gebhart/patrepeval huggingface dataset:
Tumor-associated macrophages in breast cancer: distinct subsets, distinct functions (2011)

Macrophages display remarkable plasticity, allowing these cells to adapt to changing microenvironments and perform functions as diverse as tissue development and homeostasis, inflammation, pathogen clearance and wound healing. Macrophage activation can be triggered by Th1 cytokines and pathogen-associated or endogenous danger signals, leading to the formation of classically activated or M1 macrophages. On the other hand, anti-inflammatory mediators, including IL-4, IL-10, TGF-β and M-CSF, induce diverse anti-inflammatory types of macrophages, known under the generic term M2. In human breast carcinomas, tumor-associated macrophage (TAM) density correlates with poor prognosis. In mouse models of breast cancer, eliminating macrophages from the tumor site, either via genetic or therapeutic means, results in retarded tumor progression. Over the years, multiple signals from the mammary tumor microenvironment have been reported to influence the TAM phenotype and TAM have been propagated as anti-inflammatory M2-like cells. Recent developments point to the existence of at least two distinct TAM subpopulations in mammary tumors, based on a differential expression of markers such as CD206 or MHC II and different in vivo behaviour: perivascular, migratory TAM which are less M2-like, and sessile TAM found at tumor-stroma borders and/or hypoxic regions that resemble more M2-like or "trophic" macrophages. Hence, a further refinement of the molecular and functional heterogeneity of TAM is an avenue for further research, with a potential impact on the usefulness of these cells as therapeutic targets.
Micro-specialization: dynamic code specialization in dbmses (2012)

Database management systems (DBMSes) form a cornerstone of modern IT infrastructure, and it is essential that they have excellent performance. In this research, we exploit the opportunities of applying dynamic code specialization to DBMSes, particularly by focusing on runtime invariant present in DBMSes during query evaluation. Query evaluation involves extensive references to the relational schema, predicate values, and join types, which are all invariant during query evaluation, and thus are subject to dynamic value-based code specialization. 
We observe that DBMSes are general in the sense that they must contend with arbitrary schemas, queries, and modifications; this generality is implemented using runtime metadata lookups and tests that ensure that control is channelled to the appropriate code in all cases. Unfortunately, these lookups and tests are carried out even when information is available that renders some of these operations superfluous, leading to unnecessary runtime overheads. 
We introduce micro-specialization, an approach that uses relation- and query-specific information to specialize the DBMS code at runtime and thereby eliminate some of these overheads. We develop a taxonomy of approaches and specialization times and propose a general architecture that isolates most of the creation and execution of the specialized code sequences in a separate DBMS-independent module. We show that this approach requires minimal changes to a DBMS and can improve the performance simultaneously across a wide range of queries, modifications, and bulk-loading, in terms of storage, CPU usage, and I/O time of the TPC-H and TPC-C benchmarks. We also discuss an integrated development environment that helps DBMS developers apply micro-specializations to identified target code sequences.
Integrated Mikaelian Lens Implemented by Subwavelength Grating (2020)

An integrated Mikaelian lens was designed with subwavelength grating. The device was numerically simulated and experimentally demonstrated in a compact mode size converter and an efficient S-bend connector.
Effects of Age and Dietary β-Carotene on Immunological Variables in Dogs (2003)

