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Tripathi M, Deokar G, Casanova-Chafer J, Jin J, Sierra-Castillo A, Ogilvie SP, Lee F, Iyengar SA, Biswas A, Haye E, Genovese A, Llobet E, Colomer JF, Jurewicz I, Gadhamshetty V, Ajayan PM, Schwingenschlögl U, Costa PMFJ, Dalton AB. Vertical heterostructure of graphite-MoS 2 for gas sensing. NANOSCALE HORIZONS 2024. [PMID: 38808602 DOI: 10.1039/d4nh00049h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
2D materials, given their form-factor, high surface-to-volume ratio, and chemical functionality have immense use in sensor design. Engineering 2D heterostructures can result in robust combinations of desirable properties but sensor design methodologies require careful considerations about material properties and orientation to maximize sensor response. This study introduces a sensor approach that combines the excellent electrical transport and transduction properties of graphite film with chemical reactivity derived from the edge sites of semiconducting molybdenum disulfide (MoS2) through a two-step chemical vapour deposition method. The resulting vertical heterostructure shows potential for high-performance hybrid chemiresistors for gas sensing. This architecture offers active sensing edge sites across the MoS2 flakes. We detail the growth of vertically oriented MoS2 over a nanoscale graphite film (NGF) cross-section, enhancing the adsorption of analytes such as NO2, NH3, and water vapor. Raman spectroscopy, density functional theory calculations and scanning probe methods elucidate the influence of chemical doping by distinguishing the role of MoS2 edge sites relative to the basal plane. High-resolution imaging techniques confirm the controlled growth of highly crystalline hybrid structures. The MoS2/NGF hybrid structure exhibits exceptional chemiresistive responses at both room and elevated temperatures compared to bare graphitic layers. Quantitative analysis reveals that the sensitivity of this hybrid sensor surpasses other 2D material hybrids, particularly in parts per billion concentrations.
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Biswas A, Pal S. Plant-nano interactions: A new insight of nano-phytotoxicity. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108646. [PMID: 38657549 DOI: 10.1016/j.plaphy.2024.108646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/23/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024]
Abstract
Whether nanoparticles (NPs) are boon or bane for society has been a centre of in-depth debate and key consideration in recent times. Exclusive physicochemical properties like small size, large surface area-to-volume ratio, robust catalytic activity, immense surface energy, magnetism and superior biocompatibility make NPs obligatory in many scientific, biomedical and industrial ventures. Nano-enabled products are newer entrants in the present era. To attenuate environmental stress and maximize crop yields, scientists are tempted to introduce NPs as augmented supplements in agriculture. The feasible approaches for NPs delivery are irrigation, foliar spraying or seed priming. Internalization of excessive NPs to plants endorses negative implications at higher trophic levels via biomagnification. The characteristics of NPs (dimensions, type, solubility, surface charge), applied concentration and duration of exposure are prime factors conferring nanotoxicity in plants. Several reports approved NPs persuaded toxicity can precisely mimic abiotic stress effects. The signature effects of nanotoxicity include poor root outgrowth, biomass reduction, oxidative stress evolution, lipid peroxidation, biomolecular damage, perturbed antioxidants, genotoxicity and nutrient imbalance in plants. NPs stress impels mitogen-activated protein kinase signaling cascade and urges stress responsive defence gene expression to counteract stress in plants. Exogenous supplementation of nitric oxide (NO), arbuscular mycorrhizal fungus (AMF), phytohormones, and melatonin (ME) is novel strategy to circumvent nanotoxicity. Briefly, this review appraises plants' physio-biochemical responses and adaptation scenarios to endure NPs stress. As NPs stress represents large-scale contaminants, advanced research is indispensable to avert indiscriminate NPs usage for synchronizing nano-security in multinational markets.
