gebhart/patrepeval huggingface dataset:
Methods for extracting genomic DNA from whole blood samples : current perspectives (2014)

Deoxyribonucleic acid (DNA) extraction has considerably evolved since it was initially performed back in 1869. It is the first step required for many of the available downstream applications used in the field of molecular biology. Whole blood samples are one of the main sources used to obtain DNA, and there are many different protocols available to perform nucleic acid extraction on such samples. These methods vary from very basic manual protocols to more sophisticated methods included in automated DNA extraction protocols. Based on the wide range of available options, it would be ideal to determine the ones that perform best in terms of cost-effectiveness and time efficiency. We have reviewed DNA extraction history and the most commonly used methods for DNA extraction from whole blood samples, highlighting their individual advantages and disadvantages. We also searched current scientific literature to find studies comparing different nucleic acid extraction methods, to determine the best available choice. Based on our research, we have determined that there is not enough scientific evidence to support one particular DNA extraction method from whole blood samples. Choosing a suitable method is still a process that requires consideration of many different factors, and more research is needed to validate choices made at facilities around the world.
Automatic speech recognition for webcasts (2006)

The increased availability of broadband connections has recently led to an increase in the use of Internet broadcasting (webcasting). Most webcasts are archived and accessed numerous times retrospectively. One challenge to skimming and browsing through such archives is the lack of text transcripts of the webcast's audio channel. This paper describes a procedure for prototyping an Automatic Speech Recognition (ASR) system that generates realistic transcripts of any desired Word Error Rate (WER), thus overcoming the drawbacks of both prototype-based and Wizard of Oz simulations. We used such a system in a user study showing that transcripts with WERs less than 25% are acceptable for use in webcast archives. As current ASR systems can only deliver, in realistic conditions, Word Error Rates (WERs) of around 45%, we also describe a solution for reducing the WER of such transcripts by engaging users to collaborate in a wiki fashion on editing the imperfect transcripts obtained through ASR.
Dipeptidyl peptidase IV expression in cancer and stromal cells of human esophageal squamous cell carcinomas, adenocarcinomas and squamous cell carcinoma cell lines (2008)

Dipeptidyl peptidase IV (DPPIV) is a transmembrane serine protease which is involved in the process of tumor invasion and development of metastases in human cancers. The aim of this study was to investigate the expression of DPPIV in cancer and stromal cells of both esophageal adenocarcinoma and squamous cell carcinoma (SCC). Tissue material from 159 patients was analyzed using immunohistochemistry. Western blotting was performed on cell lines and fresh frozen tissue sections. Results were compared with clinicopathological features. Evaluation of the immunohistochemical findings revealed significant differences between DPPIV expression in carcinoma cells and stromal cells, depending on the histological tumor type. A significantly higher level of DPPIV was found in adenocarcinomas compared to SCCs while no DPPIV was detected in normal esophageal epithelium. Overexpression of DPPIV in patients with adenocarcinoma was additionally associated with distant metastases. Thus, differences of DPPIV level in esophageal carcinomas compared with normal epithelium showed that esophageal malignancies were associated with an increased amount of cell surface-bound DPPIV. Radiotherapy in patients had no impact on DPPIV expression in analyzed tissue samples. There was no correlation between DPPIV expression in cancer or stromal cells and survival of the patients.
Marburg Hemorrhagic Fever in Durba and Watsa, Democratic Republic of the Congo: Clinical Documentation, Features of Illness, and Treatment (2007)

The objective of the present study was to describe day of onset and duration of symptoms of Marburg hemorrhagic fever (MHF), to summarize the treatments applied, and to assess the quality of clinical documentation. Surveillance and clinical records of 77 patients with MHF cases were reviewed. Initial symptoms included fever, headache, general pain, nausea, vomiting, and anorexia (median day of onset, day 1-2), followed by hemorrhagic manifestations (day 5-8+), and terminal symptoms included confusion, agitation, coma, anuria, and shock. Treatment in isolation wards was acceptable, but the quality of clinical documentation was unsatisfactory. Improved clinical documentation is necessary for a basic evaluation of supportive treatment.
Exploring sparsity of firing activities and clock gating for energy-efficient recurrent spiking neural processors (2017)

