gebhart/patrepeval huggingface dataset:
Resolving the spatial and cellular architecture of lung adenocarcinoma by multi-region single-cell sequencing (2020)

ABSTRACT Little is known of the geospatial architecture of individual cell populations in lung adenocarcinoma (LUAD) evolution. Here, we perform single-cell RNA sequencing of 186,916 cells from 5 early-stage LUADs and 14 multi-region normal lung tissues of defined spatial proximities from the tumors. We show that cellular lineages, states, and transcriptomic features geospatially evolve across normal regions to LUADs. LUADs also exhibit pronounced intratumor cell heterogeneity within single sites and transcriptional lineage-plasticity programs. T regulatory cell phenotypes are increased in normal tissues with proximity to LUAD, in contrast to diminished signatures and fractions of cytotoxic CD8+ T cells, antigen-presenting macrophages and inflammatory dendritic cells. We further find that the LUAD ligand-receptor interactome harbors increased expression of epithelial CD24 which mediates pro-tumor phenotypes. These data provide a spatial atlas of LUAD evolution, and a resource for identification of targets for its treatment. Statement of significance The geospatial ecosystem of the peripheral lung and early-stage LUAD is not known. Our multi-region single-cell sequencing analyses unravel cell populations, states, and phenotypes in the spatial and ecological evolution of LUAD from the lung that comprise high-potential targets for early interception.
The effect of increased frequency of hemodialysis on serum cystatin C and β2‐microglobulin concentrations: A secondary analysis of the frequent hemodialysis network (FHN) trial (2019)

β2-M may be a better biomarker of dialysis dose than CysC. Reduction in the concentration of potentially toxic long-lived proteins of the size of β-2M is one potential long-term benefit of more intensive dialysis that may be explored.
Human HL-60 myeloid leukemia cells transport dehydroascorbic acid via the glucose transporters and accumulate reduced ascorbic acid (1994)

The cellular accumulation of vitamin C, a substance critical to human physiology, is mediated by transporters located at the cell membrane, and is regulated in a cell-specific manner. Neoplastic cells may have special needs for vitamin C. Therefore, we investigated the transport of vitamin C in a human myeloid leukemia cell line (HL-60). The HL-60 cells lacked the capacity to transport the reduced form of vitamin C, ascorbic acid, but they showed a remarkable ability to transport the oxidized form of vitamin C, dehydroascorbic acid (DHA). Uptake-accumulation studies indicated that the HL-60 cells accumulated ascorbic acid when provided with DHA. Kinetic analysis showed the presence of two functional activities involved in the uptake of DHA, one with low affinity and one with high affinity. Cytochalasin B and phloretin, which inhibit the passage of glucose through the facilitative glucose transporters, also inhibited the transport of DHA by HL-60 cells. Transport of DHA was completed by D- but not L-hexoses, and was sensitive to D-hexose-dependent counter transport acceleration. These data support the concept that HL-60 myeloid leukemic cells transport DHA through the facilitative hexose transporters (glucose transporters) and accumulate the reduced form of ascorbic acid.
Implanted Cell-Dense Prevascularized Tissues Develop Functional Vasculature That Supports Reoxygenation After Thrombosis (2014)

Achieving adequate vascularization within implanted engineered tissues is a significant obstacle to maintaining viability and functionality. In vitro prevascularization of engineered tissues has been explored as a potential solution to this challenge. The traditional paradigm of in vitro prevascularization is to implant an engineered tissue with a preformed vascular network that is perfused after anastomosis with the host circulation. We investigated the efficacy of this strategy by implanting cell-dense prevascularized tissues created via cell-mediated contraction and composed of collagen and a collagen-fibrin mixture into dorsal window chambers surgically prepared on immunocompromised mice. We found that host-implant anastomosis takes place in 2-6 days and that perfusion of vessels within the implants is subsequently restricted by thrombosis. However, by day 7, a functional vascular network composed of host and implant vessels developed. Prevascularization enhanced intra-implant pO2 significantly as early as 2 days postimplantation, reaching a maximum of 55 mmHg by day 8, which was significantly greater than the maximum within cellularized control tissues (18 mmHg). By day 14, collagen tissues supported ∼ 0.51 × 10(9) implanted and host-derived cells per mL. Our findings elucidate key features of in vitro prevascularization that can be used toward the design of larger and more functionally complex engineered tissues.
Synthesis of empagliflozin, a novel and selective sodium‐glucose co‐transporter‐2 inhibitor, labeled with carbon‐14 and carbon‐13 (2014)

