gebhart/patrepeval huggingface dataset:
Multi-gene signature of microcalcification and risk prediction among Taiwanese breast cancer (2020)

Microcalcification is one of the most common radiological and pathological features of breast ductal carcinoma in situ (DCIS), and to a lesser extent, invasive ductal carcinoma. We evaluated messenger RNA (mRNA) transcriptional profiles associated with ectopic mammary mineralization. A total of 109 breast cancers were assayed with oligonucleotide microarrays. The associations of mRNA abundance with microcalcifications and relevant clinical features were evaluated. Microcalcifications were present in 86 (79%) patients by pathological examination, and 81 (94%) were with coexistent DCIS, while only 13 (57%) of 23 patients without microcalcification, the invasive diseases were accompanied with DCIS (χ<sup>2</sup>-test, P < 0.001). There were 69 genes with differential mRNA abundance between breast cancers with and without microcalcifications, and 11 were associated with high-grade (comedo) type DCIS. Enriched Gene Ontology categories included glycosaminoglycan and aminoglycan metabolic processes and protein ubiquitination, indicating an active secretory process. The intersection (18 genes) of microcalcificaion-associated and DCIS-associated genes provided the best predictive accuracy of 82% with Bayesian compound covariate predictor. Ten genes were further selected for prognostic index score construction, and five-year relapse free survival was 91% for low-risk and 83% for high-risk group (log-rank test, P = 0.10). Our study suggested that microcalcification is not only the earliest detectable radiological sign for mammography screening but the phenomenon itself may reflect the underling events during mammary carcinogenesis. Future studies to evaluate the prognostic significance of microcalcifications are warranted.
Nonlinear photonic crystal waveguide structures based on barium titanate thin films and their optical properties (2007)

Nonlinear photonic crystal waveguide structures were fabricated from barium titanate thin films using nanolithography. A cascaded Bragg reflector using a strip waveguide was designed and analyzed. Both simulation and experimental results show that there is sufficient refractive index contrast to form a stop band by only etching through the Si3N4 strip layer. The band gap of the Bragg reflector can be engineered through control of the Bragg spacing, thickness, and etching depth of the strip layer. The transmission spectrum of the Bragg reflector waveguide was measured over the spectral range of 1500–1580nm. A 27nm wide stop band was obtained for a millimeter long sample. The nonlinear photonic crystal waveguides are potentially suitable as tunable filters, optical switches, and ultrawide bandwidth modulators.
The Role of a Long-Acting Somatostatin Analogue (SMS 201-995) in the Management of a Patient with a Benign Insulin-Secreting Adenoma of the Pancreas and a Postoperative Pancreatic Fistula (1986)

(1986). The Role of a Long-Acting Somatostatin Analogue (SMS 201-995) in the Management of a Patient with a Benign Insulin-Secreting Adenoma of the Pancreas and a Postoperative Pancreatic Fistula. Scandinavian Journal of Gastroenterology: Vol. 21, No. sup119, pp. 217-222.
A Comparison of the Host Responses to Syngeneic and Xenogeneic Islet Transplantation Using Noninvasive In Vivo Imaging (2012)

