gebhart/patrepeval huggingface dataset:
Homogeneous upconversion in Er-doped fibers under steady state excitation: analytical model and its Monte Carlo verification (2005)

We present an extension to our earlier proposed statistical model [Phys. Rev. B 62, 15628 (2002)] for studying migration-assisted homogeneous upconversion in erbium-doped fibers. The extension takes into account minimum proximity distance between erbium ions randomly distributed in the host material and the nonuniformity of the excitation distribution among them. We derive a transcendental equation for the population inversion and find the dependence of the upconversion rate on the population inversion and the pump power for the entire range of feasible Er concentrations. We verify the validity and accuracy of the model by means of time-resolved Monte Carlo simulations.
Low-molecular-weight RNAs of Moloney murine leukemia virus: identification of the primer for RNA-directed DNA synthesis (1977)

The small RNAs of Moloney murine leukemia virus (M-MuLV) were fractionated into at least 15 species by two-dimensional polyacrylamide gel electrophoresis. The pattern of small RNAs is significantly different from that of Rous sarcoma virus. A subset of the virion small RNAs is associated with the genome RNA in the 70S complex. One of the associated molecules, a cellular tRNA, is tightly bound to the genome RNA and serves as the major primer for M-MuLV RNA-directed DNA synthesis in vitro.
EOS determination through optical microscopy-interferometry measurements (OMI) (2016)

Abstract not provided
Non-Viral Delivery of RNA Interference Targeting Cancer Cells in Cancer Gene Therapy (2012)

RNA interference (RNAi) is a collection of small RNA-directed mechanisms that result in sequence-specific inhibition of gene expression. RNAi delivery has demonstrated promising efficacy in the treatment of genetic disorders in cancer. Although viral vectors are currently the most efficient systems for gene therapy, potent immunogenicity, mutagenesis, and the biohazards of viral vectors remain their major risks. Various non-viral delivery vectors have been developed to provide a safer approach for gene delivery, including polymers, peptides, liposomes, and nanoparticles. However, some concerns and challenges of these non-viral gene delivery approaches remain to be overcome. In this review, we summarize the recent progress in the development of non-viral systems delivering RNAi and the currently available preclinical and clinical data, and discuss the challenges and future directions in cancer therapy.
Simvastatin-loaded liposome nanoparticles treatment for uterine leiomyoma in a patient-derived xenograft mouse model: a pilot study (2022)

Uterine leiomyomas are complex tumours with limited medical treatment options. Simvastatin is used to treat hypercholesterolaemia and has shown promising effects as a treatment option for leiomyomas. Previously, our group demonstrated a promising effect of simvastatin treatment in a patient-derived xenograft mouse model. Here, we tested the efficacy of simvastatin liposomal nanoparticles (NPs). After bilateral leiomyoma xenograft implantation, mice (N = 12) were divided into three treatment arms: control, simvastatin and simvastatin-loaded liposome NPs (simvastatin-NPs). Treatment with simvastatin significantly reduced tumour volume and inhibited the Ki67 expression when compared to the control group. There was a trend of reduced tumour volume and Ki67 expression after treatment with simvastatin-NP; however, the results were not significant. Due to low bioavailability and short half-life of simvastatin, liposomal NPs have the potential to enhance drug delivery, however, in this study NP did not provide improvement over simvastatin, but did demonstrate their potential for the delivery of simvastatin.Impact statement<b>What is already known on this subject?</b> Simvastatin treatment in a patient-derived xenograft mouse model reduced tumour growth and decreased proliferation.<b>What do the results of this study add?</b> Treatment with simvastatin significantly reduced tumour volume and inhibited the Ki67 expression when compared to the control group. There was a trend of reduced tumour volume and Ki67 expression after treatment with simvastatin-NP, however, it did not improve the efficacy of simvastatin at reducing tumour growth and proliferation.<b>What are the implications of these findings for clinical practice and/or further research?</b> More studies are needed to optimise the formulation of NPs to further enhance the sustainable delivery of simvastatin.
Decoherence, control and attosecond probing of XUV-induced charge migration in biomolecules. A theoretical outlook (2016)

The sudden ionization of a molecule by an attosecond pulse is followed by charge redistribution on a time scale from a few femtoseconds down to hundreds of attoseconds. This ultrafast redistribution is the result of the coherent superposition of electronic continua associated with the ionization thresholds that are reached by the broadband attosecond pulse. Thus, a correct theoretical description of the time evolution of the ensuing wave packet requires the knowledge of the actual ionization amplitudes associated with all open ionization channels, a real challenge for large and medium-size molecules. Recently, the first calculation of this kind has come to light, allowing for interpretation of ultrafast electron dynamics observed in attosecond pump-probe experiments performed on the amino acid phenylalanine [Calegari et al., Science 2014, 346, 336]. However, as in most previous theoretical works, the interpretation was based on various simplifying assumptions, namely, the ionized electron was not included in the description of the cation dynamics, the nuclei were fixed at their initial position during the hole migration process, and the effect of the IR probe pulse was ignored. Here we go a step further and discuss the consequences of including these effects in the photoionization of the glycine molecule. We show that (i) the ionized electron does not affect hole dynamics beyond the first femtosecond, and (ii) nuclear dynamics has only a significant effect after approximately 8 fs, but does not destroy the coherent motion of the electronic wave packet during at least few additional tens of fs. As a first step towards understanding the role of the probe pulse, we have considered an XUV probe pulse, instead of a strong IR one, and show that such an XUV probe does not introduce significant distortions in the pump-induced dynamics, suggesting that pump-probe strategies are suitable for imaging and manipulating charge migration in complex molecules. Furthermore, we show that hole dynamics can be changed by shaping the attosecond pump pulse, thus opening the door to the control of charge dynamics in biomolecules.
Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains (2015)

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project to sequence about 250 bacterial and archaeal genomes of elevated phylogenetic diversity. Herein, we propose to extend this approach to type strains of prokaryotes associated with soil or plants and their close relatives as well as type strains from newly described species. Understanding the microbiology of soil and plants is critical to many DOE mission areas, such as biofuel production from biomass, biogeochemistry, and carbon cycling. We are also targeting type strains of novel species while they are being described. Since 2006, about 630 new species have been described per year, many of which are closely aligned to DOE areas of interest in soil, agriculture, degradation of pollutants, biofuel production, biogeochemical transformation, and biodiversity.
Supplementary Table 1 from The Rectal Cancer microRNAome – microRNA Expression in Rectal Cancer and Matched Normal Mucosa (2023)

&lt;p&gt;XLSX file, 64K, Clinical data.&lt;/p&gt;
Rapid monitoring assay of congenital adrenal hyperplasia with microbore high‐performance liquid chromatography/electrospray ionization tandem mass spectrometry from dried blood spots (2001)

17-hydroxyprogesterone (17OHP) is the most important plasma parameter for diagnosing and monitoring congenital adrenal hyperplasia (CAH) caused by 21-hydroxylase deficiency. A rapid, simple, and specific method based on microbore high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (micro-HPLC/ESI-MS/MS) was developed to determine the presence of 17OHP on dried filter-paper blood samples from patients with CAH caused by 21-hydroxylase deficiency. 17OHP from dried blood spots formed by the action of Girard reagent P (GirP) turned out to be a water-soluble hydrazone complex. Derivatization with GirP led to higher ESI sensitivity for 17OHP. The LC/MS/MS detection of GirP-derivatized 17OHP (GirP-17OHP) was rapid (<3 min). The method is repeatable and reproducible, with CVs <7% and 12%, respectively. This new method was used for direct determination of 17OHP in dried blood specimens obtained from abnormal children and infants of various ages with a detection limit of 10 ng/mL ( approximately 12 microL blood). The method described allows for rapid and reliable measurements of 17OHP in dried blood specimens from patients affected by CAH.
Farm and abattoir sources of <i>Carnobacterium</i> species and implications for lamb meat spoilage (2018)

Data on distribution, diversity, sources and transmission routes for meat product contamination is limited for spoilage bacteria. This study highlights the importance of good hygienic slaughter practices and cleaning routines to remove accumulated detritus from the handling of animals that may lead to cross-contamination.
Characteristics of He<sup>+</sup>‐irradiated Ni Schottky diodes based on 4H‐SiC epilayer grown by sublimation (2009)

Abstract Forward and reverse current‐voltage (I‐V) and capacitance‐voltage (C‐V) characteristics of the of He + – irradiated Ni‐SiC(4H) Schottky diodes (SDs) are presented prior and after irradiation. The effect of irradiation was weakly observed in the region of small forward and reverse current, but series resistance of SD demonstrated tendency to rise with increasing irradiation dose. The most interesting effect was the big scatter of the series resistances after exposure to high irradiation dose 2×10 12 cm ‐2 . By contrast, uncompensated donor concentration had just minor changes (from 3.3×10 17 cm ‐3 prior irradiation to 1.8×10 17 cm ‐3 at highest irradiation dose) with no connection with SDs resistance. Hypothesis that localized defect‐induced current paths could explain this behaviour is discussed. (© 2009 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Author's Reply: Fecal Occult Blood Test (1984)

CA: A Cancer Journal for Clinicians publishes information about the prevention, early detection, and treatment of cancer, as well as nutrition, palliative care, survivorship, and additional topics of interest related to cancer care.
Reconstructing absorber images in a three-dimensional scattering medium by using photon-path data (1996)

The proposed averaged photon-path imaging (APPI) method uses Monte Carlo data to reconstruct the images being scanned by optical tomography. To confirm its effectiveness, simulated continuous-wave measurements of one or two absorbers located in a cubic scattering medium were performed. The three-dimensional locations of the absorbers were accurately reconstructed using the APPI method. Combining time-resolved measurement with the APPI method improved the accuracy of the reconstructed images. The APPI method can thus be applied to various measuring situation for practical image reconstruction.
Contents (2018)

Coalmining was a notoriously dangerous industry and many of its workers experienced injury and disease. However, the experiences of the many disabled people within Britain's most dangerous industry have gone largely unrecognised by historians. This book examines the British coal industry through the lens of disability, using an interdisciplinary approach to examine the lives of disabled miners and their families.The book considers the coal industry at a time when it was one of Britain's most important industries, and follows it through a period of growth up to the First World War, through strikes, depression and wartime, and into an era of decline. During this time, the statutory provision for disabled people changed considerably, most notably with the first programme of state compensation for workplace injury. And yet disabled people remained a constant presence in the industry as many disabled miners continued their jobs or took up 'light work'. The burgeoning coalfields literature used images of disability on a frequent basis and disabled characters were used to represent the human toll of the industry.A diverse range of sources are used to examine the economic, social, political and cultural impact of disability in the coal industry, looking beyond formal coal company and union records to include autobiographies, novels and oral testimony. It argues that, far from being excluded entirely from British industry, disability and disabled people were central to its development. The book will appeal to students and academics interested in disability history, disability studies, social and cultural history, and representations of disability in literature.
Survival prediction for patients with metastatic urothelial cancer after immunotherapy by machine learning (2023)

We studied the feasibility of developing a machine learning model to predict the survival of patients with metastatic urothelial cancer after immunotherapy. CT scans of 363 metastatic tumors in 49 patients undergoing immunotherapy were collected at every treatment time point. 1040 temporal triplets of metastatic cancers were formed. At every time point, a radiologist measured the tumor diameter. The patient survival data was collected from clinical records. Using the tumor diameters at prior time points as inputs, we built a model to predict patient survival after immunotherapy using artificial neural networks (PSNN). The PSNN used 3 prior time points to predict patient survival at a future time point: PS(t<sub>4</sub>)=PSNN(d(t<sub>1</sub>), d(t<sub>2</sub>), d(t<sub>3</sub>)). Specifically, PSNN was trained to predict patient survival at 4 years from the beginning of treatment (t<sub>4</sub>=4) using 3 prior time points within 3 years from the beginning of treatment (0&lt;t<sub>1</sub>&lt;t<sub>2</sub>&lt;t<sub>3</sub>&lt;3). We split the dataset into training (53 tumors, 13 patients, 335 triplets) and independent test (310 lesions, 36 patients, 705 triplets) sets. The final patient-based survival prediction scores were obtained by averaging PSNN scores of all triplets for a given patient. Area under the ROC curve (AUC) and Kaplan-Meier analysis were used for performance evaluation. The training and test AUCs for survival prediction at 4 years were 0.77&plusmn;0.13 and 0.73&plusmn;0.09, respectively. Using a decision threshold determined by the training set, the test set was stratified into two subgroups of longer and shorted survival. Median survival time for the 2 test subgroups estimated by the PSNN was 5 and 2 years, respectively (p=0.025). The PSNN shows promise for predicting patient survival after immunotherapy.
Direct Action of Opiates on Bromocriptine-Inhibited Prolactin Release by Human Prolactinoma Cells in Primary Culture* (1985)

The present study was undertaken in order to examine the existence of opioid binding sites on cell membranes of human PRL-secreting tumors. Determination of opioid binding sites using different opiate ligands revealed one class of high affinity (KD, 1.3 nM) binding sites. Pharmacological characterization revealed kappa-1 selectivity (high affinity ethylketocyclazocine (EKC) binding, insensitive to 5 microM (D-Ala2, D-Leu5]enkephalin). Subsequently EKC was added to hPRL-secreting tumor cells in primary culture, alone or in combination with the dopaminergic agonist bromocriptine, and PRL release was measured. Opiates had no direct effect on PRL release by prolactinoma cells. When cells were preincubated with bromocriptine [6.6 +/- 4.8 (SD) X 10(-11) M], EKC (10(-11) to 10(-9) M) antagonized, in a dose-dependent manner, the dopaminergic inhibition of PRL release. The opiate effect was reversed by the opiate antagonist diprenorphine (10(-7) M). Cross-competition studies indicated that this effect was not due to the interaction of opiates with the dopaminergic receptor. In conclusion, opioid binding sites are found on prolactinoma cells. The binding of kappa-1 type opioid ligands modulates the inhibitory effect of dopamine upon PRL release.
Generative Adversarial Network for Pansharpening With Spectral and Spatial Discriminators (2021)

The pansharpening problem amounts to fusing a high-resolution panchromatic image with a low-resolution multispectral image so as to obtain a high-resolution multispectral image. Therefore, the preservation of the spatial resolution of the panchromatic image and the spectral resolution of the multispectral image is of key importance for the pansharpening problem. To cope with it, we propose a new method based on a bidiscriminator in a generative adversarial network (GAN) framework. The first discriminator is optimized to preserve textures of images by taking as input the luminance and the near-infrared band of images, and the second discriminator preserves the color by comparing the chroma components Cb and Cr. Thus, this method allows to train two discriminators, each one with a different and complementary task. Moreover, to enhance these aspects, the proposed method based on bidiscriminator, and called MDSSC-GAN SAM, considers a spatial and a spectral constraint in the loss function of the generator. We show the advantages of this new method on experiments carried out on Pléiades and World View 3 satellite images.
Single‐enzyme kinetics with fluorogenic substrates: lessons learnt and future directions (2014)

Single-molecule fluorescence techniques have developed into powerful tools for studying the kinetics of biological reactions at the single-molecule level. Using fluorogenic substrates, enzymatic reactions can be observed in real-time with single-turnover resolution. The turnover sequence contains all kinetic information, giving access to reaction substeps and dynamic processes such as fluctuations in the reaction rate. Despite their clearly proven potential, the accuracy of current measurements is limited by the availability of substrates with 1:1 stoichiometry and the signal-to-noise ratio of the measurement. In this review we summarize the state-of-the-art and discuss these limitations using experiments performed with α-chymotrypsin as an example. We are further providing an overview of recent efforts aimed at the improvement of fluorogenic substrates and the development of new detection schemes. These detection schemes utilize nanophotonic structures such as zero mode waveguides or nanoantennas. Nanophotonic approaches reduce the size of the effective detection volume and are a powerful strategy to increase the signal-to-noise ratio. We believe that a combination of improved substrates and novel detection schemes will pave the way for performing accurate single-enzyme experiments in biologically relevant conditions.
Fusion of Talking Face Biometric Modalities for Personal Identity Verification (2006)

We describe a personal identity verification system based on lip dynamics biometric. The lip shape is represented in terms of a B-spline model, tracked over time. The coordinates of the 11 control points of the B-spline model are used as features for each frame. An utterance consisting of N frames produces a sequence of 22 dimensional feature vectors that is matched to the template using dynamic time warping. The verification error rate achived by the systems on the XM2VTS database is about 14%. By fusing the system with face and voice biometrics the error rate is reduced to a fractiopn of one percent.
[P3–102]: GENETIC RISK FOR SCHIZOPHRENIA AND PSYCHOSIS IN ALZHEIMER DISEASE (2017)

Psychotic symptoms, defined as the occurrence of delusions or hallucinations, are frequent in Alzheimer Disease, affecting ∼ 40% to 60% of individuals with AD (AD with psychosis, AD+P). In comparison to AD subjects without psychosis, AD+P subjects have more rapid cognitive decline and poor outcomes. Prior studies have estimated the heritability of psychosis in AD at 61%, but the underlying genetic sources of this risk are not known. We evaluated a Discovery Cohort of 2876 AD subjects with (n=1761) or without psychosis (n=1115). All subjects were genotyped using a custom genotyping array designed to evaluate SNPs with evidence of genetic association with AD+P and include SNPs affecting or putatively affecting risk for schizophrenia and Alzheimer disease. Results were replicated in an independent cohort of 2194 AD subjects with (n=734) or without psychosis (n=1460). We found that AD+P is associated with polygenic risk for a set of novel loci and inversely associated with polygenic risk for schizophrenia. These findings provide the first clear demonstration that AD+P is associated with common genetic variation. In addition, they provide an unbiased link between polygenic risk for schizophrenia and a lower risk of psychosis in AD. This provides an opportunity to leverage progress made in identifying the biologic effects of schizophrenia alleles to identify novel mechanisms protecting against more rapid cognitive decline and psychosis risk in AD.
Professor Dr. Hans-Dieter Klenk (1938–2021) (2021)

We share with great sadness that our long-time friend and colleague Prof. Dr. Hans-Dieter Klenk passed away on 1 June 2021, at the age of 82. With the passing of Hans-Dieter Klenk, the worldwide vi...
An in vitro method to select malignant cells from surgical biopsies of breast cancer patients (2005)

To date, breast cancer (BC) research is mainly studied with cell lines. These cells were passaged multiple times, acquiring phenotypes, additional mutations and epigenetic changes. These changes make the passaged cell lines different from the original malignancy. Thus cell lines, although useful as models could be improved with additional studies with primary BC. It is difficult to obtain malignant cells from breast tissues without contamination from surrounding healthy cells. Selection and expansion of malignant cells from surgical tissues have proved to be daunting tasks. This study describes a reliable and reproducible method for isolating and expanding malignant cells from surgical breast tissues. The method uses co-cultures with BM stroma to select for the cancer cells while the healthy cells undergo rapid cell death. Studies are described to show the cloning efficiencies and sensitivity of the method using surgical samples of varying sizes, different stages of BC, and samples from needle biopsies.
Sol-Gel Synthesis of Zircon-Carbon Precursors and Coatings of Nextel 720™ Fiber Tows (2008)

A zircon-carbon precursor was continuously coated on Nextel 720™ fibers using the sol-gel method. Zircon was synthesized by the hydrolysis of zirconyl nitrate hydrate and tetraethoxysilane (TEOS) in ethanol. Polyacrylic acid was added as a carbon precursor. Ammonium vanadate was added to decrease the zircon formation temperature. The effects of prehydrolysis of TEOS and preheating of zircon and zircon-carbon precursor powders were investigated. Zircon formation was retarded by the presence of carbon.