gebhart/patrepeval huggingface dataset:
Data from Single-Cell RNA Sequencing Unveils the Clonal and Transcriptional Landscape of Cutaneous T-Cell Lymphomas (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Clonal malignant T lymphocytes constitute only a fraction of T cells in mycosis fungoides skin tumors and in the leukemic blood of Sézary syndrome, the classic types of cutaneous T-cell lymphomas. However, lack of markers specific for malignant lymphocytes prevents distinguishing them from benign T cells, thus delaying diagnosis and the development of targeted treatments. Here we applied single-cell methods to assess the transcriptional profiles of both malignant T-cell clones and reactive T lymphocytes directly in mycosis fungoides/Sézary syndrome patient samples.&lt;/p&gt;Experimental Design:&lt;p&gt;Single-cell RNA sequencing was used to profile the T-cell immune repertoire simultaneously with gene expression in CD3&lt;sup&gt;+&lt;/sup&gt; lymphocytes from mycosis fungoides and healthy skin biopsies as well as from Sézary syndrome and control blood samples. Transcriptional data were validated in additional advanced-stage mycosis fungoides/Sézary syndrome skin and blood samples by immunofluorescence microscopy.&lt;/p&gt;Results:&lt;p&gt;Several nonoverlapping clonotypes are expanded in the skin and blood of individual advanced-stage mycosis fungoides/Sézary syndrome patient samples, including a dominant malignant clone as well as additional minor malignant and reactive clones. While we detected upregulation of patient-specific as well as mycosis fungoides– and Sézary syndrome–specific oncogenic pathways within individual malignant clones, we also detected upregulation of several common pathways that included genes associated with cancer cell metabolism, cell-cycle regulation, &lt;i&gt;de novo&lt;/i&gt; nucleotide biosynthesis, and invasion.&lt;/p&gt;Conclusions:&lt;p&gt;Our analysis unveils new insights into mycosis fungoides/Sézary syndrome pathogenesis by providing an unprecedented report of the transcriptional profile of malignant T-cell clones in the skin and blood of individual patients and offers novel prospective targets for personalized therapy.&lt;/p&gt;&lt;/div&gt;
Concomitant Occurrence of Peptide 3<sub>10</sub>- and α-Helices Probed by NMR (2000)

Oligopeptides based on protein (Cα-trisubstituted) α-amino acids are known to undergo α-helix to unordered conformation transitions under appropriate experimental conditions. On the other hand, oligopeptides rich in Cα-tetrasubstituted α-amino acids present a rather peculiar stereochemistry due to significant constraints imposed on their conformational freedom by these residues. Specifically, most of the Cα-tetrasubstituted α-amino acids have been extensively documented to possess a very high intrinsic helix-forming capacity. The narrow conformational space accessible includes both the classical α-helix and the 310-helix. It was shown that among the Cα-tetrasubstituted chiral α-amino acids the β-branched Cα-methyl-L-valine [L-(αMe)Val] is the residue with the most pronounced bias toward the right-handed 310-helix. Strong initial experimental evidence has indicated that the terminally blocked −[L-(αMe)Val]8− sequence adopts a fully developed, right-handed 310-helical conformation both in the crystal state and in structure-supporting solvents. More recently, the interesting property of this peptide to fold in solution both in the 310- and in the α-helix has emerged. The type of helical conformation adopted was found to depend on experimental conditions, as clearly shown by vibrational and electronic CD techniques. Under appropriate conditions, the conformational transition from 310- to α-helix is very slow (the time scale is on the order of several days).
Software Tools for NMR Metabolomics (2011)

NMR-based metabolomics is a rapidly evolving field with applications in medicine, agriculture, food, and nutrition. Major technological advances in NMR spectrometers, coupled with advances in computing power, allow complex mixtures of metabolites derived from serum, blood, tissues, or other biofluids to be readily analyzed and interpreted in the biological context. This article provides an overview of the software tools currently available to analyze NMR spectra derived from mixtures of these small organic molecules. While commercial software is available, this article primarily focuses on the freely available open-source software products and their specific features, and it also provides a synopsis of future software developments for metabolomics applications.
Dual Function of Single Electron Transistor Coupled with Double Quantum Dot: Gating and Charge Sensing (2013)

