gebhart/patrepeval huggingface dataset:
Abstract 2162: Spatially resolved image-based transcriptomics using high-throughput single-molecule fluorescence in situ hybridization (HITSFISH) (2021)

Abstract Single-cell transcriptomics enables the study of heterogeneity by uncovering the transcriptome of individual cells, which is averaged out in bulk analyses. This facilitates the grouping of cells based on similar transcriptomic profiles, potentially identifying cell subpopulations, such as rare tumor cells that mediate drug resistance or undergo metastasis. Image-based transcriptomic techniques can go a step further in uniquely profiling cells, by providing information about the spatial co-ordinates of transcripts and cells, whilst shedding light on cell morphology for phenotypic characterization. Single-molecule Fluorescence in situ hybridization (smFISH) is one image-based method in which fluorescently labeled tiling-oligonucleotide (TO) probes are bound along the length of complementary RNA strands, allowing for the detection of transcripts at nanometer-scale resolution. However, smFISH data analysis has been difficult to implement at scale due to the tradeoff between transcript resolution and imaging area, as well as the lack of automated feature detection tools. To address this issue, we have developed a pipeline called HIgh-Throughput Single-molecule FISH (HITSFISH), which uniquely combines smFISH with structured-illumination microscopy allowing for large-area high-resolution imagery with automated feature detection and analysis. We have validated our platform by showing high transcriptomic concordance between HITSFISH and other standard methods such as bulk RNA-seq and qPCR, demonstrating its ability to accurately measure RNA levels. With our pipeline we look to answer questions pertaining to the spatiotemporal landscape of gene expression within and across normal and cancerous cells. In addition, by using immunofluorescence in tandem with our platform, we can study transcript localization at various subcellular landmarks, such as membraneless organelles, to gain insight on subcellular mechanisms of gene regulation. Citation Format: Andrej Coleski, Sethu Pitchiaya, Jeremy D'Silva, Marcin Cieslik, Arul Chinnaiyan. Spatially resolved image-based transcriptomics using high-throughput single-molecule fluorescence in situ hybridization (HITSFISH) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2162.
Age Influences on the Molecular Presentation of Tumours (2020)

Abstract Cancer is often called a disease of aging. There are numerous ways in which cancer epidemiology and behaviour change with the age of the patient. The molecular bases for these relationships remain largely underexplored. To characterize them, we analyzed age-associations in the nuclear and mitochondrial somatic mutational landscape of 20,033 tumours across 35 tumour-types. Age influences both the number of mutations in a tumour and their evolutionary timing. Specific mutational signatures are associated with age, reflecting differences in exogenous and endogenous oncogenic processes such as a greater influence of tobacco use in the tumours of younger patients, but more activity of DNA damage repair signatures in those of older patients. We find that known cancer driver genes are mutated in age-associated frequencies, and these alter the transcriptome and predict for clinical outcomes. These effects are most striking in brain cancers where alterations like SUFU loss and ATRX mutation are age-dependent prognostic biomarkers. Using three cancer datasets, we show that age shapes the somatic mutational landscape of cancer, with clinical implications.
Studies on Egg Zona Pellucida-Binding Molecule (Ligand) of Mouse Sperm. I. Sperm Maturation and Zona-Binding Ability. (1991)

