Kronos: a workflow assembler for genome analytics and informatics.

BackgroundThe field of next-generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into "best practices" for automated analysis of next-generation sequencing datasets) still requires significant programming investment and expertise.ResultsWe present Kronos, a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by compiling a text configuration file into executable Python applications. Making analysis modules would still require programming. The framework of each workflow includes a run manager to execute the encoded workflows locally (or on a cluster or cloud), parallelize tasks, and log all runtime events. The resulting workflows are highly modular and configurable by construction, facilitating flexible and extensible meta-applications that can be modified easily through configuration file editing. The workflows are fully encoded for ease of distribution and can be instantiated on external systems, a step toward reproducible research and comparative analyses. We introduce a framework for building Kronos components that function as shareable, modular nodes in Kronos workflows.ConclusionsThe Kronos platform provides a standard framework for developers to implement custom tools, reuse existing tools, and contribute to the community at large. Kronos is shipped with both Docker and Amazon Web Services Machine Images. It is free, open source, and available through the Python Package Index and at https://github.com/jtaghiyar/kronos

Graphene oxide coated aluminium as an efficient antibacterial surface

Antimicrobial coatings on metallic surfaces are rapidly emerging to combat bacterial pathogens. The excess use of conventional antibiotics increases the number of resistant strains at an alarming rate, which in turn leads to detrimental implications in the healthcare sector. Hence, it is of great importance in developing a new class of material with inherent bactericidal activity and good biocompatibility. In the present study, we have modified the aluminium surfaces by a coating of graphene oxide (GO) due to its excellent physicochemical properties, water dispersity and low cytotoxicity. Coatings were developed through facile and enviornment-friendly transfer method. The antimicrobial properties of GO coated aluminium are investigated against Gram-negative strain E. coli through agar plate counting and ‘Live/Dead’ fluorescence staining. Further, to shed light into the mechanism of antibacterial activity of GO at the molecular level, we have performed X-ray reflectivity (XRR) study considering a phospholipid multilayer as a model system to mimic bacteria cell membrane. Results show a significant bactericidal activity of the GO coatings compared to uncoated aluminium with lower concentration showing slightly better antibacterial property due to higher roughness. The obtained results may pave the way for engineering graphene-based antimicrobial coatings on a material surface using an easy, environment-friendly, cost-effective and straight forward processing route

Density functional theoretical studies on 2-methyl-4-chlorophenoxyacetic acid (MCPA)

135-142MCPA is a post-emergence herbicide for control of wild oats and annual grassy weeds found among several economically important crops. In the present work, the Eigen values and Eigen functions of the MCPA have been calculated using two basis sets of DFT. The Global DFT descriptors for the compound have also been calculated. The Fukui functions, local softness, and atomic charges for each center of MCPA have also been calculated It has been found that all the reactivity centers of MCPA are not equal in chemical reactivity. The differences in chemical reactivity of different sites have been investigated in detail in this work

Effects of pumping on entomopathogenic nematodes and temperature increase within a spray system

Exposure to hydrodynamic stresses and increased temperature during hydraulic agitation within a spray system could cause permanent damage to biological pesticides during spray application. Damage to a benchmark biopesticide, entomopathogenic nematodes (EPNs), was measured after a single passage through three different pump types (centrifugal, diaphragm, and roller) at operating pressures up to 828 kPa. No mechanical damage to the EPNs due to passage through the pumps was observed. Separate tests evaluated the effect of pump recirculation on temperature increase of water within a laboratory spray system (56.8-L spray tank) and a conventional-scale spray system (1136-L spray tank). A constant volume of water (45.4 L) was recirculated through each pump at 15.1 L/min within the laboratory spray system. After 2 h, the temperature increase for the centrifugal pump was 33.6 degrees C, and for the diaphragm and roller pumps was 8.5 degrees C and 11.2 degrees C, respectively. The centrifugal pump was also evaluated within the conventional spray system, under both a constant (757 L) and reducing volume scenario, resulting in an average temperature increase of 3.2 degrees C and 6.5 degrees C, respectively, during the 3-h test period. When comparing the number of recirculations for each test, the rate of temperature increase was the same for the conventional spray, system (for both the constant and reducing volume scenarios), while for the laboratory spray system the temperature increased at a greater rate, suggesting that the volume capacity of the spray tank is the primary factor influencing the temperature increase. Results from this study indicate that thermal influences during pump recirculation could be more detrimental to EPNs than mechanical stress. Results show that extensive recirculation of the tank mix can cause considerable increases in the liquid temperature. Diaphragm and roller pumps (low-capacity pumps) are better suited for use with biopesticides compared to the centrifugal pump, which was found to contribute significant heat to the spray system

