SHARK enables sensitive detection of evolutionary homologs and functional analogs in unalignable and disordered sequences.

Intrinsically disordered regions (IDRs) are structurally flexible protein segments with regulatory functions in multiple contexts, such as in the assembly of biomolecular condensates. Since IDRs undergo more rapid evolution than ordered regions, identifying homology of such poorly conserved regions remains challenging for state-of-the-art alignment-based methods that rely on position-specific conservation of residues. Thus, systematic functional annotation and evolutionary analysis of IDRs have been limited, despite them comprising ~21% of proteins. To accurately assess homology between unalignable sequences, we developed an alignment-free sequence comparison algorithm, SHARK (Similarity/Homology Assessment by Relating K-mers). We trained SHARK-dive, a machine learning homology classifier, which achieved superior performance to standard alignment-based approaches in assessing evolutionary homology in unalignable sequences. Furthermore, it correctly identified dissimilar but functionally analogous IDRs in IDR-replacement experiments reported in the literature, whereas alignment-based tools were incapable of detecting such functional relationships. SHARK-dive not only predicts functionally similar IDRs at a proteome-wide scale but also identifies cryptic sequence properties and motifs that drive remote homology and analogy, thereby providing interpretable and experimentally verifiable hypotheses of the sequence determinants that underlie such relationships. SHARK-dive acts as an alternative to alignment to facilitate systematic analysis and functional annotation of the unalignable protein universe.

CD-CODE: crowdsourcing condensate database and encyclopedia.

The discovery of biomolecular condensates transformed our understanding of intracellular compartmentalization of molecules. To integrate interdisciplinary scientific knowledge about the function and composition of biomolecular condensates, we developed the crowdsourcing condensate database and encyclopedia ( cd-code.org ). CD-CODE is a community-editable platform, which includes a database of biomolecular condensates based on the literature, an encyclopedia of relevant scientific terms and a crowdsourcing web application. Our platform will accelerate the discovery and validation of biomolecular condensates, and facilitate efforts to understand their role in disease and as therapeutic targets.

Preferred Spin Excitations in the Bilayer Iron-Based Superconductor CaK(Fe_{0.96}Ni_{0.04})_{4}As_{4} with Spin-Vortex Crystal Order.

Spin-orbit coupling (SOC) is a key to understand the magnetically driven superconductivity in iron-based superconductors, where both local and itinerant electrons are present and the orbital angular momentum is not completely quenched. Here, we report a neutron scattering study on the bilayer compound CaK(Fe_{0.96}Ni_{0.04})_{4}As_{4} with superconductivity coexisting with a noncollinear spin-vortex crystal magnetic order that preserves the tetragonal symmetry of the Fe-Fe plane. In the superconducting state, two spin resonance modes with odd and even L symmetries due to the bilayer coupling are found similar to the undoped compound CaKFe_{4}As_{4} but at lower energies. Polarization analysis reveals that the odd mode is c-axis polarized, and the low-energy spin anisotropy can persist to the paramagnetic phase at high temperature, which closely resembles other systems with in-plane collinear and c-axis biaxial magnetic orders. These results provide the missing piece of the puzzle on the SOC effect in iron-pnictide superconductors, and also establish a common picture of c-axis preferred magnetic excitations below T_{c} regardless of the details of magnetic pattern or lattice symmetry.

Styrene-Maleimide/Maleic Anhydride Alternating Copolymers: Recent Advances and Future Perspectives.

Alternating sequencing of styrene-maleimide/maleic anhydride (S-MI/MA) in the copolymer chain is known for a long time. But since early 2000, this class of copolymers has been extensively studied using various living/controlled polymerization techniques to design S-MI/MA alternating copolymers with tunable molecular weight, narrow dispersity (Ð), and precise chain-end functionality. The widespread diverse applications of this polymeric backbone are due to its ease of synthesis, cheap starting materials, high precision in alternating sequencing, and facile post-polymerization functionalization with simple organic reactions. Recently, S-MI/MA alternating copolymers have been rediscovered as novel polymers with unprecedented emissive behavior. It outperforms the traditional fluorophores with no aggregation caused quenching (ACQ), aqueous solubility, and greater cell viability. Herein, the origin of alternating sequence, synthesis, and recent (2010-Present) developments in applications of these polymers in different fields are elaborately discussed, including the advantages of the unconventional luminogenic property. This review article also highlights the future research directions of the versatile S-MI/MA copolymers.

Doping site identification in 112 iron pnictides through a first-principles core-electron spectroscopic study.