As a model of recurrent spiking neural networks, the Liquid State Machine (LSM) offers a powerful brain-inspired computing platform for pattern recognition and machine learning applications. While operated by processing neural spiking activities, the LSM naturally lends itself to an efficient hardware implementation via exploration of typical sparse firing patterns emerged from the recurrent neural network and smart processing of computational tasks that are orchestrated by different firing events at runtime. We explore these opportunities by presenting a LSM processor architecture with integrated on-chip learning and its FPGA implementation. Our LSM processor leverage the sparsity of firing activities to allow for efficient event-driven processing and activity-dependent clock gating. Using the spoken English letters adopted from the TI46 [1] speech recognition corpus as a benchmark, we show that the proposed FPGA-based neural processor system is up to 29% more energy efficient than a baseline LSM processor with little extra hardware overhead.
Laser medicine (1990)

Duke University, Durham, North Carolina, and US Army Environmental Hygiene Agency, Aberdeen Proving Ground, Maryland, USA
Characterization of a recombinant chimeric plasminogen activator composed of a fibrin fragment‐<scp>d</scp>‐dimer‐specific humanized monoclonal antibody and a truncated single‐chain urokinase (1992)

A recombinant chimeric plasminogen activator, MA-15C5Hu/scu-PA-32k, composed of a humanized fibrin fragment-D-dimer-specific monoclonal antibody (MA-15C5Hu) and a recombinant low-molecular-mass single-chain urokinase-type plasminogen activator, comprising amino acids Leu144-Leu411 (scu-PA-32k), was produced by cotransfecting Chinese hamster ovary (CHO) cells with the cDNA encoding the MA-15C5Hu light-chain sequence and the cDNA encoding the MA-15C5Hu heavy-chain sequence fused with the cDNA encoding scu-PA-32k. Purified MA-15C5Hu/scu-PA-32k migrated as a 215-kDa band on non-reducing SDS/PAGE, which is consistent with a molecule composed of one antibody and two scu-PA-32k moieties. However, the chimera was obtained as a mixture of single-chain u-PA-32k (37%) and amidolytically inactive (50%) and active (13%) two-chain u-PA-32k, the latter of which was removed by immunoadsorption on a monoclonal antibody specific for two-chain urokinase. The fragment-D-dimer affinity and enzymatic properties of MA-15CHu/scu-PA-32k were similar to those of MA-15C5Hu or of scu-PA-32k. In an in vitro system composed of a 125I-fibrin-labeled human plasma clot submerged in citrated human plasma, MA-15C5Hu/scu-PA-32k had a 12-fold higher fibrinolytic potency than scu-PA-32k: 50% lysis in 2 h required 0.43 +/- 0.12 micrograms u-PA-32k equivalent of the chimera/ml versus 5.4 +/- 0.3 micrograms/ml of scu-PA-32k (mean +/- SEM, n = 4). Addition of purified fibrin fragment-D dimer reduced the fibrinolytic potency of MA-15C5Hu/scu-PA-32k in a concentration-dependent way, indicating that the increased potency is the result of antibody targeting. Thus, a recombinant humanized antifibrin antibody/u-PA chimera has been obtained in which only the variable domains of the antibody moiety are of non-human origin. The chimera has intact antigen-binding capacity, u-PA enzymatic activity and a significantly increased fibrinolytic potency in a plasma medium in vitro.
Edge-Directed Error Diffusion Halftoning (2006)

