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Clade-Specific Influences of Glycans on the Interactions between HIV-1 Envelope and Broadly Neutralizing Antibodies
No full textN-linked glycans are important in the elicitation and activity of many broadly neutralizing antibodies (bNAbs) against HIV-1. The high conformational flexibility of glycans hindered detailed atomistic investigations of glycan-bNAb interactions, including the glycan shielding of bNAbs. Importantly, how these interactions vary across different HIV-1 clades remains unclear. The variability in the number and location of potential N-linked glycosylation sites (PNGS) on the HIV-1 envelope (Env) protein across clades can lead to differences in glycan dynamics and topology, potentially affecting Env-bNAb interactions and the clade-specific efficacy of bNAb-based therapies. Here, we combined comprehensive glycan conformational sampling, using the software glycoSHIELD, and molecular dynamics simulations to model fully glycosylated trimeric Env for six HIV-1 strains, one from each of the major clades A, B, C, G, CRF01 AE (01 AE), and CRF07 BC (07 BC). We assessed the interactions of 50 different bNAbs, drawn from all of the major bNAb classes, with each of these strains, quantifying glycan shielding, glycan-bNAb interactions, and their clade-specific variations for each bNAb in microscopic detail. Our findings reveal that while glycans cover most of the exposed surface area in all clades, the amount of accessible surface varies, with clade B having the minimum and clade 07 BC having the maximum antibody accessible surface area. The number of glycan conformers per glycosylation site also varies with clades, even for conserved sites. Overall, we observed that bNAbs interact with more glycans than those previously reported in experimental and computational studies. Important variations emerge in Env-bNAb interactions with the clade and bNAb-class. These atomic-level insights will be valuable for improving bNAb-based therapies and vaccine design strategies against HIV-1
Spotlight on the artifacts in next-generation sequencing in PGT-A: Reason for high mosaicism reporting
No full textThe study investigates artifacts in Next-Generation Sequencing (NGS) used for Preimplantation Genetic Testing for Aneuploidy (PGT-A) and their contribution to the high rates of mosaicism reporting. Modern PGT-A can detect mosaicism by analyzing copy number variations (CNVs) in embryonic biopsies, yet distinguishing true mosaicism from artifacts remains challenging. In a cohort of 22 embryos, NGS profiles revealed recurring artifacts on chromosomes 7, 11, 16, and 19. These artifacts likely result from errors in DNA amplification for NGS library preparation, potentially leading to false mosaicism diagnosis. The study utilized DNA extracted from trophectoderm biopsies, spent culture media, and whole blastocyst samples, with CNV analysis performed using BlueFuse Multi software. Quality control parameters such as DLR noise, read count, and quality score were considered, confirming that technical inconsistencies contribute to the observed artifacts. Findings align with prior research, suggesting the need for improved NGS protocols to minimize these errors. Enhanced internal validation and adoption of new technologies could reduce false-positive rates and improve clinical decision-making in PGT-A
Defect-Mediated Exciton Storage in Ag–In–Ga–S Nanocrystals
No full textColloidal Ag–In–Ga–S nanocrystals (NCs) represent a promising class of RoHS-compliant light emitters exhibiting narrow excitonic photoluminescence (PL). Here, we unveil a unique exciton storage mechanism in Ag–In–Ga–S NCs. Temperature-dependent PL and ultrafast transient absorption spectroscopy show that thermally activated back transfer from long-lived (∼1.8 μs) shallow defects repopulates the excitons, increasing both exciton lifetime and PL intensity. The thermally activated back transfer increases the excitonic PL lifetime systematically from a few nanoseconds at 6.5 K to about 100 ns at 300 K, a reverse trend compared to typical semiconductor NCs like CdSe. This reverse trend of Ag–In–Ga–S NCs mirrors dopant-mediated exciton dynamics in Mn-doped CdSe NCs but arises here from intrinsic defects of the undoped NCs. Our results establish a generalizable pathway for prolonging excitonic lifetime (exciton storage) with high PL intensity in semiconductor NCs (quantum dots), enabling potential applications in photocatalysis, photonic memory, and optoelectronic device
Intra‐Configurational Spin‐Flip <i>d</i> → <i>d</i> Transition of Mo (III) Doped Perovskite for Ultra‐Narrow Near Infrared‐II Emission in Ambient Conditions
