Pairs Of Lines Research Articles

Simultaneous detection of soot, temperature, and C2H2 in laminar premixed flames using a multi-pass diode laser absorption spectrometer

We report the development of a multi-pass diode laser absorption spectroscopy system for simultaneous measurements of soot volume fraction (SVF), temperature, and C2H2 concentration using a single diode laser near 1.543 µm. A line-shaped beam spot pattern is chosen for the open-path Herriott multi-pass cavity, enabling sensitive detection at various heights above the burner with an effective optical absorption path length of approximately 1.2 m in a 6 cm diameter flame region. The gas parameters (temperature and C2H2 concentration) and the SVF are determined from the absorption spectra of the target C2H2 line pair and the laser extinction of the soot, which can be extracted from the detected signal, respectively. The performance of the system was confirmed in laminar premixed ethylene and air (C2H4/air) sooting flames produced by a standard bronze plug McKenna burner at four representative equivalence ratios. All the measurement results were compared with the two-dimensional (2D) computational fluid dynamics (CFD) simulations using a skeletal mechanism with the Moss−Brookes model. The good quantitative and qualitative agreement between the TDLAS measurements and 2D CFD simulations confirms the powerful capability of the developed system.

Equiangular lines in ℂ3

Abstract A p-set of equiangular lines in ℂ3 is a set of p lines spanning ℂ3 each pair of which has the same nonzero angle arccos c, where 0 < c < 1. It is known that via a real matrix representation, a pair of lines in ℝ3 with angle arccos c yields a pair of isoclinic planes in ℝ6 with angle arccos c. In this article we characterize all p-tuples of equi-isoclinic planes in ℝ6 which come via our real matrix representation from p-tuples of equiangular lines in ℂ3. More precisely, we describe quadruples, quintuples up to nine-tuples of equiangular lines in ℂ3.

Enhancing the Sensitivity and Spatial Imaging Resolution of a Hybrid X-Ray Imaging Screen via Energy Transfer at the ZnS (Ag) and a Thermally Activated Delayed Fluorescence Interface.

Novel scintillation materials have played an indispensable role in the recent remarkable progress witnessed for X-ray imaging technology. Herein, a high-performance X-ray scintillation screen was developed based on a highly efficient hybrid system combining inorganic ZnS (Ag) with thermally activated delayed fluorescence (TADF) scintillator materials via an interfacial energy transfer (EnT) mechanism. ZnS (Ag) has a high X-ray absorption capacity and functions as the initial layer for efficiently converting high-energy X-ray photons into low-energy visible light (acting as a sensitizer) while also serving as an energy donor. The TADF component, on the contrary, is an energy acceptor and forms an active scintillating layer. By harnessing TADF chromophores that can efficiently capture both singlet and triplet excitons, our composite material offers a remarkable spatial imaging resolution of 24 line pairs per millimeter, surpassing those of the majority of existing organic and inorganic scintillators. Further, our interfacial energy transfer strategy effectively amplifies the radioluminescence intensity of the TADF scintillator by a factor of 75, offering an outstanding light yield of 38,000 photons/MeV. This advancement represents a remarkable breakthrough in organic X-ray scintillation technology and is a notable achievement within the X-ray imaging field, paving the way for novel applications in medical imaging and security inspection.

Triple Combination of Entinostat, a Bromodomain Inhibitor, and Cisplatin Is a Promising Treatment Option for Bladder Cancer.

Cisplatin is part of the first-line treatment of advanced urothelial carcinoma. Cisplatin resistance is a major problem but may be overcome by combination treatments such as targeting epigenetic aberrances. Here, we investigated the effect of the class I HDACi entinostat and bromodomain inhibitors (BETis) on the potency of cisplatin in two pairs of sensitive and cisplatin-resistant bladder cancer cell lines. Cisplatin-resistant J82cisR and T24 LTT were 3.8- and 24-fold more resistant to cisplatin compared to the native cell lines J82 and T24. In addition, a hybrid compound (compound 20) comprising structural features of an HDACi and a BETi was investigated. We found complete (J82cisR) or partial (T24 LTT) reversal of chemoresistance upon combination of entinostat, JQ1, and cisplatin. The same was found for the BETis JQ35 and OTX015, both in clinical trials, and for compound 20. The combinations were highly synergistic (Chou Talalay analysis) and increased caspase-mediated apoptosis accompanied by enhanced expression of p21, Bim, and FOXO1. Notably, the combinations were at least 4-fold less toxic in non-cancer cell lines HBLAK and HEK293. The triple combination of entinostat, a BETi, and cisplatin is highly synergistic, reverses cisplatin resistance, and may thus serve as a novel therapeutic approach for bladder cancer.

