Quasinormal modes of slowly-rotating black holes in dynamical Chern-Simons gravity

The detection of gravitational waves from compact binary mergers by the LIGO/Virgo collaboration has, for the first time, allowed us to test relativistic gravity in its strong, dynamical and nonlinear regime, thus opening a new arena to confront general relativity (and modifications thereof) against observations. We consider a theory which modifies general relativity by introducing a scalar field coupled to a parity-violating curvature term known as dynamical Chern-Simons gravity. In this theory, spinning black holes are different from their general relativistic counterparts and can thus serve as probes to this theory. We study linear gravito-scalar perturbations of black holes in dynamical Chern-Simons gravity at leading-order in spin and (i) obtain the perturbed field equations describing the evolution of the perturbed gravitational and scalar fields, (ii) numerically solve these equations by direct integration to calculate the quasinormal mode frequencies for the dominant and higher multipoles and tabulate them, (iii) find strong evidence that these rotating black holes are linearly stable, and (iv) present general fitting functions for different multipoles for gravitational and scalar quasinormal mode frequencies in terms of spin and Chern-Simons coupling parameter. Our results can be used to validate the ringdown of small-spin remnants of numerical relativity simulations of black hole binaries in dynamical Chern-Simons gravity and pave the way towards future tests of this theory with gravitational wave ringdown observations

Exploration of mycorrhizal fungi as potential biofertilizer in the management of plant biotic and abiotic stresses

Arbuscular mycorrhizal fungi (AMF) are fungi found in the soil and it can significantly enhance plant nutrient uptake and increase resistance to various environmental stresses. Arbuscular mycorrhizal symbiosis is the most common non-pathogenic symbiosis in the soil and is found in 80% of vascular plant roots. Most of AM fungi species belong to the sub-phylum Glomeromycotina within the phylum Mucoromycota. Arbuscular mycorrhizal (AM) fungi not only enhance the phosphorus supply to plants but also boost the absorption of zinc, copper, nitrogen and iron. AM fungi limit the uptake of Na and Cl. AM fungal hyphae make significant contributions in enhancing soil structure and its ability to retain water. Additionally, these fungi demonstrate resilience against certain root diseases and display a tolerance to drought conditions. Arbuscular mycorrhizal (AM) fungi serve as crucial endosymbionts, playing a significant role in enhancing plant productivity and contributing to the overall functioning of ecosystems. Their importance is paramount in the context of sustainable crop enhancement

cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries

BACKGROUND: Exogenous cDNA introduced into an experimental system, either intentionally or accidentally, can appear as added read coverage over that gene in next-generation sequencing libraries derived from this system. If not properly recognized and managed, this cross-contamination with exogenous signal can lead to incorrect interpretation of research results. Yet, this problem is not routinely addressed in current sequence processing pipelines. RESULTS: We present cDNA-detector, a computational tool to identify and remove exogenous cDNA contamination in DNA sequencing experiments. We demonstrate that cDNA-detector can identify cDNAs quickly and accurately from alignment files. A source inference step attempts to separate endogenous cDNAs (retrocopied genes) from potential cloned, exogenous cDNAs. cDNA-detector provides a mechanism to decontaminate the alignment from detected cDNAs. Simulation studies show that cDNA-detector is highly sensitive and specific, outperforming existing tools. We apply cDNA-detector to several highly-cited public databases (TCGA, ENCODE, NCBI SRA) and show that contaminant genes appear in sequencing experiments where they lead to incorrect coverage peak calls. CONCLUSIONS: cDNA-detector is a user-friendly and accurate tool to detect and remove cDNA detection in NGS libraries. This two-step design reduces the risk of true variant removal since it allows for manual review of candidates. We find that contamination with intentionally and accidentally introduced cDNAs is an underappreciated problem even in widely-used consortium datasets, where it can lead to spurious results. Our findings highlight the importance of sensitive detection and removal of contaminant cDNA from NGS libraries before downstream analysis

