gebhart/patrepeval huggingface dataset:
Knock-down-knock-in assay of H1299 cells conditionally expressing wt WDR12, wt Pes1 and the indicated BRCT-domain mutants of Pes1 (2011)

<b>Copyright information:</b>Taken from "The BRCT domain of mammalian Pes1 is crucial for nucleolar localization and rRNA processing"Nucleic Acids Research 2006;35(3):789-800.Published online 22 Dec 2006PMCID:PMC1807956.© 2006 The Author(s) Experimental procedure was performed as summarized in . () Metabolic labelling of nascent rRNA. Cells were incubated in phosphate-free medium for 30 min, labelled with P-orthophosphate for 1 h and subsequently cultured in regular medium for 4.5 h. Total RNA was separated by formaldehyde-agarose gel electrophoresis. The gel was dried before autoradiography. The ethidium bromide stained gel is shown as loading control. () Expression of recombinant wt WDR12, wt or mutant Pes1 proteins was analysed using the anti-HA antibody (3F10). Efficient knock-down of endogenous Pes1 by siRNA was verified with the anti-Pes1 antibody (8E9). Equal loading was verified by immunodetection of α-tubulin.
Self-Sensing and Power Conversion Comparison for Flux Weakening Surface Mounted Permanent Magnet Servo Motors Designed using Symmetric and Asymmetric Rotors (2019)

Servo motors are widely used in automation and industrial robots. These motors achieve high dynamic performance with high peak torque and acceleration rates. Flux Weakening Surface mounted Permanent Magnet Synchronous Motors (FW-SPMSMs) which are known as SPMSMs can be used in servo application. They are designed to achieve very low ripple and cogging torque to enable precise speed and position control. This can be done by shaping the magnet to achieve low airgap flux harmonics or through using shifted ring magnets with asymmetric rotor structures to cancel the airgap flux harmonics. Standard SPMSMs are not suitable for injection-based self-sensing control due to low saliencies. Many techniques have been reported in the literature to design slightly salient SPMSMs. In this paper, two SPMSMs for servo applications are designed, one using bread-loaf magnets and another with shifted ring magnets. The power conversion performance and the injection-based self-sensing properties will be fairly compared for both designs, pros and cons for each design will be highlighted.
A Detailed Simulation Model of the HP 97560 Disk Drive (1994)

We implemented a detailed model of the HP 97560 disk drive, to replicate a model devised by Ruemmler and Wilkes (both of Hewlett-Packard, HP). Our model simulates one or more disk drives attached to one or more SCSI buses. The design is broken into three components: a test driver, the disk model itself, and the discrete-event simulation support. Thus, the disk model can be easily extracted and used in other simulation environments. We validated our model using traces obtained from HP, using the same &amp;quot;demerit&amp;quot; measure as Ruemmler and Wilkes. We obtained a demerit percentage of 3.9%, indicating that our model was extremely accurate. This paper describes our implementation, and is meant for those wishing to use our model, see our validation, or understand our code. 1 Introduction A recent paper by Ruemmler and Wilkes [RW94] describes the HP 97560 disk drive in detail, their model of the disk, and general techniques for modeling disks. We implemented our own version of the model. Our mode...
Studies on the Synthesis of Phlegmarine-Type Lycopodium Alkaloids: Enantioselective Synthesis of (−)-Cermizine B, (+)-Serratezomine E, and (+)-Luciduline (2018)

The synthesis of the Lycopodium alkaloids, (-)-cermizine B, (+)-serratezomine E, and (+)-luciduline using phenylglycinol-derived tricyclic lactams as chiral scaffolds, is reported. The requisite lactams are prepared by a cyclocondensation reaction between ( R)- or ( S)-phenylglycinol and the substituted δ-keto ester 11, easily accessible from ( R)-pulegone. The factors governing the stereoselectivity of these cyclocondensation reactions are discussed. Key steps of the synthesis from the stereochemical standpoint are the stereoselective elaboration of the allyl substituent to the ( S)-2-(piperidyl)methyl moiety and the stereoselective removal of the chiral inductor to give a cis-decahydroquinoline.
Activation of CXCR2 by Extracellular Matrix Degradation Product Acetylated Pro-Gly-Pro Has Therapeutic Effects against Sepsis (2011)