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Lahiri D, Krishna KVM, Verma AK, Modak P, Vishwanadh B, Chattopadhyay S, Shibata T, Sharma SK, Sarkar SK, Clifton PH, Biswas A, Garg N, K Dey G. Comprehensive characterization of the structure of Zr-based metallic glasses. Sci Rep 2024; 14:4911. [PMID: 38418473 PMCID: PMC10902397 DOI: 10.1038/s41598-024-53509-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/01/2024] [Indexed: 03/01/2024] Open
Abstract
Structure of metallic glasses fascinates as the generic amorphous structural template for ubiquitous systems. Its specification necessitates determination of the complete hierarchical structure, starting from short-range-order (SRO) → medium-range-order (MRO) → bulk structure and free volume (FV) distribution. This link has largely remained elusive since previous investigations adopted one-technique-at-a-time approach, focusing on limited aspects of any one domain. Reconstruction of structure from experimental data inversion is non-unique for many of these techniques. As a result, complete and precise structural understanding of glass has not emerged yet. In this work, we demonstrate the first experimental pathway for reconstruction of the integrated structure, forZr 67 Ni 33 andZr 52 Ti 6 Al 10 Cu 18 Ni 14 glasses. Our strategy engages diverse (× 7) multi-scale techniques [XAFS, 3D-APT, ABED/NBED, FEM, XRD, PAS, FHREM] on the same glass. This strategy complemented mutual limitations of techniques and corroborated common parameters to generate complete, self-consistent and precise parameters. Further, MRO domain size and inter-void separation were correlated to identify the presence of FV at MRO boundaries. This enabled the first experimental reconstruction of hierarchical subset: SRO → MRO → FV → bulk structure. The first ever image of intermediate region between MRO domains emerged from this link. We clarify that determination of all subsets is not our objective; the essence and novelty of this work lies in directing the pathway towards finite solution, in the most logical and unambiguous way.
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Ivaškevičius V, Biswas A, Singh S, Stulpinaitė U, Reda S, Rühl H, Pezeshkpoor B, Pavlova A, Oldenburg J. Fibrinogen Bonn (p. Arg510Cys) in the Aα-Chain Is Associated with High Risk of Venous Thrombosis. Hamostaseologie 2023; 43:440-446. [PMID: 37442158 DOI: 10.1055/a-2094-7191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023] Open
Abstract
INTRODUCTION Inherited dysfibrinogenemia is a qualitative defect of fibrinogen caused by various mutations among three fibrinogen genes. Dysfibrinogenemia can be associated with an increased risk of thrombosis, bleeding, or both. Here, we report a 36-year-old female with dysfibrinogenemia who experienced two successful pregnancies under thromboprophylaxis after cerebral venous sinus thrombosis (CVST). PATIENTS AND METHODS In addition to plasmatic coagulation tests, fibrinogen genes FGA, FGB, and FGG were screened using direct genomic DNA sequencing. The structural-functional implications of the detected mutation were analyzed in silico. RESULTS Inherited dysfibrinogenemia was diagnosed in an index patient after CVST in a risk situation. Anticoagulation with warfarin was stopped after 12 months when the first pregnancy was planned. Pregnancy and spontaneous delivery (2020) was uncomplicated. A second pregnancy was interrupted because of acute cytomegalovirus infection and the third pregnancy was successful in 2022. Pregnancies were accompanied by thromboprophylaxis with enoxaparin 40 mg once daily until 6 weeks postpartum. Substitution of fibrinogen has not become necessary in the index patient so far. Genetic analysis revealed a novel missense mutation (p. Arg510Cys) in the FGA gene ("fibrinogen Bonn") in the index patient, as well as an asymptomatic sister, and their father who experienced recurrent pulmonary embolism. Surface exposure of wild-type Arg510 suggested the mutated Cys510 to form nonnative disulfide bonds with surface-exposed reactive cysteines from other plasma proteins like albumin leading to formation of aggregates and impaired fibrinolysis. CONCLUSIONS Fibrinogen Bonn might be associated with an increased risk of thrombosis, possibly due to impaired polymerization.
