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Temporal TCR dynamics and epitope diversity mark recovery in severe COVID-19 patients.
No full textIntroduction: Severe COVID-19 is characterized by immune dysregulation, with T cells playing a central role in disease progression and recovery. However, the longitudinal dynamics of the T cell receptor (TCR) repertoire during the course of severe illness remain unclear.
Methods: To investigate temporal changes in adaptive immunity, we analyzed peripheral blood samples from the ICU-admitted severe COVID-19 patients (n = 36) collected at three time points: Day 1 (T1), Day 4 (T2), and Day 7 (T3). Bulk RNA-sequencing was performed to extract TCR repertoires, and cytokine profiles were assessed in parallel. TCR clonotypes were annotated using VDJdb and TCRex to infer potential epitope specificities.
Results: By T3, we observed a 2.3-fold expansion in TCR clonotypes along with increased TCR-β (TRB) chain usage, indicating the emergence of a broad polyclonal T cell response. In contrast, TCR-γ (TRG) chain prevalence declined. Pro-inflammatory cytokines, including IL-1β and IL-6, were reduced over time, marking a shift toward immune resolution. Changes in CDR3 motifs and preferential TRBV gene segment usage were detected, suggesting repertoire adaptation. Additionally, annotated TCR clonotypes at T3 mapped to SARS-CoV-2 and other pathogen-associated epitopes (e.g., CMV, Plasmodium), reflecting possible cross-reactivity or memory T cell recruitment.
Discussion: These findings suggest a coordinated transition from immune dysfunction to recovery in severe COVID-19, marked by expanding TCR diversity, reduced inflammation, and predicted broadening of antigen recognition. The integrated analysis of TCR repertoire dynamics and cytokine profiles provides insights into the adaptive immune mechanisms underlying viral clearance and immune stabilization
Indian beamline at Photon Factory, high-energy accelerator research organization (KEK), Tsukuba, Japan
No full textSynchrotron X-ray sources play a vital role in the detailed structural characterisation of new materials and in advancing our understanding of structure-property relationships in advanced materials. Recognising the absence of intense X-ray synchrotron sources and the pressing nationwide demand for access to radiation sources to propel nanoscience and materials research forward, a national program was launched by Nano Mission, Department of Science and Technology, India. As part of this initiative, the Indian Beamline was established at the High-Energy Accelerator Research Organization (KEK) in Tsukuba, Japan, representing a flagship cooperative endeavour. This facility operates at 2.5 GeV with a storage ring current of 450 mA, providing around 4000 hours of user time annually across six different experiment types. The operational efficiency of this synchrotron facility, with an impressive ratio of actual user time to scheduled user time maintained at 96-98%, stands as a critical benchmark for the planning and execution of synchrotron-related experiments
Metal deficiency tuned charge transfer in intermetallic Ni<sub>2−<i>x</i></sub>Sn (<i>x</i> = 0.37–0.65) enhances selective conversion of furfural to furfuryl alcohol towards the theoretical limit
No full textHeterogeneous catalysis facilitated by intermetallic nanoparticles has recently been the subject of increased scrutiny, given the enhanced selectivity and stability they bestow on many chemical reactions compared to their monometallic components. This paper explores a series of Ni-Sn (Ni2-xSn, where x = 0.65, 0.5, 0.37) intermetallic compounds supported on a high-surface-area support, SBA-15, as catalysts for the selective hydrogenation of furfural to furfuryl alcohol. Rietveld refinements of the X-ray diffraction data show catalysts with mixed intermetallic phases that assist in the catalysis. At the same time, X-ray photoelectron spectroscopy (XPS) studies and X-ray absorption studies indicate the role played by charge transfer from Sn to Ni for the catalysis. Selectivity to the desired furfuryl alcohol in all the intermetallic samples was high (>97%), but Ni1.35Sn had a relatively lower conversion than the other intermetallic compounds
Comprehensive transcriptomic profiling of fusions and abnormal variant transcripts in pilocytic astrocytoma using NanoString nCounter technology
No full textBackground
Pilocytic astrocytoma (PA), a common pediatric and young adult low-grade brain tumor, exhibits MAPK pathway alterations, involving recurrent fusion and duplication events. These genetic changes are crucial for diagnosis, therapy guidance, and predicting patient survival. BRAF alterations are commonly detected using FISH and RT-PCR; however their cost is intensive and they lack multiplexing capacity. This study utilizes NanoString technology to provide a broader analysis of alterations in PA, aiming to improve diagnostic accuracy.
