gebhart/patrepeval huggingface dataset:
Adenovirus-Mediated Transduction of Intestinal Cells <i>In Vivo</i> (1998)

The intestinal tract has many features that make it an attractive target for therapeutic gene transfer. In this study, replication-defective adenoviral vectors were used to explore parameters that may be important in administering gene therapy vectors to the intestine. After surgically accessing the intestine, an E1-, E3-deleted adenoviral vector encoding beta-galactosidase (beta-Gal) was directly injected into various regions of the small and large intestine of rats and rabbits. Significant transduction of the tissue was observed and histochemical staining was used to identify enterocytes as the primary targets of gene transfer. Expression of beta-Gal did not differ substantially when the virus was administered to the duodenum, ileum, or colon. When the vector was directly administered to segments of the distal ileum containing a Peyer's patch, transgene expression was approximately 10-fold higher than in segments lacking a Peyer's patch. In the Peyer's patches, a high level of expression was localized to epithelial cells, potentially M cells, overlying the lymphoid follicle domes. Transduction of these cells could have application in DNA-mediated oral vaccination. Administration of an adenoviral vector encoding a secreted alkaline phosphatase to the lumen resulted in expression and secretion of this gene product into the circulation. This finding demonstrates the potential of enterocytes to serve as heterotopic sites for the synthesis of heterologous gene products that would be secreted into the lumen of the intestinal tract or into the bloodstream.
Divergent Synthesis and Biological Evaluation of Carbocyclic α-, <i>iso</i>- and 3′-<i>epi</i>-Nucleosides and their Lipophilic Nucleotide Prodrugs (2006)

A new divergent approach towards carbocyclic α-, iso- and 3′-epi-nucleosides starting from enantiomerically pure (1S,2R)-2-benzyloxymethylcyclopent-3-enol (5) is described. In the key step, isomeric cyclopentanols were condensed with a N3-protected pyrimidine nucleobase using a modified Mitsunobu protocol. Moreover, the conversion into the cycloSal-pronucleotides and the effect of the orientation of the nucleobase on anti-HIV activity are reported.
Fast viewpoint-invariant articulated hand detection combining curve and graph matching (2008)

We present an approach to viewpoint invariant hand detection which merges model based representation of shape and exact curve matching with graph search in order to achieve a very low false alarm rate system able to work in real time. The method proposed makes few assumptions on the articulated object nature and can be applied to recognize other articulated objects as well.
Mesenchymal stem cells derived from synovium, meniscus, anterior cruciate ligament, and articular chondrocytes share similar gene expression profiles (2008)

Mesenchymal stem cells (MSCs) can be obtained from various tissues, and contain common features. However, an increasing number of reports have described variant properties dependent of cell sources. We examined (1) whether MSCs existed in several intraarticular tissues, (2) whether gene expression profiles in intraarticular tissue MSCs closely resembled each other, and (3) whether identified genes were specific to intraarticular tissue MSCs. Human synovium, meniscus, intraarticular ligament, muscle, adipose tissue, and bone marrow were harvested, and colony-forming cells were analyzed. All these cells showed multipotentiality and surface markers typical of MSCs. Gene profiles of intraarticular tissue MSCs and chondrocytes were closer to each other than those of extraarticular tissues MSCs. Among three characteristic genes specific for intraarticular tissue MSCs, we focused on proline arginine-rich end leucine-rich repeat protein (PRELP). Higher expression of PRELP was confirmed in chondrocytes and intraarticular tissue MSCs among three elderly and three young donors. Synovium MSCs stably expressed PRELP, contrarily, bone marrow MSCs increased PRELP expression during in vitro chondrogenesis. In conclusion, MSCs could be isolated from various intraarticular tissues including meniscus and ligament, gene expression profiles of intraarticular tissue MSCs closely resembled each other, and the higher expression of PRELP was characteristic of intraarticular tissue MSCs.
Lipidomics reveals control of <i>Mycobacterium tuberculosis</i> virulence lipids via metabolic coupling (2007)