Empagliflozin, (2S,3R,4R,5S,6R)-2-[4-chloro-3-[[4-[(3S)-oxolan-3-yl]oxyphenyl]methyl]phenyl]-6-(hydroxymethyl)oxane-3,4,5-triol was recently approved by the FDA for the treatment of chronic type 2 diabetes mellitus. Herein, we report the synthesis of carbon-13 and carbon-14 labeled empagliflozin. Carbon-13 labeled empagliflozin was prepared in five steps and in 34% overall chemical yield starting from the commercially available α-D-glucose-[(13)C6]. For the radiosynthesis, the carbon-14 atom was introduced in three different positions of the molecule. In the first synthesis, Carbon-14 D-(+)-gluconic acid δ-lactone was used to prepare specifically labeled empagliflozin in carbon-1 of the sugar moiety in four steps and in 19% overall radiochemical yield. Carbon-14 labeled empagliflozin with the radioactive atom in the benzylic position was obtained in eight steps and in 7% overall radiochemical yield. In the last synthesis carbon-14 uniformly labeled phenol was used to give [(14)C]empagliflozin in eight steps and in 18% overall radiochemical yield. In all these radiosyntheses, the specific activities of the final compounds were higher than 53 mCi/mmol, and the radiochemical purities were above 98.5%.
Wireless Monitoring of Workpiece Material Transitions and Debris Accumulation in Micro-Electro-Discharge Machining (2009)

Wireless signals are inherently generated with each discharge in micro-electro-discharge machining (¿EDM), allowing direct observation of discharge quality. While traditional methods of monitoring machining quality rely on electrical characteristics at the discharge supply terminals, the wireless method provides more accurate information because it is less affected by electrical parasitics in the supply loop and by spatial averaging. The depth location of a metal-metal interface can be distinguished in the wireless signal. This is useful for determining the stop depth in certain processes. For example, in machining through samples of stainless steel into an electroplated copper backing layer, the metal transition is identified by a 10-dBm change in wireless-signal strength for the 300-350-MHz band and a 5-dBm average change across the full 1-GHz bandwidth. As debris accumulate in the discharge gaps, shifts in the wireless spectra can also indicate spurious discharges that could damage the workpiece and tool. For example, when copper micromachining becomes debris dominated, the 800-850-MHz band drops 4 dBm in signal strength, with a 2.2-dBm average drop across the full 1-GHz bandwidth.
The effect of stationary ultraviolet excitation on the optical properties of electrochemically self-assembled semiconductor nanowires (2007)

The optical behavior of electrochemically self-assembled nanowire arrays excited by stationary ultraviolet light is investigated. The wires are fabricated by electrodepositing CdS, ZnO, and ZnSe in anodic porous alumina templates with 50, 25, and 10nm diameter pores. We have developed a theoretical model to calculate nanowire permittivity, refractive index, and absorption coefficient under such stationary excitation. This model is incorporated in an electromagnetic wave simulation to obtain the optical response of the array of wires. The behavior is also investigated experimentally using a pump-probe excitation scheme in an optical interferometer. We report a strong nonmonotonic optical activity as a function of wire diameter in the nanowire arrays. This result implies a sharp increase in the optically pumped change in refractive index and permittivity in narrower nanowires.
Modular Design and Integration of In-Cycle Closed-Loop Combustion Controllers for a Wide-Range of Operating Conditions (2021)

This paper investigates how multiple in-cycle closed-loop combustion controllers can be integrated for a seamless operation under a wide-range of operating conditions. The stochastic cyclic variations of the combustion can be successfully compensated by the adjustment of the fuel injection pulses within the same cycle. The feedback information and controllability obtained relies on the different operating conditions, emissions regulations and fuels. Various in-cycle closed-loop combustion controllers are found in the literature to overcome the numerous challenges of the combustion control. In this paper, the modularization for the controller design and their integration is investigated, and how the transition between the available information, control actions and control strategy affects the final combustion behaviour. The approach consists in the design of a finite-state machine that supervises the transition between virtual sensors and measurements, regulators and the possibility of additional fuel injections. The proposed approach was tested in a Scania D13 engine for a wide-range of operating conditions. The results confirm the improved controllability and reduced steady-state RMSE of the controlled parameters, with a smoother transition between set-points, regardless of operating conditions and fuel.
Inside Cover (2020)