CXCR2 and Ac-PGP are thus novel target and starting molecules, respectively, for the development of therapeutic agents against sepsis.
Halftone Processing In The Xerox 7650 Image Scanner (1989)

A review of the halftone processing techniques used in the Xerox 7650 Pro Imager document scanner is presented. The halftone processing techniques which are necessary for high quality, continuous tone document scanners to function in lithographic, xerographic and similar graphic arts environments are described. These processing techniques include image histogram manipulation, electronic screening, halftone removal and image enhancement. A method of automatic contrast adjustment which compensates for low contrast continuous tone or colored background images is shown. The need for programmable halftone generation to adapt to a wide variety of printer reproduction characteristics is discussed. A programmable halftone removal technique, and its application to halftoned pictorials, is addressed from a practical perspective. This discussion focuses particularly on the problem of the moire encountered when applying halftone patterns to scanned images which contain halftone pictorials themselves. Utilizing several example images, it is shown that by combining the described halftone image processing techniques available in the 7650 scanner, high quality, hardcopy images can be obtained on a variety of high contrast printers from a variety of continuous tone and halftone input documents.
The Caudal-related homeodomain protein CDX1 activates proliferating cell nuclear antigen expression in hepatocellular and colorectal carcinoma cells (2002)

Cdx1 and Cdx2 are known as Caudal-related homeodomain transcription factors important in the early differentiation and maintenance of intestinal epithelial cells. Cdx1 and Cdx2 are expressed in the small intestine and colon of fetus and adult. Most previous studies suggested that Cdx2 inhibits proliferation. Several target genes of Cdx2 have been identified. However, the effect of Cdx1 on cell proliferation is currently controversial and its target genes except for Hox-A7 remain unknown. In this study, we found several potential Caudal-related homeodomain binding sequences in the 5'-flanking region of human PCNA gene. Cotransfection experiments, using human PCNA reporter plasmid and CDX1 and CDX2 expression plasmids, showed that CDX1 transactivates human PCNA gene promoter activity in hepatocellular cell line (HepG2) and colorectal carcinoma cell lines (Colo320HSR and HCT116), while CDX2 does not. CDX1-induced PCNA expression was also detected in immunoblot and cytochemistry experiments. In BrdU incorporation experiments, CDX1 enhanced the incorporated BrdU. Taken together, our results suggest that CDX1 have a pro-proliferative effect on proliferation through transactivation of PCNA promoter activity.
Salt gradient and ion-pair mediated anion exchange of intact messenger ribonucleic acids (2022)

Small molecule drugs and protein-based therapeutics are widely used to treat various diseases, yet even more aspects of human health can be addressed through new modalities, like messenger RNA (mRNA). The complex nature and chemical structure of an mRNA molecule will require the development of new analytical methods. In this work, we propose the use of ion exchange and relatively mild elution conditions as the basis for alternative analytical methods. We have found that a gradient of weak ion-pairing cations can produce intriguing AEX separations of mRNA. This so-called ion pairing anion exchange “IPAX” method provides different recovery and selectivity effects compared to classical sodium chloride salt gradients. We have also shown there to be value in combining the use of an ion-pairing agent as a mobile phase additive along with the implementation of a classical salt gradient. It might be most appropriate to refer to this separation technique as an “ion-pairing mediated salt gradient”. The column temperature has been found to be a very important factor that should be applied to test for effects on various chromatographic values and to learn about an mRNA molecule while confirming its optimal separation conditions. In a classical salt gradient separation, relatively low temperatures (T = 30–40 °C) resulted in better recoveries while in the IPAX separation, higher temperatures up to 60 °C seemed to be more beneficial. An ion-pairing mediated salt gradient appeared to be best matched to temperatures between 30 and 45 °C. Plotting van't Hoff data has also elucidated new information and that a classical salt gradient seems to be an entropy driven process, while the IPAX separation seems to be more complex. It exhibits an entropy driven process at lower temperatures and then an enthalpy controlled one at higher temperatures.
Abstract IA24: Molecular imaging agents for prostate cancer: Focus on PSMA (2012)

