gebhart/patrepeval huggingface dataset:
Nanomolar Responsiveness of Marine <b><i>Phaeobacter inhibens</i></b> DSM 17395 toward Carbohydrates and Amino Acids (2022)

Phaeobacter inhibens DSM 17395 is a heterotrophic member of the ubiquitous, marine Roseobacter group and specializes in the aerobic utilization of carbohydrates and amino acids via pathways widespread among roseobacters. The in vivo responsiveness of P. inhibens DSM 17395 was studied with nonadapted cells (succinate-grown), which were exposed to a single pulse (100-0.01 µM) each of N-acetylglucosamine, mannitol, xylose, leucine, phenylalanine, or tryptophan (effectors). Responsiveness was then determined by time-resolved transcript analyses (quantitative reverse transcription-PCR) of "degradation" and "uptake" genes selected based on previously reported substrate-specific proteome profiles. The transcriptional response thresholds were: 50-100 nM for nagK (N-acetylglucosamine kinase), paaA (ring 1,2-phenylacetyl-CoA epoxidase), and kynA (tryptophan 2,3-dioxygenase), 10-50 nM for xylA (xylose isomerase), and around 10 nM for mtlK (mannitol 2-dehydrogenase). A threshold for leucine could not be determined due to the elevated intrinsic presence of leucine in the exometabolome of succinate-grown cells (no effector addition). Notably, the response thresholds for presumptive carbohydrate-binding proteins of ABC-transporters were in the same range or even lower: 0.1-1 µM for c27930 (N-acetylglucosamine) and even below 10 nM for c13210 (mannitol) and xylF (xylose). These results shed new light on the sensory/regulatory sensitivity of a well-studied roseobacter for recognizing potential substrates at low ambient concentrations and on the concentration threshold below which these might escape biodegradation ("emergent recalcitrance" concept of dissolved organic matter persistence).
Sherry Apple Resident Travel Scholarship 194 Assessment of Treatment Response in Isocitrate Dehydrogenase-Mutant Gliomas by Quantification of 2-Hydroxyglutarate With In Vivo 3-Dimensional Magnetic Resonance Spectroscopy (2014)

INTRODUCTION: Mutations in isocitrate dehydrogenase (IDH)—present in a distinct subset of human gliomas characterized by younger age and improved prognosis- cause a marked elevation of the metabolite 2-hydroxyglutarate (2HG) [1,2]. This excess production of 2HG represents an ideal biomarker for these gliomas and can be measured with in-vivo magnetic resonance spectroscopy [3]. We previously demonstrated that 2HG can be detected reliably in IDH-mutant gliomas with 3-dimensional (3-D) spectral-edited magnetic resonance spectroscopic imaging (MRSI) [4]. Here, we aimed to show that 3-D metabolomic mapping of 2HG can be utilized to evaluate treatment response in IDH-mutant gliomas. METHODS: 3-D metabolomic maps were measured in 18 IDH-mutant glioma patients prior to adjuvant radiation or chemotherapy with a robust and efficient 3-D MRSI sequence. All measurements were performed with a whole-body 3T MR scanner (Siemens Tim Trio with VB17 software). Spectra were fitted with LCModel software. All patients with detectable levels of 2HG in the baseline scan were subjected to a post-treatment 3-D MRSI to measure changes of 2HG-levels after adjuvant therapy. RESULTS: Sixteen of 18 patients (88.9%) demonstrated detectable levels of 2HG on their baseline scan. Matched pre- and post-treatment 3-D metabolomic maps indicated varying response to treatment: 4 patients demonstrated significant reduction of 2HG intensities after radiation therapy (Fig 1), while the remaining patients demonstrated mixed response (partial reduction of 2HG) to adjuvant treatment. CONCLUSION: Assessment of treatment response is feasible with in-vivo 3-D MRSI of 2HG in IDH-mutant glioma patients. Significant reduction of 2HG-levels in patients after completion of radiotherapy is suggestive of positive response to treatment. Further validation and longitudinal quantification of 2HG in IDH-mutant gliomas with 3-D MRSI is needed to evaluate the ability of the presented approach to reliably determine treatment response. Nevertheless, this non-invasive method yields great potential for clinical applicability and could tremendously improve the management of IDH-mutant glioma patients.
Magnetic Separation of Ores (1941)

