Mining genomic regions associated with agronomic and biochemical traits in quinoa through GWAS.

Quinoa (Chenopodium quinoa Willd.), an Andean crop, is a facultative halophyte food crop recognized globally for its high nutritional value and plasticity to adapt to harsh conditions. We conducted a genome-wide association study on a diverse set of quinoa germplasm accessions. These accessions were evaluated for the following agronomic and biochemical traits: days to 50% flowering (DTF), plant height (PH), panicle length (PL), stem diameter (SD), seed yield (SY), grain diameter (GD), and thousand-grain weight (TGW). These accessions underwent genotyping-by-sequencing using the DNBSeq-G400R platform. Among all evaluated traits, TGW represented maximum broad-sense heritability. Our study revealed average SNP density of ≈ 3.11 SNPs/10 kb for the whole genome, with the lowest and highest on chromosomes Cq1B and Cq9A, respectively. Principal component analysis clustered the quinoa population in three main clusters, one clearly representing lowland Chilean accessions, whereas the other two groups corresponded to germplasm from the highlands of Peru and Bolivia. In our germplasm set, we estimated linkage disequilibrium decay to be ≈ 118.5 kb. Marker-trait analyses revealed major and consistent effect associations for DTF on chromosomes 3A, 4B, 5B, 6A, 7A, 7B and 8B, with phenotypic variance explained (PVE) as high as 19.15%. Nine associations across eight chromosomes were also found for saponin content with 20% PVE by qSPN5A.1. More QTLs were identified for PL and TGW on multiple chromosomal locations. We identified putative candidate genes in the genomic regions associated with DTF and saponin content. The consistent and major-effect genomic associations can be used in fast-tracking quinoa breeding for wider adaptation across marginal environments.

Seafloor primary production in a changing Arctic Ocean.

Phytoplankton and sea ice algae are traditionally considered to be the main primary producers in the Arctic Ocean. In this Perspective, we explore the importance of benthic primary producers (BPPs) encompassing microalgae, macroalgae, and seagrasses, which represent a poorly quantified source of Arctic marine primary production. Despite scarce observations, models predict that BPPs are widespread, colonizing ~3 million km2 of the extensive Arctic coastal and shelf seas. Using a synthesis of published data and a novel model, we estimate that BPPs currently contribute ~77 Tg C y-1 of primary production to the Arctic, equivalent to ~20 to 35% of annual phytoplankton production. Macroalgae contribute ~43 Tg C y-1, seagrasses contribute ~23 Tg C y-1, and microalgae-dominated shelf habitats contribute ~11 to 16 Tg C y-1. Since 2003, the Arctic seafloor area exposed to sunlight has increased by ~47,000 km2 y-1, expanding the realm of BPPs in a warming Arctic. Increased macrophyte abundance and productivity is expected along Arctic coastlines with continued ocean warming and sea ice loss. However, microalgal benthic primary production has increased in only a few shelf regions despite substantial sea ice loss over the past 20 y, as higher solar irradiance in the ice-free ocean is counterbalanced by reduced water transparency. This suggests complex impacts of climate change on Arctic light availability and marine primary production. Despite significant knowledge gaps on Arctic BPPs, their widespread presence and obvious contribution to coastal and shelf ecosystem production call for further investigation and for their inclusion in Arctic ecosystem models and carbon budgets.

Detecting topological index of randomly scattered V-point singularities using Stokes correlations.

Topological defects in vector fields constitute polarization singularities that have numerous applications in classical and quantum optics. These beams are inhomogeneously polarized and are shown to self-heal under symmetric amplitude perturbations. Polarization singular beams are characterized using a singularity index that can be detected using Stokes polarimetry or other interferometric and diffraction approaches. However, the information about the singularity index is lost when these beams travel through random scattering media; this results in a spatially fluctuating polarization pattern known as polarization speckle. This paper proposes and experimentally demonstrates a new method to detect the topological index of these randomly scattered V-point singularities using higher-order Stokes correlations in a lensless condition. A detailed theoretical basis is developed, and the performance of the technique is demonstrated by retrieving the signature of polarization singularities with Poincaré-Hopf index |η|=1 and |η|=2. We also demonstrate that by studying the intensity-intensity correlations of the polarization speckle, it is possible to differentiate between different vector beams having the same magnitude as the Poincaré-Hopf index.