Methodology
Sixty histologically confirmed PA cases were analyzed using RT-PCR and FISH with 30 positive for KIAA1549-BRAF fusions. A customized NanoString fusion panel was developed to detect other possible fusions. RNA was isolated from FFPE samples, followed by gene fusion assessment using NanoString nCounter platform. Radiological and pathological features were analysed to evaluate their association with molecular alterations.
Results
Fusions were identified in 91 % of cases using the NanoString nCounter platform. KIAA1549-BRAF fusions were observed in majority of cases (74 %) with the most common fusion being KIAA1549-BRAF_e16-e9, present in 28 % of cases, followed by KIAA1549-BRAF_e15-e9 (22 %). Fusion events showed a significant correlation with anatomical location, particularly in the posterior fossa. However, no significant correlation was found between specific radiological features and fusion subtypes. The NanoString assay demonstrated 97 % sensitivity in detecting BRAF fusion variants, with 100 % specificity.
Conclusion
The NanoString nCounter platform demonstrated high sensitivity and specificity and identified additional fusion events, highlighting its potential as a powerful tool for high throughput analyses in clinical settings, particularly for the evaluation of PAs
Comparison of Long-Term Outcomes in Patients with Supratentorial Spontaneous Intracerebral Hemorrhage Treated with and without Surgical Intervention
No full textOriginal Article
Comparison of Long-Term Outcomes in Patients with Supratentorial Spontaneous Intracerebral Hemorrhage Treated with and without Surgical Intervention
Sharma, Agrata*; Agarwal, Ayush*; Garg, Ajay1; Vishnu, Venugopalan Y; Nilima, N2; Bhatia, Rohit; Garg, Divyani; Pandit, Awadh K; Joseph, Leve1; Billa, Srujana; Singh, Manmohan3; Suri, Ashish3; Kale, Shashank S3; Gaikwad, Shailesh B1; Srivastava, MV Padma
Author Information
Annals of Indian Academy of Neurology 28(2):p 220-226, Mar–Apr 2025. | DOI: 10.4103/aian.aian_497_24
Open
Abstract
Background and Objectives:
Intracerebral hemorrhage (ICH) is associated with high mortality and morbidity. Uncertainty still exists regarding the benefit of surgery in the management of supratentorial spontaneous ICH (sICH), especially of the basal ganglia and thalamus. Studies have not shown the clinical benefit of early surgical management compared to best medical management plus delayed surgery, when necessary. Our aim was to compare the efficacy of different neurosurgical interventions with best medical management and best medical management alone.
Methods:
We conducted a single-center, retrospective study at a tertiary care center in India in sICH patients between January 2015 and December 2022. The primary outcome was functional disability evaluated by the modified Rankin Scale (mRS) at 3, 6, and 12 months. Time-to-event outcomes were compared using the Kaplan–Meier curve.
Results:
Among 2600 stroke patients screened, 661 had sICH. Median age was 55 years, and 250 patients (37.8%) underwent neurosurgical intervention. The most common intervention was craniotomy and hematoma evacuation. The median mRS at discharge and follow-up at 3, 6, and 12 months was lower in the conservatively managed group (4, 3, 3, and 3, respectively) compared to the surgical intervention group (5, 5, 5, 4, respectively). However, the ICH score at admission was lower in the conservatively managed group and after adjustment for ICH score, there was no statistically significant difference between the two. Among the interventions, patients undergoing decompression craniectomy had the best functional outcome.