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Biswas A, Roy S, Ghosh V, Kumar L, Sharma A, Gupta R, Mallick S. Clinical Outcome and Patterns of Failure in Patients with Solitary Plasmacytoma Treated with Radical Radiotherapy. Int J Radiat Oncol Biol Phys 2023; 117:S109. [PMID: 37784287 DOI: 10.1016/j.ijrobp.2023.06.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) We intended to assess the patterns of care and failure in patients with solitary plasmacytoma (SP), treated at our institute from 2011-21. MATERIALS/METHODS Data pertaining to the management of patients with SP was abstracted by retrospective chart review. Progression free survival (PFS) and overall survival (OS) were defined as the time intervals from the date of diagnosis to the date of progression (local, systemic or both) and death or last follow up, respectively. PFS and OS were analyzed by Kaplan Meier method. RESULTS Atotal of 72 patients were diagnosed with SP (61-bone plasmacytoma; 11-extramedullary plasmacytoma) in between 2011 and 2021. The median age at diagnosis was 52 years. The male: female ratio was 2.27. The ECOG PS were 0, 1, 2, 3, and 4 in 1, 46, 11, 10, and 3 patients, respectively. The median diameter of the lesion was 6.7 cm (range 2.3-18.4 cm). The median M protein was 0.375 g/dl (range 0.63-5.3 g/dl). On bone marrow examination, 8 and 64 patients had no and minimal marrow involvement, respectively (median bone marrow plasma cells 4%). Radical radiotherapy (RT) was administered in 71 patients, the techniques being 2D-conventional in 35, 3D-conformal in 14, IMRT in 8 and VMAT in 5 patients (details not available in 9). The median RT dose was 45 Gy in 25 fractions over 5 weeks (range 45-50 Gy). In addition, 5(7%) patients underwent surgery prior to RT and 6(8.5%) patients received systemic chemotherapy. After RT, the median quantum of symptom relief was 75% (range 0-100%). The best response to RT was CR, PR, SD and PD in 41(57.7%),18(25.4%),3(4.2%) and 4(5.6%) patients, respectively (response assessment could not be done in 5). Local control with primary RT was achieved in 58(81.7%) patients. No RT related grade 3/4 acute or late toxicity was reported. The median follow up was 48.3 months (range 1.3-141.6 months). A total of 28(39.4%) patients experienced disease progression (systemic in 15, local in 7 and both in 6), out of which 13 could be successfully salvaged with further systemic chemotherapy (mostly bortezomib, lenalidomide/pomalidomide and dexamethasone based) with or without local treatment. On progression to multiple myeloma, 9 patients underwent high dose chemotherapy(melphalan) followed by autologous stem cell transplant. Nine (12.7%) patients died, the causes being COVID-19 infection in 1, surgical complications in 1, PD in 2, second malignancies in 3 and unknown in 2. The actuarial rates of PFS & OS were 58.4% & 92.5% at 3 years and 50.3% & 89.4% at 5 years, respectively. Metachronous second malignancies were noted in 4 patients (B-ALL-1, lung cancer-1, metastatic carcinoma cervix-1, metastatic carcinoma gall bladder-1). CONCLUSION In patients with SP, radical RT with a modest dose (45-50 Gy) leads to satisfactory symptom relief, response and local control. Close to 40% patients eventually progress to multiple myeloma, out of which 50% can be successfully salvaged with further systemic chemotherapy. The 5-year OS approaches 90% in this cohort.
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Pattanaik J, Bhasker S, Biswas A, R AV, Sharma A, Pramanik R, Kumar R, Sanyal S, Samala SK, Ghosh V, Sushant S, Pandey S, Tanwar MS, Praveen DVS, Mandal S. Patient-Reported Outcomes Evaluating the Impact of Hypo-Fractionated Palliative Quadshot Radiotherapy and Concurrent CDDP Treatment on Health-Related Quality of Life in Patients with Locally Advanced Squamous Cell Carcinoma of the Head and Neck. Int J Radiat Oncol Biol Phys 2023; 117:S122. [PMID: 37784316 DOI: 10.1016/j.ijrobp.2023.06.461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) In locally advanced squamous cell carcinoma of the head and neck (LAHNSCC), the main goal of treatment remains survival while improving quality of life (QOL). In recent decades, there has been a paradigm shift in the measurement of clinical outcomes in patients diagnosed with cancer, focusing on the patient perspective by incorporating patient-reported outcomes (PROs). The primary objective of this study was to evaluate the improvement in quality of life with the use of cyclic hypo-fractionated palliative QUAD SHOT radiotherapy (RT) with concurrent cisplatin (CDDP) in previously untreated patients with incurable LAHNSCC. MATERIALS/METHODS In this prospective interventional phase- II study, 60 patients with locally advanced squamous cell carcinoma of the head and neck, majority stage IVB, ECOG PS ≤ 3, were treated with QUAD SHOT RT (14 Gy/4 fractions/2 days - BD with 6-hour interval and concurrent CDDP at 6 mg/m2. This treatment was repeated at 4-week intervals for 2 additional cycles if tumor progression did not occur. Serial changes in HR -QoL were assessed using EORTC QLQ C-30 and H&N-35) at 4 different time points. Statistical methods such as the Wilcoxon signed-rank test and Friedman test were used to compare QoL values at different time points with Bonferroni correction for multiple comparisons to control for type I errors. RESULTS The median global health score (GHS) at baseline was 41.667, with an initial increase in score at 4 weeks (50.00) and at 8 weeks (54.167) that did not continue at 12 weeks (41.667). Symptoms related to toxicities (speech, social contact, sticky saliva, dry mouth, senses in H&N 35) were lower after 4 weeks. Application of the Friedman test for four time points revealed significant improvement in role function at 4 weeks, which remained constant at 8 weeks but was not sustained at 12 weeks. Comparison of HN-35 symptom scores between the four time points showed improvement in symptoms such as pain, swallowing, and mouth opening at 4 and 8 weeks. The mean QLQ C30 summary score for these patients improved at four weeks but did not remain constant at 8 and 12 weeks. CONCLUSION Our study showed significant improvement in quality-of-life parameters and reduction in symptom burden at 4 and 8 weeks due to disease control and symptom palliation by QUADSHOT CTRT, while quality-of-life scores worsened and symptom scores were not maintained at 12 weeks due to disease progression and occurrence of acute toxicities. This phase II study may serve as the basis for designing a phase III randomized control trial to compare quality of life changes with QUADSHOT CTRT and other palliative CTRT regimens.