Electric field components within a micro-scaled DBD measured by Stark shifting and splitting of helium lines

Abstract Atmospheric pressure dielectric barrier discharges (DBDs), such as the micro cavity plasma array (MCPA), have emerged as promising technologies for the conversion of volatile gases. These conversion processes’ effectiveness can be enhanced by integrating catalytically active surfaces. To deepen the understanding of the plasma-catalyst interaction, it is crucial to study the transport dynamics of charged species to the catalytic surface, which, due to collisions with neutrals, also directly affects the transport of reactive species to the catalyst. Thereby the transport of the charged species is in particular influenced by the electric field perpendicular to the catalytic surface. However, experimental data on the component-wise electric field strength within SDBDs are rare. To address this issue, we performed polarized optical emission spectroscopy on the shifting and splitting of the allowed 492.19 nm (1D → 1P0) and forbidden 492.06 nm (1F0 → 1P0) helium line pair. This diagnostic approach requires a non-radially symmetric geometry, which leads to an adapted reactor design of the MCPA allowing the side-on observation of the discharge. The discharge operates in pure helium at atmospheric pressure, utilizing a triangular excitation voltage with a frequency of 15 kHz and an amplitude of 600 V. We performed phase-resolved measurements of the electric field components with a temporal resolution of 1 µs. Our results revealed an electric field strength of approximately 22 kV cm−1 for the component perpendicular to the dielectric surface, while the component parallel to the dielectric surface is about 5 kV cm−1 larger during the decreasing potential phase of the applied voltage.

A repository of Ogden syndrome patient derived iPSC lines and isogenic pairs by X-chromosome screening and genome-editing.

Amino-terminal (Nt-) acetylation (NTA) is a common protein modification, affecting 80% of cytosolic proteins in humans. The human essential gene, NAA10, encodes the enzyme NAA10, as the catalytic subunit for the N-terminal acetyltransferase A (NatA) complex, including the accessory protein, NAA15. The first human disease directly involving NAA10 was discovered in 2011, and it was named Ogden syndrome (OS), after the location of the first affected family residing in Ogden, Utah, USA. Since that time, other variants have been found in NAA10 and NAA15. Here we describe the generation of 31 iPSC lines, with 16 from females and 15 from males. This cohort includes CRISPR-mediated correction to the wild-type genotype in 4 male lines, along with editing one female line to generate homozygous wild-type or mutant clones. Following the monoclonalizaiton and screening for X-chromosome activation status in female lines, 3 additional pairs of female lines, in which either the wild type allele is on the active X chromosome (Xa) or the pathogenic variant allele is on Xa, have been generated. Subsets of this cohort have been successfully used to make cardiomyocytes and neural progenitor cells (NPCs). These cell lines are made available to the community via the NYSCF Repository.

Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations.

Mutations in splicing factor 3B subunit 1 (SF3B1) frequently occur in patients with chronic lymphocytic leukemia (CLL) and myelodysplastic syndromes (MDS). These mutations have different effects on the disease prognosis with beneficial effect in MDS and worse prognosis in CLL patients. A full-length transcriptome approach can expand our knowledge on SF3B1 mutation effects on RNA splicing and its contribution to patient survival and treatment options. We applied long-read transcriptome sequencing (LRTS) to 44 MDS and CLL patients, as well as two pairs of isogenic cell lines with and without SF3B1 mutations, and found >60% of novel isoforms. Splicing alterations were largely shared between cancer types and specifically affected the usage of introns and 3' splice sites. Our data highlighted a constrained window at canonical 3' splice sites in which dynamic splice site switches occurred in SF3B1-mutated patients. Using transcriptome-wide RNA binding maps and molecular dynamics simulations, we showed multimodal SF3B1 binding at 3' splice sites and predicted reduced RNA binding at the second binding pocket of SF3B1K700E Our work presents the hitherto most complete LRTS study of the SF3B1 mutation in CLL and MDS and provides a resource to study aberrant splicing in cancer. Moreover, we showed that different disease prognosis most likely results from the different cell types expanded during carcinogenesis rather than different mechanisms of action of the mutated SF3B1 These results have important implications for understanding the role of SF3B1 mutations in hematological malignancies and other related diseases.

