rate of 51.11%, 37.77% and 73.91% respectively. PPR was confirmed by RT-PCR with M gene specific primers (191bp) and CCPP was confirmed by PCR with 16S rRNA gene fragment (316 bp). Affected animals showed clinical signs of pyrexia, anorexia, marked depression, mild erosions in the oral mucosa, nasal and ocular discharge, coughing and diarrhoea. Necropsy examination revealed congested oral mucosa, extensive pleuritis with large fibrin clots on lung surface and greyish pink consolidation of cranial lobes and anterior parts of diaphragmatic lobes. On section, consolidated areas were granular in appearance. Histopathology of lung revealed thickening of pleura, interlobular septa and alveolar wall by fibrin deposition and infiltration of inflammatory cells. Pulmonary congestion, infiltration of neutrophils and mononuclear cells, syncytial cell formation with eosinophilic intracytoplasmic and intranuclear inclusions were also noticed. Visceral organs showed degenerative and necrotic changes.
Benthic Diatom Communities in an Alpine River Impacted by Waste Water Treatment Effluents as Revealed Using DNA Metabarcoding

Freshwater ecosystems are continuously affected by anthropogenic pressure. One of the main sources of contamination comes from wastewater treatment plant (WWTP) effluents that contain wide range of micro- and macropollutants. Chemical composition, toxicity levels and impact of treated effluents (TEs) on the recipient aquatic ecosystems may strongly differ depending on the wastewater origin. Compared to urban TEs, hospital ones may contain more active pharmaceutical substances. Benthic diatoms are relevant ecological indicators because of their high species and ecological diversity and rapid response to human pressure. They are routinely used for water quality monitoring. However, there is a knowledge gap on diatom communities’ development and behavior in treated wastewater in relation to prevailing micro- and macropollutants. In this study, we aim to (1) investigate the response of diatom communities to urban and hospital TEs, and (2) evaluate TEs effect on communities in the recipient river. Environmental biofilms were colonized in TEs and the recipient river up- and downstream from the WWTP output to study benthic diatoms using DNA metabarcoding combined with high-throughput sequencing (HTS). In parallel, concentrations of nutrients, pharmaceuticals and seasonal conditions were recorded. Diatom metabarcoding showed that benthic communities differed strongly in their diversity and structure depending on the habitat. TE sites were generally dominated by few genera with polysaprobic preferences belonging to the motile guild, while river sites favored diverse communities from oligotrophic and oligosaprobic groups. Seasonal changes were visible to lower extent. To categorize parameters important for diatom changes we performed redundancy analysis which suggested that communities within TE sites were associated to higher concentrations of beta-blockers and non-steroidal anti-inflammatory drugs in urban effluents vs. antibiotics and orthophosphate in hospital effluents. Furthermore, indicator species analysis showed that 27% of OTUs detected in river downstream communities were indicator for urban or hospital TE sites and were absent in the river upstream. Finally, biological diatom index (BDI) calculated to evaluate the ecological status of the recipient river suggested water quality decrease linked to the release of TEs. Thus, in-depth assessment of diatom community composition using DNA metabarcoding is proposed as a promising technique to highlight the disturbing effect of pollutants in Alpine rivers.
Prognosis Prediction of Colorectal Cancer Using Gene Expression Profiles