Background: Xenotransplantion provides a solution to human islet donor scarcity. However, the rapid, immune-mediated destruction of transplanted islets in the absence of potent and prolonged immunosuppression makes it an unattractive solution. Studies have demonstrated that biomaterial encapsulation of xenograft islets prolongs their survival and obviates the need for immunosuppression. However with encapsulation, islet survival is compromised due to insufficient oxygen delivery via the microcirculation. Thus, a brisk vascular response is vital to reduce the risk of hypoxia in the transplanted islets. We aim to compare the responses to isograft and xenograft islets by employing a combination of the mouse dorsal window-chamber model, Wide-field Functional Imaging (WiFI) and Laser Speckle Imaging(LSI). Methods: Dorsal window chambers were installed on C57BL/6 albino mice. The implants were placed in intimate contact with the underside of the dermis of the opposing skin, within the viewing port of the model. We studied the host vascular response to the introduction of either a high guluronate alginate sheet containing islets isolated from C57Bl/6 mice or one containing islets isolated from 3 week old Yorkshire pigs. Two modes of WiFI were used to monitor hemodynamics over the ensuing 7-day period. Laser speckle imaging enables mapping of blood flow, and multispectral imaging enables mapping of hemoglobin oxygen saturation. Results: Our data demonstrates that the dorsal window chamber enables longitudinal monitoring and an easy comparison of the host vascular response to transplanted isograft and xenograft islets over a one week period. Vascular changes that are readily noted include arteriolar, venular and venous dilatation and the formation of nascent arteriovenous connections. Peri-implant neovascularization, while noted in both groups was significantly more in the porcine islet group. We hypothesize that this is presumably due to a greater metabolic demand by porcine islets when compared to syngeneic murine islets. An increase in the relative rate of blood flow (Fig. 1C,G and Fig. 2 C,G) and hemoglobin oxygen saturation (Fig 1D,H and Fig 2D,H.) can also be observed. Future experiments will compare islet viability and the host responses between the two groups for upto two weeks after transplantation.Figure: [Host Vascular Response To Syngeneic Islets]Figure: [Host Vascular Response to Xenogeneic Islets]
Regional Localization of over 300 Loci on Human Chromosome 22 Using a Somatic Cell Hybrid Mapping Panel (1996)

A somatic cell hybrid panel, consisting of 25 cell lines, has been developed to localize loci subregionally on chromosome 22. Over 300 markers in the form of STSs or hybridization probes have been assigned to one of 24 unique regions or "bins" using this panel. This ordered collection of markers will aid in the assembly of physical maps and contigs of chromosome 22 and assist in positional cloning of disease loci mapped to chromosome 22.
Fullerene-Based Proton-Conductive Material for the Electrolyte Membrane and Electrode of a Direct Methanol Fuel Cell (2008)

A fullerene-based compound with proton-conductive functional groups was synthesized and characterized for fuel cell applications. The fullerene-based proton conductor was mixed with polyvinylidene difluoride (PVdF) as a binder to form the electrolyte membranes. The film property can be tuned by changing the ratio of the fullerene derivatives. The proton conductivity of the electrolyte membranes with 67 wt % fullerene derivative was higher than 4.5 × 10-3 S cm-1 at 25 {degree sign}C under relative humidity (RH) of 70%. The membrane-electrolyte assemblies with these materials showed high DMFC performance under ambient conditions.
The Effect of Chromosome 9p21 Variants on Cardiovascular Disease May Be Modified by Dietary Intake: Evidence from a Case/Control and a Prospective Study (2011)

The risk of MI and CVD conferred by Chromosome 9p21 SNPs appears to be modified by a prudent diet high in raw vegetables and fruits. Please see later in the article for the Editors' Summary.
Microwave-accelerated plasmonics: application to ultrafast and ultrasensitive clinical assays (2007)

In recent years our laboratory has described the favorable effects of fluorophores in close proximity to metallic
nanostructures (1-6). These include, increased system quantum yields (increased detectability) and much improved
fluorophore photostabilities. These effects have led to many applications of metal-enhanced fluorescence (MEF)
including, improved DNA detection (7, 8), enhanced ratiometric sensing (5), metal-enhanced phosphorescence (9) and
chemiluminescence signatures (10), as well as to the development of nano-rod (6), triangular nano-plate (4) and
modified plastic surfaces (1, 3) for their multifarious applications. In all of our applications of MEF to date, we have
been able to significantly optically amplify luminescence based signatures, but have been unable to modify the rates of
the respective biochemical reactions being either studied or utilized, as these are dependent on the usual solution
parameters of temperature, viscosity and their bioaffinity etc.
However, our laboratory has recently shown that low power microwaves, when applied to the metallic nanostructures
which are suitable for MEF, are preferentially heated, rapidly accelerating local biochemical reactions (11).
Subsequently, ultra-fast and ultra-sensitive assays can be realized. We have recently termed the amalgamation of both
MEF with microwave heating as Metal-Enhanced Fluorescence (MAMEF). In this conference
proceeding, we summarize our MAMEF work on ultra-fast and sensitive myoglobin detection for rapid cardiac risk
assessment and DNA detection for bioterrorism applications. In addition we present two new platform technologies,
namely, Microwave-Accelerated Surface Plasmon-Coupled Directional Luminescence (MA-SPCL) for ultra fast assays
using clinical samples and a Microwave-Accelerated Aggregation Assay (MA-AA) technology, for ultra fast solutionbased
nanoparticle aggregation assays.
Mechanisms for nonmitotic activation of Aurora-A at cilia (2017)

