Material platform for realization of a "fiber-like" lossy mode resonance response in a simple Kretschmann-Raether geometry.

The lossy mode resonance (LMR) phenomenon is almost exclusively limited to fiber optics, since the thin film configuration yields a relatively shallow resonance dip compared to its fiber counterpart. In this Letter, we bridge this frustrating intensity gap between these basic configurations by choosing vacuum-deposited metallic indium-rich indium tin oxide as the coating material. LMR attenuation as high as -14.3dB for transverse electric and -6.4dB for transverse magnetic polarization is achieved experimentally via a commonly used Kretschmann-Raether geometry and that too for a film thickness of ≈70nm. Such a high degree of LMR response is attributed to the metallic indium generated interbands, leading to a high extinction coefficient in the visible range. A modified transfer matrix method, which takes into account the surface roughness of the films through application of the anisotropic Bruggeman effective medium approximation, is developed to realize the experimental LMR spectra numerically.

Material platform for realization of a "fiber-like" lossy mode resonance response in a simple Kretschmann-Raether geometry: publisher's note.

This publisher's note contains corrections to Opt. Lett.46, 3065 (2021).OPLEDP0146-959210.1364/OL.431787.

Enzymatic pretreatment of algal biomass has different optimal conditions for biogas and bioethanol routes.

Enzymatic pretreatment is emerging as an efficient tool for the extraction of biofuel precursors from algal biomass. However, yardsticks for end-use directed selection of optimal pretreatment conditions are not yet identified. The present study, for the first time, reveals different optimal conditions for algal biomass solubilization and sugar release. Algal biomass pretreatment optimization was carried out using the Taguchi method. Crude enzyme from Aspergillus fischeri was found effective for pretreatment of Chlorella pyrenoidosa. Maximum sugar yield (190 mg g-1 biomass) from algal biomass was observed at a substrate concentration of 4 g L-1, with a 5% enzyme load at temperature 60°C, pH 5.5, and shaking speed of 80 rpm. In contrast, maximum sCOD (1350 mg g-1 biomass) was obtained at 2 g L-1 substrate concentration with enzyme load of 20% v/v, at 60°C, pH 4, and shaking speed of 100 rpm. Hence, the first set of conditions would be more beneficial for bioethanol production. Whereas another set of conditions would improve the biofuel production that requires maximum solubilization of algal biomass, such as fermentative methane production. Overall, the present observations established that process conditions required for enzymatic pretreatment of algal biomass should be selected according to the desired biofuel type.

The endogenous cellular protease inhibitor SPINT2 controls SARS-CoV-2 viral infection and is associated to disease severity.

COVID-19 outbreak is the biggest threat to human health in recent history. Currently, there are over 1.5 million related deaths and 75 million people infected around the world (as of 22/12/2020). The identification of virulence factors which determine disease susceptibility and severity in different cell types remains an essential challenge. The serine protease TMPRSS2 has been shown to be important for S protein priming and viral entry, however, little is known about its regulation. SPINT2 is a member of the family of Kunitz type serine protease inhibitors and has been shown to inhibit TMPRSS2. Here, we explored the existence of a co-regulation between SPINT2/TMPRSS2 and found a tightly regulated protease/inhibitor expression balance across tissues. We found that SPINT2 negatively correlates with SARS-CoV-2 expression in Calu-3 and Caco-2 cell lines and was down-regulated in secretory cells from COVID-19 patients. We validated our findings using Calu-3 cell lines and observed a strong increase in viral load after SPINT2 knockdown, while overexpression lead to a drastic reduction of the viral load. Additionally, we evaluated the expression of SPINT2 in datasets from comorbid diseases using bulk and scRNA-seq data. We observed its down-regulation in colon, kidney and liver tumors as well as in alpha pancreatic islets cells from diabetes Type 2 patients, which could have implications for the observed comorbidities in COVID-19 patients suffering from chronic diseases.

Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma.

