gebhart/patrepeval huggingface dataset:
Genome-Scale Analysis of the Uses of the Escherichia coli Genome: Model-Driven Analysis of Heterogeneous Data Sets (2003)

The recent availability of heterogeneous high-throughput data types has increased the need for scalable in silico methods with which to integrate data related to the processes of regulation, protein synthesis, and metabolism. A sequence-based framework for modeling transcription and translation in prokaryotes has been established and has been extended to study the expression state of the entire Escherichia coli genome. The resulting in silico analysis of the expression state highlighted three facets of gene expression in E. coli: (i) the metabolic resources required for genome expression and protein synthesis were found to be relatively invariant under the conditions tested; (ii) effective promoter strengths were estimated at the genome scale by using global mRNA abundance and half-life data, revealing genes subject to regulation under the experimental conditions tested; and (iii) large-scale genome location-dependent expression patterns with approximately 600-kb periodicity were detected in the E. coli genome based on the 49 expression data sets analyzed. These results support the notion that a structured model-driven analysis of expression data yields additional information that can be subjected to commonly used statistical analyses. The integration of heterogeneous genome-scale data (i.e., sequence, expression data, and mRNA half-life data) is readily achieved in the context of an in silico model.
Evolution of Non-Terrestrial Networks From 5G to 6G: A Survey (2021)

Non-terrestrial networks (NTNs) traditionally have certain limited applications. However, the recent technological advancements and manufacturing cost reduction opened up myriad applications of NTNs for 5G and beyond networks, especially when integrated into terrestrial networks (TNs). This article comprehensively surveys the evolution of NTNs highlighting their relevance to 5G networks and essentially, how it will play a pivotal role in the development of 6G ecosystem. We discuss important features of NTNs integration into TNs and the synergies by delving into the new range of services and use cases, various architectures, technological enablers, and higher layer aspects pertinent to NTNs integration. Moreover, we review the corresponding challenges arising from the technical peculiarities and the new approaches being adopted to develop efficient integrated ground-air-space (GAS) networks. Our survey further includes the major progress and outcomes from academic research as well as industrial efforts representing the main industrial trends, field trials, and prototyping towards the 6G networks.
Impaired Hypoxic Ventilatory Drive in Diabetic Patients with Autonomic Neuropathy* (1986)

The mortality of diabetic patients with autonomic neuropathy (DAN) is higher than that in those without autonomic neuropathy (DM). To test the hypothesis that this may be due to respiratory rather than cardiac dysfunction, we evaluated ventilatory responses to isocapnic-hypoxic and hyperoxic-hypercapnic conditions in 14 diabetic patients (8 DAN and 6 DM) and compared the results with those in 8 normal subjects. In all groups tested there was a significant linear correlation between end-tidal CO2 and minute ventilation and between end-tidal CO2 and mouth occlusion pressure (p100), as an index of the drive to breathe. There were no significant differences between the slopes and intercepts in the groups tested. A significant linear correlation was found between the O2 saturation and both minute ventilation and p100. There were no significant differences in the relationship between minute ventilation and O2 saturation, but the slopes and the intercepts of the regression lines of p100 vs. O2 saturation were significantly different in the DAN compared with those in normal subjects and DM. Additionally, five of eight patients with DAN lost their ventilatory drive and ventilatory responses to hypoxemia compared with only one of six DM. These findings suggest that a disorder in the ventilatory response to hypoxemia exists in some DAN.
Low-cost uncooled MWIR PbSe quantum dots photodiodes (2019)

A mid-wave infrared (MWIR) uncooled PbSe-QDs/CdS p-n heterojunction photodiode has been fabricated using a wet-chemical synthesis route. This offers a low-cost alternative to traditional monocrystalline photodiodes relying on molecular beam epitaxy (MBE) technology. It was demonstrated that the post-annealing is critical to tailor the photoresponse wavelength and to improve the performance of photodiodes. After annealing at 673 K in air for 0.5 h, the ligand-free PbSe-QDs/CdS photodiode exhibits a MWIR spectral photoresponse with a cutoff wavelength of 4.2 μm at room temperature. Under zero-bias photovoltaic mode, the peak responsivity and specific detectivity at room temperature are 0.36 ± 0.04 A W<sup>-1</sup> and (8.5 ± 1) ×10<sup>8</sup> cm Hz<sup>1/2</sup> W<sup>-1</sup>, respectively. Temperature-dependent spectral response shows an abnormal intensity variation at temperatures lower than 200 K. This phenomenon is attributed to the band alignment transition from type II to type I, resulting from the positive temperature coefficient of PbSe. In addition, it was proved that In doped CdSe (CdSe:In) films could be used as a promising new candidate of infrared transparent conductive electrodes, paving the way for monolithic integration of uncooled low-cost MWIR photodiodes on Si readout circuitry.
A coldness metric for cache optimization (2013)

