Disentangled Representation Learning and Generation With Manifold Optimization.

Disentanglement is a useful property in representation learning, which increases the interpretability of generative models such as variational autoencoders (VAE), generative adversarial models, and their many variants. Typically in such models, an increase in disentanglement performance is traded off with generation quality. In the context of latent space models, this work presents a representation learning framework that explicitly promotes disentanglement by encouraging orthogonal directions of variations. The proposed objective is the sum of an autoencoder error term along with a principal component analysis reconstruction error in the feature space. This has an interpretation of a restricted kernel machine with the eigenvector matrix valued on the Stiefel manifold. Our analysis shows that such a construction promotes disentanglement by matching the principal directions in the latent space with the directions of orthogonal variation in data space. In an alternating minimization scheme, we use the Cayley ADAM algorithm, a stochastic optimization method on the Stiefel manifold along with the Adam optimizer. Our theoretical discussion and various experiments show that the proposed model is an improvement over many VAE variants in terms of both generation quality and disentangled representation learning.

Regulatory non-coding RNAs: a new frontier in regulation of plant biology.

Beyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, the regulatory role of many non-coding RNAs (ncRNAs) in plant biology has been recognized. ncRNAs act as riboregulators by recognizing specific nucleic acid targets through homologous sequence interactions to regulate plant growth, development, and stress responses. Regulatory ncRNAs, ranging from small to long ncRNAs (lncRNAs), exert their control over a vast array of biological processes. Based on the mode of biogenesis and their function, ncRNAs evolved into different forms that include microRNAs (miRNAs), small interfering RNAs (siRNAs), miRNA variants (isomiRs), lncRNAs, circular RNAs (circRNAs), and derived ncRNAs. This article explains the different classes of ncRNAs and their role in plant development and stress responses. Furthermore, the applications of regulatory ncRNAs in crop improvement, targeting agriculturally important traits, have been discussed.

Omics resources and omics-enabled approaches for achieving high productivity and improved quality in pea (Pisum sativum L.).

Pea (Pisum sativum L.), a cool-season legume crop grown in more than 85 countries, is the second most important grain legume and one of the major green vegetables in the world. While pea was historically studied as the genetic model leading to the discovery of the laws of genetics, pea research has lagged behind that of other major legumes in the genomics era, due to its large and complex genome. The evolving climate change and growing population have posed grand challenges to the objective of feeding the world, making it essential to invest research efforts to develop multi-omics resources and advanced breeding tools to support fast and continuous development of improved pea varieties. Recently, the pea researchers have achieved key milestones in omics and molecular breeding. The present review provides an overview of the recent important progress including the development of genetic resource databases, high-throughput genotyping assays, reference genome, genes/QTLs responsible for important traits, transcriptomic, proteomic, and phenomic atlases of various tissues under different conditions. These multi-faceted resources have enabled the successful implementation of various markers for monitoring early-generation populations as in marker-assisted backcrossing breeding programs. The emerging new breeding approaches such as CRISPR, speed breeding, and genomic selection are starting to change the paradigm of pea breeding. Collectively, the rich omics resources and omics-enable breeding approaches will enhance genetic gain in pea breeding and accelerate the release of novel pea varieties to meet the elevating demands on productivity and quality.

Translational genomics for achieving higher genetic gains in groundnut.

KEY MESSAGE: Groundnut has entered now in post-genome era enriched with optimum genomic and genetic resources to facilitate faster trait dissection, gene discovery and accelerated genetic improvement for developing climate-smart varieties. Cultivated groundnut or peanut (Arachis hypogaea), an allopolyploid oilseed crop with a large and complex genome, is one of the most nutritious food. This crop is grown in more than 100 countries, and the low productivity has remained the biggest challenge in the semiarid tropics. Recently, the groundnut research community has witnessed fast progress and achieved several key milestones in genomics research including genome sequence assemblies of wild diploid progenitors, wild tetraploid and both the subspecies of cultivated tetraploids, resequencing of diverse germplasm lines, genome-wide transcriptome atlas and cost-effective high and low-density genotyping assays. These genomic resources have enabled high-resolution trait mapping by using germplasm diversity panels and multi-parent genetic populations leading to precise gene discovery and diagnostic marker development. Furthermore, development and deployment of diagnostic markers have facilitated screening early generation populations as well as marker-assisted backcrossing breeding leading to development and commercialization of some molecular breeding products in groundnut. Several new genomics applications/technologies such as genomic selection, speed breeding, mid-density genotyping assay and genome editing are in pipeline. The integration of these new technologies hold great promise for developing climate-smart, high yielding and more nutritious groundnut varieties in the post-genome era.