Overexpression of the Aurora kinase A (AURKA) is oncogenic in many tumors. Many studies of AURKA have focused on activities of this kinase in mitosis, and elucidated the mechanisms by which AURKA activity is induced at the G2/M boundary through interactions with proteins such as TPX2 and NEDD9. These studies have informed the development of small molecule inhibitors of AURKA, of which a number are currently under preclinical and clinical assessment. While the first activities defined for AURKA were its control of centrosomal maturation and organization of the mitotic spindle, an increasing number of studies over the past decade have recognized a separate biological function of AURKA, in controlling disassembly of the primary cilium, a small organelle protruding from the cell surface that serves as a signaling platform. Importantly, these activities require activation of AURKA in early G1, and the mechanisms of activation are much less well defined than those in mitosis. A better understanding of the control of AURKA activity and the role of AURKA at cilia are both important in optimizing the efficacy and interpreting potential downstream consequences of AURKA inhibitors in the clinic. We here provide a current overview of proteins and mechanisms that have been defined as activating AURKA in G1, based on the study of ciliary disassembly.
Widely tunable and narrow linewidth chip-scale lasers from deep visible to near-IR (2021)

Widely-tunable and narrow-linewidth integrated lasers across all visible wavelengths are necessary to enable on-chip technologies such as quantum photonics, optical trapping, and biophotonics. However, such lasers have not been realized due to the strong wavelength sensitivity and high loss of integrated optical devices at short wavelengths. Here we overcome these challenges and demonstrate a chip-scale visible lasers platform by using tightly-confined, micrometer-scale silicon nitride resonators and commercial Fabry-Perot laser diodes. We achieve tunable and narrow-linewidth lasing in the deep blue (450 nm), blue (488 nm), green (520 nm), red (660 nm) and near-IR (785 nm) with coarse tuning up to 12 nm, fine tuning up to 33.9 GHz, linewidth down to sub-kHz, side-mode suppression ratio &gt; 35 dB, and fiber-coupled power up to 10 mW. These specifications of our chip-scale lasers are comparable to those of state-of-the-art commercial laser systems, making them stand out as powerful tools for the next generation of visible-light technologies.
180nm 4Mb High Speed High Reliability Embedded SONOS Flash Memory (2006)

A 1.8/3.3V 4Mb (512K times 8 bit) embedded SONOS flash memory has been successfully developed and verified with 180nm CMOS logic compatible integrated technology, in which a reverse programming array architecture and a novel high speed sensing circuit with dual-phase precharge path and self-adjusted load are proposed to improve read speed. Moreover, a novel threshold voltage tracking technique is also introduced to improve the reliability. Finally, a 4.4 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> core size and a 0.40 mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> (12.4F <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /bit) cell size are obtained, and the test results show that the read speed and the endurance characteristics are 17ns and 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> , respectively
Anogenital Human Papillomavirus Prevalence is Unaffected by Therapeutic Tumour Necrosis Factor-alpha Inhibition (2015)

Patients receiving tumour necrosis factor alpha (TNF-α) inhibitors are at increased risk of exacerbation of (myco-)bacterial and some viral infections. However, information on anogenital human papillomavirus (HPV) infection in these patients is sparse or conflicting. In this study 222 patients with psoriasis or inflammatory bowel disease (IBD), who received either anti-TNF-α inhibitors or alternatives (purine-, folic acid analogues, phototherapy, fumaric ester, mesalazine) continuously for at least 6 months, were evaluated for the presence of anogenital HPV-induced lesions, mucosal HPV DNA, and serological status of mucosal low-risk HPV6 and high-risk HPV16/HPV18. Hallmarks of anogenital HPV infection were more frequently detected in patients with psoriasis than in those with IBD. HPV-induced lesions, viral DNA, and seroprevalence were not elevated in participants with psoriasis or IBD, who received TNF-α inhibitors for a mean duration of 31.4 months (range 6-96 months) compared with recipients of alternative or no treatment. TNF-α blockade for a mean period of 31.4 months does not increase detectable anogenital HPV infection or disease.
Characterization and Comparison of the Human and MouseGLC1A Glaucoma Genes (1998)

