Implementation of Databox

Databox is a file hosting service[1]. It’s one of its typical usage is being implemented here as an example. This project implements databox as an online learning portal. This finds the usage across domains. The admin of the website uploads the files in the form of images, videos and PDFs. Only the registered users are allowed to access the material stored in the website. The registered student will have a private key to see the document after decrypting it. The private key will be made available to the registered student after registering into the website. DOI: 10.17762/ijritcc2321-8169.150510

Heterogeneous Host Susceptibility Enhances Prevalence of Mixed-Genotype Micro-Parasite Infections

Dose response in micro-parasite infections is usually shallower than predicted by the independent action model, which assumes that each infectious unit has a probability of infection that is independent of the presence of other infectious units. Moreover, the prevalence of mixed-genotype infections was greater than predicted by this model. No probabilistic infection model has been proposed to account for the higher prevalence of mixed-genotype infections. We use model selection within a set of four alternative models to explain high prevalence of mixed-genotype infections in combination with a shallow dose response. These models contrast dependent versus independent action of micro-parasite infectious units, and homogeneous versus heterogeneous host susceptibility. We specifically consider a situation in which genome differences between genotypes are minimal, and highly unlikely to result in genotype-genotype interactions. Data on dose response and mixed-genotype infection prevalence were collected by challenging fifth instar Spodoptera exigua larvae with two genotypes of Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV), differing only in a 100 bp PCR marker sequence. We show that an independent action model that includes heterogeneity in host susceptibility can explain both the shallow dose response and the high prevalence of mixed-genotype infections. Theoretical results indicate that variation in host susceptibility is inextricably linked to increased prevalence of mixed-genotype infections. We have shown, to our knowledge for the first time, how heterogeneity in host susceptibility affects mixed-genotype infection prevalence. No evidence was found that virions operate dependently. While it has been recognized that heterogeneity in host susceptibility must be included in models of micro-parasite transmission and epidemiology to account for dose response, here we show that heterogeneity in susceptibility is also a fundamental principle explaining patterns of pathogen genetic diversity among hosts in a population. This principle has potentially wide implications for the monitoring, modeling and management of infectious diseases

Pyrosequencing-Based Assessment of Bacterial Community Structure Along Different Management Types in German Forest and Grassland Soils

BACKGROUND: Soil bacteria are important drivers for nearly all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformations in soil. In contrast to the importance of soil bacteria for ecosystem functioning, we understand little how different management types affect the soil bacterial community composition. METHODOLOGY/PRINCIPAL FINDINGS: We used pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to identify changes in bacterial diversity and community structure in nine forest and nine grassland soils from the Schwäbische Alb that covered six different management types. The dataset comprised 598,962 sequences that were affiliated to the domain Bacteria. The number of classified sequences per sample ranged from 23,515 to 39,259. Bacterial diversity was more phylum rich in grassland soils than in forest soils. The dominant taxonomic groups across all samples (>1% of all sequences) were Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Firmicutes. Significant variations in relative abundances of bacterial phyla and proteobacterial classes, including Actinobacteria, Firmicutes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes and Alphaproteobacteria, between the land use types forest and grassland were observed. At the genus level, significant differences were also recorded for the dominant genera Phenylobacter, Bacillus, Kribbella, Streptomyces, Agromyces, and Defluviicoccus. In addition, soil bacterial community structure showed significant differences between beech and spruce forest soils. The relative abundances of bacterial groups at different taxonomic levels correlated with soil pH, but little or no relationships to management type and other soil properties were found. CONCLUSIONS/SIGNIFICANCE: Soil bacterial community composition and diversity of the six analyzed management types showed significant differences between the land use types grassland and forest. Furthermore, bacterial community structure was largely driven by tree species and soil pH