Basal Insulin Titration: Moving Towards a More Patient-Centric Approach with Gla-100 in India.

Owing to the progressive nature of the disease, patients with type 2 diabetes mellitus (T2DM) eventually require adjustment or titration of insulin doses to achieve the desired glycemic control. Titration inertia, or the inability to dose-titrate, is one of the key barriers to optimized insulin therapy and is common in Asian countries such as India. Simple and effective titration algorithms involving the use of basal insulin, which has the lowest hypoglycemia risk, that can be individualized by physicians and easily followed by patients aid in tackling titration inertia. In this context, insulin glargine 100 U/mL (Gla-100) appears to be the ideal insulin to overcome titration inertia, owing to its low risk of hypoglycemia and effective glycemic control. Different guidelines recommend the use of basal insulin, such as Gla-100, and encourage a patient-centric approach for dose titration. Although the effective implementation of the patient-centric approach in India is challenging, it is nevertheless achievable.

Repeated domestication of melon (Cucumis melo) in Africa and Asia and a new close relative from India.

PREMISE OF THE STUDY: The domestication history of melon is still unclear. An African or Asian origin has been suggested, but its closest wild relative was recently revealed to be an Australian species. The complicated taxonomic history of melon has resulted in additional confusion, with a high number of misidentified germplasm collections currently used by breeders and in genomics research. METHODS: Using seven DNA regions sequenced for 90% of the genus and the major cultivar groups, we sort out described names and infer evolutionary origins and domestication centers. KEY RESULTS: We found that modern melon cultivars go back to two lineages, which diverged ca. 2 million years ago. One is restricted to Asia (Cucumis melo subsp. melo), and the second, here described as C. melo subsp. meloides, is restricted to Africa. The Asian lineage has given rise to the widely commercialized cultivar groups and their market types, while the African lineage gave rise to cultivars still grown in the Sudanian region. We show that C. trigonus, an overlooked perennial and drought-tolerant species from India is among the closest living relatives of C. melo. CONCLUSIONS: Melon was domesticated at least twice: in Africa and Asia. The African lineage and the Indian C. trigonus are exciting new resources for breeding of melons tolerant to climate change.

A Spectrum of Chemoport-Associated Complications and Their Management in Cancer Patients.

INTRODUCTION: Chemotherapy is part and parcel of the multimodality approach to cancer treatment. Chemoports are frequently used to administer chemotherapy, preventing complications associated with the use of peripheral lines. However, chemoports have their own set of complications and can be very debilitating at times. Accurate knowledge and correct technique can help prevent and manage these complications properly. METHODS: We retrospectively analyzed all patients who underwent chemoport insertion for chemotherapy infusion over three years between July 2020 and June 2023. The patient's profile, type of cancer, the technique of chemoport insertion, complications related to chemoport, and its management were recorded retrospectively from patient records. RESULTS: The total number of patients in our study was 119. The age group of patients ranged from 13 years to 76 years. Of the 119 patients, 55 had breast cancer, 23 had ovarian cancers, 29 had GI cancers including gastroesophageal junction (GEJ)/ stomach/periampullary/colorectal, and 12 had leukemias. The most common intraoperative complication was catheter tip malposition (9.2%). The most common postoperative complications were infection (7.5%), followed by drug extravasation (5.0%), thrombosis (3.3%), wound dehiscence (2.5%), and skin necrosis (0.8%) in decreasing order of frequency. Serious complications such as hemothorax, pneumothorax, air emboli, brachial plexus injury, and pericardial tamponade, commonly reported in the literature, were not seen in any of our cases. CONCLUSION:  Totally implanted venous access devices (TIVAD)/chemoports are indispensable in the management of cancer patients, especially in patients requiring long duration of infusion and prolonged treatment. Although chemoports are associated with a spectrum of complications, proper technique of implantation and use makes it a safe and reliable tool.