Abstract Access to sterile personal protective equipment, in particular for filtered face respirators is critical in the current pandemic for front line healthcare workers. Extended use may be required during supply shortages or due to economic considerations. UVC sterilization can be a cost‐effective technique capable of high throughput. The suitability of various N95 respirator designs for UV mediated reuse were evaluated based on the materials utilized. (Background image: with permission from Prescient x . Virus image: Sophia Lilge. Further details can be found in the article by Lothar Lilge, Angelica Manalac, Madrigal Weersink, Fynn Schwiegelshohn, Tanner Young‐Schultz, Abdallatif Satti Abdalrhman, Chengjin Wang, Aldrich Ngan, Frank X. Gu, Vaughn Betz, Ron Hofmann ( e202000232 ). image
The Oxygen Isotopic Composition of the Sun Inferred from Captured Solar Wind (2011)

All planetary materials sampled thus far vary in their relative abundance of the major isotope of oxygen, (16)O, such that it has not been possible to define a primordial solar system composition. We measured the oxygen isotopic composition of solar wind captured and returned to Earth by NASA's Genesis mission. Our results demonstrate that the Sun is highly enriched in (16)O relative to the Earth, Moon, Mars, and bulk meteorites. Because the solar photosphere preserves the average isotopic composition of the solar system for elements heavier than lithium, we conclude that essentially all rocky materials in the inner solar system were enriched in (17)O and (18)O, relative to (16)O, by ~7%, probably via non-mass-dependent chemistry before accretion of the first planetesimals.
Differential roles of STAT1 and STAT1 in fludarabine-induced cell cycle arrest and apoptosis in human B cells (2004)

Signal transducer and activator of transcription 1 (STAT1), a transcription factor known to participate in antiviral responses, acts as a tumor suppressor inhibiting cell growth and promoting apoptosis. To study the role of STAT1 in DNA damage-induced apoptosis in B lymphocytes, its active form, STAT1alpha, was specifically inhibited by the overexpression of STAT1beta, the STAT1alpha truncated inhibitory isoform. An episomal vector with a tetracycline-inducible bidirectional promoter was created to induce the expression of 2 proteins, STAT1beta and enhanced green fluorescence protein (EGFP). The same vector was used to overexpress STAT1alpha as a control. Expression of STAT1beta inhibited the phosphorylation, the DNA-binding activity, and the transcriptional activity of STAT1alpha, as well as the expression of STAT1alpha target genes such as p21WAF1/CIP1, TAP1, IRF1, and PKR. Inhibiting STAT1alpha by STAT1beta increased the growth rate of transfected cells and their resistance to fludarabine-induced apoptosis and cell cycle arrest. Overexpressing STAT1beta reversed the negative regulation of Mdm2 expression observed after treatment with interferon-gamma (IFN-gamma), which activates STAT1, or with fludarabine. Nuclear translocation of p53 after fludarabine treatment was decreased when STAT1beta was overexpressed, and it was increased when STAT1alpha was induced. Oligonucleotide pull-down experiments showed a physical STAT1/p53 interaction. Our results show that imbalance between the antiproliferative/proapoptotic isoform STAT1alpha and the proliferative isoform STAT1beta is likely to play a crucial role in the regulation of proliferation and apoptosis and that STAT1alpha may regulate p53 activity and sensitize B cells to fludarabine-induced apoptosis.
Photo-Oxidative Polymerization of Bis(3,5-dimethylphenyl) Disulfide for Synthesis of Poly(thioarylene) (1993)

Abstract Bis(3,5-dimethylphenyl) disulfide was subject to photo-oxidation in the presence of 2,3-dicyanonaphthalene as a sensitizer. The photo-redox system enabled efficient formation of poly(thio-2,6-dimethyl-1,4-phenylene) non-contaminated with metal salt at room temperature through the electrophilic reaction of the sulfonium cation produced by the photo-oxidation.
Structural chromosomal mosaicism and prenatal diagnosis (2004)