In this letter, we propose two simple extensions of the existing error diffusion (ED) halftoning technique: one stops the diffusion at edge pixels, and the other tunes the support of the diffusion kernel to match the local edge orientation. Experimental results are used to show that the proposed edge-directed ED schemes achieve noticeably better performance over existing ED with edge enhancement for a certain class of gray-scale images.
Conceptual and statistical issues in the validation of analytic dilution assays for pharmaceutical applications (1998)

The discovery, research, and development of a pharmaceutical product relies on the availability of validated assays for assessing product characteristics and drug effects in vivo and in vitro. Development of a validated assay is a multifaceted activity that provides many interesting challenges for bioanalytical chemists and statisticians. In this paper, the similarity condition for fundamental validity of an analytic dilution assay is reviewed as a basic concept underlying the validation of assays for pharmaceutical applications. The distinction between the validity and the acceptability of an assay is considered in terms of the characteristics evaluated during four stages of validation. Recent guidelines on the validation of analytical procedures published by the U.S. Food and Drug Administration are appraised from a statistical perspective, and statistical issues in the validation process are discussed.
Gaussian mixture modeling for indoor positioning WIFI systems (2015)

Different location determination methods using wireless signal strength have been proposed to improve the location accuracy and mitigate the multipath problem in indoor environment. In this paper, a fingerprinting-probabilistic approach for indoor localization using wireless technology is proposed. The method is based on the use of the Gaussian Mixture Model (GMM) to approximate the probability distribution of the strength of the signal received by a mobile from Access Points (AP). This probability distribution is then used to infer the mobile location. The performance of the proposed method is compared experimentally to that of another powerful method. The comparison shows the effectiveness of the GMM method.
Stereochemistry of Endogenous Palmitic Acid Ester of 9-Hydroxystearic Acid and Relevance of Absolute Configuration to Regulation (2017)

Lipids have fundamental roles in the structure, energetics, and signaling of cells and organisms. The recent discovery of fatty acid esters of hydroxy fatty acids (FAHFAs), lipids with potent antidiabetic and anti-inflammatory activities, indicates that our understanding of the composition of lipidome and the function of lipids is incomplete. The ability to synthesize and test FAHFAs was critical in elucidating the roles of these lipids, but these studies were performed with racemic mixtures, and the role of stereochemistry remains unexplored. Here, we synthesized the R- and S- palmitic acid ester of 9-hydroxystearic acid (R-9-PAHSA, S-9-PAHSA). Access to highly enantioenriched PAHSAs enabled the development of a liquid chromatography-mass spectrometry (LC-MS) method to separate and quantify R- and S-9-PAHSA, and this approach identified R-9-PAHSA as the predominant stereoisomer that accumulates in adipose tissues from transgenic mice where FAHFAs were first discovered. Furthermore, biochemical analysis of 9-PAHSA biosynthesis and degradation indicate that the enzymes and pathways for PAHSA production are stereospecific, with cell lines favoring the production of R-9-PAHSA and carboxyl ester lipase (CEL), a PAHSA degradative enzyme, selectively hydrolyzing S-9-PAHSA. These studies highlight the role of stereochemistry in the production and degradation of PAHSAs and define the endogenous stereochemistry of 9-PAHSA in adipose tissue. This information will be useful in the identification and characterization of the pathway responsible for PAHSA biosynthesis, and access to enantiopure PAHSAs will elucidate the role of stereochemistry in PAHSA activity and metabolism in vivo.
Rapid-sweep polarography of cystine (1971)

Research Article| February 01 1971 Rapid-sweep polarography of cystine W Lee W Lee Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1971) 121 (3): 563–565. https://doi.org/10.1042/bj1210563 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation W Lee; Rapid-sweep polarography of cystine. Biochem J 1 February 1971; 121 (3): 563–565. doi: https://doi.org/10.1042/bj1210563 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1971 The Biochemical Society1971 Article PDF first page preview Close Modal You do not currently have access to this content.
Pathogenesis of Arteriovenous Malformations in the Absence of Endoglin (2010)