beta-Carotene is a naturally occurring carotenoid reported to have health-promoting effects in several species. Advancing age is known to have a negative impact on various immune variables in several species. This study was conducted in order to assess the effect of age on immune response in dogs and to determine whether beta-carotene is able to reverse this age-associated decline. To test this hypothesis, young and old dogs (n = 36) were fed either a control diet or experimental diets containing supplemental beta-carotene for 2-month periods. Age significantly (P < .05) lowered CD4+ T cell populations (47.2% versus 33.7%; young-control versus old-control, respectively) and beta-carotene restored percent distributions in old dogs to nonsignificance versus younger controls (41.0%). T cell proliferation was lower in old dogs (30,254 +/- 2,248 versus 14,811 +/- 2,497 cCPM; young-control versus old-control, respectively; P < .05), and beta-carotene supplementation significantly improved responses in this age group (21,329 +/- 2,275 cCPM). Although B cell proliferation was depressed with age (17,967 +/- 1,384 versus 7,535 +/- 1,469 cCPM; young-control versus old-control, respectively; P < .05), beta-carotene supplementation improved B cell proliferation in young dogs (23,500 +/- 1,339 cCPM). Old dogs displayed lower delayed-type hypersensitivity test (DTH) responses versus younger controls to both phytohemagglutinin-P (PHA; 11.1 +/- 0.95 versus 7.57 +/- 1.15 mm; young-control versus old-control, respectively; P < .05) and sheep red blood cell (RBC; 9.12 +/- 0.62 versus 8.08 +/- 0.75 mm; young-control versus old-control, respectively; P < .10). beta-Carotene improved these responses, mostly within the first 24-48 hours after injection. In summary, older dogs have lower immunological responses compared with younger controls. beta-Carotene supplementation significantly restored immune responses in older dogs when compared with their age-matched controls and younger counterparts.
Optimizing synonym extraction using monolingual and bilingual resources (2003)

Automatically acquiring synonymous words (synonyms) from corpora is a challenging task. For this task, methods that use only one kind of resources are inadequate because of low precision or low recall. To improve the performance of synonym extraction, we propose a method to extract synonyms with multiple resources including a monolingual dictionary, a bilingual corpus, and a large monolingual corpus. This approach uses an ensemble to combine the synonyms extracted by individual extractors which use the three resources. Experimental results prove that the three resources are complementary to each other on synonym extraction, and that the ensemble method we used is very effective to improve both precisions and recalls of extracted synonyms.
ChemInform Abstract: Microwave‐Enhanced Solid‐Phase Peptide Synthesis (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Metabolic and Immunologic Consequences of Limited Adenosine Deaminase Expression in Mice (1996)

Adenosine deaminase (ADA; EC 3.5.4.4) deficiency in humans is an autosomal recessive genetic disorder that results in severe combined immunodeficiency disease. ADA-deficient mice generated by targeted gene disruption die perinatally, preventing postnatal analysis of ADA deficiency. We have recently rescued ADA-deficient fetuses from perinatal lethality by expression of an ADA minigene in the placentas of ADA-deficient fetuses, thus generating postnatal mice admissible to analysis of ADA deficiency. The minigene used also directed ADA expression to the forestomach postnatally, producing adult animals that lacked ADA enzymatic activity in all tissues outside the gastrointestinal tract. Mice with limited ADA expression exhibited profound disturbances in purine metabolism, including thymus-specific accumulations of deoxyadenosine and dATP, and inhibition of S-adenosylhomocysteine hydrolase in the thymus, spleen, and, to a lesser extent, the liver. Lymphopenia and mild immunodeficiency were associated with these tissue-specific metabolic disturbances. These mice represent the first genetic animal model for ADA deficiency and provide insight into the tissue-specific requirements of ADA.
Ligand Conjugated Multimeric siRNAs Enable Enhanced Uptake and Multiplexed Gene Silencing (2019)

Small interfering RNAs (siRNAs) conjugated to <i>N</i>-acetylgalactosamine (GalNAc) ligands have been used to treat disease in patients. However, conjugates with other ligands deliver siRNA less efficiently, limiting the development of new targeted therapies. Most approaches to enhancing the potency of such conjugates have concentrated on increasing ligand effectiveness and/or the chemical stability of the siRNA drug. One complementary and unexplored alternative is to increase the number of siRNAs delivered per ligand. An ideal system would be a single chemical entity capable of delivering multiple copies of an oligonucleotide drug and/or several such drugs simultaneously. Here we report that siRNAs can be stably linked together under neutral aqueous conditions to form chemically defined siRNA "multimers," and that these multimers can be delivered <i>in vivo</i> by a GalNAc ligand. Conjugates containing multiple copies of the same siRNA showed enhanced activity per unit of ligand, whereas siRNAs targeting different genes linked to a single ligand facilitated multigene silencing <i>in vivo</i>; this is the first demonstration of silencing several genes simultaneously <i>in vivo</i> using ligand-directed multimeric siRNA. Multimeric oligonucleotides represent a powerful and practical new approach to improve intracellular conjugate delivery.
Investigation of the Enhanced Sensitivity of Interdigitated Electrodes for Cellular Biosensing With Geometric, Nanostructured Surface Area, and Surface Plasmon Resonance Modes (2020)