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Singh UB, Ray Y, Kanswal S, Sharma HP, Aayilliath AK, Wig N, Ahuja V, Biswas A, Velpandian T. Low rifampicin levels in plasma associated with a poor clinical response in patients with abdominal TB. Int J Tuberc Lung Dis 2023; 27:787-789. [PMID: 37749829 PMCID: PMC10519389 DOI: 10.5588/ijtld.23.0149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/15/2023] [Indexed: 09/27/2023] Open
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Bhasker S, Pattanaik J, Biswas A, R AV, Sharma A, Pramanik R, Sanyal S, Praveen DVS, Kumar R, Sushant S, Ghosh V, Mandal S, Samala SK, Tanwar MS, Pandey S. Hypo-Fractionated Palliative QUADSHOT Radiotherapy and Concurrent CDDP in Patients with LAHNSCC: Toxicities and Clinical Outcomes. Int J Radiat Oncol Biol Phys 2023; 117:e567. [PMID: 37785734 DOI: 10.1016/j.ijrobp.2023.06.1893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Shorter palliative hypo-fractionated radiotherapy regimens given concurrently with chemotherapy, preferably cisplatin (radiosensitizer), increase response rates with acceptable toxicity, leading to better compliance of patients with locally advanced squamous cell carcinoma of the head and neck (LAHNSCC) in whom late toxicities due to chemoradiotherapy are less relevant. This single institution prospective interventional phase II study was conducted with the goal of achieving high rates of locoregional control with acceptable treatment-related toxicity. MATERIALS/METHODS In this prospective interventional phase- II study, 60 patients with LAHNSCC (treatment naive), the majority in stage IVB and ECOG PS ≤ 3, were treated with QUAD SHOT RT using the conventional 2D technique (14Gy in 4 fractions on 2 consecutive days twice daily with a 6-hour interval between the two fractions) and concurrent cisplatin (CDDP) at a dose of 6 mg/m2. This treatment was repeated at 4-week intervals for 2 additional cycles if tumor progression did not occur. The Kaplan-Meier method was used to determine survival probability for progression-free survival (PFS) and overall survival (OS). Descriptive statistics with number and percentage were used for each toxicity and tumor response at different time points. A P value of less than 0.05 was considered significant. RESULTS In our study, all patients received at least one cycle of QUADSHOT chemoradiotherapy (CTRT), while 35 and 18 patients received the 2nd and 3rd QUADSHOT CTRT, respectively. Of the patients who completed the first cycle of QUADSHOT CTRT, 27 (45%) patients had a partial response (PR) and 22 (36.7%) had stable disease (SD). Of the patients who completed the second cycle QUADSHOT CTRT, 77.2% had SD, while 11.4% had PR and 11.4% had PD. After the 3rd QUADSHOT CTRT, 72.2% had SD, while 11.1% had PR and 16.7% had PD. The overall response rate (SD +PR) in our study was 81%, 88.6%, and 83% after the 1st, 2nd, and 3rd QUADSHOT CTRT, respectively. After the 3rd QUADSHOT CTRT, no patient showed grade 4 toxicity. Most patients had grade I/ II toxicities e.g., skin (grade I -83%), mucositis (grade II -50%), salivary gland toxicity (grade II -50%), grade I laryngitis (83.3%). Grade- III oral mucositis and pharyngitis were seen in 27% and 6.7% of patients, respectively. Median OS and PFS were 7.9 months and 6.2 months, respectively. CONCLUSION Concurrent chemotherapy acts as a radiosensitizer and provides a synergistic effect when coupled with hypo-fractionated radiation, resulting in more effective control of locoregional disease in locally advanced head and neck tumors with acceptable toxicities. This study is hypothesis-generating and may serve as a basis for developing optimal CTRT regimens for patients with LAHNSCC who are not suitable for curative treatment.