GO promotes detoxification of nicosulfuron in sweet corn by enhancing photosynthesis, chlorophyll fluorescence parameters, and antioxidant enzyme activity

Although graphene oxide (GO) has extensive recognized application prospects in slow-release fertilizer, plant pest control, and plant growth regulation, the incorporation of GO into nano herbicides is still in its early stages of development. This study selected a pair of sweet corn sister lines, nicosulfuron (NIF)-resistant HK301 and NIF-sensitive HK320, and sprayed them both with 80 mg kg–1 of GO-NIF, with clean water as a control, to study the effect of GO-NIF on sweet corn seedling growth, photosynthesis, chlorophyll fluorescence, and antioxidant system enzyme activity. Compared to spraying water and GO alone, spraying GO-NIF was able to effectively reduce the toxic effect of NIF on sweet corn seedlings. Compared with NIF treatment, 10 days after of spraying GO-NIF, the net photosynthetic rate (A), stomatal conductance (Gs), transpiration rate (E), photosystem II photochemical maximum quantum yield (Fv/Fm), photochemical quenching coefficient (qP), and photosynthetic electron transfer rate (ETR) of GO-NIF treatment were significantly increased by 328.31%, 132.44%, 574.39%, 73.53%, 152.41%, and 140.72%, respectively, compared to HK320. Compared to the imbalance of redox reactions continuously induced by NIF in HK320, GO-NIF effectively alleviated the observed oxidative pressure. Furthermore, compared to NIF treatment alone, GO-NIF treatment effectively increased the activities of superoxide dismutase (SOD), guaiacol peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) in both lines, indicating GO induced resistance to the damage caused by NIF to sweet corn seedlings. This study will provides an empirical basis for understanding the detoxification promoting effect of GO in NIF and analyzing the mechanism of GO induced allogeneic detoxification in cells.

Histone H3-K27 and H3-K9 methylation does not predict lifespan in divergent populations of Drosophila melanogaster

A universal theory of aging remains elusive despite decades of research. Traditional gerontological research has focused on genetic alterations as the driving unit of the aging processes. Recent breakthroughs in cellular reprogramming, transgenerational epigenetic inheritance, and molecular aging clocks have motivated theories proposing that the disruption of epigenetic regulation is the proximal cause of aging. The claim that aging is fundamentally an epigenetic process, however, is largely based on studies using clonal cell populations and genetically identical organisms. Consequently, there has been limited experimental evidence demonstrating the correlation between epigenetic differences and longevity differences among genetically diverse populations. To address this gap in literature we leveraged laboratory populations of the model organism Drosophila melanogaster. Using sister populations with evolved differences in longevity after more than 1 500 generations of divergent life history selection, we measured the methylation at the H3K27 and H3K9 sites which have previously been shown to become dysregulated with age. Here we report that there were no differences in the amount of H3K27me3 or H3K9me2 between 3 replicate population pairs of the divergent lines. These results do not support that epigenetic dysregulation is the underlying cause of aging. Future studies investigating additional indicators of epigenetic dysregulation are required to clarify the role of epigenetics in aging.

Non-magnetic layers with a single symmetry-protected Dirac cone: Which additional dispersions must appear?

In two-dimensional (2D), non-magnetic materials, a single Dirac cone at high-symmetry point (HSP) of the Brillouin zone (BZ), akin to the one in graphenes’ band structure, cannot appear as the only quasiparticle at the Fermi level. Here we found two layer groups with time-reversal symmetry, among all possible both without and with spin-orbit coupling, that host one Dirac cone at HSP and we show which additional dispersions appear: a pair of Dirac lines on opposite BZ edges and a pair of Dirac cones that can be moved but not removed by symmetry preserving perturbations, on the other two BZ edges. We illustrate our theory by a tight-binding band structure and discuss real 2D materials that belong to one of the two symmetry groups. Finally, we single out smaller or bigger discrepancies among the published papers on the same or related topic.