Abstract Although most clinical diagnostic imaging studies employ anatomic techniques such as computed tomography and magnetic resonance imaging, much of radiology research currently focuses on adapting these conventional methods to physiologic imaging as well as on introducing new techniques and probes for studying processes at the cellular and molecular levels in vivo, i.e. molecular imaging. Molecular imaging promises to provide new methods for the detection of minimal disease and support for personalized therapy. This summary will focus on experimental and near-term translational molecular imaging agents and methods for prostate cancer, with a focus on radiopharmaceuticals and optical agents, the former primarily for staging and the latter for surgical guidance. Citation Format: Martin G. Pomper. Molecular imaging agents for prostate cancer: Focus on PSMA [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr IA24.
Optical lattice clocks with non-interacting bosons and fermions (2008)

We discuss configurations of optical lattice clocks from the viewpoint of lattice geometries and quantum statistics of interrogated atoms. This leads to two promising schemes; one-dimensional lattice loaded with spin-polarized fermions and three-dimensional lattice loaded with bosons. These two optical lattice clocks based on fermionic <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">87</sup> Sr and bosonic <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">88</sup> Sr were demonstrated by measuring the frequency stability as well as their isotope shift. In addition, we address our ongoing experimental challenges for optical lattice clocks.
LED induced autofluorescence (LIAF) imager with eight multi-filters for oral cancer diagnosis (2016)

Oral cancer is one of the serious and growing problem in many developing and developed countries. The simple oral visual screening by clinician can reduce 37,000 oral cancer deaths annually worldwide. However, the conventional oral examination with the visual inspection and the palpation of oral lesions is not an objective and reliable approach for oral cancer diagnosis, and it may cause the delayed hospital treatment for the patients of oral cancer or leads to the oral cancer out of control in the late stage. Therefore, a device for oral cancer detection are developed for early diagnosis and treatment. A portable LED Induced autofluorescence (LIAF) imager is developed by our group. It contained the multiple wavelength of LED excitation light and the rotary filter ring of eight channels to capture ex-vivo oral tissue autofluorescence images. The advantages of LIAF imager compared to other devices for oral cancer diagnosis are that LIAF imager has a probe of L shape for fixing the object distance, protecting the effect of ambient light, and observing the blind spot in the deep port between the gumsgingiva and the lining of the mouth. Besides, the multiple excitation of LED light source can induce multiple autofluorescence, and LIAF imager with the rotary filter ring of eight channels can detect the spectral images of multiple narrow bands. The prototype of a portable LIAF imager is applied in the clinical trials for some cases in Taiwan, and the images of the clinical trial with the specific excitation show the significant differences between normal tissue and oral tissue under these cases.
Parametric-Rate Inference for One-Sided Differentiable Parameters (2017)

Suppose one has a collection of parameters indexed by a (possibly infinite dimensional) set. Given data generated from some distribution, the objective is to estimate the maximal parameter in this collection evaluated at the distribution that generated the data. This estimation problem is typically non-regular when the maximizing parameter is non-unique, and as a result standard asymptotic techniques generally fail in this case. We present a technique for developing parametric-rate confidence intervals for the quantity of interest in these non-regular settings. We show that our estimator is asymptotically efficient when the maximizing parameter is unique so that regular estimation is possible. We apply our technique to a recent example from the literature in which one wishes to report the maximal absolute correlation between a prespecified outcome and one of <i>p</i> predictors. The simplicity of our technique enables an analysis of the previously open case where <i>p</i> grows with sample size. Specifically, we only require that log <i>p</i> grows slower than <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msqrt><mml:mi>n</mml:mi></mml:msqrt></mml:math> , where <i>n</i> is the sample size. We show that, unlike earlier approaches, our method scales to massive data sets: the point estimate and confidence intervals can be constructed in <i>O</i>(<i>np</i>) time.
Further SAR on the (Phenylsulfonyl)piperazine Scaffold as Inhibitors of the Aedes aegypti Kir1 ( Ae Kir) Channel and Larvicides (2020)