Conclusions:
Neurosurgical intervention was not associated with better functional outcome when compared to conservative management
A unique high performing nanofiltration membrane using complementary phase additives in tuning polyamide layer to treat salt rich stream of cellulosic fibre industry.
No full textA thin-film composite (TFC) nanofiltration (NF) membrane was developed using additives polysodium 4-styrenesulfonate (PSS) and tri-n-butyl phosphate (TBP) in the aqueous and organic phases to attain the synergistic effects. The effects of concentration of PSS and TBP in the respective phases were investigated on the interfacial polymerization (IP) reaction and their impact on the membrane performance. Use of sole additives led to the enhanced cross-linking and denser polyamide (PA) layer but incorporation of complementary phase additives resulted thinner and looser morphology with higher negative surface charge enhancing the nano-filtration performance. The TFC-3 membrane with optimum PSS (0.05 wt%) and TBP concentration (0.005 wt%) showed the best performance with water flux (31.4 L.m−2.h−1), rejection of sodium sulfate (90 %), and flux recovery ratio (95 %) at 8.3 bar pressure and 100 L.h−1 crossflow rate in the synthetic solution. The efficacy of the membranes was tested at the same operating conditions with the sulfate-rich industrial stream using the TFC-3 membrane and achieved 17.3 −2.h−1 average permeate flux, 75 % rejection of total dissolved salts, and 80 % rejection of organics during long-run filtration study. Further, a multi-component coupled concentration polarization and pore flow model was formulated to describe the transport of the ions as well as organic (uncharged hemicellulose) in order to predict the concentration of salt, COD in the permeate as well as the permeate flux. The membrane pore charge density was found to −21.6 mEq.L−1. The model predictions agreed closely with the experimental data. This work not only demonstrated the influence of the synergistic effects of complementary phase additives during interfacial polymerization but also provided a sustainable TFC nanofiltration membrane suitable for the treatment of the industrial process stream
Arabidopsis GELP53 overexpression modulates polysaccharide acetylation and defense through oligosaccharide-mediated signaling
No full textO-acetylation is a crucial substitution found in hemicelluloses and pectin, which are necessary for maintaining the flexibility and structural integrity of the cell. Cell wall acetyl transferases and esterases maintain balanced polysaccharide O-acetylation levels; however, the role of esterases in cell wall polysaccharide O-acetylation metabolism is not well explored. Therefore, we investigated the role of the Arabidopsis (Arabidopsis thaliana) GDSL Esterase/Lipase Protein (GELP) family member AtGELP53. Here, we show that AtGELP53 is localized in the plasma membrane. Analysis of AtGELP53-overexpressing independent transgenic lines revealed a decrease in xyloglucan acetylation, changes in acetylation of other polysaccharides, and alterations in cell wall composition. Molecular docking and in vitro protein activity assays showed that AtGELP53 might deacetylate xyloglucan and xylan. Elicitor-based, transcriptomic, and proteomic analyses in AtGELP53-overexpressing lines suggested that oligosaccharide-mediated signaling activates the cell wall and defense-related genes primarily through xyloglucan deacetylation. Furthermore, AtGELP53-overexpressing plants showed resistance against Pseudomonas syringae and Ralstonia solanacearum through activation of elicitor-mediated defense responses. Overall, our findings outline the role of AtGELP53 in polysaccharide acetylation, cell wall remodeling, and defense through oligosaccharide signaling
Correlated evolution of multiple traits gives butterflies a false head