The epididymis has three major regions; the caput, corpus and cauda. Sperm were obtained from each region, and their binding ability to egg zona pellucida was assayed. In the case of intact sperm: cauda sperm bound in high number, corpus sperm bound at an intermediate level (an average of 30% of cauda sperm binding level), and caput sperm bound rarely (1% of cauda sperm binding level). In the case of sperm immobilized by pretreatment with LaCl3, when eggs and sperm were shaken in order to allow them to come into collision with each other, the caput and corpus sperm were able to bind to zona pellucida as well as the caudal sperm could. These results suggest that the difference in binding efficiency of the native caput and corpus sperm to bind to the zona pellucida was not due to a defect in a ligand molecule on the plasma membrane but rather to their lack of motility. When a sperm-egg binding assay was done in the presence of a binding inhibitor of caudal sperm, the binding of caudal sperm was significantly inhibited by fetuin or N-acetylgalactosamine, but the binding of caput and corpus sperm was only slightly inhibited by them. We prepared a plasma membrane fraction from each epididymal sperm, and solubilized it with sodium dodecyl sulfate (SDS). Each SDS-solubilizable fraction inhibited the binding of corresponding epididymal sperm to egg zona pellucida but didn't inhibit the binding of sperm from different regions of epididymis. These results suggested that a ligand molecule of caudal sperm was different from that of caput and corpus sperm.
Sex, androgens and regulation of pulmonary AR, TMPRSS2 and ACE2 (2020)

The sex discordance in COVID-19 outcomes has been widely recognized, with males generally faring worse than females and a potential link to sex steroids. A plausible mechanism is androgen-induced expression of TMPRSS2 and/or ACE2 in pulmonary tissues that may increase susceptibility or severity in males. This hypothesis is the subject of several clinical trials of anti-androgen therapies around the world. Here, we investigated the sex-associated TMPRSS2 and ACE2 expression in human and mouse lungs and interrogated the possibility of pharmacologic modification of their expression with anti-androgens. We found no evidence for increased <i>TMPRSS2</i> expression in the lungs of males compared to females in humans or mice. Furthermore, in male mice, treatment with the androgen receptor antagonist enzalutamide did not decrease pulmonary TMPRSS2. On the other hand, ACE2 and AR expression was sexually dimorphic and higher in males than females. ACE2 was moderately suppressible with enzalutamide therapy. Our work suggests that sex differences in COVID-19 outcomes attributable to viral entry are independent of TMPRSS2. Modest changes in ACE2 could account for some of the sex discordance.
Supplementary Figure 3 from Systems Analysis of the NCI-60 Cancer Cell Lines by Alignment of Protein Pathway Activation Modules with “-OMIC” Data Fields and Therapeutic Response Signatures (2023)

&lt;p&gt;PDF file - 142K, Unsupervised hierarchical clustering representing the NCI-60 cell lines (horizontal axis) and the calculated six pathway activation module scores (vertical axis): IGF1-R, apoptosis, integrin, mTOR, AKT and EGFR. The NCI-60 cell lines have been colorized according to their tissue origin: orange - kidney, blue - lung, pink - breast, red - blood, green - colon, brown - prostate, purple - ovary, black - skin and gray - central nervous system.&lt;/p&gt;
Complexity of dissolved organic matter in the molecular size dimension: insights from coupled size exclusion chromatography electrospray ionisation mass spectrometry (2019)

This paper investigates the relationship between apparent size distribution and molecular complexity of dissolved organic matter from the natural environment. We used a high pressure size exclusion chromatography (HPSEC) method coupled to UV-Vis diode array detection (UV-DAD) and electrospray ionisation mass spectrometry (ESI-MS) in order to compare the apparent size of natural organic matter, determined by HPSEC-UV and the molecular mass determined online by ESI-MS. We found that there was a clear discrepancy between the two methods, and found evidence for an important pool of organic matter that has a strong UV absorbance and no ESI-MS signal. Contrary to some previous research, we found no evidence that apparently high molecular weight organic matter is constituted by aggregates of low molecular weight (<1000 Da) material. Furthermore, our results suggest that the majority of apparent size variability within the ESI ionisable pool of organic matter is due to secondary interaction and exclusion effects on the HPSEC column, and not true differences in hydrodynamic size or intermolecular aggregation.
Hypervisor Event Logs as a Source of Consistent Virtual Machine Evidence for Forensic Cloud Investigations (2013)