We demonstrate gating and charge sensing functions of a lithographically defined single electron transistor (SET). The electrochemical potential of the SET is modulated by applying a voltage to both the source and drain electrodes. The SET integrated with a double quantum dot (DQD) works as a gate electrode for the DQD. Charge transitions in the DQD are detected by the SET through its charge sensing function. This dual function of the SET is useful for saving space in crowded devices with many gates and charge sensors, toward the integration of multiqubits for quantum computation.
A gene desert required for regulatory control of pleiotropic <i>Shox2</i> expression and embryonic survival (2020)

ABSTRACT Gene deserts are defined as genomic regions devoid of protein coding genes and spanning more than 500 kilobases, collectively encompassing about 25% of the human genome. Approximately 30% of all gene deserts are enriched for conserved elements with cis -regulatory signatures. These are located predominantly near developmental transcription factors (TFs) but despite predicted critical functions, the transcriptional contributions and biological necessity of most gene deserts remain elusive. Here, we explore the cis -regulatory impact of a gene desert flanking the Shox2 gene, a TF indispensable for proximal limb, craniofacial and cardiac pacemaker development. Using a functional genomics approach in mouse embryos we identify the gene desert as a hub for numerous Shox2 -overlapping enhancers arranged in a globular chromatin domain with tissue-specific features. In accordance, using endogenous CRISPR deletion, we demonstrate that the gene desert interval is essential for Shox2 transcriptional control in developing limbs, craniofacial compartments, and the heart. Phenotypically, gene desert ablation leads to pacemaker-related embryonic lethality due to Shox2 depletion in the cardiac sinus venosus. We show that this role is partially mediated through a distal gene desert enhancer, providing evidence for intra-gene desert regulatory robustness. Finally, we uncover a multi-layered functional role of the gene desert by revealing an additional requirement for stylopod morphogenesis, mediated through an array of proximal limb enhancers (PLEs). In summary, our study establishes the Shox2 gene desert as a fundamental genomic unit that controls pleiotropic gene expression through modular arrangement and coordinated dynamics of tissue-specific enhancers.
Recognition of Recurrent Stent Failure Due to Calcified Nodule (2020)

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Beam structure for CMUT with desired frequency spectrum (2008)

Capacitive Micro-machined Ultrasound Transducers (CMUTs) with beam structures independently control resonance frequency and fractional band width (FBW). We used a theoretical approach to calculate equivalent stiffness and mass with CMUT diaphragm with rectangular beams. We also investigated the relationship between a base diaphragm's thickness and width and those of beams in terms of resonance frequency, FBW and collapse voltage. We found that a CMUT's frequency spectrum can be controlled merely by controlling base diaphragm and beam thickness. To effectively change the frequency spectrum, the beam width is made as small as possible compared with the pitch of the beams. We examined a simple three-dimensional (3-D) model in which rectangular beams were placed on a uniform rectangular diaphragm aligned in one direction with constant pitch and compared its characteristics to those obtained with theoretical approach. The resonance frequency and collapse voltage calculated by the theoretical model showed good agreement with those obtained with the 3-D model. We concluded that beam structures are one means of enabling CMUTs to be designed more freely.
A Semiconducting Conjugated Radical Polymer: Ambipolar Redox Activity and Faraday Effect (2018)

Investigations of magnetism in electronically coupled polyradicals have largely focused on applications in photonic and magnetic devices, wherein radical polymers were found to possess molecularly tunable and cooperative magnetic properties. Radical polymers with nonconjugated insulating backbones have been intensively investigated previously; however the integration of radical species into conducting polymer backbones is at an early stage. We report herein 1,3-bisdiphenylene-2-phenylallyl (BDPA)-based conjugated radical polymers that display ambipolar redox activities and conductivities. Moreover, these radical polymers were demonstrated to be promising magneto-optic (MO) materials with Faraday rotations wherein the sign is modulated by the radical character and display absolute Verdet constants up to (2.80 ± 0.84) × 10<sup>4</sup> deg T<sup>-1</sup> m<sup>-1</sup> at 532 nm. These values rival the performance of the present-day commercial inorganic MO materials (e.g., terbium gallium garnet, V = -1.0 × 10<sup>4</sup> deg T<sup>-1</sup> m<sup>-1</sup> at 532 nm). The structure property studies detailed herein reveal the promise of multifunctional conjugated radical polymers as responsive MO materials.
A study on snoop cache systems for single-chip multiprocessors (1997)