In this work, preliminary investigations into the different sources of sensitivity enhancement of Interdigitated Electrodes (IDEs) on polymer substrates utilized in cell-based biosensing are evaluated. In studying underlying modalities involved in this IDE sensitivity enhancement, we have found that this phenomenon has several components - geometric (electrode gap width), nanostructuring of the substrate, and surface plasmon resonance (SPR) enhancement modes. By isolating these three modes, this article investigates and reports on the individual contribution of each of these modes in enhancing the sensitivity of IDEs during a short five days in vitro (5 DIV) assay of the HL-1 cardiomyocytes cultured on these devices. [2020-0121]
Fabrication of three-dimensional Yablonovite photonic crystals by multiple-exposure UV interference lithography (2005)

We present a method for fabricating three-dimensional photonic crystal structures by interference lithography, capable of generating face-centered cubic lattices with lattice periods that can be controllably varied over a wide range. The method consists of three separate exposures of a layer of photoresist by interfering laser beams, where each exposure generates a two-dimensional interference pattern, specifically a tilted set of parallel rods. When properly oriented, superimposing these three rod arrays within a common volume of resist material yields an fcc lattice. The lattice period is controlled by the spacing of the rod arrays, which can be tuned independently of the laser wavelength by varying the relative orientations of the interfering beams. We have developed a method for generating the necessary laser beams that is highly repeatable and requires zero alignment, using an array of diffraction gratings patterned on a single mask plate and a rotating beam blocker to select which subset of the grating array is to be used for any given exposure. This paper contains a description of the method and our fabrication setup, and presents the samples that have been fabricated using this method.
Compact non‐contact total emission detection for <i>in vivo</i> multiphoton excitation microscopy (2013)

We describe a compact, non-contact design for a total emission detection (c-TED) system for intra-vital multiphoton imaging. To conform to a standard upright two-photon microscope design, this system uses a parabolic mirror surrounding a standard microscope objective in concert with an optical path that does not interfere with normal microscope operation. The non-contact design of this device allows for maximal light collection without disrupting the physiology of the specimen being examined. Tests were conducted on exposed tissues in live animals to examine the emission collection enhancement of the c-TED device compared to heavily optimized objective-based emission collection. The best light collection enhancement was seen from murine fat (5×-2× gains as a function of depth), whereas murine skeletal muscle and rat kidney showed gains of over two and just under twofold near the surface, respectively. Gains decreased with imaging depth (particularly in the kidney). Zebrafish imaging on a reflective substrate showed close to a twofold gain throughout the entire volume of an intact embryo (approximately 150 μm deep). Direct measurement of bleaching rates confirmed that the lower laser powers, enabled by greater light collection efficiency, yielded reduced photobleaching in vivo. The potential benefits of increased light collection in terms of speed of imaging and reduced photo-damage, as well as the applicability of this device to other multiphoton imaging methods is discussed.
Synthesis and Pharmacological in Vitro and in Vivo Evaluations of Novel Triazole Derivatives as Ligands of the Ghrelin Receptor. 1 (2007)

A new series of growth hormone secretagogue (GHS) analogues based on the 1,2,4-triazole structure were synthesized and evaluated for their in vitro binding and their ability to stimulate intracellular calcium release to the cloned hGHS-1a ghrelin receptor expressed in LLC PK-1 cells. We have synthesized potent ligands of this receptor, some of them behaving as agonists, partial agonists, or antagonists. Some compounds among the most potent, i.e., agonist 29c (JMV2873), partial agonists including 21b (JMV2810), antagonists 19b (JMV2866) and 19c (JMV2844), were evaluated for their in vivo activity on food intake, after sc injection in rodents. Some compounds were found to stimulate food intake like hexarelin; some others were identified as potent hexarelin antagonists in this assay. Among the tested compounds, 21b was identified as an in vitro ghrelin receptor partial agonist, as well as a potent in vivo antagonist of hexarelin-stimulated food intake in rodents. Compound 21b was without effect on GH release from rat. However, in this series of compounds, it was not possible to find a clear correlation between in vitro and in vivo results.
Isolation of monoclonal antibodies that react preferentially with Listeria monocytogenes (1991)