Report issued by the Bureau of Mines over studies conducted on the removal of magnetic materials from iron ores. As stated in the introduction, "this report discusses briefly operations and trends in magnetic separation, explains magnetic separation, describes and classifies the machines used, and outlines their development" (p. 1). This report includes tables, and illustrations.
3D numerical reconstruction of the hyperthermia induced temperature distribution in human sarcomas using DE-MRI measured tissue perfusion: validation against non-invasive MR temperature measurements (2001)

Essential to the success of optimized thermal treatment during hyperthermia is accurate modelling. Advection of energy due to blood perfusion significantly affects the temperature. Without accurate estimates of the magnitude of the local tissue blood perfusion, accurate estimates of the temperature distribution can not be made. It is shown here that the blood mass flow rate per unit volume of tissue in the Pennes' bio-heat equation can be modelled using a relative perfusion index (RPI) determined with dynamic-enhanced magnetic resonance imaging (DE-MRI). Temperature distributions in two patients treated with hyperthermia at Duke University Medical Center for high-grade leg tissue sarcomas are modelled, and the resultant temperatures are compared to measured temperatures using a non-invasive MR thermometry technique. Significant correlations are found between the DE-MRI perfusion images, the MR temperature images, and the numerical simulation of the temperature field. The correlation between DE-MRI measured values and advective heat loss in tissue is used to scale the perfusion distribution, thereby allowing the continuum model to account for the local thermal impact of vasculature in the tumour. Large vessels in tumour and neighbouring healthy tissue need to be taken into account in order to accurately describe the complete temperature distribution.
Structure and Reactivity of Small Ring Compounds. IV. Photochemistry of Spirocyclopropyl Ketones (1972)

Abstract The photochemical transformations of a series of spriocyclopropyl ketones (1–4) have been investigated in dilute n-hexane solutions. Spirocyclopropyl ketones 1 and 2 give mainly the ’Type I’ photoproducts of cycloalkanones, i.e., 1-(2′-propenyl)cyclopropanecarboxaldehyde (5, 34%) and 1-(3′-butenyl)cyclopropanecarboxaldehyde (7, 37%), respectively, in marked contrast to the usual photochemical cleavage of cyclopropyl ketones. Ethylidenecycloalkanones are not detected, but their hydrogenated derivatives, 2-ethylcycloalkanones, are produced in a small amount. The photoreaction of 1 has been found to be quenched by piperylene, so that it is highly probable that the reaction products are derived from the n-π* triplet states of the ketones. The irradiations of nonconjugated spiroketones 3 and 4 afford ring-enlarged 4-methylenecycloalkanones, 9 and 10, respectively.
Molecular cloning, gene organization and expression of the human UDP-GalNAc:Neu5Acalpha2-3Galbeta-R beta1,4-N-acetylgalactosaminyltransferase responsible for the biosynthesis of the blood group Sda/Cad antigen: evidence for an unusual extended cytoplasmic domain (2003)

The nucleotide sequence of the short and long transcripts of beta1,4- N -acetylgalactosaminyltransferase have been submitted to the DDBJ, EMBL, GenBank(R) and GSDB Nucleotide Sequence Databases under accession nos AJ517770 and AJ517771 respectively. The human Sd(a) antigen is formed through the addition of an N -acetylgalactosamine residue via a beta1,4-linkage to a sub-terminal galactose residue substituted with an alpha2,3-linked sialic acid residue. We have taken advantage of the previously cloned mouse cDNA sequence of the UDP-GalNAc:Neu5Acalpha2-3Galbeta-R beta1,4- N -acetylgalactosaminyltransferase (Sd(a) beta1,4GalNAc transferase) to screen the human EST and genomic databases and to identify the corresponding human gene. The sequence spans over 35 kb of genomic DNA on chromosome 17 and comprises at least 12 exons. As judged by reverse transcription PCR, the human gene is expressed widely since it is detected in various amounts in almost all cell types studied. Northern blot analysis indicated that five Sd(a) beta1,4GalNAc transferase transcripts of 8.8, 6.1, 4.7, 3.8 and 1.65 kb were highly expressed in colon and to a lesser extent in kidney, stomach, ileum and rectum. The complete coding nucleotide sequence was amplified from Caco-2 cells. Interestingly, the alternative use of two first exons, named E1(S) and E1(L), leads to the production of two transcripts. These nucleotide sequences give rise potentially to two proteins of 506 and 566 amino acid residues, identical in their sequence with the exception of their cytoplasmic tail. The short form is highly similar (74% identity) to the mouse enzyme whereas the long form shows an unusual long cytoplasmic tail of 66 amino acid residues that is as yet not described for any other mammalian glycosyltransferase. Upon transient transfection in Cos-7 cells of the common catalytic domain, a soluble form of the protein was obtained, which catalysed the transfer of GalNAc residues to alpha2,3-sialylated acceptor substrates, to form the GalNAcbeta1-4[Neu5Acalpha2-3]Galbeta1-R trisaccharide common to both Sd(a) and Cad antigens.
Measurement of tracheal wall pressure: a comparison of three different in vitro techniques (2008)