Neuroblastoma is a pediatric tumor of the developing sympathetic nervous system. However, the cellular origin of neuroblastoma has yet to be defined. Here we studied the single-cell transcriptomes of neuroblastomas and normal human developing adrenal glands at various stages of embryonic and fetal development. We defined normal differentiation trajectories from Schwann cell precursors over intermediate states to neuroblasts or chromaffin cells and showed that neuroblastomas transcriptionally resemble normal fetal adrenal neuroblasts. Importantly, neuroblastomas with varying clinical phenotypes matched different temporal states along normal neuroblast differentiation trajectories, with the degree of differentiation corresponding to clinical prognosis. Our work highlights the roles of oncogenic MYCN and loss of TFAP2B in blocking differentiation and may provide the basis for designing therapeutic interventions to overcome differentiation blocks.

Kalirin-RAC controls nucleokinetic migration in ADRN-type neuroblastoma.

The migrational propensity of neuroblastoma is affected by cell identity, but the mechanisms behind the divergence remain unknown. Using RNAi and time-lapse imaging, we show that ADRN-type NB cells exhibit RAC1- and kalirin-dependent nucleokinetic (NUC) migration that relies on several integral components of neuronal migration. Inhibition of NUC migration by RAC1 and kalirin-GEF1 inhibitors occurs without hampering cell proliferation and ADRN identity. Using three clinically relevant expression dichotomies, we reveal that most of up-regulated mRNAs in RAC1- and kalirin-GEF1-suppressed ADRN-type NB cells are associated with low-risk characteristics. The computational analysis shows that, in a context of overall gene set poverty, the upregulomes in RAC1- and kalirin-GEF1-suppressed ADRN-type cells are a batch of AU-rich element-containing mRNAs, which suggests a link between NUC migration and mRNA stability. Gene set enrichment analysis-based search for vulnerabilities reveals prospective weak points in RAC1- and kalirin-GEF1-suppressed ADRN-type NB cells, including activities of H3K27- and DNA methyltransferases. Altogether, these data support the introduction of NUC inhibitors into cancer treatment research.

Super enhancers define regulatory subtypes and cell identity in neuroblastoma.

Half of the children diagnosed with neuroblastoma (NB) have high-risk disease, disproportionately contributing to overall childhood cancer-related deaths. In addition to recurrent gene mutations, there is increasing evidence supporting the role of epigenetic deregulation in disease pathogenesis. Yet, comprehensive cis-regulatory network descriptions from NB are lacking. Here, using genome-wide H3K27ac profiles across 60 NBs, covering the different clinical and molecular subtypes, we identified four major super-enhancer-driven epigenetic subtypes and their underlying master regulatory networks. Three of these subtypes recapitulated known clinical groups; namely, MYCN-amplified, MYCN non-amplified high-risk and MYCN non-amplified low-risk NBs. The fourth subtype, exhibiting mesenchymal characteristics, shared cellular identity with multipotent Schwann cell precursors, was induced by RAS activation and was enriched in relapsed disease. Notably, CCND1, an essential gene in NB, was regulated by both mesenchymal and adrenergic regulatory networks converging on distinct super-enhancer modules. Overall, this study reveals subtype-specific super-enhancer regulation in NBs.

Are we missing 'previously treated' smear-positive pulmonary tuberculosis under programme settings in India? A cross-sectional study.

Background: In 2007, a field observation from India reported 11% misclassification among 'new' patients registered under the revised national tuberculosis (TB) control programme. Ten years down the line, it is important to know what proportion of newly registered patients has a past history of TB treatment for at least one month (henceforth called 'misclassification'). Methods: A study was conducted among new smear-positive pulmonary TB patients registered between March 2016 and February 2017 in 18 randomly selected districts to determine the effectiveness of an active case-finding strategy in marginalised and vulnerable populations. We included all patients detected through active case-finding. An equal number of randomly selected patients registered through passive case-finding from marginalised and vulnerable populations in the same districts were included. Before enrolment, we enquired about any history of previous TB treatment through interviews. Results: Of 629 patients, we interviewed 521, of whom, 11% (n=56) had past history of TB treatment (public or private) for at least a month: 13% (34/268) among the active case-finding group and 9% (22/253) among the passive case-finding group (p=0.18). No factors were found to be significantly associated with misclassification. Conclusion: Around one in every ten patients registered as 'new' had previous history of TB treatment. Corrective measures need to be implemented, followed by monitoring of any change in the proportion of 'previously treated' patients among all registered patients treated under the programme at national level.

Patient characteristics, health seeking and delays among new sputum smear positive TB patients identified through active case finding when compared to passive case finding in India.

