gebhart/patrepeval huggingface dataset:
Preclinical and clinical advances in transposon-based gene therapy (2017)

Transposons derived from <i>Sleeping Beauty</i> (SB), <i>piggyBac</i> (PB), or <i>Tol2</i> typically require cotransfection of transposon DNA with a transposase either as an expression plasmid or mRNA. Consequently, this results in genomic integration of the potentially therapeutic gene into chromosomes of the desired target cells, and thus conferring stable expression. Non-viral transfection methods are typically preferred to deliver the transposon components into the target cells. However, these methods do not match the efficacy typically attained with viral vectors and are sometimes associated with cellular toxicity evoked by the DNA itself. In recent years, the overall transposition efficacy has gradually increased by codon optimization of the transposase, generation of hyperactive transposases, and/or introduction of specific mutations in the transposon terminal repeats. Their versatility enabled the stable genetic engineering in many different primary cell types, including stem/progenitor cells and differentiated cell types. This prompted numerous preclinical proof-of-concept studies in disease models that demonstrated the potential of DNA transposons for <i>ex vivo</i> and <i>in vivo</i> gene therapy. One of the merits of transposon systems relates to their ability to deliver relatively large therapeutic transgenes that cannot readily be accommodated in viral vectors such as full-length dystrophin cDNA. These emerging insights paved the way toward the first transposon-based phase I/II clinical trials to treat hematologic cancer and other diseases. Though encouraging results were obtained, controlled pivotal clinical trials are needed to corroborate the efficacy and safety of transposon-based therapies.
Mutual-information-based registration for ultrasound and CT datasets (2004)

In many applications for minimal invasive surgery the acquisition of intra-operative medical images is helpful if not absolutely necessary. Especially for Brachytherapy imaging is critically important to the safe delivery of the therapy. Modern computed tomography (CT) and magnetic resonance (MR) scanners allow minimal invasive procedures to be performed under direct imaging guidance. However, conventional scanners do not have real-time imaging capability and are expensive technologies requiring a special facility. Ultrasound (U/S) is a much cheaper and one of the most flexible imaging modalities. It can be moved to the application room as required and the physician sees what is happening as it occurs. Nevertheless it may be easier to interpret these 3D intra-operative U/S images if they are used in combination with less noisier preoperative data such as CT. The purpose of our current investigation is to develop a registration tool for automatically combining pre-operative CT volumes with intra-operatively acquired 3D U/S datasets. The applied alignment procedure is based on the information theoretic approach of maximizing the mutual information of two arbitrary datasets from different modalities. Since the CT datasets include a much bigger field of view we introduced a bounding box to narrow down the region of interest within the CT dataset. We conducted a phantom experiment using a CIRS Model 53 U/S Prostate Training Phantom to evaluate the feasibility and accuracy of the proposed method.
<i>In vivo</i> biochemistry: Physical monitoring of recombination induced by site‐specific endonucleases (1995)

The recombinational repair of chromosomal double-strand breaks (DSBs) is of critical importance to all organisms, who devote considerable genetic resources to ensuring such repair is accomplished. In Saccharomyces cerevisiae, DSB-mediated recombination can be initiated synchronously by the conditional expression of two site-specific endonucleases, HO or I-Scel. DNA undergoing recombination can then be extracted at intervals and analyzed. Recombination initiated by meiotic-specific DSBs can be followed in a similar fashion. This type of 'in vivo biochemistry' has been used to describe several discrete steps in two different homologous recombination pathways: gene conversion and single-strand annealing. The roles of specific proteins during recombination can be established by examining DNA in strains deleted for the corresponding gene. These same approaches are now becoming available for the study of recombination in both higher plants and animals. Physical monitoring can also be used to analyze nonhomologous recombination events, whose mechanisms appear to be conserved from yeast to mammals.
Sparse Antenna Array Design for MIMO Radar Using Multiobjective Differential Evolution (2016)