We compared three different tracheal wall pressure measuring techniques in vitro. Using a high-volume, low-pressure, cuffed tracheal tube with an internal diameter of 7.5 mm and a model trachea, the pressure difference technique, the wall pressure membrane technique and the microchip sensor probe technique with and without lubrication were studied. Wall pressures were measured after sequential injections of 0.5 ml of air into the cuff at cuff pressures ranging from 0 to 50 mmHg. The coefficient of variance was largest for the microchip sensor probe technique with lubrication (29%) and without lubrication (214%), and was lower for the wall pressure membrane technique (22%) and the pressure difference technique (19%). The wall pressure membrane and pressure difference techniques provided comparable results. The microchip sensor probe technique considerably underestimated wall pressure. These findings have an impact on the interpretation of published data on tracheal or pharyngeal wall pressure using the microchip sensor probe technique.
Plasticity of Both Excitatory and Inhibitory Synapses Is Associated With Seizures Induced by Removal of Chronic Blockade of Activity in Cultured Hippocampus (2006)

One factor common to many neurological insults that can lead to acquired epilepsy is a loss of afferent neuronal input. Neuronal activity is one cellular mechanism implicated in transducing deafferentation into epileptogenesis. Therefore the effects of chronic activity blockade on seizure susceptibility and its underlying mechanisms were examined in organotypic hippocampal slice cultures treated chronically with the sodium channel blocker, tetrodotoxin (TTX), or the N-methyl-D-aspartate receptor (NMDAR) antagonist, D-2-amino-5-phosphonovaleric acid (D-APV). Granule cell field potential recordings in physiological buffer revealed spontaneous electrographic seizures in 83% of TTX-, 9% of D-APV-, but 0% of vehicle-treated cultures. TTX-induced seizures were not associated with membrane property alterations that would elicit granule cell hyperexcitability. Seizures were blocked by glutamate receptor antagonists, suggesting that plasticity in excitatory synaptic circuits contributed to seizures. The morphology of granule cells and their mossy fiber axons remained largely unchanged, and the number of synapses onto granule cells measured immunohistochemically was not increased in TTX- or D-APV-treated cultures. However, voltage-clamp recordings revealed that miniature excitatory postsynaptic current frequency and kinetics were increased and miniature inhibitory postsynaptic current kinetics were decreased in D-APV- and TTX-treated cultures compared with vehicle. Changes were more profound and qualitatively different in TTX- compared with D-APV-treated cultures, consistent with the dramatic effects of TTX treatment on seizure expression. We propose that chronic blockade of action potentials by TTX induces homeostatic responses including plasticity of both excitatory and inhibitory synapses. Removal of TTX unmasks the impact of these synaptic plasticities on local circuit excitability, resulting in spontaneous seizures.
In vivo selection and characterization of a murine mammary tumor subline with high potential for spontaneous lymph node metastasis (1990)

A transplantable mammary adenocarcinoma, grown in Balb/c mice, with a marked enhancement in its draining lymph node metastatic ability (MM3LN), was obtained through an in vivo procedure from a variant tumor moderately metastatic to lymph nodes (MM3). Both MM3 and MM3LN presented a similar latency and tumor growth rate and reached the same tumor mean diameter at death. MM3LN tumor-bearing mice exhibited a larger mean survival time. The new variant showed a 2.5-fold higher incidence of tumor-draining lymph node metastases than MM3 line, with no differences in the incidence of lung metastases. Morphology as well as cytogenetic and in vitro adhesion properties were studied in order to characterize the new subline. This murine tumor model has potential application in the study of the metastatic process in lymphoid tissue.
Topographic imaging of an absorbing object in a tissue-like scattering medium using a single source-detector pair (2019)