Background: Investigation on prognostic markers for colorectal cancer (CRC) deserves efforts, but data from China are scarce. This study aimed to build a prognostic algorithm using differentially expressed gene (DEG) profiles and to compare it with the TNM staging system in their predictive accuracy for CRC prognosis in Chinese patients. Methods: DEGs in six paired tumor and corresponding normal tissues were determined using RNA-Sequencing. Subsequently, matched tumor and normal tissues from 127 Chinese patients were assayed for further validation. Univariate and multivariate Cox regressions were used to identify informative DEGs. A predictive index (PI) was derived as a linear combination of the products of the DEGs and their Cox regression coefficients. The combined predictive accuracy of the DEGs-based PI and tumors' TNM stages was also examined by a logistic regression model including the two predictors. The predictive performance was evaluated with the area under the receiver operating characteristics (AUCs). Results: Out of 75 candidate DEGs, we identified 10 DEGs showing statistically significant associations with CRC survival. A PI based on these 10 DEGs (PI-10) predicted CRC survival probability more accurately than the TNM staging system [AUCs for 3-year survival probability 0.73 (95% confidence interval: 0.64, 0.81) vs. 0.68 (0.59, 0.76)] but comparable to a simplified PI (PI-5) using five DEGs (LOC646627, BEST4, KLF9, ATP6V1A, and DNMT3B). The predictive accuracy was improved further by combining PI-5 and the TNM staging system [AUC for 3-year survival probability: 0.72 (0.63, 0.80)]. Conclusion: Prognosis prediction based on informative DEGs might yield a higher predictive accuracy in CRC prognosis than the TNM staging system does.
Peekbank: Exploring children's word recognition through an open, large-scale repository for developmental eye-tracking data

The ability to rapidly recognize words and link them to referents in context is central to children's early language development. This ability, often called word recognition in the developmental literature, is typically studied in the looking-while-listening paradigm, which measures infants' fixation on a target object (vs. a distractor) after hearing a target label. We present a large-scale, open database of infant and toddler eye-tracking data from looking-while-listening tasks. The goal of this effort is to address theoretical and methodological challenges in measuring vocabulary development. We present two analyses of the current database (N=1,320): (1) capturing age-related changes in infants' word recognition while generalizing across item-level variability and (2) assessing how a central methodological decision -- selecting the time window of analysis -- impacts the reliability of measurement. Future efforts will expand the scope of the current database to advance our understanding of participant-level and item-level variation in children's vocabulary development.
In the literature: February 2019

Malignant pleural mesothelioma (MPM) is a rare and lethal cancer associated to asbestos exposure. Currently, the pemetrexed and cisplatin combination chemotherapy remains the only approved treatment. In the last 5 years, a growing knowledge on mesothelioma pathobiology has translated into the development of multiple novel therapeutic strategies.1 One of the largest reports of comprehensive genomic profiling of MPM was conducted by Bueno and colleagues. Using RNA-seq data, they identified four distinct molecular subtypes, and through exome analysis, they found that BAP1 , NF2 , TP53 , SETD2 , DDX3X , ULK2 , RYR2 , CFAP45 , SETDB1 and DDX51 were significantly mutated.2 In an article recently published in Cancer Discovery , Hmeljak and colleagues3 report on a genomic study of 74 MPM samples as part of The Cancer Genome Atlas where they performed a comprehensive molecular profiling, including whole-exome sequencing (WES), copy-number arrays, mRNA sequencing, non-coding RNA expression, DNA methylation and proteomic data. Some interesting observations derive from their work. Using WES, the authors report a low tumour mutational burden (TMB) with <2 non-synonymous mutations per megabase in all but one sample which places mesothelioma at the low bottom of TMB among cancers. A low TMB may represent a negative predictive biomarker for immunotherapy. However, TMB may have been underestimated as recent studies have revealed that minute deletions are frequent in mesothelioma and are often missed by the approaches used in this study.4 Moreover, an interesting finding of this work is a strong expression of the immune-checkpoint gen VISTA in epitheloid MPM, on the tumour cells themselves. It remains to be seen if this finding will translate into a valuable clinical target for emerging anti-VISTA therapy. The authors confirm that, from a genomic standpoint, mesothelioma is characterised by a preponderance of tumour suppressor alterations. Indeed, they …
Navigating High-Choice European Political Information Environments: a Comparative Analysis of News User Profiles and Political Knowledge