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Gupta N, Kodan P, Baruah K, Soneja M, Biswas A. Zika virus in India: past, present and future. QJM 2023; 116:644-649. [PMID: 31642501 DOI: 10.1093/qjmed/hcz273] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/31/2022] Open
Abstract
Zika virus (ZIKV) is an arthropod-borne flavivirus that presents with acute febrile illness associated with rash, arthralgia and conjunctivitis. After years of sporadic reports in Africa, the three major outbreaks of this disease occurred in Yap Islands (2007), French Polynesia (2013-14) and South Americas (2015-16). Although, serological surveys suggested the presence of ZIKV in India in 1950s, cross-reactivity could not be ruled out. The first four proven cases of ZIKV from India were reported in 2017. This was followed by major outbreaks in the states of Rajasthan and Madhya Pradesh in 2018. Fortunately, the outbreaks in India were not associated with neurological complications. These outbreaks in India highlighted the spread of this disease beyond geographical barriers owing to the growing globalization, increased travel and ubiquitous presence of its vector, the Aedes mosquito. In this review, we discuss the epidemiology, clinical features and management of ZIKV in India.
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Dey S, Nath S, Alam Ansari T, Biswas A, Barman F, Mukherjee S, Gopal G, Bhattacharyya A, Mukherjee A, Kundu R, Paul S. Application of green synthesized bimetallic nZVI-Cu nanoparticle as a sustainable alternative to chemical fertilizers to enhance growth and photosynthetic efficiency of rice seedlings. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107837. [PMID: 37331074 DOI: 10.1016/j.plaphy.2023.107837] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/23/2023] [Accepted: 06/12/2023] [Indexed: 06/20/2023]
Abstract
Application of nanomaterials in agriculture has been extensively explored over the past decade leading to a wide ambit of nanoparticle-based agrochemicals. Metallic nanoparticles consisting of plant macro- and micro-nutrients have been used as nutritional supplements for plants through soil amendments, foliar sprays, or seed treatment. However, most of these studies emphasize monometallic nanoparticles which limit the range of usage and effectivity of such nanoparticles (NPs). Hence, we have employed a bimetallic nanoparticle (BNP) consisting of two different micro-nutrients (Cu & Fe) in rice plants to test its efficacy in terms of growth and photosynthesis. Several experiments were designed to assess growth (root-shoot length, relative water content) and photosynthetic parameters (pigment content, relative expression of rbcS, rbcL & ChlGetc.). To determine whether the treatment induced any oxidative stress or structural anomalies within the plant cells, histochemical staining, anti-oxidant enzyme activities, FTIR, and SEM micrographs were undertaken. Results indicated that foliar application of 5 mg L-1 BNP increased vigor and photosynthetic efficiency whereas 10 mg L-1 concentration induced oxidative stress to some extent. Furthermore, the BNP treatment did not perturb the structural integrity of the exposed plant parts and also did not induce any cytotoxicity. Application of BNPs in agriculture has not been explored extensively to date and this study is one of the first reports that not only documents the effectivity of Cu-Fe BNP but also critically explores the safety of its usage on rice plants making it a useful lead to design new BNPs and explore their efficacy.
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Biswas A, McNamara C, Gowda VK, Gala F, Sudhakar S, Sidpra J, Vari MS, Striano P, Blaser S, Severino M, Batzios S, Mankad K. Neuroimaging Features of Biotinidase Deficiency. AJNR Am J Neuroradiol 2023; 44:328-333. [PMID: 36759144 PMCID: PMC10187823 DOI: 10.3174/ajnr.a7781] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023]
Abstract
Biotinidase deficiency is an autosomal recessive condition caused by pathogenic variants in the BTD gene. Resultant deficiency of free biotin leads to impaired activity of the enzyme carboxylase and related neurologic, dermatologic, and ocular symptoms. Many of these are reversible on treatment, but early recognition and commencement of biotin supplementation are critical. This practice is especially important in countries where routine neonatal screening for biotinidase deficiency is not performed. In this report comprising 14 patients from multiple centers, we demonstrate the MR imaging patterns of this disorder at various age groups. Knowledge of these patterns in the appropriate clinical context will help guide early diagnosis of this treatable metabolic disorder.
