Assessing and assuring interoperability of a genomics file format

Background: Bioinformatics software tools operate largely through the use of specialized genomics file formats. Often these formats lack formal specification, and only rarely do the creators of these tools robustly test them for correct handling of input and output. This causes problems in interoperability between different tools that, at best, wastes time and frustrates users. At worst, interoperability issues could lead to undetected errors in scientific results. Methods: We sought (1) to assess the interoperability of a wide range of bioinformatics software using a shared genomics file format and (2) to provide a simple, reproducible method for enhancing interoperability. As a focus, we selected the popular BED file format for genomic interval data. Based on the file format's original documentation, we created a formal specification. We developed a new verification system, Acidbio (https://github.com/hoffmangroup/acidbio), which tests for correct behavior in bioinformatics software packages. We crafted tests to unify correct behavior when tools encounter various edge cases—potentially unexpected inputs that exemplify the limits of the format. To analyze the performance of existing software, we tested the input validation of 80 Bioconda packages that parsed the BED format. We also used a fuzzing approach to automatically perform additional testing. Results: Of 80 software packages examined, 75 achieved less than 70% correctness on our test suite. We categorized multiple root causes for the poor performance of different types of software. Fuzzing detected other errors that the manually designed test suite could not. We also created a badge system that developers can use to indicate more precisely which BED variants their software accepts and to advertise the software's performance on the test suite. Discussion: Acidbio makes it easy to assess interoperability of software using the BED format, and therefore to identify areas for improvement in individual software packages. Applying our approach to other file formats would increase the reliability of bioinformatics software and data.

ANATOMICAL VARIATIONS AND VARIOUS TECHNIQUES OF IDENTIFICATION OF MULTIPLE ROOT CANALS: A REVIEW

Variations in root canal morphology presents a constant challenge for clinicians in their detection and management. Locating and treating these extra canals is important in order to achieve favorable prognosis in endodontic therapy. This review article presents the anatomical variations, frequency of occurrence of aberrant root canal configuration and methods of identification using advanced imaging techniques like CBCT, DOM and loupes.

Ancient Relatives of Modern Maize From the Center of Maize Domestication and Diversification Host Endophytic Bacteria That Confer Tolerance to Nitrogen Starvation

Plants can adapt to their surroundings by hosting beneficial bacteria that confer a selective advantage in stressful conditions. Endophytes are a class of beneficial bacteria that exist within the internal spaces of plants and many species can improve plant nitrogen use efficiency. Nitrogen is an essential plant macronutrient, and is often a limiting factor to plant growth, especially in cereal crops such as maize. Every year farmers apply over 100 million metric tonnes of synthetic nitrogen fertilizer to meet the growing demand for stable food crops. Breeding efforts in maize over the past several decades has focused heavily on yield in response to nitrogen inputs, and so may have selected against adaptations that allow plants to survive in nitrogen stressed conditions. Data suggests that our heavy dependence on synthetic nitrogen fertilizer is not sustainable in the long term, and so there is on-going research efforts to reduce and replace this currently essential part of modern agriculture. Bacteria that improve plant tolerance to nitrogen stressed environments would allow farmers to reduce the amount of fertilizer they apply. The selection of maize under high nitrogen conditions to create modern varieties may have caused the plant to lose these beneficial bacteria that allowed wild maize ancestors to thrive in low nitrogen soil. Here in this study, we examine the root and shoot microbiomes of the wild ancestor of all maize, Parviglumis, and an ancient Mexican landrace (Mixteco) from Oaxaca, the area of early maize diversification. Both of these maize genotypes have thrived for thousands of years with little to no nitrogen inputs and so we hypothesized that they host beneficial bacteria that allow them to thrive in nitrogen stressed conditions. We identified multiple root endophyte species from each ancient maize relative that increased the growth of annual ryegrass (model maize relative) under nitrogen starvation. Furthermore, research infers these strains were vertically transmitted to new generations of plants, potentially through seed, indicating selection pressure for Parviglumis and Mixteco to maintain them in their microbiome.

