gebhart/patrepeval huggingface dataset:
Molecular genetic analysis of easily accessible breast tumour DNA, purified from tissue left over from hormone receptor measurement (1998)

In order to establish a large panel of normal and tumour DNA from primary breast cancer patients, we looked for a source of easily accessible, good quality breast tumour DNA. Following routine hormone receptor analysis at the hospital the leftover pellets contained the nuclei from the tumour tissue. We collected 670 pellets over a period of 2 1/4 years and isolated a large amount of DNA (on average 400 microg per pellet). To control the quality of this tumour DNA, we analysed 41 pellets and matching normal DNA for loss of heterozygosity (LOH), with 11 microsatellite markers along chromosome 17. This chromosome is well described for breast cancer. LOH is a sensitive method, requiring good quality and pure tumour DNA. Contamination with normal DNA will blur the results. We found a high rate of LOH, ranging from 33 to 74%, which is in agreement with other reports, and therefore recommend this rich source of breast tumour DNA for molecular biological analysis.
ANKRD11 pathogenic variants and 16q24.3 microdeletions share an altered DNA methylation signature in patients with KBG syndrome (2022)

Pathogenic variants in ANKRD11 or microdeletions at 16q24.3 are the cause of KBG syndrome (KBGS), a neurodevelopmental syndrome characterized by intellectual disability, dental and skeletal anomalies, and characteristic facies. The ANKRD11 gene encodes the ankyrin repeat-containing protein 11A transcriptional regulator, which is expressed in the brain and implicated in neural development. Syndromic conditions caused by pathogenic variants in epigenetic regulatory genes show unique patterns of DNA methylation (DNAm) in peripheral blood, termed DNAm signatures. Given ANKRD11's role in chromatin modification, we tested whether pathogenic ANKRD11 variants underlying KBGS are associated with a DNAm signature. We profiled whole-blood DNAm in 21 individuals with ANKRD11 variants, 2 individuals with microdeletions at 16q24.3 and 28 typically developing individuals, using Illumina's Infinium EPIC array. We identified 95 differentially methylated CpG sites that distinguished individuals with KBGS and pathogenic variants in ANKRD11 (n = 14) from typically developing controls (n = 28). This DNAm signature was then validated in an independent cohort of seven individuals with KBGS and pathogenic ANKRD11 variants. We generated a machine learning model from the KBGS DNAm signature and classified the DNAm profiles of four individuals with variants of uncertain significance (VUS) in ANKRD11. We identified an intermediate classification score for an inherited missense variant transmitted from a clinically unaffected mother to her affected child. In conclusion, we show that the DNAm profiles of two individuals with 16q24.3 microdeletions were indistinguishable from the DNAm profiles of individuals with pathogenic variants in ANKRD11, and we demonstrate the diagnostic utility of the new KBGS signature by classifying the DNAm profiles of individuals with VUS in ANKRD11.
Phononic crystals (2004)

Abstract Phononic crystals are periodic composite materials with lattice spacings comparable to the acoustic wavelength. They are of interest not only because of the profound effects of their periodic structure on wave propagation (e.g., the existence of acoustic band gaps), but also because of potential applications (e.g., their possible role in sound filters, transducer design and acoustic mirrors). In this paper, we summarize recent progress using ultrasonic experiments to investigate both two‐ and three‐dimensional phononic crystals. By measuring the ultrasonic wave field transmitted through slab‐shaped samples of different thicknesses, both the dispersion curves and amplitude transmission coefficient can be determined. Because the field is pulsed, the dynamics of the wave fields can also be investigated; this has allowed us to make a systematic study of ultrasonic wave tunneling in phononic crystals. New results on resonant tunneling, focussing and negative refraction phenomena in phononic crystals are also presented. Our data are well explained using Multiple Scattering Theory, giving additional insight into the physical properties and potential applications of these novel materials. (© 2004 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Surface Finishing of High Speed Print Bands: II. An Electrochemical Process for Microfinishing of Hardened Fe‐13Cr Stainless Steel (1998)

An electrochemical process has been developed to obtain microfinishing of hardened Fe‐13Cr stainless steel. The electrolyte is a mixture of phosphoric acid, sulfuric acid, and glycerol. Optimum conditions have been determined that lead to mirror finishing of the work piece over a wide range of current density. The process operates at ambient temperature and is insensitive to slight variations in temperature of the electrolyte. The beneficial effects of glycerol is due to its influence on the transport properties of the electrolyte and the diffusing species. The process is suitable for surface finishing of high speed print bands.
Temporal Starvation in CSMA Wireless Networks (2011)

It is well known that links in CSMA wireless networks are prone to starvation. Prior works focused almost exclusively on equilibrium starvation. In this paper, we show that links in CSMA wireless networks are also susceptible to temporal starvation. Specifically, although some links have good equilibrium throughputs and do not suffer from equilibrium starvation, they can still have no throughput for extended periods from time to time. For real-time applications such as VoIP and video streaming, it is desirable to understand and characterize temporal starvation in CSMA wireless networks. To this end, we develop a "trap theory" to analyze the temporal throughput fluctuations. Based on the trap theory, we can develop analytical tools for computing the "degrees of starvation" for CSMA networks to aid network design. For example, given a CSMA wireless network, we can determine whether it suffers from starvation, and if so, which links will starve. Furthermore, the likelihood and durations of temporal starvation can also be computed. We believe that the ability to identify and characterize temporal starvation as established in this paper will serve as an important first step toward the design of effective remedies for it.
PPAR.GAMMA.-gene therapy using an adenovirus vector for inflammatory bowel disease. (2003)

Peroxisome proliferator-activated receptor gamma (PPARgamma) is one of the nuclear receptors that plays a central role in adipocyte differentiation and insulin sensitivity. Recently, PPARgamma has also been recognized as a suppressive regulator of inflammation in the gastrointestinal tract. We summarize here the therapeutic benefits of PPARgamma-gene therapy using a replication-deficient adenovirus vector expressing PPARgamma (AdRGD-PPARgamma). We demonstrate that PPARgamma- protein levels are decreased in dextran sodium sulfate-induced colitis and restored in this model by intraperitoneal administration of the AdRGD-PPARgamma. Treatment with AdRGD-PPARgamma and PPARgamma-specific ligands resulted in a marked amelioration of tissue inflammation associated with the colitis, including reduction in intercellular adhesion molecule-1, cyclooxygenase-2, and tumor necrosis factor-alpha expression. Our results suggest that gene delivery of PPARgamma may open up a novel therapeutic approach for inflammatory bowel diseases such as Crohn's disease and ulcerative colitis.
Thermo-Gelation of Surface-Modified Polyethylene Microgels from Fragmentation and Immiscible Blends (2008)

Polyethylene microgels were created by swollen‐state grinding and ultrasonic fragmentation of bulk crosslinked polyethylene (XLPE) suspended in squalane, and by the extraction of crosslinked‐polyethylene micro‐domains from an immiscible blend of polyethylene (PE) and polystyrene (PS). Crosslinking of the polyethylene micro‐domains in the blend was achieved by exposure to an electron beam. Suspensions of both microgels in squalane exhibit thermal gelation upon cooling where both G′ and G″ increase by up to five‐orders in magnitude when probed using small‐angle oscillatory shear. We propose that this phenomenon is attributed to weak short‐range interactions among the particles whereby surface terminal chains on the microgels can co‐crystallize forming inter‐particle bonds. However, these interactions are mild enough that the systems may be reverted to its original state by applying higher shear stresses at elevated temperatures.
Capacity degradation due to interleaving and multiplexing (1974)

The capacity of an M-ary channel with N-ary coding is computed. It is found that the capacity of a very noisy channel is reduced by the factor (N-1)(log M)/(M-1)(log N). The results are applied to channels with noncoherent multifrequency shift keying and to concatenation of codes and interleaving.
Room temperature single-photon superfluorescence from a single epitaxial cuboid nano-heterostructure (2021)