A two-stage design approach is proposed to address the sparse antenna array design for multiple-input multiple-output radar. In the first stage, the cyclic algorithm (CA) is used to establish a covariance matrix that satisfies the beam pattern approximation for a full array. In the second stage, a sparse antenna array with a beam pattern is designed to approximate the desired beam pattern. This paper focuses on the second stage. The optimization problem for the sparse antenna array design aimed at beam pattern synthesis is formulated, where the peak side lobe (PSL) is weakly constrained by the mean squared error. To solve this optimization problem, the differential evolution (DE) algorithm with multistrategy is introduced and PSL suppression is treated as an inequality constraint. However, in doing so, a new multiobjective optimization problem is created. To address this new problem, a multiobjective differential evolution algorithm based on Pareto technique is proposed. Numerical examples are provided to demonstrate the advantages of the proposed approach over state-of-the-art methods, including DE and genetic algorithm.
Myeloid cell leukemia-1 is associated with tumor progression by inhibiting apoptosis and enhancing angiogenesis in colorectal cancer. (2015)

Myeloid cell leukemia-1 (Mcl-1) is a highly expressed anti-apoptotic Bcl-2 protein in cancer. Therefore, inhibition of its expression induces apoptosis in cancer cells and enhances sensitivity to cancer treatment. The aims of this study were to evaluate whether Mcl-1 affects the oncogenic behaviors of colorectal cancer cells, and to document the relationship of its expression with various clinicopathological parameters in colorectal cancer. Mcl-1 knockdown induced apoptosis by activating cleaved caspase-3 and -9, and increasing the expression of the pro-apoptotic protein, PUMA. Mcl-1 knockdown induced cell cycle arrest by decreasing cyclin D1, CDK4 and 6, and by increasing p27 expression. Mcl-1 knockdown decreased both endothelial cell invasion and tube formation, and decreased the expression of VEGF. The phosphorylation level of STAT3 was decreased by Mcl-1 knockdown. The mean apoptotic index value of Mcl-1 positive tumors was significantly lower than that of Mcl-1 negative tumors. The mean microvessel density value of Mcl-1 positive tumors was significantly higher than that of negative tumors. Mcl-1 expression was significantly increased in colorectal cancer, also associated with tumor stage, lymph node metastasis, and poor survival. These results indicate Mcl-1 is associated with tumor progression through its inhibition of apoptosis and enhancement of angiogenesis in colorectal cancer.
Effects of fibrinolytic inhibitors on mortality from upper gastrointestinal haemorrhage. (1989)

Treatment with tranexamic acid may be of value to patients considered to be at risk of dying after an upper gastrointestinal haemorrhage.
Effects of rebamipide on bile acid‐induced inhibition of gastric epithelial repair in a rabbit cell culture model (1996)

Deoxycholic acid significantly retarded restoration by the inhibition of both cell migration and proliferation, potentially through an effect on the cytoskeleton. Rebamipide protected the mucosal cells from bile acid mediated injury.
Plasma levels of the cis- and trans-isomers of doxepin and desmethyldoxepin after administration of doxepin to patients. (1981)

In depressed patients treated with doxepin (Sinequan), a 15:85% mixture of cis- and trans-isomers, plasma levels of the cis- and trans-forms of doxepin and desmethyldoxepin were measured using a GLC-method with a capillary column and a nitrogen detector. A gradual increase of the concentration of the products in the plasma is seen in the first days of administration. There is a remarkable variation from patient to patient in the steady-state concentrations of trans-doxepin and of cis- and trans-desmethyldoxepin. cis-Doxepin levels are always very low. It is suggested that for studies of correlation between plasma levels and therapeutic and toxic effects of doxepin, the isomers of the parent compound and its metabolite should be measured separately.
Copper: Role of the 'Endogenous' and 'Exogenous' Metal on the Development and Control of Inflammatory Processes (2006)

Article Copper: Role of the 'Endogenous' and 'Exogenous' Metal on the Development and Control of Inflammatory Processes was published on July 1, 2006 in the journal Reviews on Environmental Health (volume 21, issue 3).
In Vitro Evaluation of Frozen-Thawed Stallion Semen: A Review (2001)

The article reviews methods used for in vitro evaluation of sperm, with particular emphasis on frozen-thawed stallion sperm. The techniques, limitations of the methods and correlations with fertility results are discussed. Very few studies have tried to find correlation between fertility of frozen stallion semen and laboratory tests. It is difficult and expensive to inseminate an adequate number of mares to achieve statistically significant differences. Significant, but low correlations have been demonstrated between the foaling rate and subjective motility of sperm incubated for 2 h and 4 h at 37 degrees C and hypoosmotic swelling test after 0 and 3 h of incubation. Significant correlations have been reported between the pregnancy rate and viability of propidium iodide-stained sperm assessed by flow cytometry as well as for glass wool and Sephadex filtration tests. No correlations have been detected between fertility and motility immediately after thawing. In spite of that, motility estimation by light microscope is the most commonly used method to evaluate frozen-thawed stallion sperm. Computer assisted automatic sperm analyzers have replaced light microscopy in research projects, but so far nobody has been able to demonstrate a correlation between fertility of frozen stallion semen and any of the motility parameters obtained by these instruments.
TransRPPG: Remote Photoplethysmography Transformer for 3D Mask Face Presentation Attack Detection (2021)

3D mask face presentation attack detection (PAD) plays a vital role in securing face recognition systems from emergent 3D mask attacks. Recently, remote photoplethysmography (rPPG) has been developed as an intrinsic liveness clue for 3D mask PAD without relying on the mask appearance. However, the rPPG features for 3D mask PAD are still needed expert knowledge to design manually, which limits its further progress in the deep learning and big data era. In this letter, we propose a pure rPPG transformer (TransRPPG) framework for learning intrinsic liveness representation efficiently. At first, rPPG-based multi-scale spatial-temporal maps (MSTmap) are constructed from facial skin and background regions. Then the transformer fully mines the global relationship within MSTmaps for liveness representation, and gives a binary prediction for 3D mask detection. Comprehensive experiments are conducted on two benchmark datasets to demonstrate the efficacy of the TransRPPG on both intra- and cross-dataset testings. Our TransRPPG is lightweight and efficient (with only 547 K parameters and 763 M FLOPs), which is promising for mobile-level applications.
Four-photon laser spectroscopy of solids in 0–0.15 THz (2005)

Four-photon coherent spectroscopy of fused quartz, crown glass K8 and NaCl crystal in 0–5 cm -1 have been done. It was established that the spectra contain the Brillouin resonances on longitudinal and transversal hypersound, as well as distinct resonances at ∼1.6 cm -1 , which can be attributed to hydroxyl (OH) rotations. The fine structure of Rayleigh wing scattering in fused quartz has been observed for the first time. The detected lines 0.18 cm -1 and 0.37 cm -1 (5.4 and 11.1 GHz, respectively) are attributed to spheroidal modes ν 22 and ν 32 of SiO 2 spheres with the diameter ∼760 nm.
Computing Gaussian Mixture Models with EM Using Equivalence Constraints (2003)

Density estimation with Gaussian Mixture Models is a popular generative technique used also for clustering. We develop a framework to incorporate side information in the form of equivalence constraints into the model estimation procedure. Equivalence constraints are defined on pairs of data points, indicating whether the points arise from the same source (positive constraints) or from different sources (negative constraints). Such constraints can be gathered automatically in some learning problems, and are a natural form of supervision in others. For the estimation of model parameters we present a closed form EM procedure which handles positive constraints, and a Generalized EM procedure using a Markov net which handles negative constraints. Using publicly available data sets we demonstrate that such side information can lead to considerable improvement in clustering tasks, and that our algorithm is preferable to two other suggested methods using the same type of side information. 1
REPENSANDO A ADMINISTRAÇÃO COMO CIÊNCIA: UM ENSAIO TEÓRICO (2013)

