gebhart/patrepeval huggingface dataset:
US Backscatter for Liver Fat Quantification: An AIUM-RSNA QIBA Pulse-Echo Quantitative Ultrasound Initiative (2022)

Nonalcoholic fatty liver disease (NAFLD) is believed to affect one-third of American adults. Noninvasive methods that enable detection and monitoring of NAFLD have the potential for great public health benefits. Because of its low cost, portability, and noninvasiveness, US is an attractive alternative to both biopsy and MRI in the assessment of liver steatosis. NAFLD is qualitatively associated with enhanced B-mode US echogenicity, but visual measures of B-mode echogenicity are negatively affected by interobserver variability. Alternatively, quantitative backscatter parameters, including the hepatorenal index and backscatter coefficient, are being investigated with the goal of improving US-based characterization of NAFLD. The American Institute of Ultrasound in Medicine and Radiological Society of North America Quantitative Imaging Biomarkers Alliance are working to standardize US acquisition protocols and data analysis methods to improve the diagnostic performance of the backscatter coefficient in liver fat assessment. This review article explains the science and clinical evidence underlying backscatter for liver fat assessment. Recommendations for data collection are discussed, with the aim of minimizing potential confounding effects associated with technical and biologic variables.
Supplementary Table S8 from Cancers as Wounds that Do Not Heal: Differences and Similarities between Renal Regeneration/Repair and Renal Cell Carcinoma (2023)

Supplementary Table S8 from Cancers as Wounds that Do Not Heal: Differences and Similarities between Renal Regeneration/Repair and Renal Cell Carcinoma
Short Peptide Induces an “Uncultivable” Microorganism To Grow In Vitro (2008)

Microorganisms comprise the bulk of biodiversity, but only a small fraction of this diversity grows on artificial media. This phenomenon was noticed almost a century ago, repeatedly confirmed, and termed the "great plate count anomaly." Advances in microbial cultivation improved microbial recovery but failed to explain why most microbial species do not grow in vitro. Here we show that at least some of such species can form domesticated variants capable of growth on artificial media. We also present evidence that small signaling molecules, such as short peptides, may be essential factors in initiating growth of nongrowing cells. We identified one 5-amino-acid peptide, LQPEV, that at 3.5 nM induces the otherwise "uncultivable" strain Psychrobacter sp. strain MSC33 to grow on standard media. This demonstrates that the restriction preventing microbial in vitro growth may be different from those offered to date to explain the "great plate count anomaly," such as deficiencies in nutrient composition and concentrations in standard media, medium toxicity, and inappropriate incubation time. Growth induction of MSC33 illustrates that some microorganisms do not grow in vitro because they are removed from their native communities and the signals produced therein. "Uncultivable" species represent the largest source of unexplored biodiversity, and provide remarkable opportunities for both basic and applied research. Access to cultures of some of these species should be possible through identification of the signaling compounds necessary for growth, their addition to standard medium formulations, and eventual domestication.
Cripto-1: an extracellular protein – connecting the sequestered biological dots (2015)

Cripto-1 (CR-1) is a multifunctional embryonic protein that is re-expressed during inflammation, wound repair, and malignant transformation. CR-1 can function either as a tethered co-receptor or shed as a free ligand underpinning its flexible role in cell physiology. CR-1 has been shown to mediate cell growth, migration, invasion, and induce epithelial to mesenchymal transition (EMT). The main signaling pathways mediating CR-1 effects include Nodal-dependent (Smad2/3) and Nodal-independent (Src/p44/42/Akt) signaling transduction pathways. In addition, there are several naturally occurring binding partner proteins (BPPs) for CR-1 that can either agonize or antagonize its bioactivity. We will review the collective role of CR-1 as an extracellular protein, discuss caveats to consider in developing a quantitation assay, define possible mechanistic avenues applicable for drug discovery, and report on our experimental approaches to overcome these problematic issues.
Clozapine—lithium combined treatment and agranulocytosis (1993)

A case report of clozapine-induced agranulocytosis in a patient treated concomitantly with lithium is reported. The possible role of lithium in the mechanism of clozapine myelosuppression is discussed.
One-Pot Formal Dehydrogenative Ketone Synthesis from Aldehydes and Non-activated Hydrocarbons (2020)

Ketones are a fundamental functionality found throughout a range of natural and synthetic compounds, making their synthesis essential throughout the chemical disciplines. Herein, we describe a one-pot synthesis of ketones via decatungstate-mediated formal dehydrogenative coupling between aldehydes and non-activated hydrocarbons. A variety of substituted benzaldehydes and cycloalkanes could be used in the optimized reaction to produce the desired ketones in moderate yields. The decatungstate photocatalyst functions in two reactions in this synthesis, catalyzing both the coupling and oxidation steps of the process. Notably, the reaction displays both high atom economy and sustainability, as it uses light and oxygen as key energy sources.
Scintigraphic images of tumor-bearing mice 24 hours post-injection with: a) CasKi tumor, E6-specific mAb <sup>188</sup>Re-C1P5 mAb; b) CasKi tumor, control <sup>188</sup>Re-18B7 mAb; c) Hep 3B2.1-7 and A2058 human metastatic melanoma tumors, HBx-specific <sup>188</sup>Re-4H9 mAb. (2015)

&lt;p&gt;Scintigraphic images of tumor-bearing mice 24 hours post-injection with: a) CasKi tumor, E6-specific mAb &lt;sup&gt;188&lt;/sup&gt;Re-C1P5 mAb; b) CasKi tumor, control &lt;sup&gt;188&lt;/sup&gt;Re-18B7 mAb; c) Hep 3B2.1-7 and A2058 human metastatic melanoma tumors, HBx-specific &lt;sup&gt;188&lt;/sup&gt;Re-4H9 mAb.&lt;/p&gt;
Urinary microRNA-1913 to microRNA-3659 expression ratio as a non-invasive diagnostic biomarker for prostate cancer (2021)

The urinary miR-1913 to miR-3659 expression ratio was increased in PCa and may serve as a useful supplemental biomarker to PSA for the diagnosis of PCa, particularly in patients within the PSA gray zone.
Offline recognition of handwritten Chinese characters using Gabor features, CDHMM modeling and MCE training (2002)

We've been developing a Chinese OCR engine for handwritten Chinese scripts. Currently, our OCR engine supports a vocabulary of 4616 characters which include 4516 simplified Chinese characters in GB2312-80, 62 alphanumeric characters, 38 punctuation marks and symbols. By using 1,384,800 character samples to train our recognizer, an averaged character recognition accuracy of 96.34% is achieved on a testing set of 1,025,535 character samples. An arguably best Chinese OCR product on the market achieves an accuracy of 94.07% for the recognizable Chinese characters in the above testing set. In this paper, we describe key techniques used in our recognizer that contribute to the high recognition accuracy, namely the use of Gabor features and their spatial derivatives as raw features, the use of LDA for feature extraction and dimension reduction, the use of CDHMMs for modeling Chinese characters along both horizontal and vertical directions, and the use of minimum classification error as a criterion for model training.
A new polymorphic probe on chromosome 3p: LIB46-95(D3S620) (1991)

XLIB46-95(D3S620) is a 1.4 kb EcoRI fragment isolated from a Charon 21A human chromosome 3 library (1). Polymorphism: TaqI digestion of genomic DNA and hybridization with the probe detects a two-allele polymorphism: 3.6 kb (Ti) and 3.4 kb (T2). Frequency: Estimated from 30 unrelated Caucasians. T1 :0.42 T2:0.58 Frequency of heterozygosity: 0.49 Not Polymorphic For: BamHI, BglII, DraI, EcoRI, HindIII, Hinfi, MspI, PvuI and RsaI. Chromosomal Localization: Using a somatic cell hybrid panel (2) which was based on linkage groups anchored to physically localized markers, the probe was assigned to the short arm of chromosome 3 between 3p24-3p26. Mendelian Inheritance: Mendelian inheritance has been demonstrated in a two generation von Hippel-Lindau disease (VHL) family. Probe
Electroluminescent, Polycrystalline Cadmium Selenide Nanowire Arrays (2013)