Progress in device design and implementation technologies will change the structure of bus-connected multi-processors and allow them to be implemented on a single chip. In such an implementation, the speed of the bus inside the chip is far faster than that of the backplane bus, and data transfer between the chip and external devices will become a bottleneck. Many studies on snoop cache protocols have been made, but they generally assume that the cache memory is on a printed circuit board. In this paper, we first classify the snoop cache protocols in terms of accesses to off-chip shared memory, which will be the principal cause of performance degradation, and then compare them quantitatively. Evaluations are made with an instruction-level multiprocessor simulator and practical parallel applications, varying the cache size or the access latency of shared memory. The results show that an I/N/C protocol that actively uses the line transfers between caches achieves the highest performance under all conditions. © 1997 Scripta Technica, Inc. Syst Comp Jpn, 28(2): 62–72, 1997
How to “digitize” metamaterials (2015)

Inspired by the Boolean algebra, the notion of digital electronics and the binary number theory, we have developed the methodologies to “digitize” metamaterials. We explore how an arbitrary value of the permittivity function can, in principle, be synthesized by judicious combinations of only two constituent materials with two different permittivity parameters. We have analyzed the conditions upon which one can achieve such synthesis, and have investigated theoretically issues such as the role of loss, shape and dimensions of the constituent elements. Two different digital systems have been considered: (1) the “rectangular bytes” and (2) the “core-shell bytes”. We have investigated the various features of these two systems, and their advantages and constraints. We present some of our theoretical results on this concept as utilized in several case studies.
Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH (2022)

Single-molecule DNA fluorescence in situ hybridization (FISH) techniques enable studying the three-dimensional (3D) organization of the genome at the single cell level. However, there is a major unmet need for open access, high quality, curated and reproducible DNA FISH datasets. Here, we describe a dataset obtained by applying our recently developed iFISH method to simultaneously visualize 16 small (size range: 62-73 kilobases, kb) DNA loci evenly spaced on chromosome 2 in human cells, in a single round of hybridization. We show how combinatorial color coding can be used to precisely localize multiple loci in 3D within single cells, and how inter-locus distances scale inversely with chromosome contact frequencies determined by high-throughput chromosome conformation capture (Hi-C). We provide raw images and 3D coordinates for nearly 10,000 FISH dots. Our dataset provides a free resource that can facilitate studies of 3D genome organization in single cells and can be used to develop automatic FISH analysis algorithms.
Transcription factor‐mediated molecular mechanisms involved in the functional cross‐talk between cytokines and glucocorticoids (2001)

After antigenic stimulation the increase in cytokine levels constitutes a fundamental event in the host defense and mediates many processes such as inflammation, B- and T-cell growth and differentiation and activation of effector cells. Most of these processes depend on the cytokine-induced activation of transcription factors that modulate the expression of target genes. Cytokines induce a rise in glucocorticoid levels, which are instrumental in controlling immune-cytokine overreactions. Because of their anti-inflammatory and immunosuppressive actions, glucocorticoids are highly useful as therapeutic drugs in a range of diseases. The cross-talk between cytokine-induced transcription factors such as nuclear factor-kappaB, activating protein-1, cAMP responsive element binding protein and nuclear factor of activated T cells, and glucocorticoid receptors involves both genomic and non-genomic actions, and constitutes the mechanism by which glucocorticoid repressive effects on cytokine synthesis and action take place. These molecular interactions represent the key for the study of physiological compensatory actions of corticosteroids, the interactions of cytokines and glucocorticoids at their target cells, as well as the therapeutic benefits and side-effects of synthetic steroids. For this reason, we will focus on the molecular aspects of cytokine-glucocorticoid interactions, represented by the cross-coupling between cytokine-mediated transcription factors and glucocorticoid receptors.
The SQUID sounding rocket experiment (2011)

