gebhart/patrepeval huggingface dataset:
Abstract 3693: Single cell RNA-Seq of primary lymphomas reveals the diverse transcriptional states of the cancer immunologic milieu (2017)

Abstract Follicular lymphoma (FL) is an incurable B-cell malignancy that has the potential to transform into highly aggressive, lethal lymphomas. To resolve the cellular characteristics of the underlying cancer immunologic milieu at single cell resolution, we leveraged droplet-based barcoding technology for highly parallel single cell RNA-Seq. We analyzed the transcriptomes across tens of thousands of indviidual cells derived from five primary FL tumors (average &amp;gt; 5,000 cells per sample). These tumors were obtained via direct surgical biopsies. In parallel, we conducted multi-dimensional flow cytometry that orthogonally confirmed our characterization of the various cell types including the various subsets of T cells that existed within each tumor. We identified multiple cellular subpopulations, matching known hematopoietic lineages that were present within each tumor. Despite some common features, such as MYC and BCL overexpression, transcriptional patterns and regulatory programs destinguished the different tumors from each other. We compared the transcriptional profiles of malignant cellular subpopulations to the matched normal B-cells within each sample. Malignant B-cells were characterized by expression of restricted immunoglobulin light chain type (either kappa or lambda), BCL2 expression, and CD20 expression. In each case a minor population of normal B-cells was characterized by expression of the opposite light chain type and a pattern of gene expression common to B cells in all tumor samples and normal peripheral blood. Tumor B cells consistently demonstrated downregulation of β-2-microglobulin and for those cases that harbored a founder CREBBP mutation, a downregulation of MHC II, that would cause an alteration in antigen presentation and evasion of the T cell immune system. Moreover, we characterized the transcriptional profiles of the infiltrating T-cell populations within each tumor, providing a high-resolution perspective of immunologic cellular interactions. Overall, we identified the diverse transcriptional states at single cell resolution among different tumors and discovered specific genes that were aberrantly expressed compared to normal B cells within the same microenvironment. Our findings provide an unprecedented resolution of distinct immune lineages as seen by transcriptionally characterized cell diversity. Studies using single cell genomics may have implications for considering immunotherapeutic efficacy. Citation Format: Noemi Andor, Erin Simonds, Jiamin Chen, Christina Wood, Susan Grimes, Debra Czerwinski, Grace Zheng, Ronald Levy, Hanlee P. Ji. Single cell RNA-Seq of primary lymphomas reveals the diverse transcriptional states of the cancer immunologic milieu [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 3693. doi:10.1158/1538-7445.AM2017-3693
In Vitro Cultivation of the Syphilis Spirochete Treponema pallidum (2021)

For over a century, investigation of Treponema pallidum subsp. pallidum, the spiral-shaped bacterium that causes syphilis, was hindered by an inability to culture the organism in vitro. A recent breakthrough has enabled continuous in vitro growth of this organism in co-culture with mammalian tissue culture cells. This article contains the protocols needed to culture T. pallidum in the standard laboratory environment. In addition, protocols for growing and maintaining the required tissue culture cells, for generating isogenic strains by limiting dilution, and for quantitating T. pallidum by darkfield microscopy are included. © 2021 Wiley Periodicals LLC. Basic Protocol 1: In vitro cultivation of Treponema pallidum Basic Protocol 2: Generation of isogenic strains Support Protocol 1: Alternate harvest procedure Support Protocol 2: Culture of Sf1Ep cells Support Protocol 3: Assessment of T. pallidum number and viability.
Microstructure Evolution in Nanostructured High-Performance Thermoelectrics: The case of p-type Pb 1-x Na x Te-SrTe (2016)

Thermoelectric (TE) materials, which convert waste heat to useful electricity, have had their widespread deployment limited by low energy conversion efficiencies. Recent collaborative work has introduced an innovative all-scale hierarchical architecturing approach [1] . In this approach, structural features across multiple length scales are introduced, ranging from point defects to nanoscale precipitates to microscale grain boundaries, which effectively scatter phonons across these disparate length-scales to achieve low thermal conductivity without significantly increasing charge carrier scattering. However, predictive control over synthesis and processing is required to control the microstructural constituents, especially the size, number and distribution of nanoscale precipitates, to achieve the targeted TE performance.
Research on Environment Materials with Progress on Regeneration of Active Carbon (2014)