The transition from low- to high-choice media environments has had far-reaching implications for citizens’ media use and its relationship with political knowledge. However, there is still a lack of comparative research on how citizens combine the usage of different media and how that is related to political knowledge. To fill this void, we use a unique cross-national survey about the online and offline media use habits of more than 28,000 individuals in 17 European countries. Our aim is to (i) profile different types of news consumers and (ii) understand how each user profile is linked to political knowledge acquisition. Our results show that five user profiles – news minimalists, social media news users, traditionalists, online news seekers, and hyper news consumers – can be identified, although the prevalence of these profiles varies across countries. Findings further show that both traditional and online-based news diets are correlated with higher political knowledge. However, online-based news use is more widespread in Southern Europe, where it is associated with lower levels of political knowledge than in Northern Europe. By focusing on news audiences, this study provides a comprehensive and fine-grained analysis of how contemporary European political information environments perform and contribute to an informed citizenry.
The Virulence-Related MYR1 Protein of Toxoplasma gondii as a Novel DNA Vaccine Against Toxoplasmosis in Mice

Toxoplasma gondii causes serious public health problems, but there is no effective treatment strategy against it currently. DNA vaccines have shown promising findings in this regard. MYR1 is a new virulence factor identified in T. gondii that may have potential as a DNA vaccine candidate. We constructed a recombinant eukaryotic plasmid, pVAX1-MYR1, as a DNA vaccine, injected it intramuscularly into BALB/c mice, and evaluated its immunoprotective effects. pVAX1-MYR1 immunization induced a sequential Th1 and Th2 T-cell response, as indicated by high levels of Th1 and mixed Th1/Th2 cytokines at 2 and 6 weeks after immunization, respectively. These findings were corroborated by the antibody assays too. In addition, increased levels of antigen-specific lymphocyte proliferation, CD4+ and CD8+ T lymphocytes, cytotoxic T lymphocyte activity and cytokine (IFN-γ, IL-12, and IL-10) production were also observed in the immunized mice. These findings showed that pVAX1-MYR1 stimulated humoral and cellular immune responses in the immunized mice. The increased production of IFN-γ and IL-12 was correlated with increased expression of the T-bet and p65 genes of the NF-κB pathway. However, no significant increase was observed in the level of IL-4. The survival of mice immunized with pVAX1-MYR1 was also significantly prolonged compared with the control group mice. Based on all the above findings, the current study proposes that pVAX1-MYR1 can induce a T. gondii-specific immune response and should therefore be considered as a promising vaccine candidate against toxoplasmosis. To the best of our knowledge, this is the first report to evaluate the immunoprotective value of an MYR1-based DNA vaccine against T. gondii.
Apelin and chemerin as promising adipokines in children with type 1 diabetes mellitus

Background Type 1 diabetes mellitus (T1DM) is one of the most common chronic diseases in children that may be due to micro or macrovascular complications. Diabetic renal disease or nephropathy is a common complication of DM, clinically silent and the only detectable abnormality due to the presence of microalbuminuria. Subjects and methods This study was a case–control study. Participants were classified into two groups. The first group included 40 children with T1DM and the second group included 30 matched healthy controls. Serum apelin (APLN), chemerin, cholesterol, and triglycerides (TG) levels were measured for each case. Also, albumin/creatinine ratio was analyzed in random urine sample. Results Comparison between T1DM patients and controls revealed that serum apelin, chemerin, cholesterol, TG levels, and albuminuria were significantly increased in cases compared to their controls. Significant positive correlations were found between HbA1c% and albuminuria for APLN and chemerin in the diabetic group. Whereas significant negative correlations were found between apelin and glomerular filtration rate (GFR). Conclusion Increased levels of serum apelin and chemerin in T1DM patients may be considered as promising adipokines for the development of diabetic complication.
Estimating HIV-1 Genetic Diversity in Brazil Through Next-Generation Sequencing