Finding the Needles in the Metagenome Haystack

In the collective genomes (the metagenome) of the microorganisms inhabiting the Earth’s diverse environments is written the history of life on this planet. New molecular tools developed and used for the past 15 years by microbial ecologists are facilitating the extraction, cloning, screening, and sequencing of these genomes. This approach allows microbial ecologists to access and study the full range of microbial diversity, regardless of our ability to culture organisms, and provides an unprecedented access to the breadth of natural products that these genomes encode. However, there is no way that the mere collection of sequences, no matter how expansive, can provide full coverage of the complex world of microbial metagenomes within the foreseeable future. Furthermore, although it is possible to fish out highly informative and useful genes from the sea of gene diversity in the environment, this can be a highly tedious and inefficient procedure. Microbial ecologists must be clever in their pursuit of ecologically relevant, valuable, and niche-defining genomic information within the vast haystack of microbial diversity. In this report, we seek to describe advances and prospects that will help microbial ecologists glean more knowledge from investigations into metagenomes. These include technological advances in sequencing and cloning methodologies, as well as improvements in annotation and comparative sequence analysis. More significant, however, will be ways to focus in on various subsets of the metagenome that may be of particular relevance, either by limiting the target community under study or improving the focus or speed of screening procedures. Lastly, given the cost and infrastructure necessary for large metagenome projects, and the almost inexhaustible amount of data they can produce, trends toward broader use of metagenome data across the research community coupled with the needed investment in bioinformatics infrastructure devoted to metagenomics will no doubt further increase the value of metagenomic studies in various environments

Culture Enriched Molecular Profiling of the Cystic Fibrosis Airway Microbiome

The microbiome of the respiratory tract, including the nasopharyngeal and oropharyngeal microbiota, is a dynamic community of microorganisms that is highly diverse. The cystic fibrosis (CF) airway microbiome refers to the polymicrobial communities present in the lower airways of CF patients. It is comprised of chronic opportunistic pathogens (such as Pseudomonas aeruginosa) and a variety of organisms derived mostly from the normal microbiota of the upper respiratory tract. The complexity of these communities has been inferred primarily from culture independent molecular profiling. As with most microbial communities it is generally assumed that most of the organisms present are not readily cultured. Our culture collection generated using more extensive cultivation approaches, reveals a more complex microbial community than that obtained by conventional CF culture methods. To directly evaluate the cultivability of the airway microbiome, we examined six samples in depth using culture-enriched molecular profiling which combines culture-based methods with the molecular profiling methods of terminal restriction fragment length polymorphisms and 16S rRNA gene sequencing. We demonstrate that combining culture-dependent and culture-independent approaches enhances the sensitivity of either approach alone. Our techniques were able to cultivate 43 of the 48 families detected by deep sequencing; the five families recovered solely by culture-independent approaches were all present at very low abundance (<0.002% total reads). 46% of the molecular signatures detected by culture from the six patients were only identified in an anaerobic environment, suggesting that a large proportion of the cultured airway community is composed of obligate anaerobes. Most significantly, using 20 growth conditions per specimen, half of which included anaerobic cultivation and extended incubation times we demonstrate that the majority of bacteria present can be cultured

Prognostic model to predict postoperative acute kidney injury in patients undergoing major gastrointestinal surgery based on a national prospective observational cohort study.

Background: Acute illness, existing co-morbidities and surgical stress response can all contribute to postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery. The aim of this study was prospectively to develop a pragmatic prognostic model to stratify patients according to risk of developing AKI after major gastrointestinal surgery. Methods: This prospective multicentre cohort study included consecutive adults undergoing elective or emergency gastrointestinal resection, liver resection or stoma reversal in 2-week blocks over a continuous 3-month period. The primary outcome was the rate of AKI within 7 days of surgery. Bootstrap stability was used to select clinically plausible risk factors into the model. Internal model validation was carried out by bootstrap validation. Results: A total of 4544 patients were included across 173 centres in the UK and Ireland. The overall rate of AKI was 14·2 per cent (646 of 4544) and the 30-day mortality rate was 1·8 per cent (84 of 4544). Stage 1 AKI was significantly associated with 30-day mortality (unadjusted odds ratio 7·61, 95 per cent c.i. 4·49 to 12·90; P < 0·001), with increasing odds of death with each AKI stage. Six variables were selected for inclusion in the prognostic model: age, sex, ASA grade, preoperative estimated glomerular filtration rate, planned open surgery and preoperative use of either an angiotensin-converting enzyme inhibitor or an angiotensin receptor blocker. Internal validation demonstrated good model discrimination (c-statistic 0·65). Discussion: Following major gastrointestinal surgery, AKI occurred in one in seven patients. This preoperative prognostic model identified patients at high risk of postoperative AKI. Validation in an independent data set is required to ensure generalizability

Environmental degradation amplifies species’ responses to temperature variation in a trophic interaction