Diffuse optical tomography is an emerging biomedical imaging technique, due to its numerous advantages, such as low cost and non-ionizing radiation. In this work, we have developed a very simple setup, which included a single source – photodiode (SP) pair for scanning a sample of water with diluted Intralipid, simulating a biological tissue. LEDs emitting at 470, 525 and 624 nm, as well as a 650 nm Fabry Perot laser, were used as light sources. Scattered light from the sample was detected by the photodiode placed next to the LED. The SP distance could vary and the phantom could be scanned by moving the SP pair in precise, small and automated steps without any intervention during the measurements. Therefore, we obtained measurements from multiple locations on the sample, with just one SP pair. The presented experimental system verified the feasibility of deploying extremely low cost devices for detection and imaging absorbing objects of 1 cm height, placed inside a scattering medium. Maximum depth detection was 2.5 cm. As expected, the quality of the obtained images was degrading, as the object’s depth or the scanning step was increasing. Additionally, we developed Monte Carlo simulations of the setup, which achieved good agreement with the experimental results. We also conducted another set of simulations, studying the depth sensitivity of a single static SP pair considering a scattering medium similar to the experimental phantom with and without object. We observed that the depth sensitivity increases as the source wavelength increases from 450 nm to 650 nm.
The Gene Controlling Marijuana Psychoactivity (2004)

Delta(1)-tetrahydrocannabinolic acid (THCA) synthase is the enzyme that catalyzes oxidative cyclization of cannabigerolic acid into THCA, the precursor of Delta(1)-tetrahydrocannabinol. We cloned a novel cDNA (GenBank trade mark accession number AB057805) encoding THCA synthase by reverse transcription and polymerase chain reactions from rapidly expanding leaves of Cannabis sativa. This gene consists of a 1635-nucleotide open reading frame, encoding a 545-amino acid polypeptide of which the first 28 amino acid residues constitute the signal peptide. The predicted molecular weight of the 517-amino acid mature polypeptide is 58,597 Da. Interestingly, the deduced amino acid sequence exhibited high homology to berberine bridge enzyme from Eschscholtzia californica, which is involved in alkaloid biosynthesis. The liquid culture of transgenic tobacco hairy roots harboring the cDNA produced THCA upon feeding of cannabigerolic acid, demonstrating unequivocally that this gene encodes an active THCA synthase. Overexpression of the recombinant THCA synthase was achieved using a baculovirus-insect expression system. The purified recombinant enzyme contained covalently attached FAD cofactor at a molar ratio of FAD to protein of 1:1. The mutant enzyme constructed by changing His-114 of the wild-type enzyme to Ala-114 exhibited neither absorption characteristics of flavoproteins nor THCA synthase activity. Thus, we concluded that the FAD binding residue is His-114 and that the THCA synthase reaction is FAD-dependent. This is the first report on molecular characterization of an enzyme specific to cannabinoid biosynthesis.
Two Different Contact Sites Are Recruited by Cardiotrophin-like Cytokine (CLC) to Generate the CLC/CLF and CLC/sCNTFRα Composite Cytokines (2004)

The cytokines of the interleukin-6 family are multifunctional proteins that regulate cell growth, differentiation, and other cell functions in a variety of biological systems including the immune, inflammatory, hematopoietic, and nervous systems. One member of this family, ciliary neurotrophic factor (CNTF), displays biological functions more restricted to the neuromuscular axis. We have recently identified two additional ligands for the CNTF receptor complex. Both are composite cytokines formed by cardiotrophin-like cytokine (CLC) associated to either the soluble type I cytokine receptor CLF or the soluble form of CNTF receptor alpha (CNTFRalpha). The present study was aimed at analyzing the interactions between the cytokine CLC and its different receptor chains. For this purpose, we modeled CLC/receptor interactions to define the residues potentially involved in the contact sites. We then performed site-directed mutagenesis on these residues and analyzed the biological interactions between mutants and receptor chains. Importantly, we found that CLC interacts with the soluble forms of CNTFRalpha and CLF via sites 1 and 3, respectively. For site 1, the most crucial residues involved in the interaction are Trp67, Arg170, and Asp174, which interact with CNTFRalpha. Surprisingly, the residues that are important for the interaction of CLC with CLF are part of the conserved FXXK motif of site 3 known to be the interaction site of LIFRbeta. Obtained results show that the Phe151 and Lys154 residues are effectively involved in the interaction of CLC with LIFRbeta. This study establishes the molecular details of the interaction of CLC with CLF, CNTFRalpha, and LIFRbeta and helps to define the precise role of each protein in this functional receptor complex.
Wafer bonding for 3D integration of MEMS/CMOS (2006)