Approximately 36.7 million people were living with the human immunodeficiency virus (HIV) at the end of 2016 according to UNAIDS, representing a global prevalence rate of 0.8%. In Brazil, an HIV prevalence of 0.24% has been estimated, which represents approximately 830,000 individuals living with the virus. As a touristic and commercial hub in Latin America, Brazil harbors an elevated HIV genetic variability, further contributed by the selective pressure exerted by the host immune system and by antiretroviral treatment. Through the progress of the next-generation sequencing (NGS) techniques, it has been possible to expand the study of HIV genetic diversity, evolutionary, and epidemic processes, allowing the generation of HIV complete or near full-length genomes (NFLG) and improving the characterization of intra- and interhost diversity of viral populations. Greater sensitivity in the detection of viral recombinant forms represents one of the major improvements associated with this development. It is possible to identify unique or circulating recombinant forms using the near full-length viral genomes with increasing accuracy. It also permits the characterization of multiple viral infections within individual hosts. Previous Brazilian studies using NGS to analyze HIV diversity were able to identify several distinct unique and circulating recombinant forms and evidenced dual infections. These data unveiled unprecedented high rates of viral recombination and highlighted that novel recombinants are continually arising in the Brazilian epidemic. In the pooled analysis depicted in this report, HIV subtypes have been determined from HIV-positive patients in five states of Brazil with some of the highest HIV prevalence, three in the Southeast (Rio de Janeiro, São Paulo, and Minas Gerais), one in the Northeast (Pernambuco) and one in the South (Rio Grande do Sul). Combined data analysis showed a significant prevalence of recombinant forms (29%; 101/350), and a similar 26% when only NFLGs were considered. Moreover, the analysis was able to evidence the occurrence of multiple infections in some individuals. Our data highlight the great HIV genetic diversity found in Brazil and unveils a more accurate scenario of the HIV evolutionary dynamics in the region.
AMPLIFY: a randomized, Phase III study evaluating the efficacy and safety of aclidinium/formoterol vs monocomponents and tiotropium in patients with moderate-to-very severe symptomatic COPD

Background AMPLIFY assessed the efficacy and safety of aclidinium bromide/formoterol fumarate (AB/FF) vs its monocomponents and tiotropium (TIO) in patients with moderate-to-very severe symptomatic COPD (NCT02796677). Methods In this 24-week, Phase III, double-dummy, active-controlled study, symptomatic patients (COPD Assessment Test score ≥10) were randomized to twice-daily AB/FF 400/12 µg, AB 400 µg, or FF 12 µg, or once-daily TIO 18 µg. Co-primary endpoints were change from baseline at week 24 in 1-hour morning post-dose FEV1 (AB/FF vs AB) and in pre-dose (trough) FEV1 (AB/FF vs FF). Non-inferiority of AB vs TIO in pre-dose FEV1 was also an objective. Normalized area under the curve (AUC)0–3/3 h FEV1 and nighttime and early morning symptoms were also assessed. A subgroup participated in a 24-hour serial spirometry sub-study. Results A total of 1,594 patients were randomized; 566 entered the sub-study. At week 24, 1-hour post-dose FEV1 significantly improved with AB/FF vs AB, FF, and TIO (84, 84, and 92 mL; all P<0.0001). AB/FF significantly improved trough FEV1 vs FF (55 mL, P<0.001) and AB was non-inferior to TIO. AB/FF significantly improved AUC0–3/3 h FEV1 vs all comparators (P<0.0001) and provided significant improvements in early morning symptoms vs TIO. The 24-hour spirometry demonstrated significantly greater improvements with AB/FF in AUC12–24/12 h vs all comparators, and in AUC0–24/24 h vs FF or TIO at week 24. Conclusion In patients with moderate-to-very severe symptomatic COPD, twice-daily AB/FF significantly improved lung function vs monocomponents and TIO, and early morning symptom control vs TIO.
DiGraph: An Efficient Path-based Iterative Directed Graph Processing System on Multiple GPUs

