Ethnobotanical Observation on Tuberous Plants from Tribal Area of Rajasthan (India)

The present paper gives an account of 42 tuberous plants of Ethnobotanical interest from Aravalli hills of Rajasthan. Main tribes inhabiting the study area are Bhil, Meena, Garasia, Damor and Kathodi. These tribes use the tuberous plants for various purposes in their daily life. Health, vitality and longevity enjoyed by the tribals have been attributed by them to these wild tuberous plants. On account of environmental changes and lack of insight of conservation of tuberous plants, many of them have become rare, threatened and endangered. If proper attention is not given, extinction of these plant species is certain and this is beyond doubt. Therefore identification and utility of these tuberous plants and compilation of a database on local information held by the tribes is stressed. Ethnobotanical information about tuberous plants is given by mentioning their botanical name, family, local name, time of flowering and fruiting, ecology and uses

A random search approach to the machine loading problem of an FMS

This paper discusses a modelling framework that addresses operational planning, problems of flexible manufacturing systems (FMSs). A generic 0-1 mixed integer programming formulation integrating the part selection and loading problems has been proposed. The constraints considered in the problems are mainly the availability of tool slots and machining time on the machining centres. The above problem is solved using an algorithm based on Simulated Annealing (SA). The potential capability of the approach is demonstrated via a small set of test problems. ©2004 IEEE.published_or_final_versio

Constitutive activation of IKK2/NF-κB impairs osteogenesis and skeletal development

Pathologic conditions impair bone homeostasis. The transcription factor NF-κB regulates bone homeostasis and is central to bone pathologies. Whereas contribution of NF-κB to heightened osteoclast activity is well-documented, the mechanisms underlying NF-κB impact on chondrocytes and osteoblasts are scarce. In this study, we examined the effect of constitutively active IKK2 (IKK2ca) on chondrogenic and osteogenic differentiation. We show that retroviral IKK2ca but not GFP, IKK2WT, or the inactive IKK2 forms IKK2KM and IKK2SSAA, strongly suppressed osteogenesis and chondrogenesis, in vitro. In order to explore the effect of constitutive NF-κB activation on bone formation in vivo, we activated this pathway in a conditional fashion. Specifically, we crossed the R26StopIKK2ca mice with mice carrying the Col2-cre in order to express IKK2ca in osteoblasts and chondrocytes. Both chondrocytes and osteoblasts derived from Col2Cre/IKK2ca expressed IKK2ca. Mice were born alive yet died shortly thereafter. Histologically, newborn Col2Cre+/RosaIKK2ca heterozygotes (Cre+IKK2ca_w/f (het)) and homozygotes (Cre+IKK2ca_f/f (KI)) showed smaller skeleton, deformed vertebrate and reduced or missing digit ossification. The width of neural arches, as well as ossification in vertebral bodies of Cre+IKK2ca_w/f and Cre+IKK2ca_f/f, was reduced or diminished. H&E staining of proximal tibia from new born pups revealed that Cre+IKK2ca_f/f displayed disorganized hypertrophic zones within the smaller epiphysis. Micro-CT analysis indicated that 4-wk old Cre+IKK2ca_w/f has abnormal trabecular bone in proximal tibia compared to WT littermates. Mechanistically, ex-vivo experiments showed that expression of differentiation markers in calvarial osteoblasts derived from newborn IKK2ca knock-in mice was diminished compared to WT-derived cells. In situ hybridization studies demonstrated that the hypertrophic chondrocyte marker type-X collagen, the pre-hypertrophic chondrocyte markers Indian hedgehog and alkaline phosphatase, and the early markers Aggrecan and type-II collagen were reduced in Cre+IKK2ca_w/f and Cre+IKK2ca_f/f mice. Altogether, the in-vitro, in vivo and ex-vivo evidence suggest that IKK2ca perturbs osteoblast and chondrocyte maturation and impairs skeletal development