Zika virus (ZIKV), dengue fever (DENV) and chikungunya (CHIKV) are arboviruses that are spread to humans from the bite of an infected adult female Aedes aegypti mosquito. As there are no effective vaccines or therapeutics for these diseases, the primary strategy for controlling the spread of these viruses is to prevent the mosquito from biting humans through the use of insecticides. Unfortunately, the commonly used classes of insecticides have seen a significant increase in resistance, thus complicating control efforts. Inhibiting the renal inward rectifier potassium (Kir) channel of the mosquito vector Aedes aegypti has been shown to be a promising target for the development of novel mosquitocides. We have shown that Kir1 channels play key roles in mosquito diuresis, hemolymph potassium homeostasis, flight, and reproduction. Previous work from our laboratories identified a novel (phenylsulfonyl)piperazine scaffold as potent AeKir channel inhibitors with activity against both adult and larval mosquitoes. Herein, we report further SAR work around this scaffold and have identified additional compounds with improved in vitro potency and mosquito larvae toxicity.
Origin of the HIV-1 group O epidemic in western lowland gorillas (2015)

HIV-1, the cause of AIDS, is composed of four phylogenetic lineages, groups M, N, O, and P, each of which resulted from an independent cross-species transmission event of simian immunodeficiency viruses (SIVs) infecting African apes. Although groups M and N have been traced to geographically distinct chimpanzee communities in southern Cameroon, the reservoirs of groups O and P remain unknown. Here, we screened fecal samples from western lowland (n = 2,611), eastern lowland (n = 103), and mountain (n = 218) gorillas for gorilla SIV (SIVgor) antibodies and nucleic acids. Despite testing wild troops throughout southern Cameroon (n = 14), northern Gabon (n = 16), the Democratic Republic of Congo (n = 2), and Uganda (n = 1), SIVgor was identified at only four sites in southern Cameroon, with prevalences ranging from 0.8-22%. Amplification of partial and full-length SIVgor sequences revealed extensive genetic diversity, but all SIVgor strains were derived from a single lineage within the chimpanzee SIV (SIVcpz) radiation. Two fully sequenced gorilla viruses from southwestern Cameroon were very closely related to, and likely represent the source population of, HIV-1 group P. Most of the genome of a third SIVgor strain, from central Cameroon, was very closely related to HIV-1 group O, again pointing to gorillas as the immediate source. Functional analyses identified the cytidine deaminase APOBEC3G as a barrier for chimpanzee-to-gorilla, but not gorilla-to-human, virus transmission. These data indicate that HIV-1 group O, which spreads epidemically in west central Africa and is estimated to have infected around 100,000 people, originated by cross-species transmission from western lowland gorillas.
Incidence and Risk Factors for Invasive Pneumococcal Disease in HIV-Infected and Non-HIV-Infected Individuals Before and After the Introduction of Combination Antiretroviral Therapy: Persistent High Risk Among HIV-Infected Injecting Drug Users (2014)

The incidence of IPD in HIV-infected individuals remained significantly higher than the incidence observed in non-HIV-infected subjects, despite the widespread use of cART. IDUs have a persistently high risk of IPD. Injecting drug use, smoking, and the receipt of cART are suitable targets for preventive measures in the future.
Development of Advanced Coatings for Laser Modifications Through Process and Materials Simulation (2004)

A simulation‐based system is currently being constructed to aid in the development of advanced coating systems for laser cladding and surface alloying. The system employs loosely coupled material and process models that allow rapid determination of material compatibility over a wide range of processing conditions. The primary emphasis is on the development and identification of composite coatings for improved wear and corrosion resistance. The material model utilizes computational thermodynamics and kinetic analysis to establish phase stability and extent of diffusional reactions that may result from the thermal response of the material during virtual processing. The process model is used to develop accurate thermal histories associated with the laser surface modification process and provides critical input for the non‐isothermal materials simulations. These techniques were utilized to design a laser surface modification experiment that utilized the addition of stainless steel alloy 431 and TiC produced using argon and argon and nitrogen shielding. The deposits representing alloy 431 and TiC powder produced in argon resulted in microstructures retaining some TiC particles and an increase in hardness when compared to deposits produced using only the 431 powder. Laser deposits representing alloy 431 and TiC powder produced with a mixture of argon and nitrogen shielding gas resulted in microstructures retaining some TiC particles, as well as fine precipitates of Ti(CN) formed during cooling and a further increase in hardness of the deposit.
DEFECTS 2008 (2008)