A "hot" concept in program optimization is hotness. For example, program optimization targets hot paths, and register allocation targets hot variables. Cache optimization, however, has to target cold data, which are less frequently used and tend to cause cache misses whenever they are accessed. Hot data, in contrast, as they are small and frequently used, tend to stay in cache. In this paper, we define a new metric called "coldness" and show how the coldness varies across programs and how much colder the data we have to optimize as the cache size on modern machines increases.
Zinc Alkoxide Catalyzed Allylations of Ketones with Allyl Pinacol Boronates (2010)

An efficient, general allylation of a wide range of ketones with allyl boronates is disclosed. A zinc alkoxide (2 mol%) serves as catalyst, enabling relatively short reaction times.
Minocycline suppresses disease-associated microglia (DAM) in a model of photoreceptor cell degeneration (2022)

As the resident immune cells in the retina, microglia play important homeostatic roles in retinal immune regulation and neuroprotection. However, chronic microglia activation is a common hallmark of many degenerative retinal diseases. The semi-synthetic tetracycline antibiotic, minocycline, appears to inhibit pro-inflammatory microglia which coincides with protection against photoreceptor cell degeneration. A sub-type of microglia termed disease associated microglia (DAM) have recently been associated with a wide range of central nervous system (CNS) diseases. In this study we examine the kinetics of microglia infiltration towards the outer retina of rhodopsin knockout mice (Rho−/−) by immunofluorescence, and undertake transcriptional and spatial localization analysis of markers for evidence of both homeostatic function and appearance of DAM. We demonstrate in the Rho−/− mice, IBA1+ and P2RY12+ microglia take on an activated morphology early in disease, prior to notable photoreceptor loss and are capable of infiltrating the subretinal space. Expression of lipid processing enzyme and DAM-marker lipoprotein lipase (LPL) is primarily observed only after microglia have traversed the ONL. Administration of minocycline to Rho−/− mice induced loss of phagocytic/DAM microglia in the outer retina in vivo coinciding with photoreceptor survival and amelioration of retinal degeneration. Overall, we show that minocycline suppresses many DAM markers, in particular those associated with lipid metabolism indicating that suppression of this process is one mechanism by which minocycline protects against inflammation induced photoreceptor cell death.
ChemInform Abstract: Ir‐Catalyzed Functionalization of C—H Bonds (2011)

Abstract Review: 138 refs.
Antenna selection for space-time communication with covariance feedback (2005)

We consider space-time communication for a cellular downlink in which the base station (BS) transmitter has multiple antennas, while the mobile receiver has one or two. Only a subset of the available antennas at the BS are used for transmission, thus reducing the number of RF chains and the complexity of the baseband signal processing. It is assumed that the BS does not know the instantaneous downlink channel realization, but has estimates of the covariance of the space-time channel: covariance information can be easily obtained in wideband systems by averaging uplink channel measurements over frequency. Based on the optimization of a lower bound for capacity, we are able to provide rules of thumb for antenna selection as a function of the physical channel characteristics and the number of receive antennas. This procedure is shown to be optimal or near-optimal (relative to exhaustive computation of the best antenna subset) at moderate SNR.
HEAT TRANSFER TO DISPERSED SWIRL FLOW OF HIGH-PRESSURE WATER WITH LOW WALL SUPERHEAT (1991)

Heat transfer was studied to two-phase flow in the post-CHF dispersed flow regime under swirl conditions. Data were used for post-CHF water flow at high pressure, 15.9 MPa, inside a vertical tube with twisted-tape inserts. Data used were obtained under test conditions typical of heat exchanger operation with low wall superheats of 5-40°C. The mass flux range of the data was 910-1878 kg/m2 s, and three tape-twist ratios were used: 2.55, 5.03, and 7.52. The low wall superheat and the relatively high mass fluxes resulted in higher than predicted drop-wall heat transfer. The only existing heat transfer correlation for this flow situation was modified to include this heat exchanger parameter range.
Peripheral Blood Gene Expression as a Novel Genomic Biomarker in Complicated Sarcoidosis (2012)