We have isolated and characterized three monoclonal antibodies that preferentially recognize the pathogen Listeria monocytogenes. Mouse monoclonal antibodies were produced by fusion of spleen cells from a Balb/c mouse, which was immunized with live L. monocytogenes, to an NS-1 myeloma partner. Hybridomas that produced antibodies which preferentially reacted with L. monocytogenes were identified by a direct binding enzyme-linked immunoabsorbent assay (ELISA) using a panel of bacteria which included L. ivanovii, Streptococcus faecalis, L. seeligeri, L. innocua and L. monocytogenes Scott A. Three hybridomas, Mab 20-10-2, Mab 36-6-12 and Mab 56-9-16 which preferentially reacted with L. monocytogenes were selected for further analysis. An indirect ‘sandwich’ ELISA was developed and used to further confirm that these hybridomas reacted with a number of L. monocytogenes isolates and not with other common cross-reacting bacteria including Kurthia sp.
Peptide Retention Standards and Hydrophobicity Indexes in Reversed-Phase High-Performance Liquid Chromatography of Peptides (2009)

The growing utility of peptide retention prediction in proteomics would benefit from the development of a universal peptide retention standard for better alignment of chromatographic data obtained using various liquid chromatography (LC) platforms. We describe a six-peptide mixture designed for this purpose; its members cover a wide range of hydrophobicity for the most popular modes of reversed-phase peptide high-performance liquid chromatography (HPLC): C18 sorbents with trifluoroacetic/formic acid as the ion-pairing modifier and separations at pH 10. We propose a hydrophobicity index (HI) describing the concentration of organic solvent (typically acetonitrile) that yields a retention factor of 10 under isocratic elution conditions for any peptide. This measure is a fundamental characteristic of peptide-sorbent interaction, depending only on the type of sorbent and the ion-pairing modifier used. Spiking a sample with a standard peptide mixture provides a measurement of the HI values of all detected species during gradient separation. In addition to alignment of data and calibration of chromatographic runs when peptide retention prediction protocols are used, these values obtained from proteomics experiments can be utilized directly in method development for large-scale preparative separations.
A novel method of temperature compensation for multiplexed liquid crystal displays (1978)

A new, simple technique for compensating the drive voltages to allow for temperature changes of multiplexed liquid crystal displays is described. No components apart from the display and drive electronics are required and compensation over the temperature range 0°C to 50°C has been achieved.
Measurement of the noise power spectrum in digital x-ray detectors (2001)

The noise power spectrum, NPS, is a key imaging property of a detector and one of the principle quantities needed to compute the detective quantum efficiency. NPS is measured by computing the Fourier transform of flat field images. Different measurement methods are investigated and evaluated with images obtained from an amorphous silicon flat panel x-ray imaging detector. First, the influence of fixed pattern structures is minimized by appropriate background corrections. For a given data set the effect of using different types of windowing functions is studied. Also different window sizes and amounts of overlap between windows are evaluated and compared to theoretical predictions. Results indicate that measurement error is minimized when applying overlapping Hanning windows on the raw data. Finally it is shown that radial averaging is a useful method of reducing the two-dimensional noise power spectrum to one dimension.
100 mm 4HN-SiC Wafers with Zero Micropipe Density (2008)

Recent advances in PVT c-axis growth process have shown a path for eliminating micropipes in 4HN-SiC, leading to the demonstration of zero micropipe density 100 mm 4HN-SiC wafers. Combined techniques of KOH etching and cross-polarizer inspections were used to confirm the absence of micropipes. Crystal growth studies for 3-inch material with similar processes have demonstrated a 1c screw dislocation median density of 175 cm-2, compared to typical densities of 2x103 to 4x103 cm-2 in current production wafers. These values were obtained through optical scanning analyzer methods and verified by x-ray topography.
Anti-Phase Driven Rate Gyroscope with Multi-Degree of Freedom Sense Mode (2007)