Cloud Computing is an emerging model of computing where users can leverage the computing infrastructure as a service stack or commodity. The security and privacy concerns of this infrastructure arising from the large co-location of tenants are, however, significant and pose considerable challenges in its widespread deployment. The current work addresses one aspect of the security problem by facilitating forensic investigations to determine if these virtual tenant spaces were maliciously violated by other tenants. It presents the design, application and limitations of a software prototype called the Virtual Machine (VM) Log Auditor that helps in detecting inconsistencies within the activity timelines for a VM history. A discussion on modeling a consistent approach is also provided.
Location-based Initial Access for Wireless Power Transfer with Physically Large Arrays (2022)

Radio frequency (RF) wireless power transfer (WPT) is a promising technology for 6G use cases. It enables a massive, yet sustainable deployment of batteryless energy neutral (EN) devices at unprecedented scale. Recent research on 6G is exploring high operating frequencies up to the THz spectrum, where antenna arrays with large apertures are capable of forming narrow, "laser-like" beams. At sub-10 GHz frequencies, physically large antenna arrays are considered that are operating in the array near field. Transmitting spherical wavefronts, power can be focused in a focal point rather than a beam, which allows for efficient and radiation-safe WPT. We formulate a multipath channel model comprising specular components and diffuse scattering to find the WPT power budget in a realistic indoor scenario. Specular components can be predicted by means of a geometric model. This is used to transmit power via multiple beams simultaneously, increasing the available power budget and expanding the initial access distance. We show that exploiting this "beam diversity" reduces the required fading margin for the initial access to EN devices.
Polydactyly in the Strong's luxoid mouse is suppressed by limb deformity alleles (1996)

The study of limb development has provided insight into pattern formation during vertebrate embryogenesis. Genetic approaches offer powerful ways to identify the critical molecules and their pathways of action required to execute a complex morphogenetic program. We have applied genetic analysis to the process of limb development by studying two mouse mutants, limb deformity (Id) and Strong's luxoid (Ist). These mutations confer contrasting phenotypic alterations to the anteroposterior limb pattern. The six mutant Id alleles are fully recessive and result in oligosyndactyly of all four limbs. By contrast, the two mutant Ist alleles result in a mirror-image polydactylous limb phenotype inherited in a semidominant fashion. Morphological and molecular analysis of embryonic limbs has shown that the Id and Ist alleles affect the extent and distribution of two key signaling centers differentially: the apical ectodermal ridge and the zone of polarizing activity. Molecular characterization of the Id gene has defined a new family of evolutionarily conserved proteins termed the formins. The underlying molecular defect in the Ist mutation has not been identified; however, both loci are tightly linked on mouse chromosome 2, suggesting the possibility that they may be allelic. In this study, we have used genetic analysis to examine the epistatic and allelic relationships of Id and Ist. We observed that in + Id/Ist + double heterozygotes, a single mutant Id allele is able to suppress the semi-dominant polydactylous Ist limb phenotype. By segregating the Ist and Id loci in a backcross, we observed that these loci recombine and are separated by a genetic distance of approximately 6 cM. Therefore, while our observations demonstrate a genetic interaction between Id and Ist, it is probable that Id and Ist are not allelic. Instead, Ist and Id may be operating either in a linear or in a parallel (bypass) genetic pathway to affect the limb signaling centers. © 1996 Wiley-Liss, Inc.
An Ultra Compact Differentially Tuned 6 GHz CMOS LC VCO with Dynamic Common-Mode Feedback (2006)

A fully integrated 0.024mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> differentially tuned 6GHz LC VCO for 6+Gbps high speed serial (HSS) links in a 90nm bulk CMOS is presented. It is smaller than any LC-VCO reported to date at this frequency. Its size is comparable with ring oscillators but it has significantly better phase noise. A circuit technique is introduced to dynamically set the common-mode (CM) voltage of the differential varactor control signals equal to the VCO's CM. Using a differential control a very wide tuning range from 4.5GHz to 7.1GHz (45%) is achieved. The VCO has a measured phase noise of -117.7dBc/Hz at a 3MHz offset from a 5.63GHz carrier while dissipating 14mW from a 1.6V supply
Photochemistry of iron atoms and dimers with ethylene in cryogenic matrixes. The FT-IR spectrum of ethenyliron hydride (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotochemistry of iron atoms and dimers with ethylene in cryogenic matrixes. The FT-IR spectrum of ethenyliron hydrideZakya H. Kafafi, Robert H. Hauge, and John L. MargraveCite this: J. Am. Chem. Soc. 1985, 107, 25, 7550–7559Publication Date (Print):December 1, 1985Publication History Published online1 May 2002Published inissue 1 December 1985https://pubs.acs.org/doi/10.1021/ja00311a054https://doi.org/10.1021/ja00311a054research-articleACS PublicationsRequest reuse permissionsArticle Views142Altmetric-Citations30LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Cortical recording with polypyrrole microwire electrodes (2008)

The ability to record from the same neuron for extended periods of time is essential to understanding how the brain reorganizes during learning. Conventional chronic recording microelectrodes are made from metal or silicon. However, the large stiffness mismatch between the electrodes and brain tissue causes shear-induced inflammation, limiting long-term recording stability. The flexibility of polypyrrole microwire has the potential to improve the chronic recording stability by minimizing the stiffness mismatch. In this paper, we report the implantation of a conducting polymer microwire electrode in a rodent brain, and the successful recording of cortical activity using such an electrode.
Progress in lithium beam focusing and beam-target interaction experiments at Sandia National Laboratories (1992)

Significant progress in the generation and focusing of ion beams generated by PBFA-II has enabled us to begin experiments in ion beam coupling and target physics. Data from these experiments indicates that we can reproducibly deliver ∼50 KJ of 5 MeV protons at an average power intensity of 3.5 TW/cm2 to a 6 mm diameter by 6 mm tall cylindrical target. The implosion of spherical exploding pusher targets and the radiation production from foam-filled cylindrical thermal targets were studied in these experiments. They demonstrated that high quality target data can be obtained on PBFA-II. Specific deposition rates of about 100 TW/g were achieved in these experiments. This deposition rate marks the boundary between the regime where enhanced ion deposition and equation-of-state (EOS) physics are studied (10–100 TW/g) and the regime where radiation-conversion and radiation-transport physics are studied (100–1000 TW/g). Experiments in the radiation-conversion regime are now of primary importance in our program because these experiments will test the target physics basis for ion-driven ICE Experiments using a thin film LiF source have produced an intensity of 1 TW/cm2 of lithium ions. This beam has a potential specific deposition rate of 300–400 TW/g in hydrocarbon foams. However, radiation conversion experiments will require an increased total energy content of this beam in order to overcome the specific internal energy of the foam. Further increases in ion beam intensity and energy content are being pursued in a multi-pronged attack. Understanding and controlling ion beam divergence is the highest program priority. Present understanding indicates that instabilities in the electron sheath cause significant ion beam divergence. Our understanding suggests that this contribution to the ion divergence can be decreased by operating the diode at a low enhancement through the use of high applied magnetic fields or by modifying the electron distribution near the anode via electron limiters. The new 9 cm radius “Compact Diode” has the capability of generating ≥8 T applied magnetic fields which will enable divergence experiments in the low-enhancement, high-B regime. Experiments with the LEVIS (Laser Evaporation Ion Source) lithium source have demonstrated the existence of a preformed plasma, as determined by visible-emission spectroscopy of the anode plasma. Work on improving lithium purity with this source is in progress. This active anode plasma will be used in experiments testing the effectiveness of electron limiters in controlling ion beam divergence. We are also working to understand the interrelation between accelerator coupling, diode physics, and ion beam focusing in order to optimize the diode configuration to maximize the power intensity on target. Success in these experiments will provide an adequate lithium beam for performing target experiments exploring radiation conversion and radiation transport physics in ion-driven ICF.
Nonmyristoylated Abl proteins transform a factor-dependent hematopoietic cell line. (1992)