Now activated carbon has been used greatly in all walks of life, thus the regeneration of spent activated carbon is of great significance. The advantages and disadvantages of the regeneration methods of the spent activated carbon are introduced and discussed in this paper, mainly including thermal regeneration, chemical regeneration, electrochemical regeneration, microwave radiation regeneration, wet air oxidation and supercritical fluid regeneration etc. Then a new recycling method of the spent activated carbon is proposed.
Supplementary Table S1 from Thyroid Cancers Exhibit Oncogene-Enhanced Macropinocytosis that Is Restrained by IGF1R and Promote Albumin–Drug Conjugate Response (2023)

&lt;p&gt;Biological and chemical reagents and their sources&lt;/p&gt;
12/15-lipoxygenase–derived lipid peroxides control receptor tyrosine kinase signaling through oxidation of protein tyrosine phosphatases (2010)

Protein tyrosine phosphatases (PTPs) are regulated through reversible oxidation of the active-site cysteine. Previous studies have implied soluble reactive oxygen species (ROS), like H(2)O(2), as the mediators of PTP oxidation. The potential role(s) of peroxidized lipids in PTP oxidation have not been described. This study demonstrates that increases in cellular lipid peroxides, induced by disruption of glutathione peroxidase 4, induce cellular PTP oxidation and reduce the activity of PDGF receptor targeting PTPs. These effects were accompanied by site-selective increased PDGF beta-receptor phosphorylation, sensitive to 12/15-lipoxygenase (12/15-LOX) inhibitors, and increased PDGF-induced cytoskeletal rearrangements. Importantly, the 12/15-LOX-derived 15-OOH-eicosatetraenoic acid lipid peroxide was much more effective than H(2)O(2) in induction of in vitro PTP oxidation. Our study thus establishes that lipid peroxides are previously unrecognized inducers of oxidation of PTPs. This identifies a pathway for control of receptor tyrosine kinase signaling, which might also be involved in the etiology of diseases associated with increased lipid peroxidation.
Endwall Pressure Measurement and Skin Friction Correction of a Compressor Cascade (2006)

This paper presents results from a endwall study of the tip-gap flow in a low-speed linear compressor cascade wind tunnel at Virginia Tech. The endwall pressure measurements were made on a stationary endwall to obtain the flow features and to determine the measurement profiles of interest. A custom-made miniature 3-orthogonal-velocity-component fiber-optic laser-Doppler velocimetry (LDV) system was used to measure all three components of velocity within a 50 µm spherical measurement volume within the viscous sublayer of the endwall. The endwall high lateral pressure gradient changed U up to 20% after the correction of the pressure gradient. The chord, pitch, and span of the blade was 30.0 cm, 18.0cm, and 43.5cm, respectively. The stagger and inlet flow angle from the axial direction was 22.2 and 45.0 . The Reynolds number based on the chord was 500,000 and the displacement thickness of the inlet endwall boundary layer 140% chord upstream was 2.9 mm. Detailed velocity profiles were acquired with 25 points across the gap at ten chordwise locations. The data displayed similar patterns of leakage flow velocity at the tip gap for two dierent gap sizes. The exit velocity results showed the relationship between the tip leakage flow and the total pressure loss. A core of very low loss fluid bounded by the endwall and a free shear layer at about 75% of the gap height occurred from near the minimum pressure location and all the downstream measurement location. Accordingly, the flow velocity and direction remained nearly invariant in the core. However, the flow direction varied 50 across the shear layer bounded on the surface of the blade tip end. The total pressure and turbulence intensity inside the 4% gap were further measured at the 65% chord plane in the same facility with the same Pitot probe above. 3 For the measurement of turbulence intensity from the near endwall to the blade tip using a single subminiature hot-wire probe with the prongs bent forward to be inserted through the endwall, it was assumed that turbulence in the gap is isotropic so that the probe stayed in the same direction to measure the fluctuating component of velocity normal to the probe. The acquired data demonstrated that the pressure loss and turbulence intensity were negligible around the mid gap while they were huge in the two shear layers bounded on the endwall and the blade tip surface. Static pressure on the blade tip end was measured with 1.0% to 4.0% gaps and provided the signature of flow attachment on the blade tip. The endwall static pressure, the tip blade loading, and the exit velocity of the gap flow were later reported in the same facility above. 4 The endwall pressure distribution exhibited the dierent
Detection of Motion Vector-Based Video Steganography by Adding or Subtracting One Motion Vector Value (2018)