Assessing the clinical utility of cancer genomic and proteomic data across tumor types

Molecular profiling of tumors promises to advance the clinical management of cancer, but the benefits of integrating molecular data with traditional clinical variables have not been systematically studied. Here we retrospectively predict patient survival using diverse molecular data (somatic copy-number alteration, DNA methylation and mRNA, miRNA and protein expression) from 953 samples of four cancer types from The Cancer Genome Atlas project. We found that incorporating molecular data with clinical variables yielded statistically significantly improved predictions (FDR < 0.05) for three cancers but those quantitative gains were limited (2.2–23.9%). Additional analyses revealed little predictive power across tumor types except for one case. In clinically relevant genes, we identified 10,281 somatic alterations across 12 cancer types in 2,928 of 3,277 patients (89.4%), many of which would not be revealed in single-tumor analyses. Our study provides a starting point and resources, including an open-access model evaluation platform, for building reliable prognostic and therapeutic strategies that incorporate molecular data

Differential diagnosis of tuberculous meningitis from partially-treated pyogenic meningitis by cell ELISA

BACKGROUND: Tuberculous meningitis (TBM) is a major global health problem, and it is sometimes difficult to perform a differential diagnosis of this disease from other diseases, particularly partially-treated pyogenic meningitis (PTPM). In an earlier study, we demonstrated the presence of a 30-kD protein antigen in cerebrospinal fluid (CSF) of TBM patients. We have also shown that lymphocytes from CSF of TBM patients respond differently to this antigen than do those from PTPM patients. The purpose of this study was to develop an assay that can discriminate between TBM and PTPM. METHODS: We developed a cell enzyme-linked immunosorbant assay (Cell ELISA) to quantitatively measure production of antibodies against the 30-kD protein in B cells from CSF of TBM and PTPM patients. RESULTS: The cell ELISA yielded 92% (11/12) sensitivity and 92% (11/12) specificity for the differential diagnosis of TBM from PTPM. CONCLUSION: When induced with the 30-kD protein antigen, B cells derived from CSF of TBM patients respond to IgG production within 24 h while those derived from PTPM patients do not respond

Recommendations for the use of next-generation sequencing (NGS) for patients with metastatic cancers: a report from the ESMO Precision Medicine Working Group

Next-generation sequencing (NGS) allows sequencing of a high number of nucleotides in a short time frame at an affordable cost. While this technology has been widely implemented, there are no recommendations from scientific societies about its use in oncology practice. The European Society for Medical Oncology (ESMO) is proposing three levels of recommendations for the use of NGS. Based on the current evidence, ESMO recommends routine use of NGS on tumour samples in advanced non-squamous non-small-cell lung cancer (NSCLC), prostate cancers, ovarian cancers and cholangiocarcinoma. In these tumours, large multigene panels could be used if they add acceptable extra cost compared with small panels. In colon cancers, NGS could be an alternative to PCR. In addition, based on the KN158 trial and considering that patients with endometrial and small-cell lung cancers should have broad access to anti-programmed cell death 1 (anti-PD1) antibodies, it is recommended to test tumour mutational burden (TMB) in cervical cancers, well- and moderately-differentiated neuroendocrine tumours, salivary cancers, thyroid cancers and vulvar cancers, as TMB-high predicted response to pembrolizumab in these cancers. Outside the indications of multigene panels, and considering that the use of large panels of genes could lead to few clinically meaningful responders, ESMO acknowledges that a patient and a doctor could decide together to order a large panel of genes, pending no extra cost for the public health care system and if the patient is informed about the low likelihood of benefit. ESMO recommends that the use of off-label drugs matched to genomics is done only if an access programme and a procedure of decision has been developed at the national or regional level. Finally, ESMO recommends that clinical research centres develop multigene sequencing as a tool to screen patients eligible for clinical trials and to accelerate drug development, and prospectively capture the data that could further inform how to optimise the use of this technology