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White K, Connor K, Meylan M, Bougoüin A, Salvucci M, Bielle F, O'Farrell AC, Sweeney K, Weng L, Bergers G, Dicker P, Ashley DM, Lipp ES, Low JT, Zhao J, Wen P, Prins R, Verreault M, Idbaih A, Biswas A, Prehn JHM, Lambrechts D, Arijs I, Lodi F, Dilcan G, Lamfers M, Leenstra S, Fabro F, Ntafoulis I, Kros JM, Cryan J, Brett F, Quissac E, Beausang A, MacNally S, O'Halloran P, Clerkin J, Bacon O, Kremer A, Chi Yen RT, Varn FS, Verhaak RGW, Sautès-Fridman C, Fridman WH, Byrne AT. Identification, validation and biological characterisation of novel glioblastoma tumour microenvironment subtypes: implications for precision immunotherapy. Ann Oncol 2023; 34:300-314. [PMID: 36494005 DOI: 10.1016/j.annonc.2022.11.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND New precision medicine therapies are urgently required for glioblastoma (GBM). However, to date, efforts to subtype patients based on molecular profiles have failed to direct treatment strategies. We hypothesised that interrogation of the GBM tumour microenvironment (TME) and identification of novel TME-specific subtypes could inform new precision immunotherapy treatment strategies. MATERIALS AND METHODS A refined and validated microenvironment cell population (MCP) counter method was applied to >800 GBM patient tumours (GBM-MCP-counter). Specifically, partition around medoids (PAM) clustering of GBM-MCP-counter scores in the GLIOTRAIN discovery cohort identified three novel patient clusters, uniquely characterised by TME composition, functional orientation markers and immune checkpoint proteins. Validation was carried out in three independent GBM-RNA-seq datasets. Neoantigen, mutational and gene ontology analysis identified mutations and uniquely altered pathways across subtypes. The longitudinal Glioma Longitudinal AnalySiS (GLASS) cohort and three immunotherapy clinical trial cohorts [treatment with neoadjuvant/adjuvant anti-programmed cell death protein 1 (PD-1) or PSVRIPO] were further interrogated to assess subtype alterations between primary and recurrent tumours and to assess the utility of TME classifiers as immunotherapy biomarkers. RESULTS TMEHigh tumours (30%) displayed elevated lymphocyte, myeloid cell immune checkpoint, programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 transcripts. TMEHigh/mesenchymal+ patients featured tertiary lymphoid structures. TMEMed (46%) tumours were enriched for endothelial cell gene expression profiles and displayed heterogeneous immune populations. TMELow (24%) tumours were manifest as an 'immune-desert' group. TME subtype transitions upon recurrence were identified in the longitudinal GLASS cohort. Assessment of GBM immunotherapy trial datasets revealed that TMEHigh patients receiving neoadjuvant anti-PD-1 had significantly increased overall survival (P = 0.04). Moreover, TMEHigh patients treated with adjuvant anti-PD-1 or oncolytic virus (PVSRIPO) showed a trend towards improved survival. CONCLUSIONS We have established a novel TME-based classification system for application in intracranial malignancies. TME subtypes represent canonical 'termini a quo' (starting points) to support an improved precision immunotherapy treatment approach.
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Della Rosa M, Duranovich F, Pacheco D, Sandoval E, Khan A, Biswas A, Jonker A. Forage type affects the temporal methane emission profiles in dairy cows fed fresh forages. Anim Feed Sci Technol 2023. [DOI: 10.1016/j.anifeedsci.2023.115604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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Phillips S, Biswas A, Watson T. An assessment of learners’ child passenger safety knowledge. Am J Med Sci 2023. [DOI: 10.1016/s0002-9629(23)00198-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Sarkar P, Biswas A, Kumar R, Rai S, Jha SN, Bhattacharyya D. Role of C and B 4C barrier layers in controlling diffusion propagation across the interface of Cr/Sc multilayers. Phys Chem Chem Phys 2023; 25:3072-3082. [PMID: 36620902 DOI: 10.1039/d2cp03785h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The optical performance of low-bilayer-thickness metallic multilayers (ML) can be improved significantly by limiting the intermixing of consecutive layers at the interfaces. Barrier layers are supposed to exhibit a decisive role in controlling diffusion across the interfaces. The element-specific grazing incidence extended X-ray absorption fine structure technique using synchrotron radiation has been used in conjunction with grazing incidence X-ray reflectivity and diffuse X-ray scattering measurements to study the impact of the two most common barrier layers, viz., C and B4C, at the interfaces of Cr/Sc MLs. The diffusion propagation is reduced by both the barrier layers; however, it is found that the improvement is more significant with the B4C barrier layer. It is seen that C forms an intermixed layer with Sc and leads to carbide formation at the interface, which then acts as shielding and prevents further interdiffusion, while B4C hardly penetrates into Sc and stops the overlap between Sc and Cr directly by wetting the corresponding interface. Thus, the above measurements reveal crucial and precise information regarding the elemental diffusion kinetics at the interfaces of Cr/Sc MLs in a non-destructive way, which is very important for technological applications of these MLs as X-ray optical devices.