Folded interferometer to measure coherence-polarization matrix.

We present and experimentally demonstrate a new, to the best of our knowledge, technique to quantitatively measure coherence-polarization (BCP) matrix with correlations of only two Stokes fluctuations. The BCP matrix is a square matrix with four elements that involves two-point correlations among orthogonal polarization components. A theoretical framework of the technique is developed, and its viability is demonstrated by a proof of principle experiment. Experimental tests and measurement of the elements of the BCP matrix of statistically stationary beams are demonstrated.

Neuroprotective responses of quercetin in regulation of biochemical, structural, and neurobehavioral effects in 28-day oral exposure of iron in rats.

BACKGROUND: Iron is one of the essential metals that functions as a cofactor in various biological cascades in the brain. However, excessive iron accumulation in the brain may lead to neurodegeneration and may show toxic effects. Quercetin, a pigment flavonoid compound, has been proven to be a potent antioxidant and anti-inflammatory that can inhibit lipid peroxidation during metal-induced neurotoxicity. Although iron-induced neuroinflammation and neurodegeneration have been reported in many studies, but the proof for its exact mechanisms needs to be explored. PURPOSE: The key target of the study was to explore the neuroprotective effect of quercetin after oral exposure of iron in rats and explore its underlying molecular mechanisms. RESULTS: The outcomes of the study have shown that oral exposure to ferrous sulfate may modulate behavioral paradigms such as locomotor activity, neuromuscular coordination, and increased anxiety level. The pro-inflammatory cytokines (TNF-α, IL-1ß and IL-6), apoptotic protein (caspase 3), beta-amyloid and phosphorylated tau were found to be increased on iron exposure. Also, the expressions of ferritin heavy and light chain, BACE-1 and GFAP expressions were altered. These behavioral, structural, and biochemical alterations in the brain were significantly and dose-dependently reversed by treatment with quercetin. CONCLUSION: The current study provides a fundamental understanding of molecular signaling pathways, and structural proteins implicated in iron-induced neurotoxicity along with the ameliorative effects of quercetin.

C2 Superior Facetal Osteotomy: A Novel Technique in Complex Craniovertebral Junction Surgery for C1 Lateral Mass Screw Placement.

Complex craniovertebral junction (CVJ) defects account for a considerable proportion of CVJ diseases. Given the heavily assimilated C1, an unfavorable C1-C2 joint orientation, an overriding C2 superior facet, a low-hanging occiput, and an abnormal vertebral artery course with a high-riding vertebral artery, placement of C1 lateral mass screws might be difficult. To address this, a novel technique for placing C1 lateral mass screws that avoid vertebral artery injury, low-hanging occiput, and overriding C2 superior facet was developed in this study. This approach enables firm fixation of C1-C2 even in difficult situations where the placement of the C1 lateral mass is challenging.

The Effect of Sepsis and Septic Shock on the Viscoelastic Properties of Clot Quality and Mass Using Thromboelastometry: A Prospective Observational Study.

Background: Sepsis is associated with wide variable coagulation abnormalities. Thromboelastography (TEG) effectively measures the viscoelastic properties of the clots. This study aims to illustrate the viscoelastic properties of clot quality and mass in sepsis and septic shock patients using TEG, as an effective tool over standard coagulation tests. Materials and methods: A single-center, prospective observational study was conducted. 50 patients each meeting the criteria for sepsis and septic shock, and a healthy group of 30 patients was included in the study. Blood samples were obtained and analyzed for standard coagulation tests, platelet count, fibrinogen, and TEG study. Results: A total of 130 patients were included. Septic shock patients had a higher sequential (sepsis-related) organ failure score. Prothrombin time (PT) and activated partial thromboplastin time (aPTT) were increased significantly as compared to the sepsis and control groups. TEG markers such as alpha angle, and maximum amplitude (MA) were significantly prolonged while reaction time (R time), was significantly shortened in the sepsis group as compared to the healthy group, suggestive of a hypercoagulable state in sepsis patients. While in septic shock patients, MA and Lysis Index 30 (LY 30) were significantly prolonged and, R time was significantly shortened compared to all other groups. Even though LY30 in sepsis patients was found to be within the normal range (p < 0.001), 18% of patients had prolonged LY30 indicating a hypercoagulable state with impaired fibrinolysis. Conclusion: Thromboelastography, as a point-of-care test combined with conventional coagulation tests can provide additional, clinically relevant information on coagulopathy, and outcome, and thus help guide treatment modality in sepsis and septic shock-induced coagulopathy. How to cite this article: Mohapatra P, Kumar A, Singh RK, Gupta R, Hussain M, Singh S, et al. The Effect of Sepsis and Septic Shock on the Viscoelastic Properties of Clot Quality and Mass Using Thromboelastometry: A Prospective Observational Study. Indian J Crit Care Med 2023;27(9):625-634.