The immediate impact of mandatory helmet law on maxillo-facial trauma: A comparative study in a major trauma center, Uttar Pradesh.

Aim: To analyze the effect of the mandatory helmet rule in helmet usage among motorcycle riders and on facial trauma and to determine the significance of difference in the possibility of facial trauma between the helmeted and non-helmeted motorcycle riders. Setting and Design: A retrospective comparative study conducted in a major trauma center at Uttar Pradesh. Material and Method: Data for the present study was obtained from records of the Emergency Department of Trauma Center, for a period of two months before and after the implementation of The Motor Vehicles Act in UP. The study included patients with a history of non-fatal motorcycle accidents who sustained facial injuries regardless of the presence of injuries to other areas of the body during the study period. Information regarding helmet usage during the accident was also recorded. The results were compared between the pre-law period and post-law period. Statistical Analysis Used: Sample t-test was applied to find the level of significance. Results: Out of 219 injured patients, 152 (69.40%) subjects were not wearing helmets, whereas only 67 (30.59%) subjects were wearing helmets. It was observed that around 68.18% of people stated wearing helmets after law implementation with a statistical significance (P value < 0.05). Conclusion: Our study shows that the mandatory helmet rule with elevated penalty rates has significantly increased the usage of helmet among the motorcycle riders, and it also proves that the possibility of facial trauma is significantly higher in non-helmeted riders when compared to helmeted riders.

A novel case of left atrial and right lung mass turned out to be unconventional metastasis of uterine leiomyosarcoma with a review of literature.

Uterine leiomyosarcoma (ULMS) is a rare malignancy arising from the myometrial smooth muscle wall, and cardiac metastases are extremely rare. Metastasis to the heart is a very unusual finding, and atrial metastasis is even rarer. Here, we report a case of a 45 year old woman who presented with dyspnea and pleural effusion and had a significant history of hysterectomy done for ULMS. Magnetic resonance imaging revealed a left atrial mass, which was resected and revealed to be a metastasis of leiomyosarcoma on histopathology and immunohistochemistry. Metastatic ULMS may rarely present as a left atrial mass with acute clinical presentation. Detailed clinical history and accurate diagnosis are vital for further management.

Bipaddled Pectoralis Major Myocutaneous Flap in Complex Oral Cancer Defects- A Single Center Experience with Quality of Life Assessment.

Introduction: Advanced stage malignancies of oral cavity commonly result in complex full thickness defects with subsequent functional and aesthetic loss. Through this article we describe our center's experience in reconstruction of such defects with bipaddled pectoralis myocutaneous (PMMC) flap through an immediate, single-staged procedure. Materials And Methods: The study included a total of 54 patients who underwent composite resection and neck dissection followed by reconstruction of the defect with bipaddled PMMC flap. All patients were followed up post-operatively for 1 year and were monitored for flap and donor site related complications. Using University of Washington Quality of life v4 questionnaire (UW-QOL4), we assessed the QOL of 54 patients. The mean scores were compared to other similar studies. Results: The overall complication rate was 66.6%, whereas, 33.3% patients had no complications. The most common complication was wound dehiscence seen in 31.5% of cases in the recipient site and 12.9% in the donor site. Other complications were seroma, hematoma, plate exposure, orocutaneous fistula etc. Around 73.7% patients reported a good, very good or outstanding overall quality of life in the post-operative period. The mean composite QOL score was 65.84. Our study showed comparable domains of pain, appearance, activity, recreation, swallowing, chewing, speech, shoulder function and taste with other similar studies. Conclusion: Bipaddled PMMC flap proves to be a considerable alternative for microvascular free flaps in reconstruction of full-thickness defects of oral cavity owing to its reliable blood supply, accessibility, easier harvesting technique, cost effectiveness, high success rate and acceptable quality of life. Supplementary Information: The online version contains supplementary material available at 10.1007/s12070-022-03324-6.