No full textMany butterflies possess a combination of characters at the posterior hindwing end, superficially resembling their head. This false head has been hypothesized to deflect predator attacks towards the false head area. A clear understanding of the diversity and evolution of false head traits across butterflies is lacking. Here, we tested whether false head traits evolved from simple to complex in order to achieve a greater resemblance to a head. We also tested if false head traits form an adaptive constellation and, thus, evolved correlatedly. Using a phylogenetic framework with 928 lycaenid species, our results illustrate evolutionary patterns of five false traits: (i) false antennae; (ii) spot; (iii) conspicuous colouration in the false head area; (iv) false head contour in the false head area; and (v) convergent lines. We found that false traits (i)–(iv) evolved in a correlated fashion across the phylogeny, likely driven by a common selective pressure. Our findings support the idea that a false head functions as an adaptive constellation for predator attack deflection
Li(Sc<sub>0.70</sub>Ga<sub>0.24</sub>Cr<sub>0.06</sub>)Ge<sub>2</sub>O<sub>6</sub> in Polylactic Acid for Robust Near-Infrared Phosphor-Converted Light-Emitting Diodes
No full textNear-infrared (NIR) phosphor-converted light-emitting diodes (pc-LEDs) are promising for various applications, including bioimaging, sensing, and security monitoring. Although there is significant attention to NIR phosphor design, systematic investigations for integrating these phosphors into pc-LED devices are still lacking. Herein, we explore the structure–property relationship of Cr3+ ion-activator-based Li(Sc0.70Ga0.24Cr0.06)Ge2O6 phosphor and its polymer composites for broadband NIR pc-LED applications. Under blue excitation (470 nm), the phosphor emits broad NIR radiation with a peak at 890 nm and a full width at half maximum of 164 nm (256 meV). Temperature-dependent (6.3–350 K) photoluminescence (PL) spectroscopy provides mechanistic insights into the excitation and emission processes originating from the Cr3+ d-d transitions. For pc-LED fabrication, Li(Sc0.70Ga0.24Cr0.06)Ge2O6 is embedded into three different polymer matrices, namely, poly(methyl methacrylate), polylactic acid (PLA), and polycarbonate. The optimized pc-LED device is found with PLA, a biodegradable polymer. PLA-based NIR pc-LEDs exhibit an output power of ∼190 mW at 800 mA with a wall-plug efficiency of 15.6% at 15 mA. Importantly, the Li(Sc0.70Ga0.24Cr0.06)Ge2O6–PLA pc-LED shows long-term stability under a high driving current and during humidity stress tests (95% RH, 353 K, 250 mA current). Finally, an NIR pc-LED panel containing 88 pc-LEDs was fabricated, demonstrating noninvasive NIR imaging. Our Li(Sc0.70Ga0.24Cr0.06)Ge2O6–PLA composite, combining properties of both phosphor and matrix, shows potential for robust and environmentally friendly NIR pc-LEDs
Piezoelectricity in a mixture of chiral 1D hybrid lead bromide and iodide systems
No full textChiral organic–inorganic hybrid perovskites possess inherent structural asymmetry and lattice flexibility, enabling a piezoelectric response suitable for energy harvesting and sensing technologies. Here, we introduced a new strategy for the development of a piezoelectric nanogenerator (PENG) constructed from a mixture of two chiral one-dimensional hybrid lead halides, (R-MBA)PbBr3 and (R-MBA)PbI3 (MBA: methylbenzylammonium). Individually, both hybrid halide systems exhibit piezoelectric behaviour, but when mixed, the piezoelectric output increases significantly. The highest performance is achieved for the optimized mixed halide mixture [75 wt% (R-MBA)PbBr3 + 25 wt% (R-MBA)PbI3]. To improve flexibility and mechanical endurance, we incorporated the optimized halide mixture into a polycaprolactone (PCL) polymer matrix. The device with 15 wt% of the optimized halide mixture embedded in PCL demonstrates the highest peak-to-peak voltage of 40.8 V with a power density of 83.1 μW cm-2. The halide mixture–PCL composite significantly enhances the device performance, facilitated by its endurance to a higher impact force of 21 N at 8 Hz compared to the neat mixture of hybrid halide salts without PCL (4 N at 6 Hz), leading to a 1.5 times enhancement in the peak-to-peak voltage. Finally, self-powered pressure sensors were fabricated by integrating multiple PENG devices and demonstrated for smart door mat applications. These findings show that physical mixing of chiral hybrid lead halides might be a useful approach to enhance piezoelectric performance