Multiple root canals in the maxillary molar: an unusual case report

Background The objective of this report was to highlight the importance of using a dental operating microscope (DOM) to locate supernumerary canals and diagnose variations in root canals using cone-beam computed tomographic (CBCT) images. Case presentation A 35-year-old Chinese female had repeated swelling in the upper right posterior maxilla for 3 months and was referred to evaluate symptomatic apical periodontitis and mesotaurodonts for upper right first permanent molar and upper right second permanent molar. Root canal therapy was proposed and conducted with the use of DOM and CBCT. Conclusions Proper diagnosis and careful clinicoradiological examination are necessary, and it is essential to reinforce the knowledge of the rare morphology of root canals for clinicians.

Toward a Comprehensive Model of Fake News: A New Approach to Examine the Creation and Sharing of False Information

The authors discuss a new conceptual model to examine the phenomenon of fake news. Their model focuses on the relationship between the creator and the consumer of fake news and proposes a mechanism by which to determine how likely users may be to share fake news with others. In particular, it is hypothesized that information users would likely be influenced by seven factors in choosing to share fake news or to verify information, including the user’s: (1) level of online trust; (2) level of self-disclosure online; (3) amount of social comparison; (4) level of FoMO anxiety; (5) level of social media fatigue; (6) concept of self and role identity; and (7) level of education attainment. The implications reach into many well-established avenues of inquiry in education, Library and Information Science (LIS), sociology, and other disciplines, including communities of practice, information acquiring and sharing, social positioning, social capital theory, self-determination, rational choice (e.g., satisficing and information overload), critical thinking, and information literacy. Understanding the multiple root causes of creating and sharing fake news will help to alleviate its spread. Relying too heavily on but one factor to combat fake news—education level, for example—may have limited impact on mitigating its effects. Establishing thresholds for a certain combination of factors may better predict the tendency of users to share fake news. The authors also speculate on the role information literacy education programs can play in light of a more complex understanding of how fake news operates.

Prosthetic Embodiment and Body Image Changes in Patients Undergoing Bionic Reconstruction Following Brachial Plexus Injury

Brachial plexus injuries with multiple-root involvement lead to severe and long-lasting impairments in the functionality and appearance of the affected upper extremity. In cases, where biologic reconstruction of hand and arm function is not possible, bionic reconstruction may be considered as a viable clinical option. Bionic reconstruction, through a careful combination of surgical augmentation, amputation, and prosthetic substitution of the functionless hand, has been shown to achieve substantial improvements in function and quality of life. However, it is known that long-term distortions in the body image are present in patients with severe nerve injury as well as in prosthetic users regardless of the level of function. To date, the body image of patients who voluntarily opted for elective amputation and prosthetic reconstruction has not been investigated. Moreover, the degree of embodiment of the prosthesis in these patients is unknown. We have conducted a longitudinal study evaluating changes of body image using the patient-reported Body Image Questionnaire 20 (BIQ-20) and a structured questionnaire about prosthetic embodiment. Six patients have been included. At follow up 2.5–5 years after intervention, a majority of patients reported better BIQ-20 scores including a less negative body evaluation (5 out of 6 patients) and higher vital body dynamics (4 out of 6 patients). Moreover, patients described a strong to moderate prosthesis embodiment. Interestingly, whether patients reported performing bimanual tasks together with the prosthetic hand or not, did not influence their perception of the prosthesis as a body part. In general, this group of patients undergoing prosthetic substitution after brachial plexus injury shows noticeable inter-individual differences. This indicates that the replacement of human anatomy with technology is not a straight-forward process perceived in the same way by everyone opting for it.

An efficient class of fourth-order derivative-free method for multiple-roots

Many optimal order multiple root techniques, which use derivatives in the algorithm, have been proposed in literature. Many researchers tried to construct an optimal family of derivative-free methods for multiple roots, but they did not get success in this direction. With this as a motivation factor, here, we present a new optimal class of derivative-free methods for obtaining multiple roots of nonlinear functions. This procedure involves Traub–Steffensen iteration in the first step and Traub–Steffensen-like iteration in the second step. Efficacy is checked on a good number of relevant numerical problems that verifies the efficient convergent nature of the new methods. Moreover, we find that the new derivative-free methods are just as competent as the other existing robust methods that use derivatives.