Prevalence and Patterns of Nodal Metastasis Among Oral Cavity Cancer Patients: A Prospective Observational Study.

Introduction: Lip and oral cavity cancer remains the most common cancer among Indian males and third most common cause of cancer-related deaths in India. Cervical lymph node metastasis is one of the most important prognostic factors in oral cavity cancer. The aim of present study was to estimate the prevalence of nodal involvement and analyse patterns of nodal metastasis in oral cavity cancer patients. Methods: This prospective observational study was conducted between January 2019 and June 2020. Patients of oral cavity squamous cell carcinoma undergoing surgery with simultaneous neck dissection were included. Data pertaining to the clinical profile, treatment and histology details were collected and analysed. Results: A total of 63 patients were included in present study. Out of 63 patients, unilateral neck dissection was performed in 47 (75%), while 16 (25%) underwent bilateral neck dissection. Overall clinical and pathological nodal positivity rates were 75% and 52%, respectively. Level I (48%) followed by IIa (20%) were most commonly involved stations. Combined involvement of level IV and V was seen in only 5%, and no skip metastasis was reported in level IV and V. Conclusion: Level I and II are the most commonly involved stations in oral cavity squamous cell carcinoma (SCC). Oral SCC has a predictable nodal spread pattern with no skip metastasis to level IV/V noted in present study. There is a need for good quality randomised control trials to optimise the treatment protocols in clinically node-positive patients with respect to level IIB and V dissection.

Transcriptome Dynamics of Common Bean Roots Exposed to Various Heavy Metals Reveal Valuable Target Genes and Promoters for Genetic Engineering.

Understanding the gene regulatory basis of plant response to heavy metals (HMs) is fundamental for the management of food safety and security. However, a comprehensive and comparative view of the plant responses to different HMs is still lacking. Here, we compared root transcriptomes in common bean under 9 HM treatments at 50 µM for three time points each. Cd, Cr, Co, Ni, and Pb caused most severe morphological and/or biochemical retardations. A total of 448 genes were found to be responsive to all nine HMs, which were mostly involved in photosynthesis, oxidization-reduction, and ion binding. Cd and Cu triggered the greatest number of unique differentially expressed genes (DEG)s, which were predominantly related to cellular transport/localization in the former and RNA binding in the latter. Short-term and prolonged HM treatments shaped very different DEG patterns. Weighted gene co-expression network analysis identified six co-expression modules showing exceptionally high transcripts abundance in specific HM × time scenarios. We experimentally verified the promoter activity of the gene GIP1 and the novel function of XTH23 under Cu/Cd stress. Collectively, the transcriptomic atlas provides valuable resources for better understanding the common and unique mechanisms of plant response to different HMs and offers a mass of candidate target genes/promoters for genetic engineering.

Understanding water conservation vs. profligation traits in vegetable legumes through a physio-transcriptomic-functional approach.

Vegetable soybean and cowpea are related warm-season legumes showing contrasting leaf water use behaviors under similar root drought stresses, whose mechanisms are not well understood. Here we conducted an integrative phenomic-transcriptomic study on the two crops grown in a feedback irrigation system that enabled precise control of soil water contents. Continuous transpiration rate monitoring demonstrated that cowpea used water more conservatively under earlier soil drought stages, but tended to maintain higher transpiration under prolonged drought. Interestingly, we observed a soybean-specific transpiration rate increase accompanied by phase shift under moderate soil drought. Time-series transcriptomic analysis suggested a dehydration avoidance mechanism of cowpea at early soil drought stage, in which the VuHAI3 and VuTIP2;3 genes were suggested to be involved. Multifactorial gene clustering analysis revealed different responsiveness of genes to drought, time of day and their interactions between the two crops, which involved species-dependent regulation of the circadian clock genes. Gene network analysis identified two co-expression modules each associated with transpiration rate in cowpea and soybean, including a pair of negatively correlated modules between species. Module hub genes, including the ABA-degrading gene GmCYP707A4 and the trehalose-phosphatase/synthase gene VuTPS9 were identified. Inter-modular network analysis revealed putative co-players of the hub genes. Transgenic analyses verified the role of VuTPS9 in regulating transpiration rate under osmotic stresses. These findings propose that species-specific transcriptomic reprograming in leaves of the two crops suffering similar soil drought was not only a result of the different drought resistance level, but a cause of it.