The objective of the SQUID project is to develop and in flight verify a miniature version of a wire boom deployment mechanism to be used for electric field measurements in the ionosphere. In Februa ...
Bayesian longitudinal segmentation of hippocampal substructures in brain MRI using subject-specific atlases (2016)

The hippocampal formation is a complex, heterogeneous structure that consists of a number of distinct, interacting subregions. Atrophy of these subregions is implied in a variety of neurodegenerative diseases, most prominently in Alzheimer's disease (AD). Thanks to the increasing resolution of MR images and computational atlases, automatic segmentation of hippocampal subregions is becoming feasible in MRI scans. Here we introduce a generative model for dedicated longitudinal segmentation that relies on subject-specific atlases. The segmentations of the scans at the different time points are jointly computed using Bayesian inference. All time points are treated the same to avoid processing bias. We evaluate this approach using over 4700 scans from two publicly available datasets (ADNI and MIRIAD). In test-retest reliability experiments, the proposed method yielded significantly lower volume differences and significantly higher Dice overlaps than the cross-sectional approach for nearly every subregion (average across subregions: 4.5% vs. 6.5%, Dice overlap: 81.8% vs. 75.4%). The longitudinal algorithm also demonstrated increased sensitivity to group differences: in MIRIAD (69 subjects: 46 with AD and 23 controls), it found differences in atrophy rates between AD and controls that the cross sectional method could not detect in a number of subregions: right parasubiculum, left and right presubiculum, right subiculum, left dentate gyrus, left CA4, left HATA and right tail. In ADNI (836 subjects: 369 with AD, 215 with early cognitive impairment - eMCI - and 252 controls), all methods found significant differences between AD and controls, but the proposed longitudinal algorithm detected differences between controls and eMCI and differences between eMCI and AD that the cross sectional method could not find: left presubiculum, right subiculum, left and right parasubiculum, left and right HATA. Moreover, many of the differences that the cross-sectional method already found were detected with higher significance. The presented algorithm will be made available as part of the open-source neuroimaging package FreeSurfer.
Abstract 5027: Exome sequencing of cancer-related genes to identify genetic markers for sensitivity to cytotoxic anticancer drugs (2017)

Abstract Although the progress in moving from a one-size-fits-all cytotoxic approach to personalized molecular medicine, majority of the patients with cancer receive chemotherapy with cytotoxic anticancer drugs. Exome sequencing of 409 cancer related genes was conducted using 59 DNAs extracted from human tumor xenografts implanted into nude mice, of which sensitivity to nine cytotoxic anticancer drugs (5-fluorouracil (5FU), Nimustine (ACNU), adriamycin (ADR), cyclophosphamide (CPM), cisplatin (DDP), mitomycin C (MMC), methotrexate (MTX), vincristine (VCR), and vinblastine (VLB)) had been examined. We investigated the relationship between the sensitivities of the xenografts to the nine anticancer drugs and single nucleotide variants (SNVs) by classifying them into three groups according to the allele frequency (≤10%, 10-90%, ≥90%). We further carried out replication study using additional set of 20 xenografts. We also estimated the correlation between the expression levels of the 409 genes and sensitivities to the nine drugs in the above xenografts. In the screening stage using 59 xenografts, three SNVs, which were associated with sensitivity to VCR or MMC, showed P &amp;lt; 0.001. We further carried out a replication study of 596 SNVs showing P &amp;lt; 0.05 in the screening stage using independent samples of 20 xenografts. A combined result of the screening and replication studies suggested possible associations of 35 SNVs with sensitivities to the nine anticancer drugs (Pcombined = 0.0011 - 0.035). A total of 35 SNVs showed possible association with sensitivity to at least one of the nine drugs. Of the 35 SNVs, SNV-1 and SNV-2 in a tumor suppressor gene and a oncogene were commonly associated with sensitivity to two or four anticancer drugs, respectively. These findings provide new insights into precision anticancer therapy for the patients with cancer. Citation Format: Chihiro Udagawa, Yasushi Sasaki, Hiroshi Suemizu, Yasuyuki Ohnishi, Hiroshi Ohnishi, Takashi Tokino, Hitoshi Zembutsu. Exome sequencing of cancer-related genes to identify genetic markers for sensitivity to cytotoxic anticancer drugs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5027. doi:10.1158/1538-7445.AM2017-5027
A high-throughput investigation of Fe–Cr–Al as a novel high-temperature coating for nuclear cladding materials (2015)