The pressure for reduction in cost and development time in new product, together with the need to pack more functions into smaller volumes in silicon chips has been fueling the system-on-chip (SOC) development. However, the current SOC technologies available essentially involve merging of chips fabricated with standard CMOS technology. These SOC technologies provide an integration solution with compatible fabrication processes that require little changes in process integration. There is no standard cost-effective solution to make 3D MEMS and optoelectronic devices together with CMOS on the same chip without compromising material compatibility, process complexity and system performance. One solution is to fabricate MEMS and CMOS components on separate wafer substrates and then stack them together with well isolated interconnected vias. In order to demonstrate this wafer-level 3D integration technology, a novel wafer-level bonding technology is being developed. This paper reports a detailed study of 3D MEMS (Micro Electro-Mechanical Systems) integration through multi-wafer anodic and polymeric wafer bonding. Different from previously reported wafer bonding studies, this study focuses on the optimization of the bonding process to improve the bonding quality.
Assembly and Stabilization of Multi-Amino Acid Zwitterions by the Zn(II) Ion: A Computational Exploration (2009)

Density functional calculations were employed to stabilize multi-amino acid zwitterions by metal ions as well as to understand the stabilizing mechanism. This work distinguishes from the previous metalations and stabilizations of a single amino acid zwitterion, where the metal ions are coordination-unsaturated. It was found that up to three Gly zwitterions can be stabilized by the Zn(2+) ion at the same time. The addition of the fourth Gly zwitterion to the Zn(Gly)(3) system causes the spontaneous transformation of one zwitterion to the neutral isomer. The single mutations of Gly in Zn(Gly)(4) with Arg or Asp render the Zn(2+)-combined four amino acid zwitterions geometrically stable. The double mutation of Gly with Arg further stabilizes the structure with four amino acid zwitterions, with its energy being lower than the one containing one neutral and three zwitterionic isomers. The systematic studies on a series of M-combined amino acid systems (M = Zn(2+), Zn(+), Li(+), Na(+)) indicated that enough charge transfers from the metal ions are essential to stabilize the amino acid zwitterions. There exist critical values of charge transfers, and for Zn(2+)-combined amino acid systems, an estimation of 0.20 |e| is required to stabilize each Gly zwitterion. Further analysis revealed that the charge transfers rather than the formations of direct M-O bonds play a more important role in the stabilizations of amino acid zwitterions.
Spintronic devices for ultra-low power neuromorphic computation (Special session paper) (2016)

Emerging spin-transfer torque mechanisms in devices like vertical spin valves, lateral spin valves, domain wall motion based devices, spin-torque oscillators and spin-orbit torque based devices have opened up new possibilities of mimicking various neural and synaptic functionalities by the underlying device physics. In this paper, we review various spintronic device structures that can provide a compact and area-efficient implementation of artificial neurons and synapses. Neuromorphic architectures based on such spintronic devices can potentially provide ~ 10-100× lower energy consumption in comparison to a baseline CMOS implementation.
On the inclusion properties for multi-level cache hierarchies (1998)

Article Free Access Share on On the inclusion properties for multi-level cache hierarchies Authors: Jean-Loup Baer Department of Computer Science, University of Washington, Seattle, WA Department of Computer Science, University of Washington, Seattle, WAView Profile , Wen-Hann Wang Department of Computer Science, University of Washington, Seattle, WA Department of Computer Science, University of Washington, Seattle, WAView Profile Authors Info & Claims ISCA '98: 25 years of the international symposia on Computer architecture (selected papers)August 1998 Pages 345–352https://doi.org/10.1145/285930.285994Published:01 August 1998Publication History 1citation667DownloadsMetricsTotal Citations1Total Downloads667Last 12 Months57Last 6 weeks10 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF