gebhart/patrepeval huggingface dataset:
Prophylactic and therapeutic activity of alkaline phosphatase in arthritic rats: single-agent effects of alkaline phosphatase and synergistic effects in combination with methotrexate (2018)

Alkaline phosphatase (AP) is a gate-keeper of innate immune system responses by detoxifying inflammation triggering moieties released from endogenous and external sources. We examined whether AP's broad mechanism of action constitutes a safe therapeutic, either as single agent or combined with methotrexate (MTX), for chronic inflammatory disorders, for example, rheumatoid arthritis (RA). A rat model for RA was used with repeated intra-articular methylated bovine serum albumin (mBSA) injections in 1 knee (“arthritic” knee), with the contralateral knee serving as internal control. AP (200 µg, subcut) was administered before mBSA injections (prophylactic setting) or after arthritis induction (therapeutic setting) or combined with MTX (0.3 mg/kg or 1 mg/kg; intraperitoneally). As end point of treatment outcome, macrophage infiltration in knees, liver, and spleen was assessed by immunohistochemistry (ED1 and ED2 expression), immunofluoresence (macrophage marker folate receptor-β [FRβ]), and [18F]fluoro-polyethylene glycol-folate positron emission tomography (PET) (macrophage imaging) and ex vivo tissue distribution. Single-agent AP treatment and combinations with MTX were well tolerated. Both prophylactic and therapeutic AP markedly reduced synovial macrophage infiltration in arthritic knees (ED1: 3.5- to 4-fold; ED2: 3.5- to 6-fold), comparable with MTX treatment. AP-MTX combinations slightly improved on single agent effects. PET monitoring and ex vivo tissue distribution studies corroborated the impact of AP, MTX, and AP-MTX on reducing synovial macrophage infiltration. Beyond localized articular effects, AP also revealed systemic anti-inflammatory effects by a 2-fold reduction of ED1, ED2, and FRβ+ macrophages in liver and spleen of arthritic rats. Collectively, single-agent AP and AP combined with MTX elicited local and systemic anti-arthritic activity in arthritic rats.
High-speed frequency-domain terahertz coherence tomography (2015)

High-speed frequency-domain terahertz (THz) coherence tomography is demonstrated using frequency sweeping of continuous-wave THz radiation and beam steering. THz frequency sweeping with a kHz sweep rate and a THz sweep range is implemented using THz photomixing in which an optical beat source consists of a wavelength-swept laser and a distributed feedback laser diode. During the frequency sweep, frequency-domain THz interferograms are measured using the coherent homodyne detection employing signal averaging for noise reduction, which are used as axial scan data via fast Fourier transform. Axial scan data for 100×100 points can be acquired in 100 s while scanning a transverse range of 100×100 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> using a THz beam scanner comprised of a two-dimensional galvanometer scanner and a telecentric f-θ lens.
Novel multi-component vaccine approaches for <i>Burkholderia pseudomallei</i> (2019)

Burkholderia pseudomallei is the causative agent of melioidosis. Historically believed to be a relatively rare human disease in tropical countries, a recent study estimated that, worldwide, there are approximately 165 000 human melioidosis cases per year, more than half of whom die. The bacterium is inherently resistant to many antibiotics and treatment of the disease is often protracted and ineffective. There is no licensed vaccine against melioidosis, but a vaccine is predicted to be of value if used in high-risk populations. There has been progress over the last decade in the pursuit of an effective vaccine against melioidosis. Animal models of disease including mouse and non-human primates have been developed, and these models show that antibody responses play a key role in protection against melioidosis. Surprisingly, although B. pseudomallei is an intracellular pathogen there is limited evidence that CD8<sup>+</sup> T cells play a role in protection. It is evident that a multi-component vaccine, incorporating one or more protective antigens, will probably be essential for protection because of the pathogen's sophisticated virulence mechanisms as well as strain heterogeneity. Multi-component vaccines in development include glycoconjugates, multivalent subunit preparations, outer membrane vesicles and other nano/microparticle platforms and live-attenuated or inactivated bacteria. A consistent finding with vaccine candidates tested in mice is the ability to induce sterilizing immunity at low challenge doses and extended time to death at higher challenge doses. Further research to identify ways of eliciting more potent immune responses might provide a path for licensing an effective vaccine.
Development and Characterization of Annexin V Mutants with Endogenous Chelation Sites for <sup>99m</sup>Tc (2000)

