An algorithm competition for automatic species identification from herbarium specimens.

PREMISE: Plant biodiversity is threatened, yet many species remain undescribed. It is estimated that >50% of undescribed species have already been collected and are awaiting discovery in herbaria. Robust automatic species identification algorithms using machine learning could accelerate species discovery. METHODS: To encourage the development of an automatic species identification algorithm, we submitted our Herbarium 2019 data set to the Fine-Grained Visual Categorization sub-competition (FGVC6) hosted on the Kaggle platform. We chose to focus on the flowering plant family Melastomataceae because we have a large collection of imaged herbarium specimens (46,469 specimens representing 683 species) and taxonomic expertise in the family. As is common for herbarium collections, some species in this data set are represented by few specimens and others by many. RESULTS: In less than three months, the FGVC6 Herbarium 2019 Challenge drew 22 teams who entered 254 models for Melastomataceae species identification. The four best algorithms identified species with >88% accuracy. DISCUSSION: The FGVC competitions provide a unique opportunity for computer vision and machine learning experts to address difficult species-recognition problems. The Herbarium 2019 Challenge brought together a novel combination of collections resources, taxonomic expertise, and collaboration between botanists and computer scientists.

Pirfenidone inhibits post-traumatic proliferative vitreoretinopathy.

PurposeThe purpose of the study was to evaluate the efficacy and safety of intravitreal pirfenidone for inhibition of proliferative vitreoretinopathy (PVR) in a model of penetrating ocular injury.Patients and methodsPenetrating trauma was induced on the retina of rabbit and treated either with 0.1 ml of phosphate-buffered saline (PBS) or 0.1 ml of 0.5% pirfenidone, and development of PVR was evaluated clinically and graded after 1 month. Histopathology and immunohistochemistry with transforming growth factor beta (TGFß), alpha smooth muscle actin (αSMA), and collagen-1 were performed to assess the fibrotic changes. Expression of cytokines in the vitro-retinal tissues at different time points following pirfenidone and PBS injection was examined by RT-PCR. Availability of pirfenidone in the vitreous of rabbit at various time points was determined by high-performance liquid chromatography following injection of 0.1 ml of 0.5% pirfenidone. In normal rabbit eye, 0.1 ml of 0.5% pirfenidone was injected to evaluate any toxic effect.ResultsClinical assessment and grading revealed prevention of PVR formation in pirfenidone-treated animals, gross histology, and histopathology confirmed the observation. Immunohistochemistry showed prevention in the expression of collagen-I, αSMA, and TGFß in the pirfenidone-treated eyes compared to the PBS-treated eyes. Pirfenidone inhibited increased gene expression of cytokines observed in control eyes. Pirfenidone could be detected up to 48 h in the vitreous of rabbit eye following single intravitreal injection. Pirfenidone did not show any adverse effect following intravitreal injection; eyes were devoid of any abnormal clinical sign, intraocular pressure, and electroretinography did not show any significant change and histology of retina remained unchanged.ConclusionThis animal study shows that pirfenidone might be a potential therapy for PVR. Further clinical study will be useful to evaluate the clinical application of pirfenidone.

Silk fibroin hydrogel as physical barrier for prevention of post hernia adhesion.

BACKGROUND: Adhesion formation remains a major complication following hernia repair surgery. Physical barriers though effective for adhesion prevention in clinical settings are associated with major disadvantages, therefore, needs further investigation. This study evaluates silk fibroin hydrogel as a physical barrier on polypropylene mesh for the prevention of adhesion following ventral hernia repair. STUDY DESIGN: Peritoneal explants were cultured on silk fibroin scaffold to evaluate its support for mesothelial cell growth. Full thickness uniform sized defects were created on the ventral abdominal wall of rabbits, and the defects were covered either with silk hydrogel coated polypropylene mesh or with plain polypropylene mesh as a control. The animals were killed after 1 month, and the adhesion formation was graded; healing response of peritoneum was evaluated by immunohistochemistry with calretinin, collagen staining of peritoneal sections, and expression of PCNA, collagen-I, TNFα, IL6 by real time PCR; and its adverse effect if any was determined. RESULTS: Silk fibroin scaffold showed excellent support for peritoneal cell growth in vitro and the cells expressed calretinin. A remarkable prevention of adhesion formation was observed in the animals implanted with silk hydrogel coated mesh compared to the control group; in these animals peritoneal healing was complete and predominantly by mesothelial cells with minimum fibrotic changes. Expression of inflammatory cytokines decreased compared to control animals, histology of abdominal organs, haematological and blood biochemical parameters remained normal. CONCLUSION: Therefore, silk hydrogel coating of polypropylene mesh can improve peritoneal healing, minimize adhesion formation, is safe and can augment the outcome of hernia surgery.

BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types.

BARD, the BioAssay Research Database (https://bard.nih.gov/) is a public database and suite of tools developed to provide access to bioassay data produced by the NIH Molecular Libraries Program (MLP). Data from 631 MLP projects were migrated to a new structured vocabulary designed to capture bioassay data in a formalized manner, with particular emphasis placed on the description of assay protocols. New data can be submitted to BARD with a user-friendly set of tools that assist in the creation of appropriately formatted datasets and assay definitions. Data published through the BARD application program interface (API) can be accessed by researchers using web-based query tools or a desktop client. Third-party developers wishing to create new tools can use the API to produce stand-alone tools or new plug-ins that can be integrated into BARD. The entire BARD suite of tools therefore supports three classes of researcher: those who wish to publish data, those who wish to mine data for testable hypotheses, and those in the developer community who wish to build tools that leverage this carefully curated chemical biology resource.

RNAi screening identifies TAK1 as a potential target for the enhanced efficacy of topoisomerase inhibitors.

In an effort to develop strategies that improve the efficacy of existing anticancer agents, we have conducted a siRNA-based RNAi screen to identify genes that, when targeted by siRNA, improve the activity of the topoisomerase I (Top1) poison camptothecin (CPT). Screening was conducted using a set of siRNAs corresponding to over 400 apoptosisrelated genes in MDA-MB-231 breast cancer cells. During the course of these studies, we identified the silencing of MAP3K7 as a significant enhancer of CPT activity. Follow-up analysis of caspase activity and caspase-dependent phosphorylation of histone H2AX demonstrated that the silencing of MAP3K7 enhanced CPT-associated apoptosis. Silencing MAP3K7 also sensitized cells to additional compounds, including CPT clinical analogs. This activity was not restricted to MDA-MB-231 cells, as the silencing of MAP3K7 also sensitized the breast cancer cell line MDA-MB-468 and HCT-116 colon cancer cells. However, MAP3K7 silencing did not affect compound activity in the comparatively normal mammary epithelial cell line MCF10A, as well as some additional tumorigenic lines. MAP3K7 encodes the TAK1 kinase, an enzyme that is central to the regulation of many processes associated with the growth of cancer cells (e.g. NF- κB, JNK, and p38 signaling). An analysis of TAK1 signaling pathway members revealed that the silencing of TAB2 also sensitizes MDA-MB-231 and HCT-116 cells towards CPT. These findings may offer avenues towards lowering the effective doses of Top1 inhibitors in cancer cells and, in doing so, broaden their application.

A study of sexual dimorphism in permanent mandibular canines and its implications in forensic investigations.

Teeth are well preserved after death and they exhibit remarkable sexual dimorphism. Hence, they provide excellent materials for forensic investigations intended for identification of sex. Present study was undertaken on permanent mandibular canines of 90 male and 90 female subjects of age group 17-23 years. The mesiodistal width for right and left mandibular canines and intercanine distance were measured. Subsequently, canine index was calculated for both sides. Significant sexual dimorphism was found in all parameters except intercanine distance. All the results were compared with previous studies and discussed in the light of genetic, evolutionary and metabolic reasons for sexual dimporhism.

Ballistic impact of single particles into gelatin: experiments and modeling with application to transdermal pharmaceutical delivery.

The impact and penetration of high speed particles with the human skin is of interest for targeted drug delivery by transdermal powder injection. However, it is often difficult to perform penetration experiments on dermal tissue using micron scale particles. To address this, a finite element model of the impact and penetration of a 2 µm gold particle into the human dermis was developed and calibrated using experiments found in the literature. Using dimensional analysis, the model was linked to a larger scale steel ball-gelatin system in order to extract key material parameters for both systems and perform impact studies. In this manner, an elastic modulus of 2.25 MPa was found for skin, in good agreement with reported values from the literature. Further gelatin experiments were performed with steel, polymethyl methacrylate, titanium, and tungsten carbide balls in order to determine the effects of particle size and density on penetration depth. Both the finite element model and the steel-gelatin experiments were able to predict the penetration behavior that was found by other investigators in the study of the impact of typical particles used for vaccine delivery into the human dermis. It can therefore be concluded that scaled up systems utilizing ballistic gelatins can be used to investigate the performance of transdermal powder injection technology.