Isolation and characterization of a novel mycobacteriophage Kashi-VT1 infecting Mycobacterium species.

Mycobacteriophages are viruses that infect members of genus Mycobacterium. Because of the rise in antibiotic resistance in mycobacterial diseases such as tuberculosis, mycobacteriophages have received renewed attention as alternative therapeutic agents. Mycobacteriophages are highly diverse, and, on the basis of their genome sequences, they are grouped into 30 clusters and 10 singletons. In this article, we have described the isolation and characterization of a novel mycobacteriophage Kashi-VT1 (KVT1) infecting Mycobacterium >smegmatis mc2 155 (M. smegmatis) and Mycobacterium fortuitum isolated from Varanasi, India. KVT1 is a cluster K1 temperate phage that belongs to Siphoviridae family as visualized in transmission electron microscopy. The phage genome is 61,010 base pairs with 66.5% Guanine/Cytosine (GC) content, encoding 101 putative open reading frames. The KVT1 genome encodes an immunity repressor, a tyrosine integrase, and an excise protein, which are the characteristics of temperate phages. It also contains genes encoding holin, lysin A, and lysin B involved in host cell lysis. The one-step growth curve demonstrated that KVT1 has a latency time of 90 min and an average burst size of 101 phage particles per infected cell. It can withstand a temperature of up to 45°C and has a maximum viability between pH 8 and 9. Some mycobacteriophages from cluster K are known to infect the pathogenic Mycobacterium tuberculosis (M. tuberculosis); hence, KVT1 holds potential for the phage therapy against tuberculosis, and it can also be engineered to convert into an exclusively lytic phage.

Randomness assisted in-line holography with deep learning.

We propose and demonstrate a holographic imaging scheme exploiting random illuminations for recording hologram and then applying numerical reconstruction and twin image removal. We use an in-line holographic geometry to record the hologram in terms of the second-order correlation and apply the numerical approach to reconstruct the recorded hologram. This strategy helps to reconstruct high-quality quantitative images in comparison to the conventional holography where the hologram is recorded in the intensity rather than the second-order intensity correlation. The twin image issue of the in-line holographic scheme is resolved by an unsupervised deep learning based method using an auto-encoder scheme. Proposed learning technique leverages the main characteristic of autoencoders to perform blind single-shot hologram reconstruction, and this does not require a dataset of samples with available ground truth for training and can reconstruct the hologram solely from the captured sample. Experimental results are presented for two objects, and a comparison of the reconstruction quality is given between the conventional inline holography and the one obtained with the proposed technique.

Development of a phenotyping protocol for combined drought and salinity stress at seedling stage in rice.

Introduction: The case of combined drought and salinity stress is increasingly becoming a constraint to rice production, especially in coastal areas and river deltas where low rainfall not only reduces soil moisture levels but also reduces the flow of river water, resulting in intrusion of saline sea-water. A standardized screening method is needed in order to systematically evaluate rice cultivars under combined drought+salinity at the same time because sequential stress of salinity followed by drought or vice-versa is not similar to simultaneous stress effects. Therefore, we aimed to develop a screening protocol for combined drought+salinity stress applied to soil-grown plants at seedling stage. Methods: The study system used 30-L soil-filled boxes, which allowed a comparison of plant growth under control conditions, individual drought and salinity stress, as well as combined drought+salinity. A set of salinity tolerant and drought tolerant cultivars were tested, together with several popular but salinity and drought-susceptible varieties that are grown in regions prone to combined drought+salinity. A range of treatments were tested including different timings of the drought and salinity application, and different severities of stress, in order to determine the most effective that resulted in visible distinction among cultivars. The challenges related to determining a protocol with repeatable seedling stage stress treatment effects while achieving a uniform plant stand are described here. Results: The optimized protocol simultaneously applied both stresses by planting into saline soil at 75% of field capacity which was then allowed to undergo progressive drydown. Meanwhile, physiological characterization revealed that chlorophyll fluorescence at seedling stage correlated well with grain yield when drought stress was applied to vegetative stage only. Discussion: The drought+salinity protocol developed here can be used for screening rice breeding populations as part of a pipeline to develop new rice varieties with improved adaptation to combined stresses.