Mycobacterium tuberculosis synthesizes specific polyketide lipids that interact with the host and are required for virulence. Using a mass spectrometric approach to simultaneously monitor hundreds of lipids, we discovered that the size and abundance of two lipid virulence factors, phthiocerol dimycocerosate (PDIM) and sulfolipid-1 (SL-1), are controlled by the availability of a common precursor, methyl malonyl CoA (MMCoA). Consistent with this view, increased levels of MMCoA led to increased abundance and mass of both PDIM and SL-1. Furthermore, perturbation of MMCoA metabolism attenuated pathogen replication in mice. Importantly, we detected increased PDIM synthesis in bacteria growing within host tissues and in bacteria grown in culture on odd-chain fatty acids. Because M. tuberculosis catabolizes host lipids to grow during infection, we propose that growth of M. tuberculosis on fatty acids in vivo leads to increased flux of MMCoA through lipid biosynthetic pathways, resulting in increased virulence lipid synthesis. Our results suggest that the shift to host lipid catabolism during infection allows for increased virulence lipid anabolism by the bacterium.
Analysis of mammalian central nervous system gene expression and function using bacterial artificial chromosome-mediated transgenesis (2000)

The anatomical complexity of the mammalian central nervous system (CNS) presents special problems for the analysis of CNS gene expression and function. The most difficult challenge is presented by the simple fact that there are hundreds of functionally and morphologically defined cell types in the CNS. Given this complexity, the interpretation of CNS phenotypes is often problematic. The preparation of transgenic mice carrying marked bacterial artificial chromosomes (BACs) provides an important avenue for improving our understanding of CNS-expressed genes and phenotypes. This approach can allow efficient analysis of patterns of gene expression, subcellular localization of their encoded products and neuronal projection patterns. BAC transgenic mice can also provide access to information relevant to gene function based on phenotypes arising from increased gene dosage or expression of activating and dominant-negative alleles. This review will concentrate on these issues and their relevance to the analysis of CNS-expressed genes.
Norepinephrine: Material-Independent, Multifunctional Surface Modification Reagent (2009)

A facile approach for material-independent surface modification using norepinephrine was investigated. pH-induced oxidative polymerization of norepinephrine forms adherent films on vastly different types of material surfaces of noble metals, metal oxides, semiconductors, ceramics, shape-memory alloys, and synthetic polymers. Secondary biochemical functionalizations such as immobilization of proteins and growth of biodegradable polyester on the poly(norepinephrine) films were demonstrated.
Building a Search Tree for a Pilot System of a Rescue Search Robot in a Discretized Random Step Environment (2011)

Rescue robotics applies search and rescue robots to expand rescue capabilities while increasing safety. Mobile robots working at a disaster site are monitored remotely by operators who may not be able to see the site well and select work paths appropriately. Our goal is to provide a “pilot system” that can propose options for traversing 3D debris environments. This requires a special debris path search algorithm and an appropriately defined search tree ensuring smooth exploration. To make a path search feasible in huge real state space we discretize search space and robot movement before a search. In this paper we present path quality estimation and search tree branching function F , which defines search tree building process online through node opening and branching. Well-defined function F removes unsuitable search directions from the search tree and enables dynamic path planning accounting for debris. Exhaustive simulation was used to structure and analyze data. Experiments confirmed the feasibility of our approach.
A Wideband LNA and High-Q Bandpass Filter for Subsampling Direct Conversion Receivers (2008)

In this paper, a cascade of a wideband amplifier and a high-Q bandpass filter (BPF) has been realized in a 0.18mm CMOS technology for the applications of subsampling direct-conversion receivers. The wideband amplifier is designed to obtain the -3dB bandwidth of 5.4GHz, and the high-Q BPF is designed to select a 2.4GHz RF signal for the Bluetooth specifications. The measured results demonstrate 18.8dB power gain at 2.34GHz with 31MHz bandwidth, corresponding to the quality factor of 75. Also, it shows the noise figure (NF) of 8.6dB, and the broadband input matching (S11) of less than -12dB within the bandwidth. The whole chip dissipates 64.8mW from a single 1.8V supply and occupies the area of .
Membrane targeted horseradish peroxidase as a marker for correlative fluorescence and electron microscopy studies (2010)