[(99m)Tc]Annexin V can be used to image organs undergoing cell death during cancer chemotherapy and organ transplant rejection. To simplify the preparation and labeling of annexin V for nuclear-medicine studies, we have investigated the addition of peptide sequences that will directly form endogenous chelation sites for (99m)Tc. Three mutant molecules of annexin V, called annexin V-116, -117, and -118, were constructed with N-terminal extensions of seven amino acids containing either one or two cysteine residues. These molecules were expressed cytoplasmically in Escherichia coli and purified to homogeneity with a final yield of 10 mg of protein/L of culture. Analysis in a competitive binding assay showed that all three proteins retained full binding affinity for erythrocyte membranes with exposed phosphatidylserine. Using SnCl(2) as reducing agent and glucoheptonate as exchange agent, all three proteins could be labeled with (99m)Tc to specific activities of at least 50-100 microCi/microg. The proteins retained membrane binding activity after the radiolabeling procedure, and quantitative analysis indicated a dissociation constant (K(d)) of 7 nmol/L for the annexin V-117 mutant. The labeling reaction was rapid, reaching a maximum after 40 min at room temperature. The radiolabeled proteins were stable when incubated with phosphate-buffered saline or serum in vitro. Proteins labeled to a specific activity of 25-100 microCi/microg were injected intravenously in mice at a dose of 100 microg/kg, and biodistribution of radioactivity was determined at 60 min after injection. Uptake of radioactivity was highest in kidney and liver, consistent with previous results obtained with wild-type annexin V. Cyclophosphamide-induced apoptosis in vivo could be imaged with [(99m)Tc]annexin V-117. In conclusion, annexin V can be modified near its N-terminus to incorporate sequences that form specific chelation sites for (99m)Tc without altering its high affinity for cell membranes. These annexin V derivatives may be useful for in vivo imaging of cell death.
<title>Lossless data embedding for all image formats</title> (2002)

Lossless data embedding has the property that the distortion due to embedding can be completely removed from the watermarked image without accessing any side channel. This can be a very important property whenever serious concerns over the image quality and artifacts visibility arise, such as for medical images, due to legal reasons, for military images or images used as evidence in court that may be viewed after enhancement and zooming. We formulate two general methodologies for lossless embedding that can be applied to images as well as any other digital objects, including video, audio, and other structures with redundancy. We use the general principles as guidelines for designing efficient, simple, and high-capacity lossless embedding methods for three most common image format paradigms - raw, uncompressed formats (BMP), lossy or transform formats (JPEG), and palette formats (GIF, PNG). We close the paper with examples of how the concept of lossless data embedding can be used as a powerful tool to achieve a variety of non-trivial tasks, including elegant lossless authentication using fragile watermarks. Note on terminology: some authors coined the terms erasable, removable, reversible, invertible, and distortion-free for the same concept.
Ccl2/Ccr2 signalling recruits a distinct fetal microchimeric population that rescues delayed maternal wound healing (2017)

Foetal microchimeric cells (FMCs) traffic into maternal circulation during pregnancy and persist for decades after delivery. Upon maternal injury, FMCs migrate to affected sites where they participate in tissue healing. However, the specific signals regulating the trafficking of FMCs to injury sites had to be identified. Here we report that, in mice, a subset of FMCs implicated in tissue repair displays CD11b<sup>+</sup> CD34<sup>+</sup> CD31<sup>+</sup> phenotype and highly express C-C chemokine receptor 2 (Ccr2). The Ccr2 ligand chemokine ligand 2 (Ccl2) enhances the recruitment of FMCs to maternal wounds where these cells transdifferentiate into endothelial cells and stimulate angiogenesis through Cxcl1 secretion. Ccl2 administration improves delayed maternal wound healing in pregnant and postpartum mice but never in virgin ones. This role of Ccl2/Ccr2 signalling opens new strategies for tissue repair through natural stem cell therapy, a concept that can be later applied to other types of maternal diseases.
An ID/Locator Architecture for P2PSIP (2008)