In last decades the Steganography is an tremendous progress, at the same time there exist issues to detect the steganalysis in motion based video where the substance is reliably in motion conduct that makes that to detect it. Analyzing the difference between the rated motion value plays a crucial role that enables us to focus on difference between the locally optimal SAD and actual SAD after adding-or-subtracting-one operation on the motion value. Based on the motion vectors to play out the classification and extraction process at last, two features sets are been used based on the fact that most motion vectors are locally optimal for most video codec’s to complete this process. The conventional approaches announced the technique for proposed prevails to meet the requirement applications and detecting the steganalysis in videos compare in the literature.
Anti-Factor V inhibitor in patients with autoimmune diseases: case report and literature review (2011)

Acquired anti-Factor V deficiency caused by inhibitor production is a rare coagulation disorder. Although this is a well known entity in the literature, choice of optimal treatment for an individual patient is difficult, given that no standard therapeutic measures are available because of rare incidence and various underlying diseases occurring in the elderly. An 88 year-old man treated for Hashimoto's disease was found to exhibit prolongation of both prothrombin time and activated partial thromboplastin time. Detailed study of coagulation factors revealed a deficiency of Factor V. Our patient's coagulation disorder resolved in two weeks with intravenous administration of prednisolone 20 mg/day. Clinical features of autoimmune disease-related Factor V deficiency are discussed, along with eight previously reported cases over the past 20 years.
POMC Biosynthesis in the Intermediate Lobe of the Spontaneously Hypertensive Rat (1989)

Pro-opiomelanocortin (POMC) synthesized in the anterior (AL) and intermediate lobe (IL) of the rat pituitary gland, is a prohormone precursor of several peptide hormones that may participate in the regulation of blood pressure. We therefore studied the biosynthesis of POMC by measuring the incorporation of 3H-tyrosine into the IL of 32-week-old spontaneously hypertensive rat (SHR) of the Aoki-Okamoto strain and their normotensive controls, the Wistar-Kyoto rat (WKY). Under basal conditions, POMC biosynthesis was significantly reduced in the SHR (1130 +/- 102 cpm/30 min/IL, n = 13) when compared to the WKY (1515 +/- 163 cpm/30 min/IL, N = 12, P less than 0.05, t test). There was also an inverse correlation between systolic blood pressure and POMC biosynthesis in both the WKY (Y = 8.4 +/- 1.38X + 2097 +/- 673, r = 0.86 +/- 0.06, N = 5), and SHR (Y = 5.7 +/- 1.8X + 1122 +/- 336 r = 0.57 +/- 0.13, N = 3). The decreased POMC biosynthesis was associated with a higher dopamine content in IL in SHR compared to WKY (1.56 +/- 0.53, n = 17 v 0.51 +/- 0.16, n = 17 pmol/IL, P less than 0.05, Mann-Whitney test). Oral administration of three different antihypertensive agents (propranolol, captopril, or hydralazine) for 12 weeks normalized blood pressure and POMC biosynthesis in the SHR but had no effect on either variable in the WKY. Because POMC biosynthesis in IL increased with normalization of blood pressure in the SHR, the decreased POMC biosynthesis in SHR may be a consequence rather than a cause of the elevated blood pressure in SHR.
Phenylethynyl Terminated Imide (PETI) Composites Made by High Temperature Vartm (2010)