Synaptic dynamics and reorganization are fundamental features of synaptic plasticity both during synaptic circuit development and in the mature CNS underlying learning, memory, and experience-dependent circuit rearrangements. Combining in vivo time-lapse fluorescence imaging and retrospective electron microscopic analysis provides a powerful technique to decipher the rules governing dynamics of neuronal structure and synaptic connections. Here we have generated a membrane-targeted horseradish peroxidase (mHRP) that allows identification of transfected cells without obscuring the intracellular ultrastructure or organelles and in particular allows identification of synaptic sites using electron microscopy. The expression of mHRP does not affect dendritic arbor growth or dynamics of transfected neurons. Co-expression of EGFP and mHRP was used to study neuronal morphology at both the light and electron microscopic levels. mHRP expression greatly facilitates 3D reconstruction based on serial EM sections. We expect this reagent will be valuable for studying the mechanisms that guide construction of neuronal networks.
Modification of natural polymer via free radical graft copolymerization of 2‐acrylamido‐2‐methyl‐1‐propane sulfonic acid in aqueous media and study of swelling and metal ion sorption behavior (2009)

Abstract In the present article, the graft copolymer of xanthan gum with 2‐acrylamido‐2‐methyl‐1‐propane sulfonic acid (AMPS) was synthesized using potassium bromate/ascorbic acid as a redox initiator in aqueous medium; reaction conditions were optimized to obtain maximum % grafting ratio (% G ). The optimum concentration of BrO ion, ascorbic acid, H + ion, and AMPS for maximum % G were 8.0 × 10 −3 , 2.8 × 10 −3 , 4.0 × 10 −3 , and 33.2 × 10 −3 mol dm −3 , respectively. The maximum % G (433.0) occurred at a minimum concentration of xanthan gum, i.e., 0.6 g dm −3 . The optimum time duration and temperature of the reaction for maximum % of grafting were 180 min and 45°C, respectively. The graft copolymer was characterized by FTIR spectroscopy. The thermal analysis of xanthan gum and prepared graft copolymer was performed in a nitrogen atmosphere to study their thermal behavior. It was observed that the PDT (polymer decomposition temperature) of graft copolymer is lower than that of xanthan gum, whereas the IPDT (integral procedural decomposition temperature) of graft copolymer is higher than that of xanthan gum, making the former more thermally stable. The swelling and metal ion sorption capability of graft copolymer was investigated. The metal ion sorption behavior of graft copolymer was studied for five metal ions (Cu ++ , Ni ++ , Zn ++ , Pb ++ , Hg ++ ). Our results show that the grafted sample absorbs a good amount of water and the metal ion. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
Risk factors and clinical presentation of hepatobiliary carcinoma in patients with primary sclerosing cholangitis: A case-control study (1998)

The reason why 10% to 20% of all patients with primary sclerosing cholangitis (PSC) develop cholangiocarcinoma (CC) remains unknown. The aim of this study was to compare the clinical and biochemical presentation in PSC patients with and without hepatobiliary malignancy and to look for risk factors for developing hepatobiliary carcinoma in PSC. All PSC patients (n = 20) with hepatobiliary carcinoma treated at Huddinge Hospital between 1984 and 1995 were age- and sex-matched to 20 PSC patients with end-stage disease without carcinoma. Clinical and biochemical data from four different occasions (time of onset of PSC, 12 and 6 months before and at the time of cancer diagnosis or liver transplantation [Ltx]) were registered. Seventeen patients had CC, 2 had hepatocellular carcinoma (HCC), and 1 had gallbladder carcinoma (GBC). Eighteen of the cancer patients and 19 controls had inflammatory bowel disease (IBD). The number of patients who smoked or were former smokers was significantly higher in the cancer group (P < .0004). The duration of IBD and PSC, extra- and intrahepatic distribution of PSC, surgical and medical treatments did not differ between the two groups. Abdominal pain was the only symptom that was more frequent among cancer patients at the time of cancer diagnosis/Ltx compared with controls. Evaluation of biochemical data did not indicate a more rapid deterioration among cancer patients. The mean value of the tumor marker, CA 19-9, in the cancer group was 700 kU/L; in the control group, it was 46 kU/L (P < .05), although data were only available in 10 cancer patients and 7 controls. Bile duct dysplasia was found in over 60% of patients with PSC and CC in nontumorous liver tissue apart from the tumor. Clinical and biochemical presentation of PSC patients with and without hepatobiliary carcinoma did not differ during the year before cancer diagnosis/Ltx. Smoking seems to be a risk factor for developing hepatobiliary carcinoma in patients with PSC.
Combining dictionary techniques with extensible markup language (XML)--requirements to a new approach towards flexible and standardized documentation. (1999)