Sarcoidosis, a systemic granulomatous syndrome invariably affecting the lung, typically spontaneously remits but in ~20% of cases progresses with severe lung dysfunction or cardiac and neurologic involvement (complicated sarcoidosis). Unfortunately, current biomarkers fail to distinguish patients with remitting (uncomplicated) sarcoidosis from other fibrotic lung disorders, and fail to identify individuals at risk for complicated sarcoidosis. We utilized genome-wide peripheral blood gene expression analysis to identify a 20-gene sarcoidosis biomarker signature distinguishing sarcoidosis (n = 39) from healthy controls (n = 35, 86% classification accuracy) and which served as a molecular signature for complicated sarcoidosis (n = 17). As aberrancies in T cell receptor (TCR) signaling, JAK-STAT (JS) signaling, and cytokine-cytokine receptor (CCR) signaling are implicated in sarcoidosis pathogenesis, a 31-gene signature comprised of T cell signaling pathway genes associated with sarcoidosis (TCR/JS/CCR) was compared to the unbiased 20-gene biomarker signature but proved inferior in prediction accuracy in distinguishing complicated from uncomplicated sarcoidosis. Additional validation strategies included significant association of single nucleotide polymorphisms (SNPs) in signature genes with sarcoidosis susceptibility and severity (unbiased signature genes - CX3CR1, FKBP1A, NOG, RBM12B, SENS3, TSHZ2; T cell/JAK-STAT pathway genes such as AKT3, CBLB, DLG1, IFNG, IL2RA, IL7R, ITK, JUN, MALT1, NFATC2, PLCG1, SPRED1). In summary, this validated peripheral blood molecular gene signature appears to be a valuable biomarker in identifying cases with sarcoidoisis and predicting risk for complicated sarcoidosis.
ChemInform Abstract: Zeolite Effects on the Cracking of Long Chain Alkyl Aromatics. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Hot sphere detection limits for a dual head coincidence imaging system (1999)

Phantom studies were performed to investigate detectability limits for a dual head coincidence imaging system. Spheres of 2.8, 2.2, 1.6, 1.2, 1.0, 0.8 cm inner diameter were placed at a radius of 5.75 cm in a 22 cm diameter cylindrical phantom. The contrast to noise ratio (CNR) of the spheres to background was used as the authors' metric of detectability. CNR values were determined for three different sphere to background ratios (10:1, 5:1, and 3:1); for three different background count densities (high, medium, and low); and for three different energy window requirements (photopeak only, photopeak and photopeak-Compton, and all combinations). Based upon the authors' visual observation, the smallest detectable spheres were 0.8 cm, 1.2 cm and 1.6 cm for a 2.5 million event photopeak-Compton image set with sphere to background ratios of 10:1, 5:1 and 3:1, respectively. The CNR values for these spheres were 5.1, 7.8, and 4.8. Over all observations, spheres with a CNR greater than 4 were detectable.
A 1 MHz BW 34.2 fJ/step Continuous Time Delta Sigma Modulator With an Integrated Mixer for Cardiac Ultrasound (2016)

Fully digitized 2D ultrasound transducer arrays require one ADC per channel with a beamforming architecture consuming low power. We give design considerations for per-channel digitization and beamforming, and present the design and measurements of a continuous time delta-sigma modulator (CTDSM) for cardiac ultrasound applications. By integrating a mixer into the modulator frontend, the phase and frequency of the input signal can be shifted, thereby enabling both improved conversion efficiency and narrowband beamforming. To minimize the power consumption, we propose an optimization methodology using a simulated annealing framework combined with a C++ simulator solving linear electrical networks. The 3rd order single-bit feedback type modulator, implemented in a 65 nm CMOS process, achieves an SNR/SNDR of 67.8/67.4 dB across 1 MHz bandwidth consuming 131 [Formula: see text] of power. The achieved figure of merit of 34.2 fJ/step is comparable with state-of-the-art feedforward type multi-bit designs. We further demonstrate the influence to the dynamic range when performing dynamic receive beamforming on recorded delta-sigma modulated bit-stream sequences.
Rolle des antimikrobiellen Peptids Hepcidin bei der hereditären Hämochromatose (2015)

