gebhart/patrepeval huggingface dataset:
Data from Detection of Early Prostate Cancer Using a Hepsin-Targeted Imaging Agent (2023)

&lt;div&gt;Abstract&lt;p&gt;Early detection and diagnosis of prostate cancer is key to designing effective treatment strategies. Microarrays have resulted in the discovery of hepsin (HPN) as a biomarker for detection of prostate cancer. In this study, we explore the development of HPN imaging probes for detection of prostate cancer. We used phage display to isolate HPN binding peptides with 190 + 2.2 nmol/L affinity in monomeric form and high specificity. The identified peptides were able to detect human prostate cancer on tissue microarrays and in cell-based assays. HPN-targeted imaging agents were synthesized by conjugating multiple peptides to fluorescent nanoparticles to further improve avidity through multivalency and to improve pharmacokinetics. When injected into mouse xenograft models, HPN-targeted nanoparticles bound specifically to HPN-expressing LNCaP xenografts compared with non–HPN-expressing PC3 xenografts. HPN imaging may provide a new method for detection of prostate cancer. [Cancer Res 2008;68(7):2286–91]&lt;/p&gt;&lt;/div&gt;
Katana: A Hot Patching Framework for ELF Executables (2010)

Despite advances in software modularity, security, and reliability,offline patching remains the predominant form of updating or protecting commodity software. Unfortunately, the mechanics of hot patching (the process of upgrading a program while it executes) remain understudied, even though such a capability offers practical benefits for both consumer and mission-critical systems. A reliable hot patching procedure would serve particularly well by reducing the downtime necessary for critical functionality or security upgrades. Yet, hot patching also carries the risk -- real or perceived -- of leaving the system in an inconsistent state, which leads many owners to forego its benefits as too risky. In this paper, we propose a novel method for hot patching ELF binaries that supports (a) synchronized global data and code updates and (b)reasoning about the results of applying the hot patch. We propose a format, which we call a Patch Object, for encoding patches as a special type of ELF relocatable object file. Our tool, Katana, automatically creates these patch objects as a by-product of the standard source build process. Katana also allows an end-user to apply the Patch Objects to a running process. In essence, our method can be viewed as an extension of the Application Binary Interface (ABI), and we argue for its inclusion in future ABI standards.
Role of interleukin 12 in hypercholesterolemia-induced inflammation (2003)

We have previously shown that T lymphocytes and interferon-gamma are involved in hypercholesterolemia-induced leukocyte adhesion to vascular endothelium. This study assessed the contribution of interleukin 12 (IL-12) to these hypercholesterolemia-induced inflammatory responses. Intravital videomicroscopy was used to quantify leukocyte adhesion and emigration and oxidant stress (dihydrorhodamine oxidation) in unstimulated cremasteric venules (wall shear rate > or =500 s-1) of wild-type (WT) C57Bl/6, lymphocyte-deficient [recombinase-activating gene knockout (RAG1-/-)], and IL-12-deficient (p35-/- and p40-/-; p35 and p40 are the two subunits of active IL-12) mice on either a normal (ND) or high-cholesterol (HC) diet for 2 wk. RAG1-/--HC mice received splenocytes from WT-HC (WT --> RAG1-/-), p35-/--HC (p35-/- --> RAG1-/-), or p40-/--HC (p40-/- --> RAG1-/-) mice. Compared with WT-ND mice, WT-HC mice exhibited exaggerated leukocyte adherence and emigration as well as increased dihydrorhodamine oxidation. The enhanced leukocyte recruitment was absent in the RAG1-/--ND, p35-/--ND, and p40-/--ND groups. Hypercholesterolemia-induced leukocyte adherence and emigration were attenuated in RAG1-/--HC vs. WT-HC mice but were similar to ND mice. Furthermore, compared with WT-HC animals, p35-/--HC and p40-/--HC mice showed significantly lower leukocyte adhesion and tissue oxidant stress responses, but these values were comparable to ND mice. Leukocyte adherence and emigration in WT --> RAG1-/- mice were similar to responses of WT-HC mice. However, p35-/- --> RAG1-/- mice had lower levels of adherence and emigration vs. the WT --> RAG1-/- and WT-HC groups. Elevated levels of leukocyte adherence and emigration were restored by approximately 50% toward WT-HC levels in p40-/- --> RAG1-/- mice. These findings implicate IL-12 in the inflammatory responses observed in the venules of hypercholesterolemic mice.
Crystal structures and ligand binding of PurM proteins fromThermus thermophilusandGeobacillus kaustophilus (2015)

Crystal structures of 5-aminoimidazole ribonucleotide (AIR) synthetase, also known as PurM, from Thermus thermophilus (Tt) and Geobacillus kaustophilus (Gk) were determined. For TtPurM, the maximum resolution was 2.2 Å and the space group was P21212 with four dimers in an asymmetric unit. For GkPurM, the maximum resolution was 2.2 Å and the space group was P21212 with one monomer in asymmetric unit. The biological unit is dimer for both TtPurM and GkPurM and the dimer structures were similar to previously determined structures of PurM in general. For TtPurM, ∼50 residues at the amino terminal were disordered in the crystal structure whereas, for GkPurM, the corresponding region covered the ATP-binding site forming an α helix in part, suggesting that the N-terminal region of PurM changes its conformation upon binding of ligands. FGAM binding site was predicted by the docking simulation followed by the MD simulation based on the SO4 (2-) binding site found in the crystal structure of TtPurM.
Transporting Timing messages over MPLS Networks (2015)

This document defines a method for transporting timing messages, such
as Precision Time Protocol (PTP) or Network Time Protocol (NTP), over
a Multiprotocol Label Switched (MPLS) network. The method facilitates
efficient recognition of timing packets to enable their port level
processing in both Label Edge Routers (LERs) and Label Switched
Routers (LSRs). The basic mechanism is to transport timing messages
inside Timing LSPs, which are dedicated MPLS Label Switched Paths
(LSPs) that carry only timing, and possibly related Operations,
Administration and Maintenance (OAM) or management packets, but do not
carry customer traffic. Two encapsulations methods are defined. The
first transports UDP/IP encapsulated timing messages directly over the
dedicated LSP. The second transports Ethernet encapsuled timing
messages inside an Ethernet pseudowire.
Precoding Schemes for the MIMO-GBC (2006)

The use of M antennas at the base station and of transmitter channel state information can boost the downlink throughput by a factor M (multiplexing gain), even though the receivers have a single antenna and do not cooperate. In this semi-tutorial work, we discuss some low-complexity alternatives to achieve a downlink throughput very close to the optimal sum capacity. We review and compare these alternatives and we show that, in the simple setting of independently fading channels, relatively traditional forms of linear beamforming achieve the best tradeoff between performance and complexity. These results somehow call for a reconsideration of the emphasis that certain recently proposed precoding techniques have enjoyed both in scientific literature and in technology development
Development of Anti-CD74 Antibody–Drug Conjugates to Target Glucocorticoids to Immune Cells (2018)

Glucocorticoids (GCs) are excellent anti-inflammatory drugs but are dose-limited by on-target toxicity. We sought to solve this problem by delivering GCs to immune cells with antibody-drug conjugates (ADCs) using antibodies containing site-specific incorporation of a non-natural amino acid, novel linker chemistry for in vitro and in vivo stability, and existing and novel glucocorticoid receptor (GR) agonists as payloads. We directed fluticasone propionate to human antigen-presenting immune cells to afford GR activation that was dependent on the targeted antigen. However, mechanism of action studies pointed to accumulation of free payload in the tissue culture supernatant as the dominant driver of activity and indeed administration of the ADC to human CD74 transgenic mice failed to activate GR target genes in splenic B cells. Suspecting dissipation of released payload, we designed an ADC bearing a novel GR agonist payload with reduced permeability which afforded cell-intrinsic activity in human B cells. Our work shows that antibody-targeting offers significant potential for rescuing existing and new dose-limited drugs outside the field of oncology.
Mechanism studies of Cu RIE for VLSI interconnections (1998)

An etch mechanism study of a chlorine based Cu RIE is presented. It has been generally accepted that the chlorination of Cu and the volatilization of (CuCl) <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> are essential steps during RIE of Cu in a chlorine based discharge. The exposure of Cl <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> to a Cu surface leads to a chlorinated surface layer whose thickness increases with exposure. Based on these results we have investigated the chlorination of Cu in a reactive plasma at elevated temperature. In order to minimize isotropic etching or chlorine residues in the remaining Cu film it is necessary to reduce the thickness of the chlorinated film. One way to do this is to lower the Cl <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> partial pressure. The influence of the Cl <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> partial pressure on the Cu chlorination is discussed. AES surface measurements at the etch bottom and the Cu sidewall after RIE interruption have been carried out showing only a very thin chlorinated surface layer.
REFLEX: Reconfigurable logic for entropy extraction (2014)