In oncology various international and national standards exist for the documentation of different aspects of a disease. Since elements of these standards are repeated in different contexts, a common data dictionary could support consistent representation in any context. For the construction of such a dictionary existing documents have to be worked up in a complex procedure, that considers aspects of hierarchical decomposition of documents and of domain control as well as aspects of user presentation and models of the underlying model of patient data. In contrast to other thesauri, text chunks like definitions or explanations are very important and have to be preserved, since oncologic documentation often means coding and classification on an aggregate level and the safe use of coding systems is an important precondition for comparability of data. This paper discusses the potentials of the use of XML in combination with a dictionary for the promotion and development of standard conformable applications for tumor documentation.
Testing embedded cores using partial isolation rings (2002)

Intellectual property cores pose a significant test challenge. The core supplier may not give any information about the internal logic of the core, but simply provide a set of test vectors for the core which guarantees a particular fault coverage. If the core is embedded within a larger design, then the problem is how to apply the specified test vectors to the core and how to test the user-defined logic around the core. A simple and fast solution is to place a full isolation ring (i.e., boundary scan) around the core, however, the area and performance overhead for this may not be acceptable in many applications. This paper presents a systematic method for designing a partial isolation ring that provides the same fault coverage as a full isolation ring, but avoids adding MUXes on critical timing paths and reduces area overhead. Efficient ATPG techniques are used to analyze the user-defined logic surrounding the core and identify a maximal set of core inputs and outputs (that includes the critical timing paths) that do not need to be included in the partial isolation ring. Several different partial isolation ring selection strategies that vary in computational complexity are described. Experimental results are shown comparing the different strategies.
A method for reducing multipath artifacts in ultrasonic computed tomography (1982)

Estimates of ultrasonic attenuation based on first-order or moment spectral estimators are often confused by multipath propagation effects. The magnitude of error in attenuation estimates due to multipath for the frequency shift technique is described. A parametric model of multipath propagation effects on the frequency spectrum is introduced and an optimization technique is used to estimate the coefficients of the model. The attenuation estimation performances of the model estimation technique, the frequency shift technique, and a cepstral liftering technique are compared.
Profit determination for vehicle-to-grid (V2G) operation in smart grid environment (2013)

Vehicle-to-Grid (V2G) operation has gained immense popularity in the smart grid environment. Furthermore V2G could offer various ancillary services to the power grid. Frequency regulation is one of the ancillary services which offer highest profit to vehicle owner once participated in regulated market. This paper presents the maximum profit for the vehicle owner who participates in the V2G operation by considering the market prices and user constraints. The profits are calculated based on Regulation Market Clearing Price (RMCP) and Locational Marginal Price (LMP). Since the data pattern for LMP and RCMP are similar throughout the week, the day-ahead price model is used to calculate time and duration of charging activity while maximizing the profit to the vehicle owner through frequency regulation. Results from the study indicated that charging sequence have significant impact on the profit function while meeting the required State-of-Charge (SOC).
A Molecular Chipper technology for CRISPR sgRNA library generation and functional mapping of noncoding regions (2016)