Electroluminescence (EL) from nanocrystalline CdSe (nc-CdSe) nanowire arrays is reported. The n-type, nc-CdSe nanowires, 400-450 nm in width and 60 nm in thickness, were synthesized using lithographically patterned nanowire electrodeposition, and metal-semiconductor-metal (M-S-M) devices were prepared by the evaporation of two gold contacts spaced by either 0.6 or 5 μm. These M-S-M devices showed symmetrical current voltage curves characterized by currents that increased exponentially with applied voltage bias. As the applied biased was increased, an increasing number of nanowires within the array "turned on", culminating in EL emission from 30 to 50% of these nanowires at applied voltages of 25-30 V. The spectrum of the emitted light was broad and centered at 770 nm, close to the 1.74 eV (712 nm) band gap of CdSe. EL light emission occurred with an external quantum efficiency of 4 × 10(-6) for devices with a 0.60 μm gap between the gold contacts and 0.5 × 10(-6) for a 5 μm gap-values similar to those reported for M-S-M devices constructed from single-crystalline CdSe nanowires. Kelvin probe force microscopy of 5 μm nc-CdSe nanowire arrays showed pronounced electric fields at the gold electrical contacts, coinciding with the location of strongest EL light emission in these devices. This electric field is implicated in the Poole-Frenkel minority carrier emission and recombination mechanism proposed to account for EL light emission in most of the devices that were investigated.
Experiments with multi-protocol RMI in Java (2002)

Remote Method Invocation is an adaptation of the remote procedure call paradigm for object-oriented environments. RMI allows clients to seamlessly invoke methods of objects within remote servers. Communication between the client and server is based upon an agreed protocol stack that defines connection management rules, message formats, and data encoding.There are numerous communication libraries for Java that enable remote method invocations over different wire protocols. Standard Java RMI is based on the Java Remote Method Protocol, JRMP. RMI-IIOP [6] is alternative implementation that enables connectivity with legacy CORBA systems. JAX-RPC [5] provides means to invoke methods via SOAP, making it possible to interact with Web Services. Also, many alternative RMI implementations have been developed in order to overcome standard Java RMI and JRMP performance issues [3, 1, 2]. The common drawback of these libraries is that they are designed to be used exclusively (e.g. they usually bind clients to a particular wire protocol via stubs generated at compile time) and they do not interoperate well.RMIX is a meta-RMI framework that, rather than itself providing communication capabilities, defines a common facade through which variety of wire protocols may be used in a uniform way. Concrete protocols are supported by independent, dynamically pluggable modules, i.e. protocol service providers. Such an approach permits removal of the dependence of distributed applications on particular communication protocols: at the server side, remote objects may be uniformly exported over various protocols; at the client side, the need for statically generated stub classes is eliminated.Some projected usage scenarios of RMIX include: (1) loosely coupled distributed systems with peer-to-peer protocol negotiation (dynamic discovery is especially beneficial in this case as it makes it possible to add or upgrade protocol providers at run-time); (2) applications that are multi-protocol by nature (e.g. distributed scientific applications that communicate using an efficient native protocol but offer SOAP endpoints for monitoring and control purposes); (3) standard Java RMI applications ported to RMIX in order to eliminate the burden associated with generation and distribution of stub classes.Currently, RMIX offers two concrete protocol providers: RMIX-JRMPX, a lightweight layer over standard Java RMI, and RMIX-XSOAP, based on XSOAP [4] and using SOAP 1.1 as its wire protocol.In addition to multiple protocol support, RMIX offer other enhancements such as customizable remote object endpoints, and asynchronous invocation mode. More information about RMIX can be found at http://www.mathcs.emory.edu/rmix/.
Cleaved high molecular weight kininogen binds directly to the integrin CD11b/CD18 (Mac-1) and blocks adhesion to fibrinogen and ICAM-1 (2000)

High molecular weight kininogen (HK) and its cleaved form (HKa) have been shown to bind to neutrophils. Based on studies using monoclonal antibodies (mAbs), we postulated that CD11b/CD18 (Mac-1) might be the receptor on the neutrophils for binding to HK/HKa. However, the direct interaction of HK/HKa and Mac-1 had not been demonstrated. We therefore transfected HEK 293 cells with human Mac-1. Cell binding assays using fluorescein isothiocyanate-labeled HKa showed increased binding to the Mac-1 transfected cells compared with the control transfected cells. The binding was specific because unlabeled HKa, Mac-1-specific antibody, and fibrinogen can inhibit the binding of biotin-HKa to Mac-1 transfected cells. HKa bound to Mac-1 transfected cells (20 000 molecules/cell) with a K(d) = 62 nmol/L. To demonstrate directly the formation of a complex between HKa and Mac-1, we examined the interaction of HKa and purified Mac-1 in a cell-free system using an IAsys resonant mirror optical biosensor. The association and dissociation rate constants (k(on) and k(off), respectively) were determined, and they yielded a dissociation constant (K(d)) of 3.2x10(-9) mol/L. The functional significance of direct interaction of HKa to Mac-1 was investigated by examining the effect of HKa on cellular adhesion to fibrinogen and intercellular adhesion molecule-1 (ICAM-1), molecules abundant in the injured vessel wall. HKa blocked the adhesion of Mac-1 transfected cells to fibrinogen and ICAM-1 in a dose-dependent manner. Thus, HKa may interrupt Mac-1-mediated cell-extracellular matrix and cell-cell adhesive interactions and may therefore influence the recruitment of circulating neutrophils/monocytes to sites of vessel injury. (Blood. 2000;95:3788-3795)
Microfluidic generation of tunable emulsions for templated monodisperse silica (2005)