No full textSharp near‐infrared‐II (NIR‐II) emissions are typically achieved through electronic transitions of rare‐earth ions, while transitions in transition metal ions are broad due to electron–ligand interactions. An exception is the intra‐configurational spin‐flip (ICSF) transition like t2g 3 t2g 3 of Mo3+ emitting sharp NIR‐II emission, but only at cryogenic temperatures under vacuum. The high oxophilicity of Mo 3+ created defects during the synthesis, quenching the emission at room temperature. Herein, we overcome this issue by synthesizing Mo 3+ − doped Cs2 NaInCl6 double perovskites in a reducing H 3 PO2 environment. [MoCl6 ]3- octahedra are formed, exhibiting ultra‐narrow ICSF ( 2 T1g / 2 Eg 4 A2g ) NIR‐II emission at 1095 nm in ambient conditions. In addition, a second ICSF 2 T2g 4 A2g emission is observed at 700 nm, violating the Kasha's rule. The intensity of ICSF emissions increase with increasing temperature (7–350 K) due to vibronic coupling relaxing the Laporte selection rule. The samples are stable for more than 6 months in ambient conditions, allowing for a detailed study of fundamental photophysics and fabrications of phosphor‐converted light emitting diodes. This is the first Mo3+ –based NIR‐II optoelectronic device, opening opportunities for applications like optical fibers and lasing
Covalent organic–inorganic layered 2D CdCl<sub>2</sub>(<i>n</i>-hexylamine)<sub>2</sub> and not Cd<sub>2</sub>S<sub>2</sub>(<i>n</i>-hexylamine)
No full textOrganic ammonium cations (A+) and inorganic [PbX4]2- (X: Cl, Br, I) anions bind to each other through electrostatic interactions, forming layered two-dimensional (2D) A2PbX4 hybrid perovskites. Thus, they dissociate in water. In contrast, charge-neutral organic amines (L) can covalently bind to metal M (M: Zn, Cd), forming M2Q2 (L) (Q: S, Se, Te) hybrid II–VI semiconductors. We attempted to explore the optoelectronic properties of such a reported hybrid II–VI compound, Cd2S2 (n-hexylamine), but surprisingly it did not form. Instead, the obtained product, referred to here as product-1, is a mixture of a new layered halide compound CdCl2 (n-hexylamine)2 and CdS nanocrystals (NCs). The quantum confinement in ∼3 nm CdS NCs shows interesting optoelectronic properties, which were initially misinterpreted as signatures of a Cd2S2 (n-hexylamine) quantum well structure. The obtained layered compound CdCl2 (n-hexylamine)2 crystallizes in the P21/c space group. Each Cd2+ is coordinated with 4 equatorial Cl− and two axial n-hexylamines, forming distorted octahedra that propagate in 2D, forming the layered structure. Note that the organic and inorganic components in CdCl2 (n-hexylamine)2 are covalently bound (coordinate bonds), making the compound water-stable, unlike the electrostatically bound A2PbX4 perovskites. The covalent organic–inorganic bonding nature of the layered 2D hybrid halide compounds might be explored further for designing water-stable hybrid halide perovskite-like materials
Visible light driven hydrogen bonding assisted complete photocatalytic degradation of selected antibiotics by lanthanide-based metal–organic frameworks
No full textMetal–organic frameworks (MOFs) could be a promising class of photocatalysts due to their high surface area, framework robustness, and tunable architectures, which enable modulation of their semiconductor properties for enhanced light harvesting and subsequent photocatalysis. In this work, a cobalt-based metalloligand has been utilized to synthesise lanthanide (Ln)-based MOFs (Ln-MOFs). The architecturally engineered Ln-MOFs exhibit significant visible light absorption and support noteworthy photocatalysis for the complete degradation of the selected antibiotics. Both Ln-MOFs enabled complete photodegradation of antibiotics, as supported by their high degradation reaction rates. The Ln-MOFs exhibited remarkably enhanced photocatalytic activity compared to the Co-based photosensitizer. This fact is attributed to an enhanced charge-carrier lifetime for both Ln-MOFs, which was corroborated by the transient absorption spectroscopy, photoluminescence, and electrochemical impedance spectroscopy analyses. These studies, along with the scavenger experiments, helped in establishing the probable mechanism for Ln-MOF-mediated photodegradation. We further illustrate the importance of hydrogen bonding-assisted encapsulation of an antibiotic molecule within the pores of Ln-MOFs, which remarkably improved its photocatalytic degradation. The present visible-light-driven Ln-MOFs are a rare example of photocatalysts exhibiting high efficiency for the complete photodegradation of antibiotics
Sub-seasonal prediction of compound hot and dry extremes in India