Myeloid lineage skewing due to exacerbated NF-κB signaling facilitates osteopenia in Scurfy mice

Immune surveillance through Foxp3+ regulatory T cells plays a crucial role in bone homeostasis. Scurfy, the mouse model of autoimmune IPEX syndrome, bears a loss-of-function mutation in Foxp3 that leads to multi-organ inflammation. Herein, we report that scurfy mice exhibit severe bone loss mediated by accelerated osteoclastogenesis. Mechanistically, Foxp3 deficiency results in the upregulation of NF-κB in T helper cells through the loss of repressive Foxp3/NEMO interaction, thereby unleashing NF-κB-mediated over-production of pro-osteoclastogenic cytokines. Flow cytometry analysis shows marked increase in lin(-)Sca-1(+)c-kit(+) hematopoietic stem cells (LSK HSCs) and granulocyte/macrophage progenitors (GMPs) in bone marrow of scurfy mice with corresponding exacerbated osteoclastogenic potential, implying that osteoclast progenitors are affected at a very primitive stage in this disorder. Scurfy LSK HSCs exhibit greater sensitivity to M-CSF and contain abundant PU.1+ Sf LSK HSCs compared with WT. Accordingly, genetic or pharmacological inhibition of M-CSF or mTOR signaling, but not IL-17 signaling, attenuates osteoclastogenesis and osteopenia in scurfy. Thus, our study suggests that Foxp3 deficiency leads to osteopenia owing to dysregulated NF-κB activity and subsequent cytokine-mediated hyper-proliferation of myeloid precursors, and positions the NF-κB pathway as a potential target for therapeutic intervention for this disorder

Text Processing Like Humans Do: Visually Attacking and Shielding NLP Systems

Visual modifications to text are often used to obfuscate offensive comments in social media (e.g., "!d10t") or as a writing style ("1337" in "leet speak"), among other scenarios. We consider this as a new type of adversarial attack in NLP, a setting to which humans are very robust, as our experiments with both simple and more difficult visual input perturbations demonstrate. We then investigate the impact of visual adversarial attacks on current NLP systems on character-, word-, and sentence-level tasks, showing that both neural and non-neural models are, in contrast to humans, extremely sensitive to such attacks, suffering performance decreases of up to 82\%. We then explore three shielding methods---visual character embeddings, adversarial training, and rule-based recovery---which substantially improve the robustness of the models. However, the shielding methods still fall behind performances achieved in non-attack scenarios, which demonstrates the difficulty of dealing with visual attacks.Comment: Accepted as long paper at NAACL-2019; fixed one ungrammatical sentenc

SOST/Sclerostin Improves Posttraumatic Osteoarthritis and Inhibits MMP2/3 Expression After Injury.

Patients with anterior cruciate ligament (ACL) rupture are two times as likely to develop posttraumatic osteoarthritis (PTOA). Annually, there are ∼900,000 knee injuries in the United States, which account for ∼12% of all osteoarthritis (OA) cases. PTOA leads to reduced physical activity, deconditioning of the musculoskeletal system, and in severe cases requires joint replacement to restore function. Therefore, treatments that would prevent cartilage degradation post-injury would provide attractive alternatives to surgery. Sclerostin (Sost), a Wnt antagonist and a potent negative regulator of bone formation, has recently been implicated in regulating chondrocyte function in OA. To determine whether elevated levels of Sost play a protective role in PTOA, we examined the progression of OA using a noninvasive tibial compression overload model in SOST transgenic (SOSTTG ) and knockout (Sost-/- ) mice. Here we report that SOSTTG mice develop moderate OA and display significantly less advanced PTOA phenotype at 16 weeks post-injury compared with wild-type (WT) controls and Sost-/- . In addition, SOSTTG built ∼50% and ∼65% less osteophyte volume than WT and Sost-/- , respectively. Quantification of metalloproteinase (MMP) activity showed that SOSTTG had ∼2-fold less MMP activation than WT or Sost-/- , and this was supported by a significant reduction in MMP2/3 protein levels, suggesting that elevated levels of SOST inhibit the activity of proteolytic enzymes known to degrade articular cartilage matrix. Furthermore, intra-articular administration of recombinant Sost protein, immediately post-injury, also significantly decreased MMP activity levels relative to PBS-treated controls, and Sost activation in response to injury was TNFα and NF-κB dependent. These results provide in vivo evidence that sclerostin functions as a protective molecule immediately after joint injury to prevent cartilage degradation. © 2018 The Authors. Journal of Bone and Mineral Research Published by Wiley Periodicals Inc