Hyperhomocysteinemia is Associated with Aortic Atheroma Progression in Stroke/TIA Patients

Significance: Aortic arch (AA) atheroma and AA atheroma progression are independent risk factors for recurrent vascular events in stroke/transient ischemic attack (TIA) patients. Total homocysteine level (tHcy) is an independent risk marker for atherosclerosis including that found in AA. The purpose of this study was to prospectively test the association between AA atheroma progression and tHcy. Methods: This is a cohort study of 307 consecutive hospitalized stroke/TIA patients undergoing transesophageal echocardiogram (TEE) as a part of their clinical workup. Measurable AA atheroma was detected in 167 patients of whom 125 consented to a protocol-mandated follow-up TEE at 12 months. Patients had evaluation for vascular risk factors, dietary factors (folate, B12 and pyridoxine), and methylene tetrahydrofolate reductase (MTHFR) polymorphism. One hundred eighteen stroke/TIA patients had tHcy, acceptable paired AA images, and detailed plaque measurements. An increase by ≥1 grade of AA atheroma was defined as progression. Results: Of the 118 patients, 33 (28%) showed progression and 17 (14%) showed regression of their index arch lesion at 1 year. tHcy (≥14.0 μmol/l) was significantly associated with progression on both univariate (RR = 3.4, 95% CI 2.0–5.8) and multivariate analyses (adjusted RR = 3.6, 95% CI 2.2–4.6). The changes in AA plaque thickness (r2 = 0.11; p < 0.001) and AA plaque area (r2 = 0.08; p = 0.002) correlated with tHcy. tHcy was associated with change in plaque thickness over 12 months, independent of age, dietary factors, renal function and MTHFR polymorphism (Standardized β-coefficient 0.335, p = 0.02). Conclusions: Our results validate the association and a linear correlation between tHcy and progression of AA atheroma

Kikuchi-Fujimoto Disease Associated with Myasthenia Gravis: A Case Report

Kikuchi-Fujimoto disease is a self-limited benign condition of unknown etiology characterized by cervical lymphadenopathy, fever, and leucopenia. An autoimmune hypothesis has been suggested and an association with systemic lupus erythematosus, Sjogren's disease, and antiphospholipid syndrome has been noted. We report a 27-year-old male who presented for evaluation of weakness and he was diagnosed with seropositive generalized myasthenia gravis and underwent a thymectomy. He was stable until five months post-thymectomy, when he developed a high fever associated with nontender cervical lymphadenopathy, chills, and night sweats. Histopathology of a cervical lymph gland biopsy was compatible with Kikuchi-Fujimoto lymphadenitis. He improved spontaneously and was asymptomatic at the followup six months later. Our case expands the association of Kikuchi-Fujimoto disease with autoimmune disorders to include myasthenia gravis

Communication in the Gig Economy: Buying and Selling in Online Freelance Marketplaces

The proliferating gig economy relies on online freelance marketplaces, which support relatively anonymous interactions by text-based messages. Informational asymmetries thus arise that can lead to exchange uncertainties between buyers and freelancers. Conventional marketing thought recommends reducing such uncertainty. However, uncertainty reduction and uncertainty management theories indicate that buyers and freelancers might benefit more from balancing, rather than reducing, uncertainty, such as by strategically adhering to or deviating from common principles. With dyadic analyses of calls for bids and bids from a leading online freelance marketplace, this study reveals that buyers attract more bids from freelancers when they provide moderate degrees of task information and concreteness, avoid sharing personal information, and limit the affective intensity of their communication. Freelancers’ bid success and price premiums increase when they mimic the degree of task information and affective intensity exhibited by buyers. However, mimicking a lack of personal information and concreteness reduces freelancers’ success, so freelancers should always be more concrete and offer more personal information than buyers do. These contingent perspectives offer insights into buyer–seller communication in two-sided online marketplaces; they clarify that despite, or sometimes due to, communication uncertainty, both sides can achieve success in the online gig economy

Long-Term Stability of an Area-Reversible Atom-Interferometer Sagnac Gyroscope

We report on a study of the long-term stability and absolute accuracy of an atom interferometer gyroscope. This study included the implementation of an electro-optical technique to reverse the vector area of the interferometer for reduced systematics and a careful study of systematic phase shifts. Our data strongly suggests that drifts less than 96 $\mu$deg/hr are possible after empirically removing shifts due to measured changes in temperature, laser intensity, and several other experimental parameters.Comment: 4 pages, 4 figures, submitted to PR