Experimentelle Daten lassen auf eine zentrale Rolle des in der Leber exprimierten antimikrobiellen Peptids Hepcidin in der Regulation des Eisenstoffwechsels schließen. So hemmt das Akutphase-Protein Hepcidin die intestinale Eisenaufnahme und scheint entscheidend an der Pathogenese der Infekt- und Tumoranämie beteiligt zu sein. Ziel dieser Studie war es, die Expression des Hepcidins unter klinischen und experimentellen Bedingungen einer Eisenüberladung einschließlich der hereditären Hämochromatose zu untersuchen. Mittels quantitativer RT-PCR wurde die Expression des Hepcidins sowie der wesentlich am Eisenstoffwechsel beteiligten Gene in Leberbiopsien von Hämochromatosepatienten und Kontrollpersonen ohne Eisenüberladung bestimmt. Zudem wurde die Abhängigkeit der mRNA-Expression des Hepcidins von transferringebundenem Eisen, nicht-transferringebundenem freiem Eisen sowie Deferoxamin in humanen Hepatom-Zellen (HepG2) untersucht. Die erhobenen Daten zeigen, dass die Expression des Hepcidins bei Kontrollpersonen ohne Eisenüberladung signifikant mit den Ferritinspiegeln im Serum korreliert. Im Gegensatz dazu fand sich bei den Hämochromatosepatienten trotz erheblicher Eisenüberladung und hohen Ferritinspiegeln keine gesteigerte Expression des Hepcidins. Vielmehr zeigte sich eine negative Korrelation der Hepcidin-Expression mit der Serum-Transferrinsättigung. Außerdem fanden wir eine hochsignifikante Korrelation der Hepcidin-Expression mit der Transferrinrezeptor-2-Expression unabhängig von dem Vorhandensein einer Eisenüberladung. Unsere in vitro Ergebnisse deuten darauf hin, dass die Hepcidin-Expression bereits bei geringen Konzentrationen an nicht-transferringebundenem Eisen drastisch abnimmt. Dieser Zusammenhang scheint die negative Korrelation der Hepcidin-Expression mit der Serum-Transferrinsättigung zu erklären und könnte einen zentralen Mechanismus in der Pathogenese zahlreicher Eisenstoffwechselstörung einschließlich der Hämochromatose darstellen.
Gene amplification in mesenchymal stem cells and during differentiation towards adipocytes or osteoblasts (2017)

Gene amplifications are an attribute of tumor cells and have for long time been overlooked in normal cells. A growing number of investigations describe gene amplifications in normal mammalian cells during development and differentiation. Possibly, tumor cells have rescued the gene amplification mechanism as a physiological attribute of stem cells. Here, we investigated human mesenchymal stem cells (hMSCs) for gene amplification using array-CGH, single cell fluorescence <i>in situ</i> hybridization and qPCR. Gene amplifications were detected in mesenchymal stem cells and in mesenchymal stem cells during differentiation towards adipocytes and osteoblasts. Undifferentiated hMSCs harbor 12 amplified chromosomal regions, hMSCs that differentiated towards adipocytes 18 amplified chromosome regions, and hMSCs that differentiate towards osteoblasts 19 amplified regions. Specifically, hMSCs that differentiated towards adipocytes or osteoblasts harbor <i>CDK4</i> and <i>MDM2</i> amplifications both of which frequently occur in osteosarcoma and liposarcoma that are both of same cell origin. Beside the amplifications, we identified 36 under-replicated regions in undifferentiated and in differentiating hMSC cells.
MT1-MMP Regulates Hematopoiesis Through HIF-Mediated Chemo-/Cytokine Release From the Bone Marrow Niche, (2011)