The XMM-Newton and NuSTAR view of IRASF11119+3257

Context. IRASF11119+3257 is an ultra-luminous infrared galaxy with a post-merger morphology, hosting a type-1 quasar at z = 0.189. It shows a prominent ultra-fast outflow (UFO) absorption feature (vout ∼ 0.25c) in its 2013 Suzaku spectrum. This is the first system in which the energy released by the UFO was compared to that of the known galaxy-scale molecular outflow to investigate the mechanism driving active galactic nuclei (AGN) feedback. Aims. In 2021, we obtained the first XMM-Newton long look of the target, coordinated with a simultaneous NuSTAR observation, with the goal of constraining the broad band continuum and the nuclear wind physical properties and energetics with an unprecedented accuracy. Methods. The new high-quality data allowed us to clearly detect at a confidence level P > 99.8% multiple absorption features associated with the known UFO at the 9.1 and 11.0 keV rest frames. Furthermore, an emission plus absorption feature at 1.1 − 1.3 keV reveals the presence of a blueshifted P-Cygni profile in the soft band. Results. We associate the two hard band features with blends of FeXXV and FeXXVI Heα-Lyα and Heβ-Lyβ line pairs and infer a large column (NH ∼ 1024 cm−2) of highly ionized (log ξ ∼ 5) gas outflowing at vout = 0.27 ± 0.01c. The 1.3 keV absorption line can be associated with a blend of Fe and Ne transitions, produced by a lower column (NH ∼ 3 × 1021 cm−2) and ionization (log ξ ∼ 2.6) gas component outflowing at the same speed. Using a radiative-transfer disk wind model to fit the highly ionized UFO, we derive a mass outflow rate comparable with the mass accretion rate and the Eddington limit (Ṁout = 4.25−0.73+1.11 M⊙/yr, ∼1.6 Ṁacc and ∼1.0 ṀEdd), and kinetic energy (Ėkin = 1.21−0.20+0.32 Lbol and ∼0.7LEdd) and momentum flux (Ṗout = 6.37−1.09+1.67 Lbol/c) among the highest reported in the literature. We measured an extremely low high-energy cutoff (Ecut ∼ 25 − 30 keV). This and several other cases in the literature suggest that a steep X-ray continuum may be related to the formation of powerful winds. We also analyzed the ionized [OIII] component of the large-scale outflow through optical spectroscopy and derived a large outflow velocity (vout ∼ 3000 km/s) and energetics comparable with the large-scale molecular outflows. Finally, we observe a trend of decreasing outflow velocity from forbidden optical emission lines of decreasing ionization levels, interpreted as the outflow decelerating at large distances from the ionizing source. Conclusions. The lack of a significant momentum boost between the nuclear UFO and the different phases of the large-scale outflow, observed in IRASF11119 and in a growing number of similar sources, can be explained by (i) a momentum-driven expansion, (ii) an inefficient coupling of the UFO with the host interstellar medium, or (iii) by repeated energy-driven expansion episodes with a low duty cycle, that average out on long timescales to produce the observed large-scale outflow.