This document describes an architecture where peers in an overlay use
special IP addresses to identify other peers. Two of the advantages of
this approach are that (a) most existing applications can run in an
overlay without needing any changes and (b) peer mobility and NAT
traversal are handled in a way that is transparent to most
applications. Terminology Descriptions of the basic concepts and
terminology used in this document can be found in the P2PSIP Concepts
and Terminology document [Concepts].
A novel synthesis of 5,15-trimethylammonium substituted porphyrins and their evaluation as potential antimicrobial photosensitizers (2005)

The MacDonald's [2 + 2] condensation of unsubstituted dipyrromethane and 3- or 4-hydroxyalkoxybenzoaldehydes afforded 5,15-meso-hydroxyalkoxyphenylporphyrins. The hydroxyl groups on the side chains were then transformed to tertiary amines via synthesis of the mesylate and substitution with the appropriate amines or aminoalcohols. Methylation of such products afforded a series of cationic porphyrins which have been tested in vitro as photodynamic agents against microorganisms, showing high antimicrobial activity.
Novel insights into histamine H<sub>2</sub>receptor biology (1997)

Histamine exerts multiple biological actions through one of three receptor subtypes (H1, H2, and H3). This review focuses on new developments regarding the structure and function of the H2 receptor. In addition to the important role this receptor plays in stimulating gastric acid secretion, recent studies have demonstrated that it is also involved in regulating gastrointestinal motility and intestinal secretion. The potential role of the H2 receptor in regulating cell growth and differentiation has also been added to the list of actions this biogenic amine may exert in both normal and transformed tissues. Molecular cloning of the gene indicates that it has the structural characteristics of a heptahelical G protein-linked receptor. Site-directed mutagenesis studies of this receptor reveal the presence of key amino acids within the third and fifth transmembrane domains that are critical for ligand recognition. Molecular approaches have also shed light on the structural components of the H2 receptor important in regulating desensitization and internalization. Although the H2 receptor was classically thought to couple to the adenylate cyclase pathway, recent work with the cloned receptor indicates that it can also activate the phosphoinositide signaling cascade through an independent G protein-dependent mechanism. The novel observation that histamine may stimulate c-fos gene expression lends further support to the possible role of this receptor in regulating cell growth and differentiation.
Low-affinity placenta-derived receptors for human granulocyte-macrophage colony-stimulating factor can deliver a proliferative signal to murine hemopoietic cells. (1990)

Retrovirally mediated introduction of a cDNA encoding a placenta-derived low-affinity receptor for human granulocyte-macrophage colony-stimulating factor (GM-CSF) into murine FDC-P1 hemopoietic cells allowed these cells to proliferate when stimulated by human GM-CSF. The expressed human receptors on cloned lines were of low affinity (Kd = 4-6 nM), were internalized, and did not interact with endogenous GM-CSF receptors. Concentrations of human GM-CSF of 6.5-13 nM were required to stimulate 50% maximal colony formation versus a concentration of murine GM-CSF of 6 pM; this difference is comparable with the difference in relative affinities of the human and murine receptors for their respective ligands. If maintained in murine GM-CSF, cells able to bind or respond to human GM-CSF were rapidly lost due to transcriptional inactivation of the inserted cDNA. The observations indicate that low-affinity receptors for human GM-CSF can deliver a proliferative signal in appropriate cells and that the signaling mechanisms are not species-specific.
Cell proliferation as a biomarker for response to immune checkpoint inhibitors in PD-L1 negative renal cell carcinoma. (2019)

62 Background: Cell proliferation is an important marker of survival in many tumors, and we hypothesized that this attribute could be related to response to immune checkpoint inhibitors (ICIs) in RCC. Previously we reported (SITC 2018) that moderately proliferative lung cancer have a much higher response rate than either poorly or highly proliferative tumors. Methods: 69 FFPE RCC tumor samples were evaluated by RNA-seq to measure transcript levels of 394 immune related genes. Cell proliferation was defined as the mean mRNA expression of 10 genes (BUB1, CCNB2, CDK1, CDKN3, FOXM1, KIAA0101, MAD2L1, MELK, MKI67, TOP2A) which was evaluated for association with ORR to ICIs by RECIST v1.1 criteria for both PD-L1 IHC positive and negative cases. Cell proliferation for each case was split into 3 tertiles of poorly ( < 33), moderately (33-66) and highly ( > 66) proliferative versus a reference population. Poorly and highly proliferative were grouped for comparison to moderately proliferative tumors. PD-L1 IHC was performed using DAKO 22C3 antibody and scored by FDA guidelines and considered positive if TPS ≥1% and negative if < 1%. Results: In our cohort of 69 patients, the overall ORR was 18.8. The majority, 91% of tumors were PD-L1 negative, with ORR of 14.8%, as opposed to ORR of 50% in PD-L1 positive cases. 62.2% of tumors were poorly proliferative, 8.7% were highly proliferative, and 29% were moderately proliferative. ORR in moderately proliferative tumors was 30% and 14.2% in poorly/highly proliferative tumors. In PD-L1 negative tumors the ORR in moderately proliferative tumors was 20% and 13% in poorly/highly proliferative tumors. For the 5 moderately proliferative, PD-L1 positive tumors, there were 2 PR and 1 CR, and in the 3 poorly/highly proliferative tumors there was 1 PR. Conclusions: Cell proliferation may play a crucial role in distinguishing RCC patients who may have a clinical benefit to ICI, including the important subgroup of PD-L1 negative tumors. Moderately proliferative tumors have a higher ORR than their poorly/highly counterparts.
Improved watermark detection reliability using filtering before correlation (2002)

A digital watermark is a perceptually unobtrusive signal embedded in some multimedia asset carrying additional information: e.g. copyright information of a video clip. For nearly all watermarking schemes published so far, detection is based on some form of correlation. We show that the detection reliability can be significantly improved by applying filtering prior to correlation. This improvement is analysed using a theoretical model based on statistical communication and detection theory. Finally, the improvements predicted by the theory are verified in a number of experiments.
Bisulfite-converted duplexes for the strand-specific detection and quantification of rare mutations (2017)

The identification of mutations that are present at low frequencies in clinical samples is an essential component of precision medicine. The development of molecular barcoding for next-generation sequencing has greatly enhanced the sensitivity of detecting such mutations by massively parallel sequencing. However, further improvements in specificity would be useful for a variety of applications. We herein describe a technology (BiSeqS) that can increase the specificity of sequencing by at least two orders of magnitude over and above that achieved with molecular barcoding and can be applied to any massively parallel sequencing instrument. BiSeqS employs bisulfite treatment to distinguish the two strands of molecularly barcoded DNA; its specificity arises from the requirement for the same mutation to be identified in both strands. Because no library preparation is required, the technology permits very efficient use of the template DNA as well as sequence reads, which are nearly all confined to the amplicons of interest. Such efficiency is critical for clinical samples, such as plasma, in which only tiny amounts of DNA are often available. We show here that BiSeqS can be applied to evaluate transversions, as well as small insertions or deletions, and can reliably detect one mutation among >10,000 wild-type molecules.
A low SINR synchronization system for direct-sequence spread-spectrum communications: radio prototype, verification testbed and experimental results (2008)

Ability to receive signals at low signal to interference and noise ratio (SINR) improves the spatial range and reliability of wireless networks. However, it is difficult to design a communication system that operates correctly in this type of environment. Our system uses a high spreading gain in the
MHDeS (2016)

A method handle (MH) is a reference to an underlying Java method with potential method type transformations. Multiple inter-connected method handles form a method handle graph (MHG). Together with the Java Virtual Machine (JVM) instruction, invokedynamic, the implementation of MHGs is significant to dynamically typed language implementations on the JVM.
Promoter hypermethylation of<i>BCL6B</i>gene is a potential plasma DNA biomarker for gastric cancer (2013)

We previously showed that BCL6B acts as a tumor suppressor in gastric cancer and up to 66% gastric cancer patients have promoter hypermethylation in tumor tissues. We aimed to evaluate the feasibility of detecting BCL6B methylation in plasma DNA as a potential biomarker for gastric cancer. Hypermethylation of the CpG islands in BCL6B promoter was detected in 42.5% (17/40) plasma DNA samples from gastric cancer patients, while no methylation was found in the plasma DNA of healthy controls (p < 0.001). BCL6B methylation may serve as a novel potential non-invasive plasma biomarker for the detection of gastric cancer.
Effects of anthocyanin extracted from black soybean seed coat on spermatogenesis in a rat varicocele-induced model (2011)

Varicocele is the most common cause of primary male infertility and is associated with oxidative stress. The aim of the present study was to investigate the effects of anthocyanin on a rat model of varicocele. Twenty-four male rats were divided into four experimental groups: a normal control group, a varicocele-induced control group and two varicocele-induced groups treated with either 40 or 80mgkg(-1), p.o., anthocyanin for 4 weeks. Varicocele was induced by the partial obstruction of the left renal vein. After 8 weeks, the testes and epididymides from rats in all groups were removed, weighed and subjected to histological examination and semen analysis. Apoptosis in the testes was determined by terminal deoxyribonucleotidyl transferase-mediated dUTP-digoxigenin nick end-labelling (TUNEL) and oxidative stress was assessed by measuring 8-hydroxy-2'-deoxyguanosine (8-OHdG) levels. Although no significant differences in sperm counts were observed among the groups, anthocyanin treatment of the varicocele-induced groups resulted in significantly increased testes weight, sperm motility and spermatogenic cell density (P<0.05). Anthocyanin treatment also significantly decreased apoptotic body count and 8-OHdG concentrations (P<0.05). We suggest that the antioxidant effect of anthocyanin prevented the damage caused by varicocele-induced reactive oxygen species.
Femtosecond Laser Near-Field Ablation by Gold Nanoparticles (2006)

We describe a novel, non-thermal ablation process for selective removal of biological material. The technique takes advantage of enhanced plasmonic scattering of near-infrared, ultrashort laser pulses in the near-field of gold nanoparticles to vaporize attoliter volumes.
Fiber Grating Moisture And Chemical Sensing System (2004)

A vane for a stator of a variable-geometry turbine, in particular for aeronautical engines, has an airfoil profile and a pair of hinge portions, which are carried by the airfoil profile and enable the airfoil profile to be coupled to a support structure of the stator so as to be rotatable about an axis of adjustment; the vane also has internal channels that allow a flow of air to pass through in order to cool the hinge portions.
Enhancement of esophageal speech by injection noise rejection (2002)

Esophageal speakers, who produce a voice source by bringing about a vibration of the esophageal superior sphincter, must insufflate the esophagus with an air injection gesture before every utterance, thus creating an air reservoir to drive the vibration. The resulting noise is generally undesired by the speakers. This paper describes a method for the automatic recognition and rejection of the injection noise which occurs in esophageal speech.
Measurement of glycated hemoglobin using an aptamer/antibody assay on an integrated microfluidic system (2014)

Measurement of the ratio between glycated hemoglobin (HbA1c) and total hemoglobin (Hb) is now recommended for screening and diagnosing diabetes, in addition to monitoring long-term glycemic control for patient management. The costly and time-consuming traditional assay methods, which involve multi-step, bench-top, and antibody-based immunoassays, have presented major challenges to their clinical utility. In this study, an integrated microfluidic system capable of rapidly measuring the level of HbA1c and Hb in an automated fashion was reported. Moreover, this detection assay used nucleic acid aptamers that exhibited high sensitivity and specificity to Hb and HbA1c to further enhance the robustness of the assay. Combining the advantages of microfluidics and aptamers, this system presents a promising tool for clinical diagnosis and management of diabetes. As a demonstration of its clinical utility, we analyzed patient whole blood samples with clinically-relevant concentrations of HbA1c and Hb (4.4%-12.5% and 12.1 g/dL-14.9 g/dL, respectively) on our integrated microfluidic system.