High-temperature alloy coatings that can resist oxidation are urgently needed as nuclear cladding materials to mitigate the danger of hydrogen explosions during meltdown. Here we apply a combination of computationally guided materials synthesis, high-throughput structural characterization and data analysis tools to investigate the feasibility of coatings from the Fe–Cr–Al alloy system. Composition-spread samples were synthesized to cover the region of the phase diagram previous bulk studies have identified as forming protective oxides. The metallurgical and oxide phase evolution were studied via in situ synchrotron glancing incidence x-ray diffraction at temperatures up to 690 K. A composition region with an Al concentration greater than 3.08 at%, and between 20.0 at% and 32.9 at% Cr showed the least overall oxide growth. Subsequently, a series of samples were deposited on stubs and their oxidation behavior at 1373 K was observed. The continued presence of a passivating oxide was confirmed in this region over a period of 6 h.
Glycosaminoglycans enhance megakaryocytopoiesis by modifying the activities of hematopoietic growth regulators (1996)

We have previously reported that heparin is capable of stimulating in vitro and in vivo megakaryocytopoiesis in mice and has a thrombopoietic effect when given in chronic immune thrombocytopenic purpura and that heparin and several other glycosaminoglycans (GAGs) promote the growth of human megakaryoblastic cell lines in the presence of serum. We show here that GAGs, including heparan sulfate (HS), chondroitin sulfate (CS), dermantan sulfate (DS), and hyaluronic acid (HA), also stimulate in vitro growth of murine megakaryocyte progenitors and augment the diameter of individual megakaryocytes in the presence of serum. However, in a serum-free agar system, the GAGs alone had no effect on megakaryocyte colony formation, suggesting that GAGs cooperate with some serum factor(s) to exert their activity. We also show that heparin significantly potentiates the megakaryocytopoietic activity of C-Mpl ligand and interleukin (IL)-6 but not IL3, GM-CSF, SCF, and Epo. In addition, the GAGs significantly neutralize the inhibitory action of platelet factor 4 (PF4) and transforming growth factor β1 (TGFβ1) on megakaryocyte colony growth. These results demonstrate a stimulating activity of GAGs on megakaryocytopoiesis by modifying the activity of several growth-regulating factors. © 1996 Wiley-Liss, Inc.
Rod–coil type miktoarm star copolymers consisting of polyfluorene and polylactide: precise synthesis and structure–morphology relationship (2015)

Rod–coil type miktoarm star copolymers consisting of PF and PLA have been precisely synthesized for investigating the effect of macromolecular architecture on self-assembled nanostructures.
Wave transmission in time- and space-variant helicoidal phononic crystals (2014)

We present a dynamically tunable mechanism of wave transmission in one-dimensional helicoidal phononic crystals in a shape similar to DNA structures. These helicoidal architectures allow slanted nonlinear contact among cylindrical constituents, and the relative torsional movements can dynamically tune the contact stiffness between neighboring cylinders. This results in cross-talking between in-plane torsional and out-of-plane longitudinal waves. We numerically demonstrate their versatile wave mixing and controllable dispersion behavior in both wavenumber and frequency domains. Based on this principle, a suggestion toward an acoustic configuration bearing parallels to a transistor is further proposed, in which longitudinal waves can be switched on and off through torsional waves.
PSATSim (2006)

Two of the most important design issues for modern processors are power and performance. It is important for students in computer organization classes to understand the tradeoff between these two issues. This paper presents PSATSim, a graphical simulator that allows student to configure the design of a speculative out-of-order execution superscalar processor and see the effect of the design on both power and performance. The simulator explicitly shows the relationship between instructions within a processor by visually tagging instructions. The use of a graphical simulator makes it simple for instructors to demonstrate the execution of instructions within these architectures and the interactions among processor components.