This paper describes a new approach to the formation of macroporous silica, templated using emulsions generated in a microfluidic device. With precise control over the size and uniformity of the emulsion droplets, we are able to tailor the pore size and size distribution of the resulting bulk silica gels. Using triethylenetetramine as a biomimetic catalyst, our gelation reactions occur within minutes at room temperature and neutral pH, in contrast to conventional sol-gel routes. Subsequent drying at 50/spl deg/C and calcining at 400/spl deg/C yields glassy materials with spherical pores where the emulsion droplets had been. Monodisperse porous silica with a range of pore sizes from 5-50 /spl mu/m and polydispersity less than 2.4% has been fabricated. Such materials may be produced in situ within lab-on-a-chip systems and functionalized for use in reaction and separation modules.
A proteomic study of resistance to deoxycholate-induced apoptosis (2004)

The development of apoptosis resistance appears to be an important factor in colon carcinogenesis. To gain an understanding of the molecular pathways altered during the development of apoptosis resistance, we selected three cell lines for resistance to induction of apoptosis by deoxycholate, an important etiologic agent in colon cancer. We then evaluated gene expression levels for 825 proteins in these resistant lines, compared with a parallel control line not subject to selection. Eighty-two proteins were identified as either over-expressed or under-expressed in at least two of the resistant lines, compared with the control. Thirty-five of the 82 proteins (43%) proved to have a known role in apoptosis. Of these 35 proteins, 21 were over-expressed and 14 were under-expressed. Of those that were over-expressed 18 of 21 (86%) are anti-apoptotic in some circumstances, of those that were under-expressed 11 of 14 (79%) are pro-apoptotic in some circumstances. This finding suggests that apoptosis resistance during selection among cultured cells, and possibly in the colon during progression to cancer, may arise by constitutive over-expression of multiple anti-apoptotic proteins and under-expression of multiple pro-apoptotic proteins. The major functional groups in which altered expression levels were found are post-translational modification (19 proteins), cell structure (cytoskeleton, microtubule, actin, etc.) (17 proteins), regulatory processes (11 proteins) and DNA repair and cell cycle checkpoint mechanisms (10 proteins). Our findings, overall, bear on mechanisms by which apoptosis resistance arises during progression to colon cancer and suggest potential targets for cancer treatment. In addition, assays of normal-appearing mucosa of colon cancer patients, for over- or under-expression of genes found to be altered in our resistant cell lines, may allow identification of early biomarkers of colon cancer risk.
Synthesis and Characterization of Palladium(II) and Nickel(II) Alcoholate-Functionalized NHC Complexes and of Mixed Nickel(II)–Lithium(I) Complexes (2014)