True structural chromosomal mosaicism are rare events in prenatal cytogenetics practice and may lead to diagnostic and prognostic problems. Here is described the case of a fetus carrying an abnormal chromosome 15 made of a whole chromosome 2p translocated on its short arm in 10% of the cells, in association with a normal cell line. The fetal karyotype was 46,XX,add(15)(p10).ish t(2;15)(p10;q10)(WCP2+)[3]/46,XX[27]. Pregnancy was terminated and fetus examination revealed a growth retardation associated with a dysmorphism including dolichocephaly, hypertelorism, high forehead, low-set ears with prominent anthelix and a small nose, which were characteristic of partial trisomy 2p. Possible aetiologies for prenatal mosaicism involving a chromosomal structural abnormality are discussed.
Histologic characterization of vaginal vs. abdominal surgical wound healing in a rabbit model (2007)

We aimed to compare the histologic characteristics of vaginal vs. abdominal surgical wound healing in the rabbit. Bilateral 6 mm full-thickness circular segments were excised from the vagina and abdominal skin in 34 New Zealand white female rabbits. Animals were euthanized on the day of and 4, 7, 10, 14, 21, 28, and 35 days after wounding, and their wounds were evaluated using a modified scoring system. The inter- and intraobserver agreements of the scoring system were good (weighted kappa 0.63 and 0.71, respectively). A transient fibrinous crust was evident in 75% of the abdominal and in none of the vaginal wound specimens on days 4-7 after wounding (p=0.01). Acute inflammation peaked at day 4 in both the vaginal and abdominal wounds, while chronic inflammation peaked at days 4-7 and 14-21 in the abdomen and vagina, respectively. Both neovascularization and the amount of granulation tissue peaked at days 4 and 7 in the vagina and abdomen, respectively. Maturation of granulation tissue and collagen deposition increased persistently in both tissues until postwounding day 35. Reepithelialization increased after wounding, and was completed by day 14 in both tissues. The surgical wound-healing process in both the vagina and abdomen includes transient acute and chronic inflammation, fibroblast proliferation, and neovascularization, as well as progressive maturation of granulation tissue, reepithelialization, and collagen deposition. A transient fibrinous crust forms in the abdomen but not in the vagina 4-7 days after wounding. The modified histologic scoring system described here was found to be reliable and reproducible.
Towards Breakthrough Concepts in the Industrial Synthesis of Di‐ and Short Oligopeptides (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Hyperosmolarity impedes the cross-priming competence of dendritic cells in a TRIF-dependent manner (2017)

Tissue osmolarity varies among different organs and can be considerably increased under pathologic conditions. Hyperosmolarity has been associated with altered stimulatory properties of immune cells, especially macrophages and dendritic cells. We have recently reported that dendritic cells upon exposure to hypertonic stimuli shift their profile towards a macrophage-M2-like phenotype, resulting in attenuated local alloreactivity during acute kidney graft rejection. Here, we examined how hyperosmotic microenvironment affects the cross-priming capacity of dendritic cells. Using ovalbumin as model antigen, we showed that exposure of dendritic cells to hyperosmolarity strongly inhibits activation of antigen-specific T cells despite enhancement of antigen uptake, processing and presentation. We identified TRIF as key mediator of this phenomenon. Moreover, we detected a hyperosmolarity-triggered, TRIF-dependent clustering of MHCI loaded with the ovalbumin-derived epitope, but not of overall MHCI molecules, providing a possible explanation for a reduced T cell activation. Our findings identify dendritic cells as important players in hyperosmolarity-mediated immune imbalance and provide evidence for a novel pathway of inhibition of antigen specific CD8<sup>+</sup> T cell response in a hypertonic micromilieu.
Molecular characterisation of non-absorptive and absorptive enterocytes in human small intestine (2006)