Hanbury Brown-Twiss approach for imaging through a dynamic scattering medium.

The Hanbury Brown-Twiss approach, associated with the correlation of intensity fluctuations at two different points in a wave field, unveils fundamental aspects of light. Here, we propose and experimentally demonstrate an imaging and phase recovery technique through a dynamic scattering medium using the Hanbury Brown-Twiss approach. A detailed theoretical basis is presented and verified by experimental demonstrations. To validate the application of the proposed technique, the randomness of the dynamically scattered light is exploited using temporal ergodicity for evaluating the correlation of intensity fluctuations and consequently applying it in the reconstruction of the object hidden behind the dynamic diffuser.

Solid Pseudopapillary Neoplasm of the Pancreas: A Single-Center Experience of a Rare Neoplasm.

BACKGROUND: Solid pseudopapillary neoplasm (SPN) of the pancreas is an extremely rare pancreatic exocrine tumor. The study aims to report our experience with the SPN of the pancreas. METHODS: A retrospective analysis of the prospectively maintained database was carried out of all the cases diagnosed and treated as SPN between January 2019 and January 2023. Patient characteristics including age, gender, clinical presentation, laboratory examinations, imaging features, surgical details, and histopathological and immunohistochemistry details were analyzed. RESULTS: During this period, eight cases were diagnosed with SPN. All patients were female with a median age of 25.75 years (range 14-55 years). All cases presented with pain in the abdomen, and four patients had a mass per abdomen. In all the cases, contrast-enhanced computed tomography (CECT) abdomen was done for the diagnosis and had preoperative suspicion of the pseudopapillary tumor. In four cases, the tumor was located in the head region, while in four cases, the tumor was in the body and tail of the pancreas. The median size of the tumor was 12 cm (range 3.5-15 cm). Three cases underwent Whipple's procedure and one patient was unresectable. Two out of four patients with body and tail tumors underwent distal pancreatectomy with splenectomy, one underwent spleen-preserving distal pancreatectomy, and one patient underwent central pancreatectomy. CONCLUSION: SPN is a rare neoplasm that primarily affects young women. Clinicopathologic and immunohistochemical features are diagnostic. Surgical resection is generally curative with a good long-term outcome.

Monoclonal antibodies for the management of central nervous system diseases: clinical success and future strategies.

INTRODUCTION: Recombinant monoclonal antibodies (mAbs) are highly selective and effective biologicals with proven utility as therapeutics. mAbs have demonstrated substantial promise in the treatment of several central nervous system diseases. AREAS COVERED: Databases including PubMed and Clinicaltrials.gov were used to identify clinical studies of mAbs involving patients with neurological disorders. This manuscript reviews the current status and recent advances in the development and engineering of therapeutic blood-brain barrier (BBB)-crossing mAbs and their potential in treatment of central nervous system diseases, such as Alzheimer's disease (AD), Parkinson's disease (PD), brain tumors, and neuromyelitis optica spectrum disorder (NMSOD). In addition, the clinical implications of recently developed monoclonal antibodies are also discussed, along with the strategies to enhance their BBB permeability. The adverse events associated with the administration of monoclonal antibodies are also presented in the manuscript. EXPERT OPINION: There is growing evidence that supports the therapeutic utility of monoclonal antibodies in central nervous system and neurodegenerative diseases. Several studies have offered evidence of clinical efficacy in AD through use of anti-amyloid beta antibodies and anti-tau passive immunotherapy-based strategies. Additionally, ongoing research trials have produced promising findings for the treatment of brain tumors and NMSOD.