Effects of curcumin on oral cancer at molecular level: A systematic review.

This systematic review mainly focuses on the effects of curcumin on oral cancer cells at the molecular level and summarizes the results of the studies. We searched and analyzed various databases such as Pub Med, ProQuest, Google Scholar, Science Direct, and Scopus. Searches were conducted from 2006 to 2021. This systematic review evaluated various effects of curcumin on oral cancer at the molecular level. All the studies related to the effects of curcumin on oral cancer, both in-vivo and in-vitro, were included. After abstract and text screening a total of 13 articles were finally selected for the study based on the inclusion and exclusion criteria. All most all the included studies reported that after treating the cell lines with curcumin there is a reduction in cell proliferation and cell growth, analyzed using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) assay. Curcumin also induces S phase cell cycle arrest and also prevents Tregs migration. The curcumin reverses the process of epithelial mesenchymal transition (EMT) back to mesenchymal epithelial transition (MET). From this review, it is concluded that curcumin inhibited proliferation, migration, invasion, and metastasis, and induced apoptosis via modulating multiple signaling pathways in oral cancer cell lines. But further clinical trials are needed for a detailed evaluation of the effects of curcumin on patients with oral cancer.

Prospects for developing allergen-depleted food crops.

In addition to the challenge of meeting global demand for food production, there are increasing concerns about food safety and the need to protect consumer health from the negative effects of foodborne allergies. Certain bio-molecules (usually proteins) present in food can act as allergens that trigger unusual immunological reactions, with potentially life-threatening consequences. The relentless working lifestyles of the modern era often incorporate poor eating habits that include readymade prepackaged and processed foods, which contain additives such as peanuts, tree nuts, wheat, and soy-based products, rather than traditional home cooking. Of the predominant allergenic foods (soybean, wheat, fish, peanut, shellfish, tree nuts, eggs, and milk), peanuts (Arachis hypogaea) are the best characterized source of allergens, followed by tree nuts (Juglans regia, Prunus amygdalus, Corylus avellana, Carya illinoinensis, Anacardium occidentale, Pistacia vera, Bertholletia excels), wheat (Triticum aestivum), soybeans (Glycine max), and kidney beans (Phaseolus vulgaris). The prevalence of food allergies has risen significantly in recent years including chance of accidental exposure to such foods. In contrast, the standards of detection, diagnosis, and cure have not kept pace and unfortunately are often suboptimal. In this review, we mainly focus on the prevalence of allergies associated with peanut, tree nuts, wheat, soybean, and kidney bean, highlighting their physiological properties and functions as well as considering research directions for tailoring allergen gene expression. In particular, we discuss how recent advances in molecular breeding, genetic engineering, and genome editing can be used to develop potential low allergen food crops that protect consumer health.

Autoreconstruction of the tongue in case of extensive verrucous carcinoma.

Tongue reconstruction can be simple to complex depending on the size of the defect. Reconstruction of medium-to-large size defect is technically demanding to achieve better esthetic and functional outcome. There are various options in the reconstruction of tongue defect when it comes to the type of flap. Any type of flap has its own advantages and disadvantages. Local flaps seem to be the best option, as it avoids secondary donor site morbidity and has similar tissue characteristics as native tissue, therefore provides better esthetic and functional results. This case report illustrates a case of tongue reconstruction that was performed with the help of tongue base island flap after wide local excision of verrucous carcinoma, which provided us with excellent results.

Sustainable and green manufacturing of gravure printing cylinder for flexible packaging printing application.