Single-photon superradiance can emerge when a collection of identical emitters are spatially separated by distances much less than the wavelength of the light they emit, and is characterized by the formation of a superradiant state that spontaneously emits light with a rate that scales linearly with the number of emitters. This collective phenomena has only been demonstrated in a few nanomaterial systems, all requiring temperatures below 10K. Here, we rationally design a single colloidal nanomaterial that hosts multiple (nearly) identical emitters that are impervious to the fluctuations which typically inhibit room temperature superradiance in other systems such as molecular aggregates. Specifically, by combining molecular dynamics, atomistic electronic structure calculations, and model Hamiltonian methods, we show that the faces of a heterostructure nanocuboid mimic individual quasi-2D nanoplatelets and can serve as the robust emitters required to realize superradiant phenomena at room temperature. Leveraging layer-by-layer colloidal growth techniques to synthesize a nanocuboid, we demonstrate single-photon superfluorescence via single-particle time-resolved photoluminescence measurements at room temperature. This robust observation of both superradiant and subradiant states in single nanocuboids opens the door to ultrafast single-photon emitters and provides an avenue to entangled multi-photon states via superradiant cascades.
Mouse Cellular Cementum is Highly Dependent on Growth Hormone Status (2004)

Cementum is known to be growth-hormone (GH)-responsive, but to what extent is unclear. This study examines the effects of extremes of GH status on cementogenesis in three lines of genetically modified mice; GH excess (giant), GH antagonist excess (dwarf), and GH receptor-deleted (GHR-KO) (dwarf). Age-matched mandibular molar tissues were processed for light microscope histology. Digital images of sections of first molar teeth were captured for morphometric analysis of lingual root cementum. Cross-sectional area of the cellular cementum was a sensitive guide to GH status, being reduced nearly 10-fold in GHR-KO mice, three-fold in GH antagonist mice, and increased almost two-fold in giant mice (p < 0.001). Cellular cementum length was similarly influenced by GH status, but to a lesser extent. Acellular cementum was generally unaffected. This study reveals cellular cementum to be a highly responsive GH target tissue, which may have therapeutic applications in assisting regeneration of the periodontium.
Temporal expression profiles of organic anion transport proteins in placenta and fetal liver of the rat (2004)

Physiological cholestasis linked to immature hepatobiliary transport systems for organic anions occurs in rat and human neonates. In utero, the placenta facilitates vectorial transfer of certain fetal-derived solutes to the maternal circulation for elimination. We compared the ontogenesis of organic anion transporters in the placenta and the fetal liver of the rat to assess their relative abundance throughout gestation and to determine whether the placenta compensates for the late maturation of transporters in the developing liver. The mRNA of members of the organic anion transporting polypeptide (Oatp) superfamily, the multidrug resistance protein (Mrp) family, one organic anion transporter (OAT), and the bile acid carriers Na(+)-taurocholate cotransporting polypeptide (Ntcp) and bile salt export pump (Bsep) was quantified by real-time PCR. The most abundant placental transporters were Oatp4a1, whose mRNA increased 10-fold during gestation, and Mrp1. Mrp1 immunolocalized predominantly to epithelial cells of the endoplacental yolk sac, suggesting an excretory role that sequesters fetal-derived solutes in the yolk sac cavity, and faintly to the basal syncytiotrophoblast surface. The mRNA levels of Oatp2b1, Mrp3, and Bsep in the placenta exceeded those in the fetal liver until day 20 of gestation, suggesting that the fetus relies on placental clearance of substrates when expression in the developing liver is low. Mrp3 immunolocalized to the epithelium of the endoplacental yolk sac and less abundantly in the labyrinth zone and endothelium of the maternal arteries. The placental expression of Oatp1a1, Oatp1a4, Oatp1a5, Oatp1b2, Oat, Ntcp, Mrp2, and Mrp6 was low.
Spatial distribution and source apportionment of PFASs in surface sediments from five lake regions, China (2016)

Perfluoroalkyl substances (PFASs) have been found in environment globally. However, studies on PFAS occurrence in sediments of lakes or reservoirs remain relatively scarce. In this study, two hundred and sixty-two surface sediment samples were collected from forty-eight lakes and two reservoirs all over China. Average PFAS concentrations in surface sediments from each lake or reservoir varied from 0.086 ng/g dw to 5.79 ng/g dw with an average of 1.15 ng/g dw. Among five lake regions, average PFAS concentrations for the lakes from Eastern Plain Region were the highest. Perfluorooctanoic acid, perfluoroundecanoic acid and perfluorooctane sulfonic acid (PFOS) were the predominant PFASs in surface sediments. The significant positive correlations between PFAS concentrations and total organic carbon, total nitrogen and total phosphorus contents in sediments revealed the influences of sedimentary characteristics on PFAS occurrence. A two-dimensional hierarchical cluster analysis heat map was depicted to analyze the possible origins of sediments and individual PFAS. The food-packaging, textile, electroplating, firefighting and semiconductor industry emission sources and the precious metals and coating industry emission sources were identified as the main sources by two receptor models, with contributions of 77.7 and 22.3% to the total concentrations of C4-C14- perfluoroalkyl carboxylic acids and PFOS, respectively.
Storage Mining: Where IT Management Meets Big Data Analytics (2013)

The emerging paradigm shift to cloud based data center infrastructures imposes remarkable challenges to IT management operations, e.g., due to virtualization techniques and more stringent requirements for cost and efficiency. On one hand, the voluminous data generated by daily IT operations such as logs and performance measurements contain abundant information and insights which can be leveraged to assist the IT management. On the other hand, traditional IT management solutions cannot consume and exploit the rich information contained in the data due to the daunting volume, velocity, variety, as well as the lack of scalable data mining and machine learning frameworks to extract insights from such raw data. In this paper, we present our on-going research thrust of designing novel IT management solutions by leveraging big data analytics frameworks. As an example, we introduce our project of Storage Mining, which exploits big data analytics techniques to facilitate storage cloud management. The challenges are discussed and our proof-of-concept big data analytics framework is presented.
Interferon‐inducible expression of APOBEC3 editing enzymes in human hepatocytes and inhibition of hepatitis B virus replication† (2006)

Hypermutations in hepatitis B virus (HBV) DNA by APOBEC3 cytidine deaminases have been detected in vitro and in vivo, and APOBEC3G (A3G) and APOBEC3F (A3F) have been shown to inhibit the replication of HBV in vitro, but the presumably low or even absent hepatic expression of these enzymes has raised the question as to their physiological impact on HBV replication. We show that normal human liver expresses the mRNAs of APOBEC3B (A3B), APOBEC3C (A3C), A3F, and A3G. In primary human hepatocytes, interferon alpha (IFN-alpha) stimulated the expression of these cytidine deaminases up to 14-fold, and the mRNAs of A3G, A3F, and A3B reached expression levels of 10%, 3%, and 3%, respectively, relative to GAPDH mRNA abundance. On transfection, the full-length protein A3B(L) inhibited HBV replication in vitro as efficiently as A3G or A3F, whereas the truncated splice variant A3B(S) and A3C had no effect. A3B(L) and A3B(S) were detected predominantly in the nucleus of uninfected cells; however, in HBV-expressing cells both proteins were found also in the cytoplasm and were associated with HBV viral particles, similarly to A3G and A3F. Moreover, A3G, A3F, and A3B(L), but not A3B(S), induced extensive G-to-A hypermutations in a fraction of the replicated HBV genomes. In conclusion, the editing enzymes A3B(L), A3F, and most markedly A3G, which are expressed in liver and up-regulated by IFN-alpha in hepatocytes, are candidates to contribute to the noncytolytic clearance of HBV.
Nonlinear internal model controller design for wastegate control of a turbocharged gasoline engine (2014)