Fabrication of composite structures using vacuum assisted resin transfer molding (VARTM) is generally more affordable than conventional autoclave techniques. Recent efforts have focused on adapting VARTM for the fabrication of high temperature composites. Due to their low melt viscosity and long melt stability, certain phenylethynyl terminated imides (PETI) can be processed into composites using high temperature VARTM (HT-VARTM). However, one of the disadvantages of the current HT-VARTM resin systems has been the high porosity of the resultant composites. For aerospace applications, a void fraction of <2% is desired. In the current study, two PETI resins, LARC. PETI-330 and LARC. PETI-8 have been used to fabricate test specimens using HT-VARTM. The resins were infused into carbon fiber preforms at 260 C and cured between 316 and 371 C. Photomicrographs of the panels were taken and void contents were determined by acid digestion. Modifications to the thermal cycle used in the laminate fabrication have reduced the void content significantly; typically .3% for carbon fiber biaxially woven fabric and less than 2% for carbon fiber uniaxial fabric. Mechanical properties (short beam shear and flexure) of the panels were determined at both room and elevated temperatures. The results of this work are presented herein. This paper is declared a work of the U.S. Government and is not subject to copyright protection in the United States.
Extending the focal distance without sacrificing the spatial resolution using virtual ultrasonic optical waveguides (2021)

We present a novel technique to extend the focal length of an external lens without increasing the spot size using virtual optical waveguides ultrasonically sculpted in transparent and turbid media. When used in tandem with an external lens, these non-invasive virtual waveguides can further relay the focused beam of light into the medium without losing the spatial resolution. We will also show how the optical properties of this physical-virtual cascade system can be reconfigured by changing the pattern of ultrasound. This method can find intriguing applications for manipulating the trajectory of light in transparent and turbid media, including biological tissue.
Analysis of surface geometry of the human stomach using real‐time 3‐D ultrasonography in vivo (2004)

The objective of this study was to develop an analytical method to describe the three-dimensional (3-D) geometry of the gastric antrum, gastric fundus and the whole stomach. The Fourier series method was used to simulate the organ surface geometry obtained from a 3-D ultrasound system. Data generated from eight antrums and three whole stomachs, at pressures of approximately 7 cm H(2)O, were used for lumen curvature calculations. The principal curvatures spatial distributions were non-homogeneous in the gastric antrum, gastric fundus and the stomach due to their complex geometry. The maximum longitudinal principal curvature in the antrum, fundus and total stomach were, respectively, 0.460 +/- 0.066, 0.583 +/- 0.087 and 1.123 +/- 0.328, whereas the maximum circumferential curvature were 1.192 +/- 0.090, 3.649 +/- 1.574 and 8.444 +/- 3.424, respectively. The present study provides an analytical tool for characterizing the complex 3-D geometry of an organ-like the human stomach reconstructed by clinical imaging modalities. Providing an average tension for the stomach does not reflect the large variation in tension throughout the stomach wall.
Fully scaled 0.5 μm metal–oxide semiconductor circuits by synchrotron x-ray lithography: Mask fabrication and characterization (1988)

Several sets of x-ray masks for a metal–oxide semiconductor (MOS) device program were fabricated using boron-doped silicon as the membrane and gold as the absorber. The metrology of the mask sets was characterized. Mask-to-mask overlay error is &amp;lt;0.12 μm (3σ) including measurement error. Absorber induced distortion is not the dominating mask error. (Lack of better measurement systems and techniques preclude exact analysis of errors.) Quarter-micron patterns have been resolved using a multilayer resist system. Linewidth variations are &amp;lt;0.017 μm (1σ) across the entire membrane. The mask sets have been successfully used to fabricate fully scaled n-type MOS circuits.
Silicium‐Nanokristalle und Silicium‐Polymer‐Hybridmaterialien: Synthese, Oberflächenmodifikation und Anwendungen (2015)

Abstract Aufgrund der hohen Verfügbarkeit in der Erdkruste und seiner geringen Toxizität im Vergleich zu einigen anderen Halbleitern ist Silicium der Vorreiter in der Elektroindustrie. Daher finden Silicium‐Nanokristalle (SiNKs) insbesondere aufgrund ihrer einzigartigen optoelektronischen Eigenschaften ein hohes Interesse in der Halbleiterindustrie und sie haben das Potenzial, die toxischen Quantenpunkte (Elemente der Gruppen II–VI und III–V) zu substituieren. Dennoch erhielten SiNKs wegen ihrer geringeren Photolumineszenz(PL)‐Quantenausbeuten, einer schwierig zu erzielenden monodispersen Partikelverteilung und ihrer Oxidationsanfälligkeit nicht dieselbe Aufmerksamkeit wie ihre schwermetallhaltigen Analoga. Daher wurde vermehrt an der Funktionalisierung von SiNK‐Oberflächen geforscht und die genannten Faktoren im Wesentlichen verbessert. Vor diesem Hintergrund fassen wir in diesem Aufsatz die neuesten Entwicklungen in der Funktionalisierung von SiNK‐Oberflächen, beschriebene SiNK/Polymer‐Hybridmaterialien und deren Anwendungen in den Bereichen Sensorentwicklung, Leuchtdioden, Katalyse und Akkumulatoren zusammen.
Large diameter femoral heads (2014)