BACKGROUND: Axshya SAMVAD is an active tuberculosis (TB) case finding (ACF) strategy under project Axshya (Axshya meaning 'free of TB' and SAMVAD meaning 'conversation') among marginalized and vulnerable populations in 285 districts of India. OBJECTIVES: To compare patient characteristics, health seeking, delays in diagnosis and treatment initiation among new sputum smear positive TB patients detected through ACF and passive case finding (PCF) under the national TB programme in marginalized and vulnerable populations between March 2016 and February 2017. METHODS: This observational analytic study was conducted in 18 randomly sampled Axshya districts. We enrolled all TB patients detected through ACF and an equal number of randomly selected patients detected through PCF in the same settings. Data on patient characteristics, health seeking and delays were collected through record review and patient interviews (at their residence). Delays included patient level delay (from eligibility for sputum examination to first contact with any health care provider (HCP)), health system level diagnosis delay (from contact with first HCP to TB diagnosis) and treatment initiation delays (from diagnosis to treatment initiation). Total delay was the sum of patient level, health system level diagnosis delay and treatment initiation delays. RESULTS: We included 234 ACF-diagnosed and 231 PCF-diagnosed patients. When compared to PCF, ACF patients were relatively older (≥65 years, 14% versus 8%, p = 0.041), had no formal education (57% versus 36%, p<0.001), had lower monthly income per capita (median 13.1 versus 15.7 USD, p = 0.014), were more likely from rural areas (92% versus 81%, p<0.002) and residing far away from the sputum microscopy centres (more than 15 km, 24% versus 18%, p = 0.126). Fewer patients had history of significant loss of weight (68% versus 78%, p = 0.011) and sputum grade of 3+ (15% versus 21%, p = 0.060). Compared to PCF, HCP visits among ACF patients was significantly lower (median one versus two HCPs, p<0.001). ACF patients had significantly lower health system level diagnosis delay (median five versus 19 days, p = 0.008) and the association remained significant after adjusting for potential confounders. Patient level and total delays were not significantly different. CONCLUSION: Axshya SAMVAD linked the most impoverished communities to TB care and resulted in reduction of health system level diagnosis delay.

Active case finding among marginalised and vulnerable populations reduces catastrophic costs due to tuberculosis diagnosis.

BACKGROUND: There is limited evidence on whether active case finding (ACF) among marginalised and vulnerable populations mitigates the financial burden during tuberculosis (TB) diagnosis. OBJECTIVES: To determine the effect of ACF among marginalised and vulnerable populations on prevalence and inequity of catastrophic costs due to TB diagnosis among TB-affected households when compared with passive case finding (PCF). METHODS: In 18 randomly sampled ACF districts in India, during March 2016 to February 2017, we enrolled all new sputum-smear-positive TB patients detected through ACF and an equal number of randomly selected patients detected through PCF. Direct (medical and non-medical) and indirect costs due to TB diagnosis were collected through patient interviews at their residence. We defined costs due to TB diagnosis as 'catastrophic' if the total costs (direct and indirect) due to TB diagnosis exceeded 20% of annual pre-TB household income. We used concentration curves and indices to assess the extent of inequity. RESULTS: When compared with patients detected through PCF (n = 231), ACF patients (n = 234) incurred lower median total costs (US$ 4.6 and 20.4, p < 0.001). The prevalence of catastrophic costs in ACF and PCF was 10.3 and 11.5% respectively. Adjusted analysis showed that patients detected through ACF had a 32% lower prevalence of catastrophic costs relative to PCF [adjusted prevalence ratio (95% CI): 0.68 (0.69, 0.97)]. The concentration indices (95% CI) for total costs in both ACF [-0.15 (-0.32, 0.11)] and PCF [-0.06 (-0.20, 0.08)] were not significantly different from the line of equality and each other. The concentration indices (95% CI) for catastrophic costs in both ACF [-0.60 (-0.81, -0.39)] and PCF [-0.58 (-0.78, -0.38)] were not significantly different from each other: however, both the curves had a significant distribution among the poorest quintiles. CONCLUSION: ACF among marginalised and vulnerable populations reduced total costs and prevalence of catastrophic costs due to TB diagnosis, but could not address inequity.

Copy Number Alterations in Enzyme-Coding and Cancer-Causing Genes Reprogram Tumor Metabolism.