The GLC1A gene (which encodes the protein myocilin) has been associated with the development of primary open angle glaucoma. Bacterial artificial chromosomes containing the human GLC1A gene and its mouse ortholog were subcloned and sequenced to reveal the genomic structure of the genes. Comparison of the coding sequences of the human and mouse GLC1A genes revealed a high degree of amino acid homology (82%) and the presence of several conserved motifs in the predicted GLC1A proteins. The expression of GLC1A was examined by Northern blot analysis of RNA from adult human tissues. GLC1A expression was observed in 17 of 23 tissues tested, suggesting a wider range of expression than was recognized previously. The comparison of the human and mouse GLC1A genes suggests that the mouse may be a useful model organism in studying the molecular pathophysiology of glaucoma.
Alcohol-induced vascular damage of brain can be ameliorated by administration of magnesium (1986)

Long-term as well as short-term administration of alcohol can cause neuronal and vascular damage in the brain. The authors have reported that acute administration of ethyl alcohol (ALC), either directly into the rat brain, IV or locally, can produce concentration-dependent spasms of cerebral arterioles, venules, arteries and veins followed by irreversible rupture of capillaries and veins followed by irreversible rupture of capillaries and venules. Several experiments have suggested that administration of magnesium ions (Mg/sup 2 +/) can modify vascular tone. Whether Mg/sup 2 +/ can exert direct actions on the intact cerebral microcirculation is not known. Using the above intact rat brain model, and TV-image intensification, the authors determine whether administration of Mg/sup 2 +/ : 1) exerts actions on cerebral (coritical) arterioles (A) and venules (V) (12-40..mu..m); 2) directly into the brain alters arterial blood pressure (BP); and 3) could ameliorate or prevent some of the detrimental cerebral-vascular actions ALC exerts in the brain. The data show that infusion of Mg/sup 7 +/ : 1) into the rat brain result in a rapid dose-dependent lowering of systolic and diastolic and BP; 2) IV or intra-arterially (IA) produces dose-dependent vaso-dilation of A and V; 3) IV or IA prevents spasmsmore » and rupture of A and V induced by 10% ALC. The cerebral vascular actions of Mg/sup 2 +/ may prove to be useful in treatment and prevention of ALC-induced brain damage.« less
Role of protein and RNA synthesis in the development of insulin binding sites on activated thymus-derived lymphocytes. (1979)

Quiescent T (thymus-derived) lymphocytes have no insulin receptors. Lymphocyte activation by alloantigen or mitogens stimulates receptor appearance. There are two theories that may explain the mechanism by which cellular activation leads to newly measurable receptors: 1) activation uncovers nascent receptors by alteration of membrane configuration or 2) activation initiates synthesis of the receptor or substances crucial to the integrity of the receptor. This study was designed to test the latter theory directly. T cells were activated with the mitogen phytohemagglutinin (PM) and treated with either mitomycin C (100 pg/ml), cycloheximide (0.5 mu), or actinomycin D (1 PM). Controls consisted of cells cultured with mitogen alone or with medium alone. Inhibitors reduced DNA synthesis 83% (r3H]thymidine), RNA synthesis 90% (r3H]uridine), and protein synthesis 88% (13H]leucine) in separate series of studies. Insulin binding after PHA interaction was 4.0 f 0.6 pg/106 in control and 3.93 + 0.1 in mitomycintreated cultures. In contrast, binding after PHA activation (75 gg/ml) fell from 6.3 + 1.3 to 0.4 + 0.2 pg/106 cells after RNA synthesis inhibition. Inhibition of DNAdependent, RNA synthesis by 96%, as measured by assay of RNA polymerase II, by cx-amanitin (1
Non-linear network coding in two-way relaying discrete channels (2009)