A cientificidade das Ciencias Sociais e bastante discutida no âmbito academico, sendo que a Administracao e constantemente questionada no que tange ao seu carater cientifico. Por vezes consideram-se ciencia apenas os campos pertencentes as chamadas ciencias naturais ou hard sciences. Dessa forma, o presente ensaio teorico busca repensar as Ciencias Sociais e especialmente a Administracao enquanto campo cientifico. Utilizando-se de analise do pensamento de diversos autores sobre o assunto, por meio de levantamento bibliografico, buscou-se reunir discussoes a respeito das ciencias naturais e sociais, da cientificidade das ciencias sociais e, principalmente, das discussoes acerca da Administracao e de como essa area pode se fazer enquanto ciencia. Para atingir esse objetivo, o texto esta dividido em duas secoes, alem da introducao, onde sao abordadas a cientificidade das ciencias sociais e a Administracao enquanto ciencia. Atraves das reflexoes trazidas por este ensaio e possivel afirmar que as ciencias sociais e em especial a Administracao sao, de fato, ciencias, e devem desfrutar do mesmo status das ciencias naturais. Pode-se dizer que a forca desta conclusao reside no fato de que ela esta fundamentada justamente naqueles argumentos que comumente se utiliza para provar o contrario, ou seja, provar uma superioridade das ciencias naturais frente as ciencias sociais.
Promoter-cDNA-directed heterologous protein expression in Xenopus laevis oocytes. (1992)

Heterologous proteins can be expressed in Xenopus laevis oocytes by cytoplasmic microinjection of mRNA. To circumvent limitations inherent in this approach we investigate direct nuclear injection of strong viral expression vectors to drive transcription and subsequent translation of cDNAs encoding cytoplasmic, secreted, and plasma membrane proteins. After several viral promoters had been tested, the pMT2 vector was found to be a superior expression vector for X. laevis oocytes capable of directing expression of high levels of functional heterologous proteins. Typically the amount of protein derived from transcription-translation of the microinjected cDNA accounts for approximately 1% of total non-yolk protein. Moreover, the inefficiency usually associated with nuclear injections was overcome by coinjection of pMT2 driving expression of a secreted alkaline phosphatase as an internal control to select positive-expressing oocytes. Using this method, we have successfully expressed high levels of chloramphenicol acetyltransferase, the adipocyte-specific cytosolic 422(aP2) protein, and the membrane-associated glucose transporter GLUT1. The system described should be applicable to a wide variety of proteins for which cDNAs are available. Hence, the cumbersome and often inefficient in vitro synthesis of mRNA for studying ion channels, receptors, and transporters as well as for expression cloning in Xenopus oocytes should no longer be necessary.
Multimodal deep learning enhances diagnostic precision in left ventricular hypertrophy (2021)

Abstract Determining the etiology of left ventricular hypertrophy (LVH) can be challenging due to the similarity in clinical presentation and cardiac morphological features of diverse causes of disease. In particular, distinguishing individuals with hypertrophic cardiomyopathy (HCM) from the much larger set of individuals with manifest or occult hypertension (HTN) is of major importance for family screening and the prevention of sudden death. We hypothesized that deep learning based joint interpretation of 12 lead electrocardiograms and echocardiogram videos could augment physician interpretation. We chose not to train on proximate data labels such as physician over-reads of ECGs or echocardiograms but instead took advantage of electronic health record derived clinical blood pressure measurements and diagnostic consensus (often including molecular testing) among physicians in an HCM center of excellence. Using over 18,000 combined instances of electrocardiograms and echocardiograms from 2,728 patients, we developed LVH-Fusion. On held-out test data, LVH-Fusion achieved an F1-score of 0.71 in predicting HCM, and 0.96 in predicting HTN. In head-to-head comparison with human readers LVH-Fusion had higher sensitivity and specificity rates than its human counterparts. Finally, we use explainability techniques to investigate local and global features that positively and negatively impact LVH-Fusion prediction estimates providing confirmation from unsupervised analysis the diagnostic power of lateral T wave inversion on the ECG and proximal septal hypertrophy on the echocardiogram for HCM. In conclusion, these results show that deep learning can provide effective physician augmentation in the face of a common diagnostic dilemma with far reaching implications for the prevention of sudden cardiac death.
Focused Ethnography: A Methodological Adaptation for Social Research in Emerging Contexts (2014)