Somatic copy number alterations frequently occur in the cancer genome affecting not only oncogenic or tumor suppressive genes, but also passenger and potential codriver genes. An intrinsic feature resulting from such genomic perturbations is the deregulation in the metabolism of tumor cells. In this study, we have shown that metabolic and cancer-causing genes are unexpectedly often proximally positioned in the chromosome and share loci with coaltered copy numbers across multiple cancers (19 cancer types from The Cancer Genome Atlas). We have developed an analysis pipeline, Identification of Metabolic Cancer Genes (iMetCG), to infer the functional impact on metabolic remodeling from such coamplifications and codeletions and delineate genes driving cancer metabolism from those that are neutral. Using our identified metabolic genes, we were able to classify tumors based on their tissue and developmental origins. These metabolic genes were similar to known cancer genes in terms of their network connectivity, isoform frequency, and evolutionary features. We further validated these identified metabolic genes by (i) using gene essentiality data from several tumor cell lines, (ii) showing that these identified metabolic genes are strong indicators for patient survival, and (iii) observing a significant overlap between our identified metabolic genes and known cancer-metabolic genes. Our analyses revealed a hitherto unknown generic mechanism for large-scale metabolic reprogramming in cancer cells based on linear gene proximities between cancer-causing and -metabolic genes. We have identified 119 new metabolic cancer genes likely to be involved in rewiring cancer cell metabolism. Cancer Res; 76(14); 4058-67. ©2016 AACR.

MicroRNA-30c-2-3p negatively regulates NF-κB signaling and cell cycle progression through downregulation of TRADD and CCNE1 in breast cancer.

Nuclear Factor kappa B (NF-κB) signaling is frequently deregulated in a variety of cancers and is constitutively active in estrogen receptor negative (ER-) breast cancer subtypes. These molecular subtypes of breast cancer are associated with poor overall survival. We focused on mechanisms of NF-κB regulation by microRNAs (miRNAs), which regulate eukaryotic gene expression at the post-transcriptional level. In a previous genome-wide miRNA screen, we had identified miR-30c-2-3p as one of the strongest negative regulators of NF-κB signaling. Here we have uncovered the underlying molecular mechanisms and its consequences in breast cancer. In vitro results show that miR-30c-2-3p directly targets both TNFRSF1A-associated via death domain (TRADD), an adaptor protein of the TNFR/NF-κB signaling pathway, and the cell cycle protein Cyclin E1 (CCNE1). Ectopic expression of miR-30c-2-3p downregulated essential cytokines IL8, IL6, CXCL1, and reduced cell proliferation as well as invasion in MDA-MB-231 breast cancer cells. RNA interference (RNAi) induced silencing of TRADD phenocopied the effects on invasion and cytokine expression caused by miR-30c-2-3p, while inhibition of CCNE1 phenocopied the effects on cell proliferation. We further confirmed the tumor suppressive role of this miRNA using a dataset of 781 breast tumors, where higher expression was associated with better survival in breast cancer patients. In summary we have elucidated the mechanism by which miR-30c-2-3p negatively regulates NF-κB signaling and cell cycle progression in breast cancer.

A high-throughput RNAi screen for detection of immune-checkpoint molecules that mediate tumor resistance to cytotoxic T lymphocytes.

The success of T cell-based cancer immunotherapy is limited by tumor's resistance against killing by cytotoxic T lymphocytes (CTLs). Tumor-immune resistance is mediated by cell surface ligands that engage immune-inhibitory receptors on T cells. These ligands represent potent targets for therapeutic inhibition. So far, only few immune-suppressive ligands have been identified. We here describe a rapid high-throughput siRNA-based screening approach that allows a comprehensive identification of ligands on human cancer cells that inhibit CTL-mediated tumor cell killing. We exemplarily demonstrate that CCR9, which is expressed in many cancers, exerts strong immune-regulatory effects on T cell responses in multiple tumors. Unlike PDL1, which inhibits TCR signaling, CCR9 regulates STAT signaling in T cells, resulting in reduced T-helper-1 cytokine secretion and reduced cytotoxic capacity. Moreover, inhibition of CCR9 expression on tumor cells facilitated immunotherapy of human tumors by tumor-specific T cells in vivo. Taken together, this method allows a rapid and comprehensive determination of immune-modulatory genes in human tumors which, as an entity, represent the 'immune modulatome' of cancer.