AVMs develop when an angiogenic stimulus is combined with endoglin depletion. Moreover, AVM formation appears to result from the combination of delayed vascular remodeling and an inappropriate endothelial cell proliferation response in the absence of endoglin.
Effect of Permeation Enhancers on Permeation Kinetics of Idebenone through the Bovine Buccal Mucosa (2011)

circumvent extensive first-pass metabolism and avoid degradation in the gastrointestinal tract by enzymes and bacteria. This system serves as the better solution for the administration of drugs having low bioavailability like idebenone. Idebenone is synthetic analogue of coenzyme Q10 (CoQ10), a vital cell membrane antioxidant administered in friedreich's ataxia, duchenne muscular dystrophy, becker muscular dystrophy, alzheimer's disease, leber's hereditary optic neuropathy, MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis with stroke-like episodes), parkinson's disease mitochondrial myopathies etc.. The drug is practically water insoluble and shows limited bioavailability after oral administration due to a significant degree of first pass metabolism (99%). The low bioavailability of drug demands frequent dosing, hence the aim of the study was to demonstrate in vitro enhancement of drug penetration using Keshary – Chien diffusion cell. For demonstration varying concentrations of penetration enhancers and drug were prepared. Different penetration enhancers used were sodium lauryl sulphate, disodium ethylene diamine tetraacetic acid, urea, sorbitol, oleic acid, dimethylsulphoxide, physical mixtures with beta cyclodextrin, hydroxypropyl beta cyclodextrin, and complex of drug with hydroxypropyl beta cyclodextrin through buccal drug delivery system and tested for highest penetration. Drug complex with hydroxyl propyl cyclodextrin showed maximum enhancement ratio of 45.93 when compared with the enhancement ratio of other penetration enhances which ranged from 1.08 to 13.52. Hence, when compared with different penetration enhancers, this inclusion complex of idebenone with HPsCD can itself act as a best penetration enhancer for buccal drug delivery of idebenone. Overall, we can say that Idebenone Inclusion complex with HPsCD is the best way of enhancing the permeation of drug through buccal mucosa.
Hydrogenation for Low <i>Trans</i> and High Conjugated Fatty Acids (2005)

Hydrogenated vegetable oils contain of trans fatty acids. Because of the increased health concern about trans fatty acids, new hydrogenations have been studied to seek ways for substantial reduction of the trans fatty acids in the hydrogenated vegetable oils. This paper reviews new hydrogenation processes such as electrocatalytic hydrogenation, precious catalyst hydrogenation, and supercritical fluid state hydrogen, which have shown promising results for the reduction of trans fatty acids below the level of 8%. This paper also reviews the recently introduced hydeogenation technique for high accumulation of conjugated linoleic acids, beneficiary functional components. The hydrogenated vegetable oils with high quantity conjugated linoleic acid might provide the possibility for the utilization of hydrogenated oils as health-prompting food ingredients.
Control of thermal deformation in dielectric mirrors using mechanical design and atomic layer deposition (2009)

A mechanical design technique for optical coatings that simultaneously controls thermal deformation and optical reflectivity is reported. The method requires measurement of the refractive index and thermal stress of single films prior to the design. Atomic layer deposition was used for deposition because of the high repeatability of the film constants. An Al2O3/HfO2 distributed Bragg reflector was deposited with a predicted peak reflectivity of 87.9% at 542.4 nm and predicted edge deformation of -360 nm/K on a 10 cm silicon substrate. The measured peak reflectivity was 85.7% at 541.7 nm with an edge deformation of -346 nm/K.
The BiSearch web server (2006)

BiSearch web server is a useful tool for primer-design for any DNA template and especially for bisulfite-treated genomes. The ePCR tool for fast detection of mispriming sites and alternative PCR products in cDNA libraries and native or bisulfite-treated genomes are the unique features of the new version of BiSearch software.
Synthesis and properties of 5,10,15,20‐tetra[(4‐alkoxy‐3‐ethyloxy)phenyl]porphyrin hydroxylanthanide liquid crystal complexes (2005)