The synthesis of Pd(II) and Ni(II) alcohol-functionalized N-heterocyclic carbene (NHC) complexes was explored to examine the possible influence of the functional arm attached to the NHC backbone on their structure and reactivity and, in the case of a Ni(II) complex, on its catalytic properties in ethylene oligomerization. Starting from the alcohol-functionalized imidazolium salt [ImDiPP(C2OH)]Cl (2), the new functionalized NHC palladium(II) complex [PdCl(acac){ImDiPP(C2OH)-CNHC}] (3) was synthesized and fully characterized. Two byproducts, [PdCl{μ-ImDiPP(C2O)-CNHC,O}]2 (4) and trans-[PdCl2{ImDiPP(C2OH)-CNHC}2] (5), formed during the synthesis of 3, were also fully characterized. Acids promoted the transformation of 3 into the new CNHC-bound complex [PdCl(μ-Cl){ImDiPP(C2OH)-CNHC}]2 (6), unveiling the lability of the acac ligand and the resistance of the Pd-NHC bond to acids. Complex 6 reacted with a base to afford complex 4, in which alkoxide coordination to Pd(II) has occurred to generate a CNHC,O chelate. The stability of 3 was also assessed under basic conditions, and the new complex [Pd(acac){ImDiPP(C2O)-CNHC,O}] (7) was characterized. The new nickel(II) alcoholate-functionalized NHC complex [NiCl{μ-ImDiPP(C2O)-CNHC,O}]2 (8) was synthesized by the reaction of the imidazolium salt 2 with n-BuLi and [NiCl2(dme)]. The reaction of 8 with HCl regenerates the imidazolium and alcohol functions to give [ImDiPP(C2OH)]2[NiCl4] (9). The mixed-metal Ni(II)-Li(I) complexes [Ni2{μ-ImDiPP(C2O)-CNHC,μ-O}4Li]BF4 (10), [Ni2{μ-ImDiPP(C2O)-CNHC,μ-O}4Li]Cl (11), and [Ni{ImDiPP(C2O)-CNHC,μ-O}2LiBr] (12) were isolated and characterized. However, it was not possible to synthesize a Ni(II) alcohol-functionalized NHC complex in high yield. Small amounts of the square-planar complex [NiCl2{ImDiPP(C2OH)-CNHC}2] (13) could be isolated, and this complex was characterized by single-crystal X-ray diffraction. In 13, only the CNHC atom of the alcohol-functionalized NHC ligand is bound to the metal. The structures of the imidazolium salt 2·2H2O and of the complexes 3, 4, 4-polymorph, 5, 6·CH2Cl2, and 8-13 were established by single-crystal X-ray diffraction.
Impact of nonlinear pump interactions on broadband distributed Raman amplification (2001)

Broadband distributed Raman amplification is helpful in multi-terabit transmission experiments requiring high and flat gains over a wide spectral window. We show that nonlinear pump interactions can severely degrade amplifier performance at high pump powers.
An Automated Statistical Technique for Counting Distinct Multiple Sclerosis Lesions (2018)

This study introduces a novel technique for counting pathologically distinct lesions using cross-sectional data and demonstrates its ability to recover obscured longitudinal information. The proposed count allows more accurate estimation of lesion size, which correlated more closely with disability scores than either lesion load or lesion count alone.
Lipid interaction of diphtheria toxin and mutants with altered fragment B (1987)

The interaction of diphtheria toxin and its cross-reacting mutants crm 45,228 and 1001 with small unilamellar vesicles has been followed by a turbidity assay, electron microscopy, fluorescence energy transfer and membrane permeability. All toxins at pH lower than 6 induce the aggregation and fusion of liposomes containing negatively charged phospholipids; crm 45 and crm 1001 are less potent than diphtheria toxin. Isolated diphtheria toxin fragment B is very effective while isolated fragment A is ineffective. Liposome fusion induced by the toxins at low pH occurs without release of the internal content implying that fusion does not involve vesicle breakage and resealing. The pH dependence of the membrane interaction of diphtheria toxin monitored by turbidity is in close agreement with that monitored by fluorescence energy transfer. It shows that diphtheria toxin can alter the lipid bilayer structure in the pH interval 5-6. This pH range occurs in endosomes and suggests that histidyl and carboxyl residues are likely to be involved in the conformational change of diphtheria toxin triggered by acidic pH.
Switching ruggedness of high-power diodes (2005)

The ruggedness of high-power diodes is an important quality feature in fast-switching processes from the conducting to the blocking state. In this paper, diodes with three different types of junction terminations are analyzed in detail by numerical simulations. Furthermore, the influence of positive charges in the dielectric layer covering the junction termination, and the local reduction of the charge carrier lifetime on diode ruggedness is investigated.
Use of GSO for inelastic gamma-ray spectroscopy measurements in the borehole (1992)

Gadolinium oxyorthosilicate (GSO) with its high density, high effective Z, fast decay time and good performance at high temperature, is the scintillation detector of choice for a new generation of neutron-induced, inelastic gamma-ray spectroscopy tools for borehole measurements, specifically aimed at measuring the carbon and oxygen content from the region surrounding the borehole. The ratio of the carbon and oxygen gamma-ray yields are transformed into formation oil saturation. To get the maximum benefit from GSO, the data acquisition, choice of materials, and measurement geometry were optimized for a small diameter tool at elevated temperatures and crystal characteristics. The large neutron cross section of the gadolinium in the scintillation crystal, its second decay constant, and the desired precision of the oil saturation measurement had important consequences in the tool design.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>