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Biswas A, Vega-Guzman J, Bansal A, Kara AH, Aphane M, Yildirim Y, Alshehri HM. Solitary waves, shock waves and conservation laws with the surface tension effect in the Boussinesq equation. PROCEEDINGS OF THE ESTONIAN ACADEMY OF SCIENCES 2023. [DOI: 10.3176/proc.2023.1.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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D'Arco F, Biswas A, Clement E, Rajput K, Juliano AF. Subtle Malformation of the Cochlear Apex and Genetic Abnormalities: Beyond the "Thorny" Cochlea. AJNR Am J Neuroradiol 2023; 44:79-81. [PMID: 36549853 PMCID: PMC9835904 DOI: 10.3174/ajnr.a7746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022]
Abstract
With the routine use of high-resolution heavily T2-weighted sequences to evaluate patients with hearing deficits, new, subtle phenotypes of cochlear malformations are being discovered and an increasing number of genotype-phenotype correlations are being found through a reverse phenotype approach, which can help guide geneticists. In this brief report, we present subtle malformations of the apical turn of the cochlea related to 3 genetic mutations, emphasizing the importance of a careful assessment of the cochlear apex.
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Kanodia R, Kumar R, Biswas A, Bhasker S. 251P Is QUAD SHOT palliative cyclical hypo-fractionated radiotherapy in advanced head and neck cancer the way to go? An alternative regimen in low resource countries. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.10.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
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19
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K S, T M, Biswas A, T MS. Remediation potential of mushrooms and their spent substrate against environmental contaminants: An overview. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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20
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Kerns S, Biswas A, Minnetian NM, Borovik AS. Artificial Metalloproteins: At the Interface between Biology and Chemistry. JACS AU 2022; 2:1252-1265. [PMID: 35783165 PMCID: PMC9241007 DOI: 10.1021/jacsau.2c00102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 05/22/2023]
Abstract
Artificial metalloproteins (ArMs) have recently gained significant interest due to their potential to address issues in a broad scope of applications, including biocatalysis, biotechnology, protein assembly, and model chemistry. ArMs are assembled by the incorporation of a non-native metallocofactor into a protein scaffold. This can be achieved by a number of methods that apply tools of chemical biology, computational de novo design, and synthetic chemistry. In this Perspective, we highlight select systems in the hope of demonstrating the breadth of ArM design strategies and applications and emphasize how these systems address problems that are otherwise difficult to do so with strictly biochemical or synthetic approaches.