True Random Number Generators are cryptographic primitives that harness on-chip physical phenomena to generate random bits. Variations in the fabrication process and operating conditions can decrease reliability of these circuits by decreasing the randomness of their output. Conventional lightweight post-processing techniques use an XOR tree to combine the outputs of two or more TRNGs and improve the net entropy. We present REFLEX: Reconfigurable Logic for Entropy Extraction; a post-processing technique using reconfigurable logic. REFLEX replaces each stage of XOR tree with a reconfigurable logic block that is programmed based on the entropy of TRNGs. The output of TRNGs are further reordered before entering the logic tree to provide optimal entropy extraction. Up to 55% more chips pass NIST randomness tests when using REFLEX as compared to conventional XOR tree. When implemented in IBM 32nm SOI process, REFLEX has a maximum synthesized area of 620μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . It consumes a leakage power of 70μW and an energy overhead of 0.04pJ/bit when operating at 2GHz. The design is scalable to multiple TRNGs and provides energy efficient entropy extraction for low power applications.
Digital wideband phased array calibration and beamforming using time reversal technique (2010)

A 16-channel digital wideband phased array without antenna is characterized using impulse response measurement. A chirp signal is used as probing signal. By careful chirp design, impulse response at sub-band is measured for all the channels. Spectral domain response showing dispersive phase and magnitude reveals significant imbalance among the channels. Based on time reversal technique principle, spectrum-modified time reversal impulse response is calculated. This time reversal response is applied to the chirp probing signal to verify the bandpass characteristics of the sub-band, and the waveform coherent waveform. It is also applied to the CW pilot tone to verify digital beamforming gain.
Supplementary Information from Heterogeneity of Circulating Tumor Cell–Associated Genomic Gains in Breast Cancer and Its Association with the Host Immune Response (2023)

&lt;p&gt;Includes Supplemental Figure S1 and Supplemental Tables S1-S7&lt;/p&gt;
Synthesis and characterization of ordered mesoporous silicas with high loadings of methyl groups (2002)

Ordered silicas with high loadings of pendant methyl groups were synthesized via cocondensation of tetraethyl orthosilicate and triethoxymethylsilane under basic conditions in the presence of cetyltrimethylammonium surfactant. The resulting materials were characterized using X-ray diffraction (XRD), transmission electron microscopy (TEM), 29Si and 13C NMR spectroscopy, nitrogen adsorption and thermogravimetry. For lower loadings of the organosilane in the synthesis mixture, XRD patterns were characteristic of a 2-dimensional hexagonal structure. As seen from XRD, the degree of structural ordering diminished as the loading increased, but an XRD pattern with a single pronounced peak and TEM images characteristic of a 2-dimensional hexagonal structure were recorded even for a methyl-functionalized silica with about 50% of silicon atoms carrying the organic groups. The extent of organosilane incorporation was found to be nearly quantitative. The methyl groups were stable during surfactant removal, both via solvent extraction and pyrolysis at 573 K under nitrogen. The (100) interplanar spacing and the pore diameter were found to decrease from 3.45 to 3.12 nm, and from 2.9 to 2.3 nm, respectively, as the loading of the organosilane increased up to 43%, but no further decrease was observed when the loading increased to 50%. The BET specific surface area was relatively constant (720–800 m2 g−1) for loadings of 20–50%, whereas the primary pore volume decreased as the loading of organics increased. Nitrogen adsorption provided some evidence of phase separation into organosilicate-rich and silicate-rich phases for methyl group loadings of 33% or higher and particularly for the 50% loading. Thermogravimetric data suggested that the methyl groups are highly thermally stable in both nitrogen and air atmospheres.
Effect of Molecular Weight of Polycarboxylate Superplasticizer on Its Dispersion, Adsorption, and Hydration of a Cementitious System (2015)