Prognostic value of KLFs family genes in renal clear cell carcinoma

Numerous studies have shown that the Krüppel-like factors (KLFs) family of transcription factors regulate various eukaryotic physiological processes including the proliferation, differentiation, senescence, death, and carcinogenesis of animal cells. In addition, they are involved in the regulation of key biological processes such as cell cycle, DNA repair, and immune response. Current studies focus on investigating the role of KLFs in normal physiological conditions and the incidence and development of diseases. However002C the significance of KLFs family genes in clear cell renal cell carcinoma (ccRCC) remains partly understood; therefore, an in-depth investigation of their role and clinical value in this cancer is desired. The study aimed to investigate the role of KLF family genes in the incidence, development, and prognosis of ccRCC, and to identify the related potential biomarkers and therapeutic targets. The expression of KLFs in the RNA sequencing data of 613 ccRCCs from the TCGA database was analyzed using R software, and UALCAN and GEPIA assessed the expression of KLF genes in ccRCC. Real-time fluorescence quantitative PCR analysis was performed using 10 pairs of paired ccRCC sample tissues and renal cancer cell lines from the First Affiliated Hospital of Nanchang University. Overall survival (OS), progression-free interval (PFI), and disease-specific survival (DSS) of Kidney Clear Cell Carcinoma (KIRC) samples at differential expressions of KLFs in the TCGA database were analyzed using the R software, followed by generating a nomogram prediction model. GSCALite assessed the interactions of KLF genes with miRNAs and generated network maps. Protein interaction network maps of 50 neighboring genes associated with KLF mutations were analyzed using STRING with GO and KEGG functional enrichment analyses. The cBioPortal determined the probability of KLF gene mutations and their impact on OS and disease-free survival (DFS) in patients with ccRCC. Immune cell infiltration of KLFs was analyzed using TIMER. Finally, GSCALite was used to analyze the drug sensitivity and associated pathways of action of KLFs. Correlation validation using cellular experiments. KLF3/5/9/15 were significantly downregulated in ccRCC tissues, whereas KLF16/17 were upregulated compared with the adjacent tissues. Patients with high mRNA levels of KLF16/17 showed significantly lower OS, PFI, and DSS, whereas KLF3/5/9 showed a reverse trend. In patients with ccRCC, a significant correlation was observed between KLF mutations and OS and DSS. Furthermore, the correlation of KLF3/5/9 with immune cell infiltration was stronger than that of KLF15/16, while KLF17 was significantly associated with the Epithelial-Mesenchymal Transition (EMT) pathway. Overexpression of KLF5 inhibits the proliferative and migratory capacity of renal cancer cells (786-O and OS-RC-2), as well as their sensitivity to relevant small molecule drugs. Our research revealed the expression levels and biological significance of KLF genes in ccRCC, particularly highlighting the potential of KLF5 as a promising biomarker and therapeutic target for effective prognosis and diagnosis of ccRCC.

DRN-CDR: A cancer drug response prediction model using multi-omics and drug features

Cancer drug response (CDR) prediction is an important area of research that aims to personalize cancer therapy, optimizing treatment plans for maximum effectiveness while minimizing potential negative effects. Despite the advancements in Deep learning techniques, the effective integration of multi-omics data for drug response prediction remains challenging. In this paper, a regression method using Deep ResNet for CDR (DRN-CDR) prediction is proposed. We aim to explore the potential of considering sole cancer genes in drug response prediction. Here the multi-omics data such as gene expressions, mutation data, and methylation data along with the molecular structural information of drugs were integrated to predict the IC50 values of drugs. Drug features are extracted by employing a Uniform Graph Convolution Network, while Cell line features are extracted using a combination of Convolutional Neural Network and Fully Connected Networks. These features are then concatenated and fed into a deep ResNet for the prediction of IC50 values between Drug – Cell line pairs. The proposed method yielded higher Pearson’s correlation coefficient (rp) of 0.7938 with lowest Root Mean Squared Error (RMSE) value of 0.92 when compared with similar methods of tCNNS, MOLI, DeepCDR, TGSA, NIHGCN, DeepTTA, GraTransDRP and TSGCNN. Further, when the model is extended to a classification problem to categorize drugs as sensitive or resistant, we achieved AUC and AUPR measures of 0.7623 and 0.7691, respectively. The drugs such as Tivozanib, SNX-2112, CGP-60474, PHA-665752, Foretinib etc., exhibited low median IC50 values and were found to be effective anti-cancer drugs. The case studies with different TCGA cancer types also revealed the effectiveness of SNX-2112, CGP-60474, Foretinib, Cisplatin, Vinblastine etc. This consistent pattern strongly suggests the effectiveness of the model in predicting CDR.

DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies.

Somatic variant detection is an integral part of cancer genomics analysis. While most methods have focused on short-read sequencing, long-read technologies now offer potential advantages in terms of repeat mapping and variant phasing. We present DeepSomatic, a deep learning method for detecting somatic SNVs and insertions and deletions (indels) from both short-read and long-read data, with modes for whole-genome and exome sequencing, and able to run on tumor-normal, tumor-only, and with FFPE-prepared samples. To help address the dearth of publicly available training and benchmarking data for somatic variant detection, we generated and make openly available a dataset of five matched tumor-normal cell line pairs sequenced with Illumina, PacBio HiFi, and Oxford Nanopore Technologies, along with benchmark variant sets. Across samples and technologies (short-read and long-read), DeepSomatic consistently outperforms existing callers, particularly for indels.

Development of a correction coefficient for radiographic evaluation of the alveolar bone crest: a pilot study.

To analyze the differences in cusp height on radiographs, establishing proportional relationships between cusp and alveolar bone crest (ABC) measurements. The goal of this study was to develop a correction coefficient by considering this proportion. Twenty-one artificial teeth, molars and premolars, and bovine ribs were used. Interproximal radiographs were taken with the aid of a positioner. The vertical angles used were: 0°, + 5°, and + 10°, and processed using three spatial resolutions measured in line pairs per mm (lp/mm): 20, 25 and 40. The Perio filter was applied to each image, in addition to the original one. Combinations of angle, resolution, and filter were made. Eighteen images were analyzed by three specialists, resulting in 252 measurements for each evaluator, totaling 756 measurements. The overall variability of the measurements can be explained mainly by the variation in tooth anatomy. The 0° 25 lp/mm Perio filter method was the closest one to the actual clinical scenario for both cusps and ABC. The correction factor managed to explain 71.45% of the errors. The variation in vertical angulation interferes with cusp and ABC measurements, and the angulation at 0º and spatial resolution of 25 lp/mm showed better results. The use of correction coefficients allowed approaching actual measurement values. More accurate ABC height measurements are essential even in radiographic exams that do not meet the standard of excellence because the need to repeat radiographic exams is then eliminated.

Analysis of a Prototype Multi-Detector Fast-Neutron Radiography Panel

A multi-detector fast neutron radiography panel was built using the previous work on scalable neutron radiography using the IDEAS ROSSPAD readout module. A new aluminum housing was built to accommodate a large number of detectors tiled together. Additional changes to startup and processing code were made to operate the detector as one cohesive unit. Spatial resolution of the full panel using Cs-137 gammas was reported to be 0.42 line pairs per centimeter at 90% MTF and 2.09 line pairs per centimeter at 10% MTF. Three neutron radiographs generated using a Cf-252 fission neutron source were used to determine the spatial resolution of the panel for neutrons. The experiments had 90% MTF values of 0.24, 0.3, and 0.27 line pairs per centimeter and 10% MTF values of 1.30, 1.46, and 1.40 line pairs per centimeter. An example neutron radiograph was also used to prove that the radiography panel can perform true neutron radiography.

Cell-intrinsic platinum response and associated genetic and gene expression signatures in ovarian cancer cell lines and isogenic models.

Ovarian cancers are still largely treated with platinum-based chemotherapy as the standard of care, yet few biomarkers of clinical response have had an impact on clinical decision making as of yet. Two particular challenges faced in mechanistically deciphering platinum responsiveness in ovarian cancer have been the suitability of cell line models for ovarian cancer subtypes and the availability of information on comparatively how sensitive ovarian cancer cell lines are to platinum. We performed one of the most comprehensive profiles to date on 36 ovarian cancer cell lines across over seven subtypes and integrated drug response and multiomic data to improve on our understanding of the best cell line models for platinum responsiveness in ovarian cancer. RNA-seq analysis of the 36 cell lines in a single batch experiment largely conforms with the currently accepted subtyping of ovarian cancers, further supporting other studies that have reclassified cell lines and demonstrate that commonly used cell lines are poor models of high-grade serous ovarian carcinoma. We performed drug dose response assays in the 32 of these cell lines for cisplatin and carboplatin, providing a quantitative database of IC 50 s for these drugs. Our results demonstrate that cell lines largely fall either well above or below the equivalent dose of the clinical maximally achievable dose (C max ) of each compound, allowing designation of cell lines as sensitive or resistant. We performed differential expression analysis for high-grade serous ovarian carcinoma cell lines to identify gene expression correlating with platinum-response. Further, we generated two platinum-resistant derivatives each for OVCAR3 and OVCAR4, as well as leveraged clinically-resistant PEO1/PEO4/PEO6 and PEA1/PEA2 isogenic models to perform differential expression analysis for seven total isogenic pairs of platinum resistant cell lines. While gene expression changes overall were heterogeneous and vast, common themes were innate immunity/STAT activation, epithelial to mesenchymal transition and stemness, and platinum influx/efflux regulators. In addition to gene expression analyses, we performed copy number signature analysis and orthogonal measures of homologous recombination deficiency (HRD) scar scores and copy number burden, which is the first report to our knowledge applying field-standard copy number signatures to ovarian cancer cell lines. We also examined markers and functional readouts of stemness that revealed that cell lines are poor models for examination of stemness contributions to platinum resistance, likely pointing to the fact that this is a transient state. Overall this study serves as a resource to determine the best cell lines to utilize for ovarian cancer research on certain subtypes and platinum response studies, as well as sparks new hypotheses for future study in ovarian cancer.