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21
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Biswas A, Amirabadi A, Wagner M, Ertl-Wagner B. Features of Visually AcceSAble Rembrandt Images: Interrater Reliability in Pediatric Brain Tumors. AJNR Am J Neuroradiol 2022; 43:304-308. [PMID: 35058297 PMCID: PMC8985665 DOI: 10.3174/ajnr.a7399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/20/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND AND PURPOSE At present, no evidence-based lexicon exists for pediatric intracranial tumors. The Visually AcceSAble Rembrandt Images terminology describes reproducible MR imaging features of adult gliomas for prediction of tumor grade, molecular markers, and survival. Our aim was to assess the interrater reliability of the pre-resection features of Visually AcceSAble Rembrandt Images in pediatric brain tumors. MATERIALS AND METHODS Fifty consecutive pre-resection brain MR imaging examinations of pediatric intracranial neoplasms were independently reviewed by 3 neuroradiologists. The intraclass correlation coefficient for continuous variables and the Krippendorf alpha were used to evaluate the interrater agreement. Subgroup analysis was performed for 30 gliomas. RESULTS Parameters with almost perfect agreement (α > .8) included tumor location (F1) and proportion of enhancing tumor (F5). Parameters with substantial agreement (α = .61-.80) were side of tumor epicenter (F2), involvement of eloquent brain (F3), enhancement quality (F4), proportion of non-contrast-enhancing tumor (F6), and deep white matter invasion (F21). The other parameters showed either moderate (α = .41-.60; n = 11), fair (α = .21-.40; n = 5), or slight agreement (α = 0-.20; n = 1). Subgroup analysis of 30 gliomas showed almost perfect agreement for tumor location (F1), involvement of eloquent brain (F3), and proportion of enhancing tumor (F5); and substantial agreement for side of tumor epicenter (F2), enhancement quality (F4), proportion of noncontrast enhancing tumor (F6), cysts (F8), thickness of enhancing margin (F11), and deep white matter invasion (F21). The intraclass correlation coefficient for measurements in the axial plane was excellent in both the main group (0.984 [F29] and 0.982 [F30]) and the glioma subgroup (0.973 [F29] and 0.973 [F30]). CONCLUSIONS Nine features of Visually AcceSAble Rembrandt Images have an acceptable interrater agreement in pediatric brain tumors. For the subgroup of pediatric gliomas, 11 features of Visually AcceSAble Rembrandt Images have an acceptable interrater agreement. The low degree of reproducibility of the remainder of the features necessitates the use of features tailored to the pediatric age group and is likely related to the more heterogeneous imaging morphology of pediatric brain tumors.
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Majumdar P, Mandi S, Biswas A, Nayak P, Sahu S. COVID-19 pandemic-imposed lockdown: impacts on the rural agrarian and the urban corporate workforce of India. BIOL RHYTHM RES 2022. [DOI: 10.1080/09291016.2022.2031422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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23
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Alshehri HM, Biswas A, González-Gaxiola O, Yildirim Y. Bright optical solitons with polynomial law of nonlinear refractive index by Adomian decomposition scheme. PROCEEDINGS OF THE ESTONIAN ACADEMY OF SCIENCES 2022. [DOI: 10.3176/proc.2022.3.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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24
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Alngar ME, Alzahrani AK, Belic MR, Biswas A, Ekici M, Khan S, Zayed EM. Optical solitons in fiber Bragg gratings with quadratic-cubic law of nonlinear refractive index and cubic-quartic dispersive reflectivity. PROCEEDINGS OF THE ESTONIAN ACADEMY OF SCIENCES 2022. [DOI: 10.3176/proc.2022.2.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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25
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Subramanian S, Biswas A, Alves C, Sudhakar S, Shekdar K, Krishnan P, Shroff M, Taranath A, Arrigoni F, Aldinger K, Leventer R, Dobyns W, Mankad K. ACTA2-Related Dysgyria: An Under-Recognized Malformation of Cortical Development. AJNR Am J Neuroradiol 2022; 43:146-150. [PMID: 34857515 PMCID: PMC8757559 DOI: 10.3174/ajnr.a7364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/27/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND AND PURPOSE Pathogenic variants in the ACTA2 gene cause a distinctive arterial phenotype that has recently been described to be associated with brain malformation. Our objective was to further characterize gyral abnormalities in patients with ACTA2 pathogenic variants as per the 2020 consensus recommendations for the definition and classification of malformations of cortical development. MATERIALS AND METHODS We performed a retrospective, multicentric review of patients with proved ACTA2 pathogenic variants, searching for the presence of malformations of cortical development. A consensus read was performed for all patients, and the type and location of cortical malformation were noted in each. The presence of the typical ACTA2 arterial phenotype as well as demographic and relevant clinical data was obtained. RESULTS We included 13 patients with ACTA2 pathogenic variants (Arg179His mutation, n = 11, and Arg179Cys mutation, n = 2). Ninety-two percent (12/13) of patients had peri-Sylvian dysgyria, 77% (10/13) had frontal dysgyria, and 15% (2/13) had generalized dysgyria. The peri-Sylvian location was involved in all patients with dysgyria (12/12). All patients with dysgyria had a characteristic arterial phenotype described in ACTA2 pathogenic variants. One patient did not have dysgyria or the characteristic arterial phenotype. CONCLUSIONS Dysgyria is common in patients with ACTA2 pathogenic variants, with a peri-Sylvian and frontal predominance, and was seen in all our patients who also had the typical ACTA2 arterial phenotype.
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