Roflumilast Protects against Neuroinflammatory Alterations in Brain Tissues of Lipopolysaccharide-induced Mice Model.

BACKGROUND: Microglial overactivation promotes the production of various second messengers and inflammatory markers in brain tissue, resulting in neuroinflammation and neurodegeneration, which may lead to cognitive decline. The cyclic nucleotides are one of the important second messengers involved in the regulation of neurogenesis, synaptic plasticity, and cognition. The levels of these cyclic nucleotides are maintained by phosphodiesterase enzyme isoforms, particularly PDE4B, in the brain. An imbalance between PDE4B levels and cyclic nucleotides may lead to aggravating neuroinflammation. METHODS: Lipopolysaccharides (LPS) were administered intraperitoneally on alternate days for 7 days at a dose of 500 µg/kg in mice, which triggered systemic inflammation. This may lead to the activation of glial cells and may activate oxidative stress and neuroinflammatory markers in brain tissue. Furthermore, oral administration of roflumilast (0.1, 0.2, and 0.4 mg/kg) in this model ameliorated oxidative stress markers, neuroinflammation and improved neurobehavioral parameters in these animals. RESULTS: The detrimental effect of LPS increased oxidative stress, AChE enzyme levels, and decreased catalase levels in brain tissues, along with memory impairment in animals. Moreover, it also enhanced the activity and expression of the PDE4B enzyme, resulting in a decline in cyclic nucleotide levels. Furthermore, treatment with roflumilast improved the cognitive decline, decreased AChE enzyme level, and increased the catalase enzyme level. Roflumilast also reduced the PDE4B expression in a dose-dependent manner, which LPS up-regulated. CONCLUSION: Roflumilast has shown an anti-neuroinflammatory effect and reversed the cognitive decline in LPS-induced mice model.

Assessment of Pulmonary Hypertension in Chronic Kidney Disease Patients using Doppler Echocardiography.

Background: The incidence of chronic kidney disease (CKD) is increasing globally and is associated with significant morbidity and mortality related to the cardiovascular system. There is limited data on pulmonary hypertension (PH) in CKD patients, especially from developing and underdeveloped countries. PH leads to hypoxia which is a significant cause of dyspnea in CKD patients with or without pulmonary edema. Hence, we planned this study to assess the PH in CKD patients using two-dimensional (2D) color Doppler echocardiography. Materials and Methods: This is an observational cross-sectional study. A total of 100 CKD patients on hemodialysis or conservative management were enrolled in the study. Following the collection of demographic data, and routine/specific investigations, these patients were assessed for PH using 2D color Doppler echocardiography. Results: PH was found in 47% of patients with CKD. Left ventricular (LV) hypertrophy, systolic and diastolic dysfunction, dilated right atrium/right ventricular and left atrial/LV chambers, and valvular hypertrophy were other echocardiography findings recorded in these patients. Low hemoglobin levels, high urea/creatinine levels, and duration of hemodialysis in CKD patients were found to be significantly associated with the presence of PH. Conclusion: The majority of CKD patients have PH at various stages of disease-causing unexplained dyspnea in these patients. PH is common in end-stage CKD as compared to patients with a less severe stage of CKD. Hence, CKD patients should be evaluated for PH, especially in the presence of intractable dyspnea.

Rice husk biochar - A novel engineered bio-based material for transforming groundwater-mediated fluoride cycling in natural environments.