Many systems are recently proposed for large-scale iterative graph analytics on a single machine with GPU accelerators. Despite of many research efforts, for iterative directed graph processing over GPUs, existing solutions suffer from slow convergence speed and high data access cost, because many vertices are ineffectively reprocessed for lots of rounds so as to update their states according to other active vertices regardless of their dependencies. In this paper, we propose a novel and efficient iterative directed graph processing system on a machine with the support of multiple GPUs. Compared with existing systems, the unique feature of our system is that it takes advantage of the dependencies between vertices in three novel ways. First, it represents a directed graph into a set of disjoint hot/cold directed paths and takes the path as the basic parallel processing unit, so as to help efficient vertex state propagation along the paths over GPUs for faster convergence speed and higher utilization ratio of the loaded data. Second, it tries to dispatch the paths to GPUs for parallel processing according to the topological order of the dependency graph of them. Many paths then converge along such an order after processing them for exactly once, getting lower reprocessing overhead. Third, a path scheduling strategy is further developed on each streaming multiprocessor to enable the privileged execution of the paths (e.g., the hot paths) with greater impacts on vertex state propagation for shorter convergence time according to vertex dependency. Experimental results show that our approach speeds up iterative directed graph processing by up to 3.54 times in comparison with the state-of-the-art systems.
Evaluation of The Bio-Stimulatory Effect of Platelet Rich Fibrin Augmented by Diode LASER Compared to Platelet Rich Fibrin Alone on Dental Implant Replacing Posterior Mandibular Teeth. Randomised Clinical Trial: Split Mouth Study

BACKGROUND: Restoring masticatory function and replacing missing teeth with minimal pain and discomfort are the most important issues for the patient and clinician. Nowadays dental implants became the most popular line of treatment to replace missing teeth; offering a comfortable long lasting prosthesis. Osseo-integration reflects the long term success of a dental implant. Many bio-modulators are used aiming to improve the osseointegration and healing around dental implants such as Low-Level Laser treatment (LLLT) and Platelet Rich Fibrin (PRF). PRF has been proven to improve bone repair process around the dental implant. LLLT is considered a noninvasive, safe technique that stimulates osteogenesis and alleviates post-operative pain. AIM: Evaluation of the bio-stimulatory effect of LLLT on a dental implant with PRF compared to PRF alone clinically and radiographically. METHODS: A randomised clinical trial with the split-mouth design was conducted on nine patients with bilaterally missing lower posterior tooth. All patients received one dental implant on each side with PRF. LASER application was performed to one side twice weekly for one month starting on the day of insertion. Post-operative pain was assessed daily through the first week using numerical rating pain scale (NRS) as the primary outcome. Relative peri-implant bone density was measured using direct digital intraoral radiography immediately after insertion, one, four and nine months postoperatively. Implants stability were measured using radio frequency assessment immediately after insertion, four and nine months post-operative as secondary outcomes. RESULTS: The NRS for pain was significantly decreased by the end of the first-week postoperatively in the intervention and control group with a mean of (2.22 ± 1.56) (2.11 ± 1.83) respectively. However, there was no statistically significant difference between the test groups at P-Value (0.892). The relative bone density values were decreased by the end of the ninth month of follow-up in the intervention and control group with a mean of (134.42 ± 16.13) (128.77 ± 33.54) respectively. No statistically significant difference was observed between the two test groups at P-value (0.863). The radiofrequency values for implant stability showed no statically significant difference after nine months of follow up when compared to the initial stability values at the day of insertion in the intervention and control group. The mean radiofrequency values were (67.24 ± 1.79) and (66.9 ± 2.57) respectively, and no statistically significant difference was observed between the two test groups at P-value (0.793) CONCLUSION: There are no statistically significant differences in post-operative pain values, implant stability and bone density between the implant sites treated with PRF augmented by Diode laser compared to implant sites treated by PRF alone.