No full textIn India’s summer monsoon-dominated climate, compound hot and dry extremes (CHDEs) pose considerable challenges to agriculture and water resources. However, their drivers and predictability at sub-seasonal time scale remain largely unexplored. Using observations, reanalysis datasets, and forecast products, we examine the occurrence, drivers, and prediction skills of soil moisture based CHDEs in India from 1951 to 2020. The observed warming has resulted in a significant (p-value < 0.05) rise in the frequency of CHDEs in four (Himalayan, West Central, Central Northeast, and Northeast) out of six regions from 1951 to 2020. The area affected by CHDEs has also increased significantly during the recent (1986–2020) period compared to the previous (1951–1985). The most severe CHDEs occurred during the major summer monsoon failures in 1972, 1987, 2002, 2009, 2014, and 2015. The summer monsoon breaks are the main drivers of CHDEs, as about 98% of the events occurred during the break periods. We used sub-seasonal to seasonal (S2S) forecasts from the United Kingdom Meteorological Office (UKMO) and Extended Range Forecast Systems (ERFS) to examine the prediction skills of CHDEs at different lead times. While UKMO (from S2S) and ERFS forecasts demonstrate satisfactory skills to predict CHDEs in India at a 15-day lead, UKMO provides better skills than the ERFS, which is currently operational in India. Good prediction skills from both the models for severity and area of CHDEs demonstrate their utility for the early warning of compound extremes in India, which can assist in climate adaptation
Climate change and effectiveness of dams in flood mitigation in India
No full textIndia, the third-largest dam-building nation, highly relies on dams for irrigation, hydropower, and flood control. Observations show that dams both mitigated and triggered floods across Indian river basins. However, their effectiveness in mitigating floods under current and future climates remains unknown. Using in-situ and satellite observations and model simulations for 178 major dams, we show that flood mitigation depends more on antecedent reservoir storage than upstream rainfall. Downstream floods are more likely when reservoirs exceed 90% of their full capacity. The duration with reservoir storage exceeding 90% is projected to increase threefold at 3 °C warming compared to 1 °C. A substantial rise in compound events of high inflow and high antecedent reservoir storage is also projected from 0.55 ± 0.22 events/year at 1 °C warming to 1.1 ± 0.4 events/year at 3 °C warming. Our findings highlight the need for advanced approaches for dam operations (maintaining buffer storage) integrated with early warnings of extreme inflow in India
River drought forcing of the Harappan metamorphosis
No full textHydroclimatic variations are among the factors shaping the rise and fall of the Indus Valley Civilization. Yet, constraining the role of water availability across this vast region has remained challenging owing to the scarcity of site-specific paleoclimate records. By integrating high-resolution paleoclimate archives with palaeohydrological reconstructions from transient climate simulations, we identify the likelihood of severe and persistent river droughts, lasting from decades to centuries, that affected the Indus basin between ~4400 and 3400 years before present. Basin-scale streamflow anomalies further indicate that protracted river drought coincided with regional rainfall deficits, together reducing freshwater availability. We contend that reduced water availability, accompanied by substantially drier conditions, may have led to population dispersal from major Harappan centers, while acknowledging that societal transformation was shaped by a complex interplay of climatic, social, and economic pressures
The Lunar Gravitational-wave Antenna: mission studies and science case
No full textThe Lunar Gravitational-wave Antenna (LGWA) is a proposed array of next-generation inertial sensors to monitor the response of the Moon to gravitational waves (GWs). Given the size of the Moon and the expected noise produced by the lunar seismic background, the LGWA would be able to observe GWs from about 1 mHz to 1 Hz. This would make the LGWA the missing link between space-borne detectors like LISA with peak sensitivities around a few millihertz and proposed future terrestrial detectors like Einstein Telescope or Cosmic Explorer. In this article, we provide a first comprehensive analysis of the LGWA science case including its multi-messenger aspects and lunar science with LGWA data. We also describe the scientific analyses of the Moon required to plan the LGWA mission