Two types of enterocytes were dissected at the molecular level, the non-absorptive enterocyte located in the upper part of crypts and the absorptive enterocyte found in the middle of villi. These data improve our knowledge about the physiology of the crypt-villus architecture in human small intestine and provide new insights into pathophysiological phenomena, such as villus atrophy, which is clinically important.
High Efficiency Thermoelectric Radioisotope Power Systems (2004)

The work performed and whose results presented in this report is a joint effort between the University of New Mexico s Institute for Space and Nuclear Power Studies (ISNPS) and the Jet Propulsion Laboratory (JPL), California Institute of Technology. In addition to the development, design, and fabrication of skutterudites and skutterudites-based segmented unicouples this effort included conducting performance tests of these unicouples for hundreds of hours to verify theoretical predictions of the conversion efficiency. The performance predictions of these unicouples are obtained using 1-D and 3-D models developed for that purpose and for estimating the actual performance and side heat losses in the tests conducted at ISNPS. In addition to the performance tests, the development of the 1-D and 3-D models and the development of Advanced Radioisotope Power systems for Beginning-Of-Life (BOM) power of 108 We are carried out at ISNPS. The materials synthesis and fabrication of the unicouples are carried out at JPL. The research conducted at ISNPS is documented in chapters 2-5 and that conducted at JP, in documented in chapter 5. An important consideration in the design and optimization of segmented thermoelectric unicouples (STUs) is determining the relative lengths, cross-section areas, and the interfacial temperatures of the segments of the different materials in the n- and p-legs. These variables are determined using a genetic algorithm (GA) in conjunction with one-dimensional analytical model of STUs that is developed in chapter 2. Results indicated that when optimized for maximum conversion efficiency, the interfacial temperatures between various segments in a STU are close to those at the intersections of the Figure-Of-Merit (FOM), ZT, curves of the thermoelectric materials of the adjacent segments. When optimizing the STUs for maximum electrical power density, however, the interfacial temperatures are different from those at the intersections of the ZT curves, but close to those at the intersections the characteristic power, CP, curves of the thermoelectric materials of the adjacent segments (CP = T(sup 2)Zk and has a unit of W/m). Results also showed that the number of the segments in the n- and p-legs of the STUs optimized for maximum power density are generally fewer than when the same unicouples are optimized for maximum efficiency. These results are obtained using the 1-D optimization model of STUs that is detailed in chapter 2. A three-dimensional model of STUs is developed and incorporated into the ANSYS commercial software (chapter 3). The governing equations are solved, subject to the prescribed
Impact of 3D design choices on manufacturing cost (2009)

The available options in 3D IC design and manufacturing have different impact on the cost of a 3D System-on-Chip. Using the 3D cost model developed at IMEC, the cost of different system integration options is analyzed and the cost effectiveness of different technology solutions is demonstrated. The cost model is based on the IMEC 3D integration process flows and includes the cost of manufacturing equipment, fabrication facilities, personnel, and materials. Using the IMEC 3D cost model, the cost of various 3D stacking strategies is compared to single die (i.e. 2D) integration. In addition, the effect on cost of different Through-Silicon-Via (TSV) manufacturing technologies is evaluated. The effectiveness of different 3D testing strategies and their impact on system cost is also investigated.
AMIODARONE PHOTOTOXICITY TO HUMAN ERYTHROCYTES AND LYMPHOCYTES (1984)

Abstract Amiodarone (AD) therapy for cardiac arrhythmia frequently leads to cutaneous phototoxicity. Amiodarone and its metabolite, desethylamiodarone (DEA), photosensitized hemolysis of red blood cells (RBC) and were phototoxic to lymphocytes. Hemolysis photosensitized by 3.3 μ M AD was partially oxygen dependent and was partially quenched 5 m M sodium azide, 50 m M mannitol, superoxide dismutase (251 U/me e ) and catalase (1500 U/m e ), but was unaffected when H 2 O was replaced by D 2 O. These results suggest that membrane damage may be important in the in vivo phototoxicity to AD, that both oxygen dependent and oxygen independent mechanisms may operate, and that active oxygen species such as O 2 and hydrogen peroxide may be involved. Photohemolysis was more rapid in the presence of DEA than of AD. However, this may be due to the greater fragility of the cell membrane in the presence of DEA. The greater phototoxicity of DEA than AD towards lymphocytes was not due to greater membrane fragility.