The aim of this study was to link the molecular weight (MW) of polycarboxylate superplasticizer (PCE) with the performance of cementitious system for the purpose of developing new products; PCE synthesized by copolymerization of methacrylic acid and methyl poly(ethylene oxide) methacrylate was characterized by proton nuclear magnetic resonance (H1-NMR) and gel permeation chromatography (GPC). The polycarboylate (PC) was separated into four fractions with different MWs using an ultrafiltration method. The interaction behaviors between PC fractions and cement particles were investigated by measuring the adsorption, zeta potential, and hydration. Results showed that PC fractions with medium MW showed a good dispersion and dispersion retention owing to the adsorption amount continuously increasing with time and delayed the longest cement hydration time. The highest MW of PC exhibited poor dispersion and dispersion retention, having the greatest adsorption amount on the cement surface and poor adsorption capacity in the later period, and carried out to promote hydration of cement compared with other polymers. It can be deduced that there was an ideal MW for the best different performance of the PC investigated. This can provide an important reference for optimizing the process parameters in the preparation.
Uplink comp and the applications in LTE heterogeneous networks: Principles and the field trial (2013)

Uplink Coordinated Multi-Point (CoMP) reception is one of the key technologies of LTE Advanced system. It has the potential to improve uplink capacity by joint processing the received signals from more antennas of the neighbor nodes. Uplink CoMP is implemented at the eNodeB side with no requirement on terminals or protocols and thus is easy to be introduced in the current networks. In future heterogeneous network deployment, low power remote radio units (RRU:s) are identified as one of the key components to increase the capacity of cellular networks in dense areas with high traffic demands. By coordinating low power RRU:s with macro RRU:s, uplink CoMP can get significant uplink gain from not only macro reception diversity but also uplink/downlink decoupling. This paper analyzes the principles of uplink CoMP and its applications in heterogeneous networks, and then a recent full scale field trial in Ericsson Beijing LTE trial network is introduced. The results demonstrate that best uplink reception (in a micro RRU) can be decoupled from best downlink transmission (from a macro RRU), enabling improved uplink throughput with maintained downlink throughput. Thus the problem of uplink and downlink imbalance in heterogeneous networks can be solved and moreover significant uplink reception macro diversity gain can be achieved, hence cell edge user experience can be greatly improved.
Effects of stoichiometry on electrical, optical, and structural properties of indium nitride (2005)

A series of indium nitride (InN) epilayers with different excess indium (In) concentration are grown by plasma-assisted molecular-beam epitaxy on (0001) sapphire substrates. The increasing excess In concentration of the epilayers correlates with an increasing free-electron concentration and a decreasing electron mobility. Photoluminescence (PL) illustrates a 0.77–0.84eV transition for all samples with a redshift in the peak energy with increasing In concentration (for the highest free-electron concentration of 4×1021cm−3). This suggests that the ∼0.8eV PL transition is not consistent with the band-edge transition in InN. Moreover, an additional PL transition at 0.75eV along with the In clusters observed in transmission electron microscopy analysis are found only in the 29% excess In sample. This implies a relationship between the new PL transition and the presence of In clusters. Finally, secondary-ion mass spectrometry is used to verify that the contamination, especially hydrogen (H) and oxygen (O) impurities, has no influence on the redshift of the ∼0.8eV PL peaks and the existence of the additional 0.75eV peak in the sample containing In clusters.
AVATecH: Audio/Video technology for humanities research (2022)

In the AVATecH project the Max-Planck Institute for Psycholinguistics (MPI) and the Fraunhofer institutes HHI and IAIS aim to significantly speed up the process of creating annotations of audio-visual data for humanities research. For this we integrate state-of-theart audio and video pattern recognition algorithms into the widely used ELAN annotation tool. To address the problem of heterogeneous annotation tasks and recordings we provide modular components extended by adaptation and feedback mechanisms to achieve competitive annotation quality within significantly less annotation time. Currently we are designing a large-scale end-user evaluation of the project.
Nesting and fate of transplanted stem cells in hypoxic/ischemic injured tissues: The role ofHIF1α/sirtuins and downstream molecular interactions (2020)