Metabolic network modeling approaches for investigating the "hungry cancer".

Metabolism is the functional phenotype of a cell, at a given condition, resulting from an intricate interplay of various regulatory processes. The study of these dynamic metabolic processes and their capabilities help to identify the fundamental properties of living systems. Metabolic deregulation is an emerging hallmark of cancer cells. This deregulation results in rewiring of the metabolic circuitry conferring an exploitative metabolic advantage for the tumor cells which leads to a distinct benefit in survival and lays the basis for unbound progression. Metabolism can be considered as a thermodynamic open-system in which source substrates of high value are being processed through a well established interconnected biochemical conversion system, strictly obeying physiochemical principles, generating useful intermediates and finally resulting in the release of byproducts. Based on this basic principle of an input-output balance, various models have been developed to interrogate metabolism elucidating its underlying functional properties. However, only a few modeling approaches have proved computationally feasible in elucidating the metabolic nature of cancer at a systems level. Besides this, statistical approaches have been set up to identify biochemical pathways being more relevant for specific types of tumor cells. In this review, we are briefly introducing the basic statistical approaches followed by the major modeling concepts. We have put an emphasis on the methods and their applications that have been used to a greater extent in understanding the metabolic remodeling of cancer.

Modified Pauwels' intertrochanteric osteotomy in neglected femoral neck fractures in children: a report of 10 cases followed for a minimum of 5 years.

OBJECTIVES: To evaluate the role of a modified Pauwels' intertrochanteric osteotomy (MPIO) in neglected femoral neck fractures in children. DESIGN: Prospective study with retrospective analysis. SETTING: Tertiary care Postgraduate Institute of Medical Sciences. PATIENTS: Ten children (8 males, 2 females) with an average age of 10.2 years with neglected femoral neck fractures were seen from 1990 to 1998. A femoral neck fracture was considered neglected when no proper medical treatment was instituted for at least 1 month following the fracture. Nonunion was accompanied by coxa vara and resorption of the femoral neck in 9 patients; a 10th patient had a neglected femoral neck fracture for 1 month without coxa vara. Three patients at time of presentation with Delbet Type II displaced fractures with associated nonunion and coxa vara (2 with Ratliff Type III and 1 with Type I) also had avascular necrosis using plain radiographic criteria of increased density. INTERVENTION: Modified Pauwels' intertrochanteric osteotomy. The children were immobilized in a hip spica for 6-10 weeks postoperatively and weightbearing was started after hip spica removal. MAIN OUTCOME MEASUREMENTS: Fracture healing, neck-shaft angle, avascular necrosis, and functional outcome. RESULTS: Patients were followed for an average of 8.2 years (range 5-12 years). All patients had union of their fracture within an average of 16.6 weeks (12-20 weeks) and of the osteotomy site within 8.2 weeks (7-9 weeks). Radiologic signs of avascular necrosis disappeared completely in the 3 patients who presented with avascular necrosis. In 1 patient with a preoperatively viable femoral head, radiologic signs of Ratliff Type I avascular necrosis appeared between 60 and 98 weeks. This radiologic finding became normal again, indicating viability of the femoral head somewhere between 98 to 205 weeks of follow-up. Postoperatively, an average of 135-degree neck-shaft angle was achieved (range 125-160 degrees). The average preoperative neck-shaft angle was 104.4 degrees (range 92-120 degrees) and on the normal hip side it was 127.7 degrees (range 124-132 degrees). Significant improvement in the neck-shaft angle was seen compared with the preoperative angle (P < 0.001) and normal hip angle (P < 0.05). Coxa vara and signs of chondrolysis were not observed in any of the patients. Premature proximal femoral epiphyseal closure resulting in a 1-cm and a 1.5-cm leg-length discrepancy was seen in 2 patients as compared with their normal side. A mild Trendelenburg gait was observed in 1 patient (10%). Using Ratliff's criteria, 9 patients (90%) were graded as a good result and 1 patient (10%) was graded as a fair result. The osteotomy plate was removed in 1 patient (10%). CONCLUSION: An MPIO creates a biomechanical environment conducive to healing of a neglected femoral neck nonunion in a child while simultaneously correcting an associated coxa vara. The procedure also seems to have a biological role in helping restore viability to a noncollapsed femoral head with avascular necrosis.