Nanoparticles in Endodontics - A Review

BACKGROUND The complex anatomy of root canal makes it very difficult to clean and shape to eliminate the bacteria in the canal. Multiple root canal medicaments and irrigants are used to eliminate the canal microbials. Many of the pathogens have undergone resistance to the medicaments and the irrigants used. Thus, antibacterial nanoparticles have been introduced to overcome this problem. Nano dentistry mainly infers the use of nanomaterials and dental nanorobots in the field of diagnosis and treatment, aiming improvement in complete oral health. The use of nanoparticles is extending in many oral health–related issues such as management of dentin hypersensitivity, elimination of bacterial biofilm, diagnosing as well as treating oral cancers, bone replacement and so on. It possesses a unique physical and chemical property. The usage of nanoparticles in different forms like solutions for irrigation, as intracanal medication, in conjunction with sealers or restorative materials aimed at evaluating and mainly improving the antimicrobial efficacy in endodontic and conservative treatments. These nanoparticles act on the bacteria through various mechanisms. The bactericidal effect of the nanoparticles has been investigated in many in vitro studies. In the field of endodontics, nanomaterials are inculcated mainly focusing on strategies improving antimicrobial efficacy, mechanical integrity of already diseased dentinal matrix, regeneration of the tissues and many more. Recently, many more new technologies are in process to be tested in the field, keeping an eye on overcoming the microbial challenge. This review intended to give a look on the literature available, uses, applications and advantages of the nanoparticles in endodontics. KEY WORDS Nanotechnology, Nanoparticles, Antibacterial Efficacy, Endodontics

Underground Heterosis for Melons Yield

Heterosis, the superiority of hybrids over their parents, is a major genetic force associated with plant fitness and crop yield enhancement. Understanding and predicting heterosis is crucial for evolutionary biology, as well as for plant and animal breeding. We investigated root-mediated yield heterosis in melons (Cucumis melo) by characterizing common variety grafted onto 190 hybrid rootstocks resulting from crossing 20 diverse inbreds in a diallel-mating scheme. Hybrid rootstocks improved yield by more than 40% compared to their parents and the best hybrid outperformed the reference commercial variety by 65% under both optimal and minimal irrigation treatments. To characterize the genetics of the underground heterosis we conducted whole-genome re-sequencing of the 20 founder lines, and showed that parental genetic distance was no predictor for the level of heterosis. Through inference of the 190 hybrids genotypes from their parental genomes, followed by genome-wide association analysis, we mapped multiple root-mediated yield QTLs. The yield enhancement of the four best-performing hybrid rootstocks was validated in multiple experiments with four different scion varieties. While root biology is receiving increased attention, most of the research is conducted using plants not amenable to grafting and, as a result, it is difficult to separate root and shoot effects. Here, we use the rich genetic and genomic resources ofCucumis melo, where grafting is a common practice, to dissect a unique phenomenon of root-mediated yield heterosis, by directly evaluating in the field the contribution of the roots to fruit yield. Our grafting approach is inverted to the common roots genetics research path that focuses mainly on variation in root system architecture rather than the ultimate root-mediated whole-plant performance, and is a step towards discovery of candidate genes involved in root function and yield enhancement.HighlightWe show that yield heterosis is significant in melon and controlled independently above and underground. Using common-scion grafting approach, we find that heritable rootstock-mediated variation in a diallel population is associated with substantial fruit yield heterosis.

Taraxacum mirabile, an enigmatic sexual halophilous endemic dandelion, represents a new section

Taraxacum mirabile Wagenitz (Asteraceae, Cichorieae, Crepidinae), a remarkable but taxonomically unexplored endemic species of Central Anatolia, is examined in detail. It is shown to be a sexually reproducing diploid (2n=16) species. It used to be included in Taraxacum sect. Orientalia in the literature. However, the nrDNA analysis revealed that T. mirabile is remote from that section. Moreover, it exhibits a number of unique features, such as fleshy leaves with a white, cartilaginous apex, long, dense, bright white tomentum at the plant base, multiple root heads, achenes with an extremely short conical cone and with very few minute spinules, a very narrow involucre with imbricate outer phyllaries, and white, not numerous florets. The most specific feature of T. mirabile is the fine, microscopic sculpture of achene surface, consisting of hair-like protuberances, not known in other Taraxacum species. These attributes, together with the convincing result of the nrDNA analysis, qualify T. mirabile to be recognized as a member of a separate section, T. sect. Echinulata, sect. nov. The habitat and distribution of T. mirabile are described, and the character of its endemism is discussed.