This work investigates the design of nonlinear internal model control (IMC) for wastegate control of a turbocharged gasoline engine. We extend the inverse-based IMC design for linear time-invariant (LTI) systems to nonlinear systems. To leverage the available tools for LTI IMC deign, we have explored the quasi linear parameter varying (quasi-LPV) model. IMC design through transfer function inverse of the quasi-LPV model is ruled out due to parameter variability. A new approach for nonlinear inverse, referred to as the structured quasi-LPV model inverse, is developed and validated. A fourth-order nonlinear model which sufficiently describes the dynamic behavior of the turbocharged engine is implemented to serve as the model in the IMC structure. The controller based on structured quasi-LPV model inverse is designed to achieve boost pressure tracking. Finally, simulations on a validated high fidelity model are carried out to show the feasibility of the IMC. Its closed-loop performance and robustness are compared with a well-tuned PI controller with extensive feedforward and anti-windup built in.
Front Matter: Volume 7210 (2009)

This PDF file contains the front matter associated with SPIE Proceedings Volume 7210, including the Title Page, Copyright information, Table of Contents, Introduction, and Conference Committee listing.
Nitroxyl-mediated electrooxidation of alcohols to aldehydes and ketones (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNitroxyl-mediated electrooxidation of alcohols to aldehydes and ketonesM. F. Semmelhack, Chuen S. Chou, and David A. CortesCite this: J. Am. Chem. Soc. 1983, 105, 13, 4492–4494Publication Date (Print):June 1, 1983Publication History Published online1 May 2002Published inissue 1 June 1983https://doi.org/10.1021/ja00351a070RIGHTS & PERMISSIONSArticle Views2469Altmetric-Citations258LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (448 KB) Get e-Alerts Get e-Alerts
Pathophysiology for the boards and wards : a review for USMLE step 1 (2000)

1. Neurology > 2. Head and Neck > 3. Cardiovascular > 4. Pulmonary > 5. Breast > 6. Gastroenterology and Liver > 7. Nephrology > 8. Genitourinary > 9. Endocrinology > 10. Musculoskeletal > 11. Hematology > 12. Dermatology > Appendices > A. Basic Neurology Review > B. Zebras and Syndromes > C. Basic Immunology Review > D. Toxicology > E. Pearls > F. Vitamins.
Experimental investigation of the relationship between thermal barrier coating structured porosity and homogeneous charge compression ignition engine combustion (2019)

Heat transfer has a profound influence on homogeneous charge compression ignition combustion. When a thermal barrier coating is applied to the combustion chamber, the insulating effect magnifies the wall temperature swing, decreasing heat transfer during combustion. This enables improvements in both thermal and combustion efficiency without the detrimental impacts of intake charge heating. Increasing the temperature swing requires coatings with lower thermal conductivity and heat capacity. A promising avenue for simultaneously decreasing both thermal conductivity and capacity is to increase the porosity fraction. A proprietary solution precursor plasma spray process enables discrete organization of the porosity structure, called inter-pass boundaries, which in turn produces a step-reduction in thermal conductivity for a given porosity level. In this investigation, yttria-stabilized zirconia is used to create four different thermal barrier coatings to study the potential of structured porosity as means of improving the “temperature swing” behavior in a homogeneous charge compression ignition engine. The baseline coating is “dense YSZ,” applied using a standard air-plasma spray process. Next, significant reductions of the thermal conductivity are achieved by utilizing the solution precursor plasma spray process to create inter-pass boundaries with a moderate overall porosity. Performance, efficiency, and emissions are compared against both a baseline configuration with a metal piston and an air-plasma spray “dense YSZ” coating. Experiments are carried out in a single-cylinder gasoline homogeneous charge compression ignition engine with exhaust re-induction. Experiments indicate that incorporating structured porosity into thermal barrier coatings produces tangible gains in combustion and thermal efficiencies. However, there is an upper limit to porosity levels acceptable for homogeneous charge compression ignition engine application because an elevated porosity fraction leads to excessive surface roughness and undesirable fuel interactions. Comparison of the coatings showed the best results with coating thickness of up to 150 µm. Thicker coatings led to slower surface temperature response and attenuated swing temperature magnitude.