Biochar, a promising carbon-rich and carbon-negative material, can control water pollution, harness the synergy of sustainable development goals, and achieve circular economy. This study examined the performance feasibility of treating fluoride-contaminated surface and groundwater using raw and modified biochar synthesized from agricultural waste rice husk as problem-fixing renewable carbon-neutral material. Physicochemical characterizations of raw/modified biochars were investigated using FESEM-EDAX, FTIR, XRD, BET, CHSN, VSM, pHpzc, Zeta potential, and particle size analysis were analyzed to identify the surface morphology, functional groups, structural, and electrokinetic behavior. In fluoride (F-) cycling, performance feasibility was tested at various governing factors, contact time (0-120 min), initial F- levels (10-50 mg L-1), biochar dose (0.1-0.5 g L-1), pH (2-9), salt strengths (0-50 mM), temperatures (301-328 K), and various co-occurring ions. Results revealed that activated magnetic biochar (AMB) possessed higher adsorption capacity than raw biochar (RB) and activated biochar (AB) at pH 7. The results indicated that maximum F- removal (98.13%) was achieved using AMB at pH 7 for 10 mg L-1. Electrostatic attraction, ion exchange, pore fillings, and surface complexation govern F- removal mechanisms. Pseudo-second-order and Freundlich were the best fit kinetic and isotherm for F- sorption, respectively. Increased biochar dose drives an increase in active sites due to F- level gradient and mass transfer between biochar-fluoride interactions, which reported maximum mass transfer for AMB than RB and AB. Fluoride adsorption using AMB could be described through chemisorption processes at room temperature (301 K), though endothermic sorption follows the physisorption process. Fluoride removal efficiency reduced, from 67.70% to 53.23%, with increased salt concentrations from 0 to 50 mM NaCl solutions, respectively, due to increased hydrodynamic diameter. Biochar was used to treat natural fluoride-contaminated surface and groundwater in real-world problem-solving measures, showed removal efficiency of 91.20% and 95.61%, respectively, for 10 mg L-1 F- contamination, and has been performed multiple times after systematic adsorption-desorption experiments. Lastly, techno-economic analysis was analyzed for biochar synthesis and F- treatment performance costs. Overall, our results revealed worth output and concluded with recommendations for future research on F- adsorption using biochar.

Surgical management of cystic duct stump calculi causing post-cholecystectomy syndrome: A prospective study.

Aim: Remnant cystic duct stump calculi are an uncommon but important cause of 'post-cholecystectomy syndrome'. High index of suspicion is needed to diagnose this condition in a symptomatic post-cholecystectomy patient. We present our experience with the surgical management of this condition. Patients and Methods: This prospective study included 19 patients with residual gallstone disease who underwent completion cholecystectomy between August 2016 and October 2021. Investigations included abdominal ultrasound and magnetic resonance cholangiopancreatography. The demographic, clinical, surgical and early post-operative variables of these patients were prospectively maintained and analysed. Results: The study included 14 women and 5 men. The mean age was 42.1 years (range, 14-80 years). The median duration between index surgery and completion cholecystectomy was 36 months (range, 2-178 months) (interquartile range, 105 months). The follow-up duration was 2 months. The initial surgery was open cholecystectomy in 17 and laparoscopic cholecystectomy in 2 patients. All patients with residual stump stone presented with pain, while 10 out of 19 patients complained of dyspepsia. Completion cholecystectomy could be performed laparoscopically in 16 cases, whereas 3 patients underwent open surgery. The mean operative time was 80 min (range, 55-140 min), and the mean blood loss was 100 ml (range, 50-160 ml). The mean hospital stay was 3 days (range, 2-10 days). No post-operative mortality or major morbidity was recorded in any of our patients. Conclusion: Laparoscopic excision of the cystic duct stump is feasible and safe even after previous open cholecystectomy. It is increasingly becoming the treatment of choice where expertise is available.

Use of a Single Standard Skull Model for Preparation of PMMA-Based Cranioplasty Flap: A Novel Low-Cost Technique.

AIM: To introduce a novel, low-cost technique for cranioplasty using a single standard polyvinyl chloride plastic skull model as a guide for cranioplasty flap development; to observe and to compare the functional and cosmetic outcomes. MATERIAL AND METHODS: We conducted an observational, retrospective, cohort study that included 20 patients who underwent cranioplasty at the Department of Neurosurgery, RMLIMS, Lucknow from September 2020 to September 2021. The patients were evaluated based on postoperative cosmesis and symptomatic relief. RESULTS: A total of 20 patients were included in this study. All procedures were performed without any intraoperative or long-term complications noted on follow-up. None of the patients required reoperation. We observed no evidence of bleeding, infection, or poor scar formation. The patients and their families were satisfied with the cosmetic results of the procedure. CONCLUSION: Our technique provided excellent functional outcomes, cosmetic appearance, and improved clinical symptoms. This technique is currently the most cost-effective alternative available.