N-terminal myristoylation can promote the association of proteins with the plasma membrane, a property that is required for oncogenic variants of Src and Abl to transform fibroblastic cell types. The P210bcr/abl protein of chronic myelogenous leukemia cells is not myristoylated and does not stably transform NIH 3T3 fibroblasts; however, it will transform lymphoid and myeloid cell types in vitro and in vivo, suggesting that myristoylation is not required for Abl variants to transform hematopoietic cells. To test this hypothesis, we introduced point mutations that disrupt myristoylation into two activated Abl proteins, v-Abl and a deletion mutant of c-Abl (delta XB), and examined their ability to transform an interleukin-3-dependent lymphoblastoid cell line, Ba/F3. Neither of the nonmyristoylated Abl proteins transformed NIH 3T3 fibroblasts, but like P210bcr/abl, both were capable of transforming the Ba/F3 cells to factor independence and tumorigenicity. Nonmyristoylated Abl variants did not associate with the plasma membrane in the transformed Ba/F3 cells. These results demonstrate that Abl proteins can transform hematopoietic cells in the absence of membrane association and suggest that distinct functions of Abl are required for transformation of fibroblast and hematopoietic cell types.
Suppression for DC Magnetic Flux for a Current-Fed Bi-Directional Isolated DC-DC Converter under Boost Mode (2020)

This paper describes the principle of DC flux generation of a transformer in the boost mode of a current-type bi-directional isolated DC-DC converter and the effect of DC flux on circuit operation. Then, the circuit behavior in the case where the DC magnetic flux leading to magnetic saturation is generated is analyzed. Furthermore, this paper proposes a control method for suppressing DC flux in the boost mode of a current-fed bi-directional isolated DC-DC converter. Finally, the validity of theoretical analysis and the effectiveness of the proposed control method are verified through an experiment rated in 2.5kW.
Validating a Physics-Based Simulation of a Load Carriage Task (2001)

&lt;div class="htmlview paragraph"&gt;Boston Dynamics is developing the Digital Biomechanics Laboratory (DBL), a physics-based modeling tool for simulating humans and equipment. A key distinction of the DBL is the ability to simulate actively controlled human behavior, tasks such as walking, running, and carrying loads. The DBL combines forward dynamics simulation of the body, contact detection, contact force modeling, equipment modeling, and advanced control to simulate realistic human tasks. We are using the DBL to study the biomechanics of load carriage. In this paper we report on our effort to validate the simulation through comparisons to live subject experiments.&lt;/div&gt;
Reassortment Events among Swine Influenza A Viruses in China: Implications for the Origin of the 2009 Influenza Pandemic (2011)

That pigs may play a pivotal role in the emergence of pandemic influenza was indicated by the recent H1N1/2009 human pandemic, likely caused by a reassortant between viruses of the American triple-reassortant (TR) and Eurasian avian-like (EA) swine influenza lineages. As China has the largest human and pig populations in the world and is the only place where both TR and EA viruses have been reported to cocirculate, it is potentially the source of the H1N1/2009 pandemic virus. To examine this, the genome sequences of 405 swine influenza viruses from China were analyzed. Thirty-six TR and EA reassortant viruses were identified before and after the occurrence of the pandemic. Several of these TR-EA reassortant viruses had genotypes with most segments having the same lineage origin as the segments of the H1N1/2009 pandemic virus. However, these viruses were generated from independent reassortment events throughout our survey period and were not associated with the current pandemic. One TR-EA reassortant, which is least similar to the pandemic virus, has persisted since 2007, while all the other variants appear to be transient. Despite frequent reassortment events between TR and EA lineage viruses in China, evidence for the genesis of the 2009 pandemic virus in pigs in this region is still absent.