1. Land‐use and climate change are two of the primary drivers of the current biodiversity crisis. However, we lack understanding of how single‐species and multi‐species associations are affected by interactions between multiple environmental stressors. 2. We address this gap by examining how environmental degradation interacts with daily stochastic temperature variation to affect individual life history and population dynamics in a host‐parasitoid trophic interaction, using the Indian meal moth, Plodia interpunctella, and its parasitoid wasp Venturia canescens. 3. We carried out a single generation individual life history experiment and a multi‐generation microcosm experiment during which individuals and microcosms were maintained at a mean temperature of 26 °C that was either kept constant or varied stochastically, at four levels of host resource degradation, in the presence or absence of parasitoids. 4. At the individual level, resource degradation increased juvenile development time and decreased adult body size in both species. Parasitoids were more sensitive to temperature variation than their hosts, with a shorter juvenile stage duration than in constant temperatures and a longer adult lifespan in moderately degraded environments. Resource degradation also altered the host's response to temperature variation, leading to a longer juvenile development time at high resource degradation. At the population level, moderate resource degradation amplified the effects of temperature variation on host and parasitoid populations compared to no or high resource degradation and parasitoid overall abundance was lower in fluctuating temperatures. Top‐down regulation by the parasitoid and bottom‐up regulation driven by resource degradation contributed to more than 50% of host and parasitoid population responses to temperature variation. 5. Our results demonstrate that environmental degradation can strongly affect how species in a trophic interaction respond to short‐term temperature fluctuations through direct and indirect trait‐mediated effects. The effects are driven by species differences in sensitivity to environmental conditions and modulate top‐down (parasitism) and bottom‐up (resource) regulation. This study highlights the need to account for differences in the sensitivity of species' traits to environmental stressors to understand how interacting species will respond to simultaneous anthropogenic changes

Arthroscopic lasso-loop technique for subscapularis repair with anterolateral viewing portal yields better clinical outcomes for Lafosse grade 3 and 4 tears: a prospective study with minimum 2 years of follow-up

Background: Contracted subscapularis tears, especially Lafosse grade 3 and 4, pose a significant challenge in surgical repair due to the need for extensive release of retracted tendon and the risk of cut-through due to poor tissue quality. The posterior viewing portal may hinder adequate visualization and extensive release of retracted tendons, particularly in addressing the bursal surface of the tears. Tension-free robust repair is critical to prevent retears and for achieving successful outcomes for these massive and complex retracted tears. This study investigates the clinical outcomes of the Lasso-Loop technique with an anterolateral viewing portal, aiming to enhance tendon release, improve footprint fixation, and optimize tissue grip, particularly in cases of chronic retracted Lafosse 3 and 4 tears. This innovation also eliminates the need for arthroscope switching and serves as a crucial measure for averting axillary nerve injuries during the procedure. Methods: The study included 40 patients with isolated subscapularis or combined anterosuperior rotator cuff tears (Lafosse grade 3 and 4) that underwent arthroscopic subscapularis repair using a Lasso-Loop technique through an anterolateral viewing portal. Evaluations were conducted both preoperatively and at predefined postoperative intervals: 6 weeks, 3 months, 6 months, 1 year, and 2 years. The evaluations in this study encompassed a comprehensive range of clinical assessments, which included a complete range of movements, specialized tests for subscapularis muscle functionality (specifically the lift-off test and belly press test), the utilization of the University of California at Los Angeles and Oxford shoulder scoring systems, and a postoperative ultrasonography conducted at the 6-month mark to assess the presence of any retear. Clinical outcomes were compared with that of the opposite normal shoulder. Results: There was considerable improvement in the active painless range of motion postoperatively. During the 2-year follow-up, the positive belly press test decreased from 50% (n = 20) to 2.5% (n = 1), while the positive lift-off test decreased from 100% (n = 40) to 5% (n = 2). The modified University of California at Los Angeles score increased significantly from 10.15 preoperatively to 30.17 at 2 years postoperatively (P value = .001). Oxford’s Shoulder Score increased significantly from 15.6 preoperatively to 40.64 at 2 years postoperatively (P value = .001). Conclusion: This technique has produced positive functional outcomes, in cases categorized as massive subscapularis tears and chronic tears indicating the superiority over other conventional techniques of subscapularis repair described in the literature