Density functional theory based first-principles core-electron spectroscopic studies on iron-based superconducting 112 materials are presented. The existence of an extra As zigzag chain structure along with Fe-As planes in 112 materials is emphasised. Doping on an As site belonging to a chain by Sb is found to enhance the superconducting transition temperature. This is also shown from calculations with enhanced density of states when doped on chain-As. Therefore, As site identification in 112 is crucial. Theoretically computed As K-edge absorption spectra of two different types of As atoms for Ca0.85La0.15FeAs2 show a distinctly different nature. The sensitivities of As K-edge absorption spectra in the presence and absence of the `core-hole effect' are presented for future possible identification of the same experimentally. In both cases absorption spectra contain several features, the origins of which are thoroughly described in terms of site projected density of states results.

Dimensionless Equation of State to Predict Microemulsion Phase Behavior.

Prediction of microemulsion phase behavior for changing state variables is critical to formulation design of surfactant-oil-brine (SOB) systems. SOB systems find applications in various chemical and petroleum processes, including enhanced oil recovery. A dimensional equation-of-state (EoS) was recently presented by Ghosh and Johns1 that relied on estimation of the surfactant tail length and surface area. We give an algorithm for flash calculations for estimation of three-phase Winsor regions that is more robust, simpler, and noniterative by making the equations dimensionless so that estimates of tail length and surface area are no longer needed. We predict phase behavior as a function temperature, pressure, volume, salinity, oil type, oil-water ratio, and surfactant/alcohol concentration. The dimensionless EoS is based on coupling the HLD-NAC (Hydrophilic Lipophilic Difference-Net Average Curvature) equations with new relationships between optimum salinity and solubility. An updated HLD expression that includes pressure is also used to complete the state description. A significant advantage of the dimensionless form of the EoS over the dimensional version is that salinity scans are tuned based only on one parameter, the interfacial volume ratio. Further, stability conditions are developed in a simplified way to predict whether an overall compositions lies within the single, two-, or three-phase regions. Important new microemulsion relationships are also found, the most important of which is that optimum solubilization ratio is equal to the harmonic mean of the oil and water solubilization ratios in the type III region. Thus, only one experimental measurement is needed in the three-phase zone to estimate the optimum solubilization ratio, a result which can aid experimental design and improve estimates of optimum from noisy data. Predictions with changing state variables are illustrated by comparison to experimental data using standard diagrams including a new type of dimensionless fish plot. The results show that the optimum solubilization ratio and salinity using the tuned dimensionless EoS are within average errors of 2.44% and 1.17% of experimental values for the fluids examined. We then use the dimensionless equations and thermodynamic first-principles to derive the constant in Huh's equation for interfacial tension prediction.

Methicillin resistance & inducible clindamycin resistance in Staphylococcus aureus.

BACKGROUND & OBJECTIVES: Methicillin resistant Staphylococcus aureus (MRSA) isolates with inducible clindamycin resistance (iCR) are resistant to erythromycin and sensitive to clindamycin on routine testing and inducible clindamycin resistance can only be identified by D-test. This study was aimed to detect methicillin resistance and iCR among S. aureus isolates, effectiveness of some commonly used antibiotics and correlation between methicillin resistance and iCR. METHODS: The present cross-sectional study included 46 S. aureus isolates subjected to Kirby-Bauer's disk diffusion method for antibiotic susceptibility testing (AST) to estimate MRSA and resistance to some commonly used antibiotics. D-test was employed to detect iCR. RESULTS: Eleven of the 46 (23.9%) isolates tested were MRSA. Overall, 19 (41.3%) isolates showed of iCR. Vancomycin and linezolid were found to be 100 per cent effective. A positive Karl-Pearson's coefficient of correlation (0.89) between methicillin resistance and iCR was obtained. INTERPRETATION & CONCLUSIONS: Detection of iCR is important for the use of clindamycin in MRSA infections. Methicillin resistance and iCR appear to be clinically unrelated.

Extraction of polysaccharide fraction from cadamba (Neolamarckia cadamba) fruits and evaluation of its in vitro and in vivo antioxidant activities.