The nesting mechanisms and programming for the fate of implanted stem cells in the damaged tissue have been critical issues in designing and achieving cell therapies. The fracture site can induce senescence or apoptosis based on the surrounding harsh conditions, hypoxia, and oxidative stress (OS). Respiration deficiency, disruption in energy metabolism, and consequently OS induction change the biophysical, biochemical, and cellular components of the native tissue. Additionally, the homeostatic molecular players and cell signaling might be changed. Despite all aforementioned issues, in the native stem cell niche, physiological hypoxia is not toxic; rather, it is vitally required for homing, self-renewal, and differentiation. Hence, the key macromolecular players involved in the support of stem cell survival and re-adaptation to a new dysfunctional niche must be understood for managing the cell therapy outcome. Hypoxia-inducible factor 1-alpha is the master transcriptional regulator, involved in the cell response to hypoxia and the adaptation of stem cells to a new niche. This protein is regulated by interaction with sirtuins. Sirtuins are highly conserved NAD+-dependent enzymes that monitor the cellular energy status and modulate gene transcription, genome stability, and energy metabolism in response to environmental signals to modulate the homing and fate of stem cells. Herein, new insights into the nesting of stem cells in hypoxic-ischemic injured tissues were provided and their programming in a new dysfunctional niche along with the involved complex macromolecular players were critically discussed.
Investigations of Antisense Oligonucleotides Targeted Against bcl-2 RNAs (1993)

Expression of the bcl-2 gene becomes deregulated in many non-Hodgkin lymphomas as the result of t(14;18) chromosomal translocations. Because bcl-2 regulates the survival of cells, and because its over-expression is associated with cellular resistance to killing by chemotherapeutic drugs and gamma-irradiation, this gene and its mRNA and protein products represent ideal targets for designing novel therapeutic strategies for the treatment of cancer. Here we describe the effects of an 18-mer phosphodiester oligonucleotide that is complementary to the first 6 codons of the bcl-2 mRNA's open reading frame. When tested for inhibition of in vitro protein synthesis using RNAse-H-supplemented reticulocyte lysates and RNA prepared by in vitro transcription of a human bcl-2 cDNA, the bcl-2 antisense (AS) oligomer completely abolished Bcl-2 protein production at 10 microM, but had no effect on the in vitro translation of a chicken bcl-2 RNA that contained three mismatches relative to the oligomer binding site on the human bcl-2 RNA. A control 18-mer having the same base composition as the AS oligomer but with scrambled order (SC) was not inhibitory. Addition of AS and SC oligomers to cultures of a NIH-3T3 fibroblast cell line that had been stably infected with a recombinant retrovirus containing the same human bcl-2 cDNA used for in vitro transcription/translation experiments revealed concentration-dependent reductions in the relative levels of the 26-kD human Bcl-2 protein (as determined by immunoblotting) by the AS but not by the SC oligomer. Similar results were obtained when AS and SC oligomers were applied to a t(14;18)-containing lymphoma cell line SU-DHL-4 that was cultured in low-serum media. When used at 200 microM, the bcl-2 AS oligomer produced 84-95% reductions in Bcl-2 protein levels in SU-DHL-4 cells but had relatively little effect on the levels of other mitochondrial control proteins, suggesting that the inhibitory effects were specific. Treatment of SU-DHL-4 cells with AS oligomer lead to essentially complete loss of bcl-2 mRNA from cells within 1 day of addition to cultures, but presumably because of the long half-life of the Bcl-2 protein (approximately 14 h), commensurate reductions in Bcl-2 protein levels did not occur until 3 days.(ABSTRACT TRUNCATED AT 400 WORDS)
Two-mode PLC-based mode multi/demultiplexer for mode and wavelength division multiplexed transmission (2013)

We proposed a PLC-based mode multi/demultiplexer (MUX/DEMUX) with an asymmetric parallel waveguide for mode division multiplexed (MDM) transmission. The mode MUX/DEMUX including a mode conversion function with an asymmetric parallel waveguide can be realized by matching the effective indices of the LP(01) and LP(11) modes of two waveguides. We report the design of a mode MUX/DEMUX that can support C-band WDM-MDM transmission. The fabricated mode MUX/DEMUX realized a low insertion loss of less than 1.3 dB and high a mode extinction ratio that exceeded 15 dB. We used the fabricated mode MUX/DEMUX to achieve a successful 2 mode x 4 wavelength x 10 Gbps transmission over a 9 km two-mode fiber with a penalty of less than 1 dB.