Ethnography is one of the oldest qualitative methods, yet increasingly, researchers from various disciplines are using and adapting ethnography beyond its original intents. In particular, a form of ethnography known as "focused ethnography" has emerged. However, focused ethnography remains underspecified methodologically, which has contributed to controversy about its essential nature and value. Nevertheless, an ever-evolving range of research settings, purposes, and questions require appropriate methodological innovation. Using the example of a focused ethnography conducted to study nurses' work experiences, this article will demonstrate how particular research questions, the attributes of certain cultural groups, and the unique characteristics of specific researchers compel adaptations in ethnography that address the need for methodological evolution while still preserving the essential nature of the method. URN: http://nbn-resolving.de/urn:nbn:de:0114-fqs150111
Smart Dietary Monitoring System (2015)

The constant evolution of technology has made people health conscious. The market is flooded with smart devices which track an individual's footsteps, the exercise regime followed, the calories burnt and many such health parameters. The important criterion often ignored which defines an individual's health is the food consumed. So it is imperative to constantly track what is ingested into the body and its impact on a person's health. The Smart Dietary Monitoring System (SDMS) is essentially a Wireless Sensor Network (WSN) that provides real time dietary scheduling information. The proposed system can track the user's dietary intake and replenish behavior through sensors. By integrating this WSN into the "Internet of Things", data can be aggregated in the cloud and analyzed using statistical methods which provide the correlation between the user's health and his dietary regime. This health data can be used to track as well as guide the user regarding his nutritional needs thus acting as an ideal health assistant.
Niobic acid — a new heterogeneous catalyst for processes in petrochemical and organic syntheses (1993)

Questions associated with the application of niobium compounds in catalysis are considered. Niobic acid Nb2O5.nH2O contains an appreciable amount of water, but its surface exhibits a high acidity — equivalent to the acidity of 70% sulfuric acid. This unusual solid acid manifests not only a high activity and sensitivity but also an appreciable stability as a catalyst in reactions in which water is present or is evolved (condensation, hydration, dehydration, and esterification). It may be used also as a catalyst in other reactions. The structure and properties of the surface of niobic acid are examined. The bibliography includes 54 references.
Glypican-3 as a Serum Marker for Hepatocellular Carcinoma (2005)

Glypican-3 (GPC3) is a heparan sulfate proteoglycan that is bound to the cell membrane by a glycosyl-phosphatidylinositol anchor. GPC3 is expressed by most hepatocellular carcinomas but not by normal hepatocytes and benign liver lesions. We report here that GPC3 stimulates the in vitro and in vivo growth of hepatocellular carcinoma cells by increasing autocrine/paracrine canonical Wnt signaling. Co-immunoprecipitation experiments showed that GPC3 is able to form complexes with Wnts, and cell-binding assays indicated that GPC3-expressing cells have an increased capacity to bind Wnt. Collectively, these results suggest that GPC3 stimulates Wnt activity by facilitating the interaction of this polypeptide with its signaling receptors. Surprisingly, in contrast to the current model that proposes that Wnt-glypican binding is mediated by the heparan sulfate chains, we found that the nonglycanated GPC3 core protein can form complexes with Wnts. Furthermore, we showed that the glycosaminoglycan chains are not required for the stimulatory effect on Wnt signaling and hepatocellular carcinoma growth.