Prediction of protein subcellular localization in single cells.

The subcellular localization of a protein is important for its function and interaction with other molecules, and its mislocalization is linked to numerous diseases. While atlas-scale efforts have been made to profile protein localization across various cell lines, existing datasets only contain limited pairs of proteins and cell lines which do not cover all human proteins. We present a method that uses both protein sequences and cellular landmark images to perform Predictions of Unseen Proteins' Subcellular localization (PUPS), which can generalize to both proteins and cell lines not used for model training. PUPS combines a protein language model and an image inpainting model to utilize both protein sequence and cellular images for protein localization prediction. The protein sequence input enables generalization to unseen proteins and the cellular image input enables cell type specific prediction that captures single-cell variability. PUPS' ability to generalize to unseen proteins and cell lines enables us to assess the variability in protein localization across cell lines as well as across single cells within a cell line and to identify the biological processes associated with the proteins that have variable localization. Experimental validation shows that PUPS can be used to predict protein localization in newly performed experiments outside of the Human Protein Atlas used for training. Collectively, PUPS utilizes both protein sequences and cellular images to predict protein localization in unseen proteins and cell lines with the ability to capture single-cell variability.

Phenotypic and genetic characterization of a near-isogenic line pair: insights into flowering time in chickpea

BackgroundCicer arietinum is a significant legume crop cultivated mainly in short-season environments, where early-flowering is a desirable trait to overcome terminal constraints. Despite its agricultural significance, the genetic control of flowering time in chickpea is not fully understood. In this study, we developed, phenotyped, re-sequenced and genetically characterized a pair of near-isogenic lines (NILs) with contrasting days to flowering to identify candidate gene variants potentially associated with flowering time.ResultsIn addition to days to flowering, noticeable differences in multiple shoot architecture traits were observed between the NILs. The resequencing data confirms that the NILs developed in this study serve as appropriate plant materials, effectively constraining genetic variation to specific regions and thereby establishing a valuable resource for future genetic and functional investigations in chickpea research. Leveraging bioinformatics tools and public genomic datasets, we identified homologs of flowering-related genes from Arabidopsis thaliana, including ELF3 and, for the first time in chickpea, MED16 and STO/BBX24, with variants among the NILs. Analysis of the allelic distribution of these genes revealed their preservation within chickpea diversity and their potential association with flowering time. Variants were also identified in members of the ERF and ARF gene families. Furthermore, in silico expression analysis was conducted elucidating their putative roles in flowering.ConclusionsWhile the gene CaELF3a is identified as a prominent candidate, this study also exposes new targets in chickpea, such as CaMED16b and LOC101499101 (BBX24-like), homologs of flowering-related genes in Arabidopsis, as well as ERF12 and ARF2. The in silico expression characterization and genetic variability analysis performed could contribute to their use as specific markers for chickpea breeding programs. This study lays the groundwork for future investigations utilizing this plant material, promising further insights into the complex mechanisms governing flowering time in chickpea.

Zemax Modeling Of A Self-Aligned Focusing Schlieren System With Simulated Compressible Flow

A self-aligned focusing schlieren system is simulated in the ANSYS Zemax OpticStudio software environment. The model uses a custom scatter-defining dynamic link library on the retroreflective background in order to scatter rays in the direction of the incident ray rather than the specular ray. Simulated compressible flow refractive index fields are imported into Zemax by use of the grid gradient object and a workaround to the maximum point limit is introduced. The Ronchi ruling is built as a high resolution bitmap image in MATLAB and set in Zemax as a slide object allowing the bitmap image to either transmit or terminate rays at each line pair. The Zemax simulations are compared to computational numerical schlieren and experimental conventional, path-integrated schlieren results from a hypersonic stagnation point injection flow configuration and an experimental image of a shock wave from a laser-induced breakdown. In the stagnation point injection simulations, the Zemax schlieren images capture complex flow features such as the Mach disk, shear layers, contact surface, and bow shock well, but contains long, curved features (striations) between the model and the bow shock that are not present in the synthetic schlieren image from the CFD or the experimental image. The image from Zemax of the spark-induced shock wave captures the shape and curvature of the shock but appears blurry due to grid discretization in the computational data.