Twelve 5, 10, 15, 20‐tetra[(4‐alkoxy‐3‐ethyloxy)phenyl]porphyrin hydroxylanthanide complexes Ln[(C n OEOP)4P](OH) (n = 12, 14, 16;Ln = Tb, Dy, Er, Yb) and three ligands have been synthesized and their composition, structure and spectral properties studied. Their liquid crystalline behaviour is also presented. Differential scanning calorimetry and polarizing optical microscopy reveal that all exhibit a discotic liquid crystalline phase. X‐ray diffraction shows that the mesophase is a hexagonal columnar, Colh. The lanthanide ion, which is coordinated to the four nitrogen atoms of the porphyrin and to the oxygen atom of the hydroxyl group, is out of the porphyrin molecular plane. All the complexes are stable below 200°C and undergo complete decomposition at 800°C. The fluorescence quantum yields of the lanthanide complexes are much lower than those of the corresponding ligands. The electrochemical studies show that the redox potentials do not change on varying the chain length.
Directional cloaking of flexural waves in a plate with a locally resonant metamaterial (2015)

This paper deals with the numerical design of a directional invisibility cloak for backward scattered elastic waves propagating in a thin plate (A0 Lamb waves). The directional cloak is based on a set of resonating beams that are attached perpendicular to the plate and are arranged at a sub-wavelength scale in ten concentric rings. The exotic effective properties of this locally resonant metamaterial ensure coexistence of bandgaps and directional cloaking for certain beam configurations over a large frequency band. The best directional cloaking was obtained when the resonators' length decreases from the central to the outermost ring. In this case, flexural waves experience a vanishing index of refraction when they cross the outer layers, leading to a frequency bandgap that protects the central part of the cloak. Numerical simulation shows that there is no back-scattering in these configurations. These results might have applications in the design of seismic-wave protection devices.
Coupled-cavity effects in FM semiconductor lasers (1999)

Numerical simulations of frequency modulated (FM) external cavity semiconductor lasers have been performed and a range of dynamic and spectral phenomena observed. It is shown that FM lasing action can be suppressed due to changes in the FM modulation frequency. Coupled cavity effects are seen to be significant in the development of a broad spectral emission associated with experimentally observed coherence collapse in such a configuration.
Preparation and Characteristics of Strontium Containing Bioactive CaSiO<sub>3</sub> Ceramics (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
The Light Elements: What is Known, What is Controversial (2000)

The light elements are essential, because their primordial abundances are linked to the general parameters of the universe (at least in the Big Bang theory). Some of the light elements are fragile, and the interpretation of their abundances in stars requires a good knowledge of the stellar structure. The stellar abundances have to be known with a considerable accuracy, challenging the current level of representation of the stellar atmospheres. It is also difficult to reach accurate abundances in the gas : interstellar, H II regions, PN, intergalactic¨. On the other hand, the fragile light elements are important probes of the stellar interiors, and their observation helps to the determination of reliable models, which in turn will improve the accuracy of stellar abundances. A part of this symposium is devoted to this probing aspect. The talks (and many high quality posters) which build this symposium, cover all these aspects. I will try here to point out the controversial points and the reasonably well known facts. We expect from discussions, both formal and informal, a number of (eagerly awaited for) clarifications.
Effect of reducing agents in an aerobic amino acid fermentation (1992)

This study focuses on the effects of the reducing agents, dithiothreitol (DTT) and glutathione (GSH), on amino acid production in aerobically growing Corynebacterium glutamicum. The problem of reducing agent addition affecting the dissolved oxygen level was solved by positioning the culture at a high dissolved oxygen level and feeding the reducing agent into the fermentor. We show that it is possible to lower the redox potential even in a highly aerobic environment. The addition of DTT to the fermentation during the growth phase caused a significant increase in specific amino acid production rate and total amino acids produced, as compared with a control. In contrast, GSH had an inhibitory effect.