Abstract Abstract 3409 Stem cells reside in a physical niche, a particular microenvironment. The organization of cellular niches has been shown to play a key role in regulating normal stem cell differentiation, stem cell maintenance and regeneration. Various stem cell niches have been shown to be hypoxic, thereby maintaining the stem cell phenotype, e.g. for hematopoietic stem cells (HSCs) or cancer stem cells. The bone marrow (BM) niche is a rich reservoir for tissue-specific pluripotent HSCs. Proteases, such as matrix metalloproteinases (MMPs) can modulate stem cell fate due to their proteolytic or non-proteolytic functions (abilities). We have investigated the role of membrane-type1 matrix metalloproteinase (MT1-MMP), known for its role in pericellular matrix remodeling and cell migration, in hematopoiesis. MT1-MMP is highly expressed in HSCs and stromal cells. In MT1-MMP−/− mice, release of kit ligand (KitL), stromal cell derived factor-1 (SDF-1/CXCL12), erythropoietin (Epo) and interleukin-7 were impaired resulting in erythroid, myeloid and T and B lymphoid differentiation. Addition of exogenous rec. KitL and rec. SDF-1 restored hematopoiesis in vivo and in vitro. Further mechanistic studies revealed that MT1-MMP in a non-proteolytic manner activates the HIF-1 pathway, thereby inducing the transcription of the HIF-responsive genes KitL, SDF-1 and Epo. These results suggested MT1-MMP as a critical regulator of postnatal hematopoiesis, which as a modulator of the HIF pathway alters critical hematopoietic niche factors necessary for terminal differentiation and or migration. Thus, our results indicate that MT1-MMP as a key molecular link between hypoxia and the regulation of vital HSC niche factors. Disclosures: No relevant conflicts of interest to declare.
Electron density measurements during microwave generation in a high power backward-wave oscillator (1998)

Laser interferometry is used for the first time to measure plasma electron density along the slow wave structure (SWS) wall during microwave generation in a vacuum, long pulse, high power backward-wave oscillator (BWO). The University of New Mexico long pulse backward-wave oscillator, which displays the characteristic pulse shortening phenomenon, is investigated in these studies. Although pulse shortening is observed across a wide class of high power microwave devices, its origin is not definitively understood. Many hypotheses suggest that the unintentional introduction of plasma into the interaction region near the walls of the SWS is one of several likely causes of pulse shortening in intense electron beam driven slow wave devices. This article presents initial measurements of the line-integrated, temporally resolved plasma density between an intense, relativistic, annular electron beam and SWS walls for a variety of radiated microwave peak power levels. Line-integrated electron densities, <n L="" e="" sub="" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">, between 9.10/sup 15/ and 2.410/sup 16/ cm/sup -2/ for radiated microwave powers between 20 and 120 MW have been measured. The two main sources of the measured electron density are postulated to be (i) plasma generated from the cutoff neck due to beam scrape off, and (ii) material removed and ionized from the SWS walls during microwave generation.</n>
High-Q Tunable Capacitors and Multi-Way Switches Using Microelectromechanical Systems (MEMS) for Millimeter-Wave Applications (2002)

Abstract : The objective of this project was to design new, innovative microelectromechanical systems (MEMS) to create high-Q tunable capacitors and switches that were superior to the existing on/off switches. The concept was feasible; however, it was very challenging to design and/or process MEMS to meet specific requirements balancing mm-wave and electro -mechanical performance measures, such as quality factor (Q), capacitance range, switching complexity, dynamic response, and reliability. Therefore, we planned to conduct in-depth synthesis and analysis to develop representative, well-characterized, MEMS-based, high-Q turnable capacitors, switches, and their mm-wave modules. We have successfully demonstrated innovative RF MEMS switches and variable capacitors and the associated knowledge and technology. The devices and subsystems demonstrated have confirmed the great potential of RF MEMS. More importantly, the knowledge and technologies developed for the design, packaging, and reliability of RF MEMS will assist the industry to develop cost-effective, reliable RF MEMS to support the advancement of military systems. Five major accomplishments are summarized in this report.
High-Performance Inkjet-Printed Indium-Gallium-Zinc-Oxide Transistors Enabled by Embedded, Chemically Stable Graphene Electrodes (2016)

Recent developments in solution-processed amorphous oxide semiconductors have established indium-gallium-zinc-oxide (IGZO) as a promising candidate for printed electronics. A key challenge for this vision is the integration of IGZO thin-film transistor (TFT) channels with compatible source/drain electrodes using low-temperature, solution-phase patterning methods. Here we demonstrate the suitability of inkjet-printed graphene electrodes for this purpose. In contrast to common inkjet-printed silver-based conductive inks, graphene provides a chemically stable electrode-channel interface. Furthermore, by embedding the graphene electrode between two consecutive IGZO printing passes, high-performance IGZO TFTs are achieved with an electron mobility of ∼6 cm(2)/V·s and current on/off ratio of ∼10(5). The resulting printed devices exhibit robust stability to aging in ambient as well as excellent resilience to thermal stress, thereby offering a promising platform for future printed electronics applications.