Dislocation remains among the most common complications of, and reasons for, revision of both primary and revision total hip replacements (THR). Hence, there is great interest in maximising stability to prevent this complication. Head size has been recognised to have a strong influence on the risk of dislocation post-operatively. As femoral head size increases, stability is augmented, secondary to an increase in impingement-free range of movement. Larger head sizes also greatly increase the 'jump distance' required for the head to dislocate in an appropriately positioned cup. Level-one studies support the use of larger diameter heads as they decrease the risk of dislocation following primary and revision THR. Highly cross-linked polyethylene has allowed us to increase femoral head size, without a marked increase in wear. However, the thin polyethylene liners necessary to accommodate larger heads may increase the risk of liner fracture and larger heads have also been implicated in causing soft-tissue impingement resulting in groin pain. Larger diameter heads also impart larger forces on the femoral trunnion, which may contribute to corrosion, metal release, and adverse local tissue reactions. Alternative large bearings including large ceramic heads and dual mobility bearings may mitigate some of these risks, and several of these devices have been used with clinical success.
A Model for Field Aligned Starting (2006)

Field aligned starting (FAS) is a novel technique for starting 3-phase cage induction motors on a single-phase supply lines with minimal inrush currents. It uses a simple energy storage system that is independent of the mains supply to create two spatially displaced magnetic fields so that a high starting torque can be generated as the magnetic fields seek alignment. The started motor can then be mains connected to operate in a standard Steinmetz connection without incurring high inrush currents if the transition to the mains connection is properly timed. This paper describes the special features, theoretical concepts and advantages of the field aligned starting system, and presents a transient model through which the transient behavior of a 3-phase induction motor operated with field aligned starting can be analyzed. Detailed simulated and experimental results are presented in part II of this paper.
Characterizing Biometrics and Nutrient Profiles of Fillet and Offal Components to Better Utilize Harvests of Invasive Carp in the U.S. (2020)

The successful establishment of fisheries for invasive Asian carp (AC) would help alleviate the ecological, societal, and economic bane they impose on natural U.S. waterways, all while supplementing domestic fisheries and addressing food insecurity in high-stress regions. However, fishers of AC and the post-harvest industries lack the economic resiliency needed to self-sustain operations. Providing detailed nutrient compositions and biometric yields of edible and inedible components would strengthen consumer demands and grow supplemental product-revenue streams, all supporting commercial fisheries removal of AC. To incentivize capture and utilization of silver carp (Hypophthalmichthys molitrix), the most abundant of the invasive AC, we addressed this dearth in the literature by characterizing yields and composition of silver carp fillets and offal components (edible portions: head, frame, and trimmings) (non-edible portion: viscera). Mature silver carp collected in late June from the Ohio River (Kentucky, U.S.) were separated into major components, characterized for yields, and then evaluated across length, gender, and body condition to identify trends in biometric data. Detailed nutrient parameters were then characterized for all components. Comparatively low fillet yields (< 20%) whole-weight (w/w) and high offal-component yields of heads (35.8%), frames (23.0%), and trimmings (17.1%) w/w obtained from this post-spawn sample signify ramifications of seasonal harvest and the importance of by-product utilization. Boneless fillets produced the highest proportions of crude protein (93% dry-matter basis), essential amino acids (lysine 8.0% and leucine 6.9% of crude protein), omega-3 fatty acids (18.2% of total lipids), and several important macro minerals. Still, all edible and offal components produced attractive omega-6:omega-3 (< 1.0), which is consistent with nutrient-rich marine finfish. Findings from this study provide information that can be used to increase domestic-consumptive demand and improve the economic resiliency of commercial fisheries charged with controlling the bio-invasion of AC.