Clustered regularly-interspaced palindromic repeats (CRISPR)-based genetic screens using single-guide-RNA (sgRNA) libraries have proven powerful to identify genetic regulators. Applying CRISPR screens to interrogate functional elements in noncoding regions requires generating sgRNA libraries that are densely covering, and ideally inexpensive, easy to implement and flexible for customization. Here we present a Molecular Chipper technology for generating dense sgRNA libraries for genomic regions of interest, and a proof-of-principle screen that identifies novel cis-regulatory domains for miR-142 biogenesis. The Molecular Chipper approach utilizes a combination of random fragmentation and a type III restriction enzyme to derive a densely covering sgRNA library from input DNA. Applying this approach to 17 microRNAs and their flanking regions and with a reporter for miR-142 activity, we identify both the pre-miR-142 region and two previously unrecognized cis-domains important for miR-142 biogenesis, with the latter regulating miR-142 processing. This strategy will be useful for identifying functional noncoding elements in mammalian genomes.
Continuous User Authentication Based on Context-Emphasized Behavior Profiling (2019)

The restriction of access to software systems is more important than ever. For example, critical data is increasingly being stored on web services that are accessible from anywhere in the world. Yet most primary authentication methods are still largely based on passwords, which are vulnerable to various attacks such as phishing scams and keyloggers. Advanced methods of behavior-based authentication exist, but most are designed for a specific area or system and are not generally applicable. In this paper, we propose a generic continuous authentication scheme for software systems, which supplements existing authentication schemes and works as an auxiliary layer to provide additional protection against impostors. The kernel of our scheme is a novel monitoring engine that detects impostors in real-time based on behavior and context information. We evaluate our scheme on a dataset consisting of real users' historical records provided by our industrial partner, and the results demonstrate that our approach achieves a high classification accuracy with only a short delay in detection, allowing for real-time, continuous authentication.
Standard-setting measurement issues and the relevance of research (2007)

(2007). Standard-setting measurement issues and the relevance of research. Accounting and Business Research: Vol. 37, Special Issue: International Accounting Policy Forum, pp. 7-15.
Enzyme replacement therapy in Gaucher's and Fabry's disease. (1977)

Glucocerebrosidase and ceramidetrihexoside-alpha-galactosidase were obtained in a high degree of purity from human placental tissue. The enzymes were infused in Gaucher and Fabry patients, respectively. Following the administration of the proteins to supplement the genetically determined deficiencies, there resulted a specific reduction in the accumulated hlycolipids in the circulation and liver. These results indicate that enzyme replacement may provide hope for the clinical treatment of these disorders.
[Results of the dye dilution technic in peripheral arteriovenous fistulas and hyperthyroidism]. (1975)

Dye dilution curves (DDC) from 35 patients with arteriovenous fistulas and from 22 patients with hyperthyreoidism were performed and compared with results in 122 healthy subjects. In most cases Cardiogreen was injected into an antecubital vein during reactive hyperaemia. On the arterial side, dye concentrations were recorded by ear oximetry. The appearance time was shortened in most cases. During dilution time dye curves were interrupted by an early recirculation in hyperthyreoidism, whereas in 29 patients with haemodialysis fistulas this interruption was discrete and detectable only when compared with results after occlusion of the fistulas. Different shapes of dilution curves were observed: 1. in most cases DDC seemed to be normal or near normal, often with an accelerated indicator passage; 2. DDC with an interruption of the dilution limb by an early recirculation; 3. DDD, showing a hump of the dilution limb; 4. asymmetrical DDC or DDC with a flat shoulder of the dilution limb and without a recirculation wave. Patients with hyperthyreoidism and arteriovenous fistulas had no different shapes of dilution curves. The results are discussed with special reference to the DDC in patients with central left-to-right shunts.
Hospital emergency preparedness and response during Superstorm Sandy. (2015)

This article presents the findings of a report by the HHS Office of Inspector General (OIG) on the performance of 172 Medicare-certified hospitals in the New York Metropolitan Area before, during, and after Sandy. It makes recommendations on how to close gaps that were found in emergency planning and execution for a disaster of this magnitude. To download the complete 40-page report and a Podcast based on it, go to http://oig.hhs.gov/oei/ reports/oei-06-13-00260. asp.