In this study, polysaccharide fraction (PFFNC) derived from Neolamarckia cadamba fruits showed remarkable antioxidant activity. The PFFNC was successfully extracted from the fruits by the hot water extraction process, followed by decolorization, defatting, and deproteinization. The chemical composition of PFFNC was effectively characterized by the use of UV-Vis, FT-IR, CHN, GC-MS, and 13C NMR spectroscopy. The findings indicated that PFFNC had an average molecular weight of 292 kDa and was predominantly composed of carbohydrates (76 %), with notable contributions from uronic acids (37.22 %) and proteins (12.35 %). The primary components of the sugar content were glucose (19.24 %), galactose (10.19 %), mannose (4.09 %), and glucuronic acid (2.8 %). The tertiary structural study verified the existence of a triple-helical structure. PFFNC exhibited a strong reducing power in vitro as determined by ABTS (IC50: 121 ± 0.12 µg/mL), DPPH (IC50: 146.065 ± 0.54 µg/mL), FRAP (677.788 ± 24.189 mM Fe (II)/g), hydroxyl radical scavenging (IC50: 78.736 ± 0.32 µg/mL), and phosphomolybdate assay (90.7 ± 0.43 mg AAE/g). In addition, the PFFNC furthermore showed significant in vivo antioxidant capacity, as determined using the brine shrimp (Bsmp) (Artemia salina Leach) model. The PFFNC exhibits significant antioxidant potential, suggesting broad spectrum applications in pharmaceuticals, nutraceuticals, and oxidative stress-related disorders.

Synthetic Control of Water-Stable Hybrid Perovskitoid Semiconductors.

Hybrid metal-halide perovskites and their derived materials have emerged as the next-generation semiconductors with a wide range of applications, including photovoltaics, light-emitting devices, and other optoelectronics. Over the past decade, numerous single-crystalline perovskite derivatives have been synthesized and developed. However, the synthetic methods for these derivatives mainly rely on acidic crystallization conditions. This approach leads to crystals comprising metal halide building blocks, which show problematic stability when directly exposed to water. In this study, a methodology is developed for synthesizing hybrid metal-halide compounds using lead iodide and the zwitterionic bifunctional molecule cysteamine (CYS), to form various perovskitoid structures under a broad pH range. Interestingly, the different pH conditions alter the coordination environment of lead halides, leading to lead-sulfide and lead-nitride covalent bond formation. This modification significantly enhances their stability when in direct contact with water, lasting for months. Photoluminescence measurements and first principal density functional theory (DFT) calculations reveal that the perovskitoids synthesized under basic and acidic pH conditions exhibit a direct bandgap nature, while those synthesized under neutral conditions display an indirect bandgap. This approach opens new avenues for manipulating synthetic methods to develop water-stable hybrid semiconductors suitable for a wide range of applications, such as solid-state light emitters.

Imaging in malignant peritoneal neoplasms.

Peritoneal malignancies encompass a diverse range of tumors originating within the peritoneum, including primary tumors such as mesothelioma and primary serous peritoneal carcinoma or secondary tumors resulting from the spread of cancers from gastrointestinal, gynecological, and extra-abdominal sources. The traditional approach of palliative care for these malignancies is being replaced by a multimodal strategies that integrates surgery with systemic or intraperitoneal chemotherapy. Notably, cytoreductive surgery combined with hyperthermic intraperitoneal chemotherapy has shown significant improvements in survival rates. Imaging is crucial in the multidisciplinary management of these tumors, aiding in diagnosis, staging, restaging, and monitoring therapy response. It is also vital for appropriate patient selection, using the acronym "PAUSE", which involves assessing tumor burden via the peritoneal carcinomatosis index, evaluating patients pre- and post-therapy, detecting complications following therapy, and predicting treatment outcomes. This review explores the imaging manifestations of peritoneal malignancies, distinguishing them from various mimics, and underscores the importance of imaging modalities such as CT, MRI, PET/CT, and PET/MRI in effective decision-making and management.

Comparative evaluation of pH and Ca + ion release from MTA on interaction with platelet-rich fibrin and blood clot: an in vitro study.

Background: 'Regenerative endodontics' using host-derived scaffolds and biomaterials (MTA) is popular in the management of teeth with open apex. Alkaline pH and bioactivity contribute to tissue healing and remineralization. We assessed the influence of PRF and Blood Clot on the pH and Ca + ion release from MTA. Methods: A total of 15 single-rooted human extracted teeth were sectioned at the level of the cementoenamel junction. Based on the type of scaffolds used, samples were divided into three groups. Group 1 (MTA+ PRF), Group 2 (MTA + Blood Clot), Group 3 (control MTA). The prepared specimens were transferred to a fresh falcon tube containing 10mL of distilled water and the collected solutions were analysed for pH and Ca + ion release at 3h, seventh day and 14 th day. Results: It was observed that the mean pH and Ca + ion release were significantly lower in the experimental groups as compared to the control group. Though there was an increase in the pH recorded in Group 1 and 2 at all time periods, the difference was not significant. Ca + ion release peaked at Day 7 (Group3 > Group2 > Group1) and reduced significantly on the 14 th day for all groups. Conclusions: Within the limitations of the study, it can be concluded that PRF and blood clot influence the pH and Ca + ion release from MTA.