In this paper, we present optimal network coding which can maximize achievable rate region in two-way relaying discrete channels, where there are two communicating nodes and one relaying node. We focus on a low-complexity relaying protocol termed the detect-and-forward (DtF) scheme, in which the relaying node does not require channel decoding but detection. We first analyze the achievable rate region of any digital network coding function including non-linear types. We then search for the optimal network code in favor of maximizing two kinds of performance measures: the sum rate and the product rate. For high SNR regimes, linear network codes like the exclusive-or (XOR) function can offer the maximum-achievable rate region. Whereas, for low SNR regimes, it is verified that non-linear network codes like the negate-or (NOR) function can outperform linear codes due to the effect of error occurrence at the intermediate relaying node.
Cisplatin-Resistant Neuroblastoma Cells Express Enhanced Levels of Epidermal Growth Factor Receptor (EGFR) and Are Sensitive to Treatment with EGFR-Specific Toxins (2008)

EGFR-targeted cytotoxic reagents such as scFv(14E1)-ETA and TGF-alpha-ETA represent promising candidates for further development as antineuroblastoma agents, especially in combination with cisplatin.
Artificial intelligence-rationalized balanced PPARα/γ dual agonism resets dysregulated macrophage processes in inflammatory bowel disease (2022)

A computational platform, Boolean network explorer (BoNE), has recently been developed to infuse AI-enhanced precision into drug discovery; it enables invariant Boolean Implication Networks of disease maps for prioritizing high-value targets. Here we used BoNE to query an Inflammatory Bowel Disease (IBD)-map and prioritize a therapeutic strategy that involves dual agonism of two nuclear receptors, PPARα/γ. Balanced agonism of PPARα/γ was predicted to modulate macrophage processes, ameliorate colitis, 'reset' the gene expression network from disease to health. Predictions were validated using a balanced and potent PPARα/γ-dual-agonist (PAR5359) in Citrobacter rodentium- and DSS-induced murine colitis models. Using inhibitors and agonists, we show that balanced-dual agonism promotes bacterial clearance efficiently than individual agonists, both in vivo and in vitro. PPARα is required and sufficient to induce the pro-inflammatory cytokines and cellular ROS, which are essential for bacterial clearance and immunity, whereas PPARγ-agonism blunts these responses, delays microbial clearance; balanced dual agonism achieved controlled inflammation while protecting the gut barrier and 'reversal' of the transcriptomic network. Furthermore, dual agonism reversed the defective bacterial clearance observed in PBMCs derived from IBD patients. These findings not only deliver a macrophage modulator for use as barrier-protective therapy in IBD, but also highlight the potential of BoNE to rationalize combination therapy.
Characteristics of Thermal Cavitation on a Two-Dimensional Hydrofoil (2013)

Cavitation in cryogenic rocket propellants was simulated using a surrogate fluid exhibiting thermodynamic properties similar to liquid hydrogen. A NACA 0015 hydrofoil was chosen to represent the leading edge of a turbopump inducer, and it was installed in a closed-loop facility filled with a fluid that exhibits a strong thermodynamic effect at ambient conditions. Static pressures were measured at seven locations along the hydrofoil chord and along the wall of the test section. Flow at Reynolds numbers up to and temperature high enough to produce above unity exploited the thermosensitive properties of the surrogate fluid. Sensitivity to isolated effects of velocity, cavitation number, temperature, and angle of attack were studied, and behavior of the cavity growth and collapse cycle is described. Cavitation was observed at local static pressure both above and below the vapor point corresponding to the inlet temperature. Pressure and frequency analysis of these phenomena is described.
Design and decoding of an M-array pattern for low-cost structured light 3D reconstruction systems (2013)

3D shape reconstruction is one of the most important topics in computer vision due to its wide field of application. Among various technologies, structured light is considered to be one of the most reliable techniques. This paper addresses the problem of finding correspondences in a structured-light 3D shape reconstruction system. The work is based on the 3-symbol binary M-array encoded pattern proposed by Albitar. A new 6-symbol M-array pattern is designed with guaranteed minimum Hamming distance of three among all 3 × 3 windows. Improvements to the decoding algorithm are made, which allows successful identification of most symbols, and which corrects one possible error or missing symbol in each 3 × 3 window. Finally, refinements are made to the algorithm for finding correspondences, including back-projection of the captured structured light pattern to the projector plane to eliminate projective distortion.