Previously, we reported a 3-DOF (degree of freedom) rate gyroscope design with a 1-DOF drive and 2-DOF sense mode that was shown to be robust to environmental fluctuations. In this work, we introduce a novel design concept that combines the robustness of multi-DOF sensing with the common mode rejection of tuning fork devices in the anti-phase driven 6-DOF gyroscope. Prototypes of the design were fabricated and characterized for both rotational and acceleration inputs. For acceleration loads, the device responded in a common mode resulting in a 75% reduction in amplitude for a differential signal, while for rotations, it responded in anti-phase with sensitivities of 1.687 μV/deg/s and -1.887 μV/deg/s.
Polarization-Based Sensing with a Self-Referenced Sample (1999)

We describe a new method of fluorescence sensing based on fluorescence polarization. The sensor consists of two compartments, both of which contain the sensing fluorophore. One side of the sensor contains a constant concentration of analyte, and the other contains the unknown concentration. Emission from both sides is observed through polarizers, with the polarization from the sample being rotated 90° from that of the reference. Changes in the fluorescence intensity of the sample result in changes in the measured polarization for the combined emission. We show that this approach can be used to measure glucose and calcium using fluorophores which show analyte-dependent intensity changes, and no change in the spectral shape. Only a single fluorophore is required, this being the sensing fluorophore in both sides of the sensor. We also show that polarization sensing of glucose and calcium can be performed with visual detection of the polarization. In this case the only electronic component is the light source. These simple schemes can be used with a variety of analytes. The only requirement is a change in fluorescence intensity in response to the analyte.
In Production Performance Testing of SDN Control Plane for Telecom Operators (2018)

One of the biggest emerging challenges for telco operators is to dynamically create new services while maintaining the network at its optimal performance/revenue break point. To this end, operators are moving to a much leaner cloud-based Software Defined Network (SDN) infrastructure to achieve a truly programmable network fabric. While cloud services can be provisioned in seconds and tested in-production, service provisioning in SDNs still lasts many weeks and requires substantial manual effort. A large part of this service creation time can be attributed to testing and tuning the control plane. In this paper we present SCP-CLUB (SDN Control Plane CLoUd-based Benchmarking), a platform for in-production performance testing of telco operator SDNs, offering a level of automation as available in deploying cloud services. Telco cloud SDN performance testing with SCP-CLUB focuses on the analysis of how design choices in the cloud and SDN control planes influence SLA metrics like throughput and latency. We describe the SCP-CLUB architecture and its performance testing support capabilities. Experiments are performed on an SDN telco cloud built to demonstrate SCP-CLUB under production load conditions.
Identifying coronary artery disease from photoplethysmogram (2016)

This paper presents the idea of a non invasive screening system for identifying Coronary Artery Disease (CAD) patients from fingertip Photoplethysmogram (PPG) signal. A combined feature set, related to heart rate variability (HRV) as well as shapes of PPG waveform has been defined for distinguishing CAD and non CAD subjects. Support Vector Machine (SVM) is used for classification. Our methodology yields sensitivity and specificity scores of 0.82 and 0.88 respectively in identifying CAD patients on a corpus of 112 subjects, selected from MIMIC II dataset. Further, we achieved sensitivity and specificity scores of of 0.73 and 0.87 on another dataset of 30 subjects, collected from an urban hospital using commercial oximeter device.
On the search for self-doubly orthogonal codes (2002)

In this paper we present the search and determination of a subset of orthogonal convolutional codes called convolutional self doubly orthogonal codes (CSO/sup 2/C). These codes may be advantageously utilised for the novel coding/iterative decoding technique introduced as an important amelioration of turbo codes. For this technique the code constraint length corresponds to the latency of each decoding iteration. Hence, an important parameter in the code searching is the minimisation of the code constraint length for a given error correcting capability.