Post COVID sequelae among COVID-19 survivors: insights from the Indian National Clinical Registry for COVID-19.

INTRODUCTION: The effects of COVID-19 infection persist beyond the active phase. Comprehensive description and analysis of the post COVID sequelae in various population groups are critical to minimise the long-term morbidity and mortality associated with COVID-19. This analysis was conducted with an objective to estimate the frequency of post COVID sequelae and subsequently, design a framework for holistic management of post COVID morbidities. METHODS: Follow-up data collected as part of a registry-based observational study in 31 hospitals across India since September 2020-October 2022 were used for analysis. All consenting hospitalised patients with COVID-19 are telephonically followed up for up to 1 year post-discharge, using a prestructured form focused on symptom reporting. RESULTS: Dyspnoea, fatigue and mental health issues were reported among 18.6%, 10.5% and 9.3% of the 8042 participants at first follow-up of 30-60 days post-discharge, respectively, which reduced to 11.9%, 6.6% and 9%, respectively, at 1-year follow-up in 2192 participants. Patients who died within 90 days post-discharge were significantly older (adjusted OR (aOR): 1.02, 95% CI: 1.01, 1.03), with at least one comorbidity (aOR: 1.76, 95% CI: 1.31, 2.35), and a higher proportion had required intensive care unit admission during the initial hospitalisation due to COVID-19 (aOR: 1.49, 95% CI: 1.08, 2.06) and were discharged at WHO ordinal scale 6-7 (aOR: 49.13 95% CI: 25.43, 94.92). Anti-SARS-CoV-2 vaccination (at least one dose) was protective against such post-discharge mortality (aOR: 0.19, 95% CI: 0.01, 0.03). CONCLUSION: Hospitalised patients with COVID-19 experience a variety of long-term sequelae after discharge from hospitals which persists although in reduced proportions until 12 months post-discharge. Developing a holistic management framework with engagement of care outreach workers as well as teleconsultation is a way forward in effective management of post COVID morbidities as well as reducing mortality.

Kernelized Heterogeneity-Aware Cross-View Face Recognition.

Cross-view or heterogeneous face matching involves comparing two different views of the face modality such as two different spectrums or resolutions. In this research, we present two heterogeneity-aware subspace techniques, heterogeneous discriminant analysis (HDA) and its kernel version (KHDA) that encode heterogeneity in the objective function and yield a suitable projection space for improved performance. They can be applied on any feature to make it heterogeneity invariant. We next propose a face recognition framework that uses existing facial features along with HDA/KHDA for matching. The effectiveness of HDA and KHDA is demonstrated using both handcrafted and learned representations on three challenging heterogeneous cross-view face recognition scenarios: (i) visible to near-infrared matching, (ii) cross-resolution matching, and (iii) digital photo to composite sketch matching. It is observed that, consistently in all the case studies, HDA and KHDA help to reduce the heterogeneity variance, clearly evidenced in the improved results. Comparison with recent heterogeneous matching algorithms shows that HDA- and KHDA-based matching yields state-of-the-art or comparable results on all three case studies. The proposed algorithms yield the best rank-1 accuracy of 99.4% on the CASIA NIR-VIS 2.0 database, up to 100% on the CMU Multi-PIE for different resolutions, and 95.2% rank-10 accuracies on the e-PRIP database for digital to composite sketch matching.

COVID-19-Associated Bone Marrow Necrosis-A Case Report.

We report, herein, a rare case of vertebral bone marrow necrosis in a patient at 1-month post-novel coronavirus disease 2019 (COVID-19) pneumonia complicated with disseminated intravascular coagulation (DIC). The commonly observed radiological features on the imaging modalities like computed tomography (CT), magnetic resonance imaging (MRI), and 18-F fluorodeoxyglucose positron emission tomography (FDG PET) have been discussed here followed by a brief discussion on the role of in-phase and opposed-phase imaging in differentiating the disease from malignant infiltrative pathologies. Histopathological findings on bone marrow smear that confirm the diagnosis have also been illustrated.