Rotogravure printing cylinders are engraved by electro-mechanical engraving (EME) process in India used for printing purpose. But this process has drawbacks of the emissions of hazardous gases, solid and water pollution. EME cylinders are better in cell size, depth and needed higher copper and chrome plating thickness. By laser engraving (LE) copper and chromium thickness were reduced by 75 µm and 5 µm in a cylinder by laser engraving with also a reduction in power consumption and plating time. The carbon footprints were also reduced by 227 g per cylinder with a cost-effective solution for rotogravure printing process.

Phylogenetic relationships of Indian Memecylon L. (Melastomataceae) based on nrDNA ITS and cpDNA rbcL sequence data.

Memecylon (Melastomaceae) is a large genus of the Old-World predominantly woody species. Many species of Memecylon are used for timber, ornamental and medicinal purposes. The objective of the present study was to undertake a phylogenetic analysis of Indian Memecylon based on nuclear ribosomal DNA internal transcribed spacer (nrDNA-ITS) and rbcL sequence data. Sampling included 26 species and one variety (20 endemics) representing 67% of the total Indian species. Molecular phylogeny data for analysed species revealed that the Indian Memecylon is monophyletic. Monophyly is strongly supported in the ITS, rbcL and ITS + rbcL combined analyses. Memecylon species are grouped in a major clade with strong support in ITS sequence data and moderate support in combined ITS + rbcL analyses.

Systematic Review of Intra Parotid Facial Nerve Schwannoma and a Case Report.

To evaluate the clinico-epidemiological aspects, pathological features, diagnostic methods, management protocol and functional outcome of the intra-parotid facial nerve schwannoma (IFNS) and to present a case report on intra parotid facial nerve schwannoma. PubMed, ProQuest, Google scholar, Science direct and Scopus were screened for studies. Article selection and data extraction was done by one investigator and other investigator confirmed its accuracy. After abstract and text screening a total of 69 articles were finally selected for the study with the inclusion and exclusion criteria of the systematic review as per PRISMA guidelines. With addition of one case reported to our department. The mean age of diagnosis was 43 ± 16 years with a slight female predominance. The mean duration of the tumour was 29.5 months and the mean size of the tumour on initial diagnosis was 3.6 ± 1.67 cm. Pleomorphic adenoma was the primary diagnosis in 44 cases. Superficial parotidectomy was done in 64 cases followed by resection in 47 cases. Reconstructive treatment was carried out by an end-to-end anastomosis in 3 patients and by facial-hypoglossal anastomosis in 16 patients, GAN cable grafting in 5 patients, a greater auricular nerve graft was done in18 patients and end-to-side interposed sural nerve graft in 8 patients. The type D tumours are treated by extended resection of the facial nerve, which is difficult to reconstruct and also employs a nerve graft that does not often give acceptable recovery of facial function. Facial nerve schwannomas being a rare entity poses a dilemma in diagnosis and management. Managing the lesions is also difficult as intraoperative adherence to the nerve makes a tumour free margin difficult without sacrificing the nerve. At present there is no consensus regarding the management of various types of intra-parotid facial nerve shwannoma.

The Anatomical Basis of Heavy Metal Responses in Legumes and Their Impact on Plant-Rhizosphere Interactions.

Rapid industrialization, urbanization, and mine tailings runoff are the main sources of heavy metal contamination of agricultural land, which has become one of the major constraints to crop growth and productivity. Finding appropriate solutions to protect plants and agricultural land from heavy metal pollution/harmful effects is important for sustainable development. Phytoremediation and plant growth-promoting rhizobacteria (PGPR) are promising methods for this purpose, which both heavily rely on an appropriate understanding of the anatomical structure of plants. Specialized anatomical features, such as those of epidermis and endodermis and changes in the root vascular tissue, are often associated with heavy metal tolerance in legumes. This review emphasizes the uptake and transport of heavy metals by legume plants that can be used to enhance soil detoxification by phytoremediation processes. Moreover, the review also focuses on the role of rhizospheric organisms in the facilitation of heavy metal uptake, the various mechanisms of enhancing the availability of heavy metals in the rhizosphere, the genetic diversity, and the microbial genera involved in these processes. The information presented here can be exploited for improving the growth and productivity of legume plants in metal-prone soils.