A morphometric study of human trachea and principal bronchi in different age groups in both sexes and its clinical implications.

An extensive morphometric study of human trachea and principal bronchi was undertaken in the Department of Anatomy, Institute of Post Graduate Medical Education and Research, Kolkata, West Bengal, India, on 87 specimens procured from 51 male and 36 female relatively disease free fresh cadavers from Kolkata Police Morgue. The specimens were grouped into five age groups for both sexes. The length of trachea, principal bronchi, subcarinal angle was measured in each specimen. The external transverse diameter (width), internal transverse diameter and anteroposterior diameter (depth) were recorded at two different levels of trachea (junction of upper third and middle third; middle third and lower third) and middle of principal bronchi. Then the width-depth ratio was calculated. For each component of the measurements, standard error (SE), standard deviation (SD) and test of significance were calculated using independent sample't' test and multiple comparison test. The present investigation revealed a wide variation in different dimensions viz. length, transverse and anteroposterior diameters and width-depth ratio of upper and lower trachea and right and left principal bronchi and the subcarinal angle, in a same age group as well as in different age groups in both sexes. The study of these morphometric variations is of profound clinical importance as it may help the clinicians to understand the etiology of several pulmonary diseases and the surgeons to deal with resection and reconstruction of the tracheobronchial tree. This knowledge is also helpful for smooth conduction of some maneuvers like endotracheal intubation and bronchoscopic procedures.

Agenesis of isthmus of thyroid gland, its embryological basis and clinical significance--a case report.

A wide range of morphological varieties and developmental anomalies of the thyroid gland have been reported in literature such as hypoplasia, ectopy, hemi agenesis, and agenesis. Out of these the incidence of agenesis of the isthmus of thyroid gland is rare and very few cases have been reported. In the present case report a male cadaver was found with agenesis of isthmus of thyroid gland with pyramidal lobe and levator glandulae thyroidae arising from right lobe.

Variation in relation of cords of brachial plexus and their branches with axillary and brachial arteries--a case report.

Anatomical variations in the formation, course and distribution of brachial plexus are well documented. The present report describes some rare variations with regard to relation of cords of brachial plexus, median and ulnar nerves with the third part of axillary artery and brachial artery in the left upper limb of an adult male cadaver. All three cords of brachial plexus were noted to be lateral to all three parts of axillary artery. Median nerve was lateral to brachial artery and ulnar nerve was between the brachial artery and median nerve. Further distribution of median and ulnar nerves was normal. The arterial pattern in left arm (axillary and brachial arteries) was also normal. The findings were noted after thorough and meticulous dissection of both the upper limbs (axilla, arm, cubital fossa, forearm and palm) of the same cadaver in the Department of Anatomy, College of Medical Sciences, Bharatpur, Nepal. The right upper limb revealed no abnormality. It is important to be aware of such variations while planning a surgery in the region of axilla and arm as these nerves are more liable to be injured during surgical procedures. Possible embryological explanations and clinical significance have been discussed.

Rare variations in the formation of median nerve--embryological basis and clinical significance.

During routine dissection in the Department of Anatomy, CMS, Nepal, anomalous median nerves with regard to their formation were found in three different adult male cadavers. In one cadaver, there was variation in the formation of the median nerve and its relation with the axillary artery. Another cadaver revealed the formation of the median nerve by three roots, while in the third one, the median nerve was found to be formed by four roots. However, in each of the three cadavers the distribution of the anomalous median nerve was normal in arm, forearm and palm. The arterial pattern in the arm (axillary and brachial arteries) was also found to be normal. In each case the opposite upper limb was also meticulously dissected to exclude bilateral abnormality. However, in each case the anomaly was unilateral. Photographs of the abnormalities were taken for proper documentation. The variations related to the formation of median nerve by more than two roots are relatively uncommon as compared to the other types of varations of median nerve. Some embryological explanations are available to explain these variations. Finally, knowledge of these variations is important particularly to the surgeons for carrying out surgical procedures in axilla and arm.