Bugs are everywhere in today's software and because of the huge economic damage they are actively studied. The goal of this one-day workshop is to connect the different research communities with each other and with industry.
Multifeld‐Sättigungsmagnetisierungsmessungen an oxidierter und reduzierter Ribonucleotid‐Reduktase aus Escherichia coli (1992)

Ein zweifach carboxylatoverbrücktes Dieisen( II )‐Zentrum (Bild rechts) scheint, den Ergebnissen magnetischer Messungen zufolge, in reduzierter Ribonucleotid‐Reduktase vorzuliegen: Die starke antiferromagnetische Kopplung der Eisen( III )‐Zentren in der oxidierten Form, die in Einklang mit einer Oxobrücke ist, tritt in der reduzierten Form nicht mehr auf, und man kann daher postulierten, daß die Oxobrücke während der Reduktion zur Zquabrücke wird und schließlich, nach ihrer Abspaltung, die rechts gezeigte Struktureinheit entsteht. magnified image
Elevated Glucose Concentrations 60 Minutes after an Oral Challenge in Subjects with Normal Glucose Tolerance Are Not Explained by the Rate of Meal-Derived Glucose Appearance (2018)

Glucose concentrations 60 minutes after an oral glucose tolerance test (OGTT) ≥155 mg/dL (8.6 mmol/L) identify an increased risk of progression to type 2 diabetes even in those with normal glucose tolerance (NGT). Recent data suggests that these differences can be explained by increased intestinal glucose absorption due to increased expression of the sodium/glucose cotransporter 1 (SGLT1) in the intestine. To examine the contribution of meal appearance to postprandial glucose concentrations we studied 36 subjects with NGT using a 75g OGTT, and a labelled mixed meal. Insulin secretion and action, endogenous glucose production (EGP), meal-derived glucose appearance (Meal Ra) and glucose disappearance (Rd) were subsequently calculated. Participants were grouped according to 60 minute glucose into HI (≥155 mg/dl) or LO (&amp;lt;155mg/dl). No differences in age (47±3 vs. 50±2 years, LO vs. HI respectively, p=0.59) or BMI (28±1 vs. 28±1 Kg/M2, p=0.95) were observed. Fasting (11.9±0.6 vs. 12.6±0.6 μmol/kg/min, p=0.44) and nadir (2.0±0.8 vs. 3.3±0.3 μmol/kg/min, p=0.21) EGP did not differ. Similarly, peak (86±10 vs. 92±6 μmol/kg/min, p=0.59) and integrated (9.8±1.3 vs. 10.6±1.1 mmol per 6 hour, p=0.69) Meal Ra did not differ between groups. On the other hand, when β-cell responsivity (ϕ) was expressed as a function of insulin action (Si), the resulting Disposition Index (DI) was lower in the HI group (1862±409 vs. 893±103 10-14 dl/kg/min2 per pmol/l, p=0.01). When analyzed as a continuous variable, 60 minute glucose was inversely related to DI (r = -0.37, p=0.02) but did not correlate with peak (r=0.03, p=0.96) and integrated (r=0.02, p=0.91) Meal Ra. Taken together, these data indicate that increased 60 minute glucose concentrations, even in subjects with NGT, are explained by decreased β-cell function not by an increased systemic rate of appearance of meal-derived glucose. Disclosure J. Adams: None. G. Treiber: None. M.D. Hurtado: None. M.C. Laurenti: Other Relationship; Self; GlySens Incorporated. C. Dalla Man: None. C. Cobelli: Research Support; Self; Sanofi-Aventis. Advisory Panel; Self; Novo Nordisk Inc.. R.A. Rizza: None. A. Vella: Research Support; Self; Novo Nordisk Inc., XOMA Corporation. Advisory Panel; Self; VTV Therapeutics, Bayer AG.
Chemoselective, Practical Synthesis of Cobaltocenium Carboxylic Acid Hexafluorophosphate (2014)

Cobaltocenium carboxylic acid (carboxycobaltocenium) hexafluorophosphate, a key compound for other monofunctionalized cobaltocenium salts, has been synthesized in >70% overall yield starting from cobaltocenium hexafluorophosphate by a synthetic sequence involving (i) nucleophilic addition of lithium (trimethylsilyl)ethynide, (ii) hydride removal by tritylium hexafluorophosphate, and (iii) oxidative cleavage of the alkynyl substituent by potassium permanganate.