Single dose surfactant early rescue therapy in respiratory distress syndrome-experience and outcome at a tertiary care centre

Background: Neonatal respiratory distress syndrome (RDS) is a progressive respiratory failure that is caused primarily by a deficiency of pulmonary surfactants (PS). We undertook a prospective study to evaluate outcomes of neonatal respiratory distress syndrome (RDS) patients treated with early rescue pulmonary surfactant.Methods: This was a prospective cross sectional study conducted at level III NICU. A total of 47 eligible  patients out of 142 diagnosed RDS on chest x-ray or FiO2 ≥40 was needed to reach SpO2 between 85 and 93%  received early recue surfactant therapy (within 2hrs of life) and  maternal ,neonatal and clinical data was analysed using SPSS software.Results: In this study prevalence of RDS amongst neonates admitted in NICU was 16.4%, early rescue surfactant therapy could be given only to 47 cases. There was male predominance (2.62:1). Mean age of administration of surfactant was 1.30±0.8 hr and Antenatal steroid was given in only 21.3% of mothers. Fraction of inspired oxygen concentration (Fio2) requirement also significantly decreases before and after therapy (p value˂0.0001) at 6,12, and 24 hrs. PEEP also shows decreasing trend at 24 hrs (p value ˂0.05). Sepsis was the commonest complication leading to mortality.Conclusion: Implementation of early rescue administration of surfactant in infants at high risk for developing RDS in neonatal ICU is a safe and effective modality of respiratory support which decreases ventilatory requirements, improves respiratory status, and causes early extubation.

Mechanism of non-canonical ubiquitination by ubiquitin conjugating enzyme Ubc6

Protein quality control by ubiquitination occurs due to the sequential action of three enzyme classes: ubiquitin-activating (E1), ubiquitin-conjugating (E2) and ubiquitin-ligases (E3). Conventionally, ubiquitin (Ub) attachment by these enzymes occurs via isopeptide bonds, typically to the ε-amino group of lysine residues. Seminal studies from the past have established that non-lysine residues such as serine, threonine and cysteine can also be ubiquitinated via hydroxy- and thio-ester bonds. However, the molecular basis and physiological relevance for such non-canonical ubiquitination remain elusive. Among the E2 family, yeast Ubc6 and its homologs are the only E2 enzymes known to mediate serine/threonine ubiquitination via hydroxyester linkages, but the structural or the chemical determinants for hydroxyl attachment of Ub have not been identified. To investigate the mechanism of hydroxyester ubiquitination, I have characterized Ubc6 using structural studies and in vitro biochemical assays with purified protein. I found that Ubc6 lacks conserved motifs and residues involved in ubiquitin transfer in other E2s. Instead, Ubc6 contains a highly conserved insertion proximal to its active-site Cys (C87), consisting of Ser (S89) and His (H94). The in vitro data suggest that the conserved histidine 94 (H94) within this insertion imparts reactivity towards hydroxylated amino acids. Substitution of H94 with methylated histidine showed that H94 has to exist in its neutral, non-protonated form to exert this activity. This suggests that H94 acts as a general base by abstracting a proton from the incoming hydroxyl group. However, it cannot be formally excluded that H94 acts by covalent catalysis. Moreover, I have described a crystal structure of Ubc6 in a Ub bound state which shows that the conserved serine 89 (S89) plays a role in stabilizing a reactive closed-state of Ubc6. Mutation of S89 led to a loss of E3 RING mediated activation of Ubc6 activity, suggesting that the closed conformation is disfavoured by mutating S89. In addition, in vitro assays showed that the active site of Ubc6 is selective towards serine over threonine indicating a preference towards primary hydroxylated nucleophiles. Overall, my results indicate that conserved residues in the active site proximal region of Ubc6 mediate reactivity towards hydroxylated amino acids, filling a gap in our understanding of the chemical determinants of this process. In the second part of this thesis, I investigated the functional relevance of a conserved C-terminal element (CTE) in Doa10. Doa10 is an E3 ligase involved in the conserved protein quality control pathway termed endoplasmic reticulum associated protein degradation (ERAD). During ERAD, membrane and luminal misfolded proteins are ubiquitinated and retrotranslocated back into the cytosol where they are degraded by the proteasome. The ERAD machinery also recognizes soluble and membrane bound cytoplasmic misfolded proteins, majorly by the Doa10 E3 ligase complex. However, the structural elements within Doa10 that allow recognition of cytoplasmic misfolded proteins are not known. Using co-immunoprecipitation assays combined with proteomics, I found a role of CTE in the ubiquitin ligase activity of Doa10. However, such an involvement was not recapitulated using in vitro assays, most likely due to absence of well-defined substrates. This thesis provides chemical and structural insights into the mechanism of hydroxyester ubiquitination by Ubc6. This could potentially serve as a reference for understanding non-canonical ubiquitination mediated by other E2/E3 enzymes.2024-10-1

Mechanistic differences in mouse models of heart failure with preserved ejection fraction

Heart failure (HF) is the most potent epidemic of the 21st century. Based on ejection fraction (EF), HF has been classified into two distinct entities; heart failure with reduced EF (HFrEF) and heart failure with preserved EF (HFpEF). At present, HFpEF accounts for about half of all HF cases worldwide but owing to the rising incidence of comorbid diseases and an aging population, its prevalence is expected to rise in the coming years. While the medical community has a good arsenal of therapeutics to deal with HFrEF, there exists no dedicated treatment for HFpEF as of now. An important limitation in this context is the lack of animal models to capture the multifactorial and multi-organ pathological profile of HFpEF. This dearth of reliable animal models often translates into a lack of our collective understanding of the disease. This dissertation aims to create tailor-made models of ‘’HFpEF like’’ states based on different comorbid etiologies and seeks to stratify them based on clinically relevant end-points to gather insights about their pathomechanisms. To this end, two models were created using the most common factors associated with HFpEF. The first model was made by combining dyslipidemia induced by high fat diet (HFD) and low grade pressure overload (PO) using transverse aortic constriction (TAC) to realistically reflect the metabolic syndrome in HFpEF. The other model was based on natural aging and looked at the advanced age of 18-20 months in mice in terms of HF. After 10 weeks of HFD and 2 weeks post TAC the models were assessed. For the first model we observed that the combination of HFD+PO resulted in a selective shift in EF towards a preserved state (≥50%) while control mice on normal diet (ND) + PO presented with a reduction in EF (≤40%) which reflects HFrEF. This prompted us to hypothesize that metabolic deregulation led by HFD induced dyslipidemia in presence of low grade PO was important in the differential presentation of HF. An in-depth structural characterization of the myocardium revealed a hypertrophic, apoptotic and a highly fibrotic phenotype which presented with evidence of atrial remodeling. There was significant accumulation of neutral lipid deposits in the myocardial tissue indicating global dyslipidemic effects. The model showed an overall preserved systolic function in HFD- TAC (in contrast to ND-TAC controls) as evidenced by unchanged echocardiographic parameters like EF and reverse longitudinal strain rate (r-LSR) and pressure volume (PV) loop parameters like ESPVR, dp/dtmax and PRSW when compared to HFD-Sham group. Moreover, an impairment in diastolic function was confirmed by significant changes in EDPVR, EDP and Tau. On the aspect of remodeling, the dyslipidemic HFpEF state presented with concentric hypertrophy as evidenced by higher relative wall thickness (RWT) as compared to dyslipidemic shams. Fetal gene reprogramming was highly active in both dietary groups but differed in terms of Serca-2α downregulation seen only in the HFrEF group. Perivascular fibrosis was uniquely enhanced in HFpEF state. The inflammatory cytokine profile within the two states also revealed a differential signature with more upregulation in the dyslipidemic group. VCAM-1 and PECAM-1 also presented with enhanced expression only in HFpEF group suggestive of distinct dynamics of endothelial dysfunction(ED). IL-1 showed enhanced expression in HFpEF only, while IL-6 showed no change in either groups. Endothelin-1 was exclusively upregulated in HFpEF state. Nox2 was upregulated in both HF states. In terms of cardiac kinases and calcium handling, phosphorylation levels of HDAC-4, Akt, Erk, RyR(2814) and Plb(Thr17) were only exclusively enhanced in HFpEF and cardiac troponin phosphorylation was preserved to basal levels in the HFpEF group indicating yet another differential aspect. Transcriptomic analysis of the two HF states identified several key genes involved mainly in actin-myosin structural and functional dynamics. Pathway analysis revealed an enrichment of gene-set involved in adrenergic signaling indicating that adrenergic deficits play a differentiating role between the two HF states. The second model of cardiac aging was characterized on similar levels. In contrast to dyslipidemic HFpEF, it presented with an overall non-hypertrophic, non-remodeled, highly fibrotic, highly apoptotic and non-steatotic phenotype. There was no evidence for LA remodeling and concentric hypertrophy of the LV. Systolic parameters discussed above were preserved and all studied diastolic parameters were significantly perturbed. Fetal gene reprogramming was evident but, Acta-1 showed no change in contrast to dyslipidemic HFpEF. BNP was upregulated in both HFpEF states but ANP was preserved in aging. Perivascular fibrosis as the previous HFpEF group was remarkably enhanced. Inflammatory cytokine analysis showed no changes in IFN-γ levels which was in contrast to dyslipidemic HFpEF. PECAM-1 upregulation was not observed here as well (just like dyslipidemic HFpEF) suggesting an exclusive role. IL-6 expression unlike the previous HFpEF group, was upregulated here. Endothelin-1 expression was again upregulated in this HFpEF state too. Notably, higher accumulation of CD45+ cells was seen in LV myocardium of the aging HFpEF state only. Nox2 expression was not enhanced here unlike the previous dyslipidemia induced HFpEF cohort and HFrEF. Akt phosphorylation was not upregulated while Erk, p-38 and Jnk were. The latter two are in contrast with dyslipidemic HFpEF. In terms of calcium handling, phosphorylation of CAMKII, RyR(2814) , RyR(2808), Plb (Thr17) and Plb (Ser 16) were all enhanced showing a more potent deregulation than the dyslipidemic HFpEF group. Only HDAC-4 phosphorylation which was present in the previous group, could not be seen here. Assessment of the coding transcriptome of the two HFpEF states revealed an over representation of genes involved in response to chemokine and extracellular matrix (ECM) organization and the resulting KEGG pathway showed an enrichment in ECM-receptor pathway interaction genes. It suggests that these two HFpEF states differ strongly in the context of ECM based signaling. PCA plot revealed a clustering of both HFpEF groups together despite their divergent etiologies. This further stresses on the multifactorial nature of HFpEF. The differences and similarities between the two ‘’HFpEF like’’ states and between HFpEF vs HFrEF reveal a distinct mechanistic profile. This study provides first such cross-comparative insight which ultimately may contribute to our collective understanding of different HFpEF pheno-groups and help in identifying mechanistically intuitive therapeutic targets for this elusive entity.2024-02-2