gebhart/patrepeval huggingface dataset:
Identification of anthrax toxin genes in a<i>Bacillus cereus</i>associated with an illness resembling inhalation anthrax (2004)

Bacillus anthracis is the etiologic agent of anthrax, an acute fatal disease among mammals. It was thought to differ from Bacillus cereus, an opportunistic pathogen and cause of food poisoning, by the presence of plasmids pXO1 and pXO2, which encode the lethal toxin complex and the poly-gamma-d-glutamic acid capsule, respectively. This work describes a non-B. anthracis isolate that possesses the anthrax toxin genes and is capable of causing a severe inhalation anthrax-like illness. Although initial phenotypic and 16S rRNA analysis identified this isolate as B. cereus, the rapid generation and analysis of a high-coverage draft genome sequence revealed the presence of a circular plasmid, named pBCXO1, with 99.6% similarity with the B. anthracis toxin-encoding plasmid, pXO1. Although homologues of the pXO2 encoded capsule genes were not found, a polysaccharide capsule cluster is encoded on a second, previously unidentified plasmid, pBC218. A/J mice challenged with B. cereus G9241 confirmed the virulence of this strain. These findings represent an example of how genomics could rapidly assist public health experts responding not only to clearly identified select agents but also to novel agents with similar pathogenic potentials. In this study, we combined a public health approach with genome analysis to provide insight into the correlation of phenotypic characteristics and their genetic basis.
Lytic polysaccharide monooxygenases: a crystallographer's view on a new class of biomass-degrading enzymes (2016)

Lytic polysaccharide monooxygenases (LPMOs) are a new class of microbial copper enzymes involved in the degradation of recalcitrant polysaccharides. They have only been discovered and characterized in the last 5-10 years and have stimulated strong interest both in biotechnology and in bioinorganic chemistry. In biotechnology, the hope is that these enzymes will finally help to make enzymatic biomass conversion, especially of lignocellulosic plant waste, economically attractive. Here, the role of LPMOs is likely to be in attacking bonds that are not accessible to other enzymes. LPMOs have attracted enormous interest since their discovery. The emphasis in this review is on the past and present contribution of crystallographic studies as a guide to functional understanding, with a final look towards the future.
A New Cross-Linkable Oxygen Sensor Covalently Bonded into Poly(2-hydroxyethyl methacrylate)-<i>co</i>-Polyacrylamide Thin Film for Dissolved Oxygen Sensing (2010)

A new oxygen sensor, compound 2, was synthesized through a chemical modification of a popularly used oxygen sensor of platinum(II)-5,10,15,20-tetrakis-(2,3,4,5,6-pentafluorophenyl)-porphyrin (PtTFPP). The new sensor compound 2 possesses four crosslinkable methacrylate functional moieties, enabling it to be polymerized and crosslinked with other monomers for polymer sensing film (also called membrane) preparation. Using this characteristic, compound 2 was covalently bonded to hydrophilic poly(2-hydroxyethyl methacrylate)-co-polyacrylamide (referred to as PHEMA to simplify) and hydrophobic polystyrene (PS) films. To better understand the advantages and disadvantages of chemical crosslinking approaches and the influence of polymer matrices on sensing performance, PtTFPP was physically incorporated into the same PHEMA and PS matrices to compare. Response to dissolved oxygen (DO), leaching of the sensor molecules from their matrices, photostability of the sensors, and response time to DO changes were studied. It was concluded that the chemical crosslinking of the sensor compound 2 in polymer matrices: (i) alleviated the leaching problem of sensor molecules which usually occurred in the physically doped sensing systems and (ii) significantly improved sensors' photostability. The PHEMA matrix was demonstrated to be more suitable for oxygen sensing than PS, because for the same sensor molecule, the oxygen sensitivity in PHEMA film was higher than that in PS and response time to DO change in the PHEMA film was faster than that in PS. It was the first time oxygen sensing films were successfully prepared using biocompatible hydrophilic PHEMA as a matrix, which does not allow leaching of the sensor molecules from the polymer matrix, has a faster response to DO changes than that of PS, and does not present cytotoxicity to human lung adenocarcinoma epithelial cells (A549). It is expected that the new sensor compound 2 and its similar compounds with chemically crosslinking characteristics can be widely applied to generate many interesting oxygen sensing materials for studying biological phenomena.
A second locus for hereditary hemorrhagic telangiectasia maps to chromosome 12. (1995)

Hereditary hemorrhagic telangiectasia (HHT) or Osler-Rendu-Weber (ORW) disease is an autosomal dominant vascular dysplasia. Initial linkage studies identified an ORW gene localized to 9q33-q34 but with some families clearly excluding this region. A probable correlation in clinical phenotype between the 9q3-linked families and unlinked families was described with a significantly lower incidence of pulmonary arteriovenous malformations observed in the unlinked families. In this study we examined four unrelated ORW families for which linkage to chromosome 9q33-q34 has been previously excluded. Linkage was established for all four families to markers on chromosome 12, with a combined maximum lod score of 10.77 (theta = 0.04) with D12S339. Mapping of crossovers using haplotype analysis indicated that the candidate region lies in an 11-CM interval between D12S345 and D12S339, in the pericentromeric region of chromosome 12. A map location for a second ORW locus is thus established that exhibits a significantly reduced incidence of pulmonary involvement.
Laser sintering of blended Al‐Si powders (2012)

Purpose The purpose of this paper is to study the effects of particle size distribution, component ratio, particle packing arrangement, and chemical constitution on the laser sintering behaviour of blended hypoeutectic Al‐Si powders. Design/methodology/approach A range of bimodal and trimodal powder blends were created through mixing Al‐12Si and pure aluminium powder. The powder blends were then processed using selective laser sintering to investigate the effect of alloy composition, powder particle size and bed density on densification and microstructural evolution. Findings For all of the powder blends the sintered density increases with the specific laser energy input until a saturation level is reached. Beyond this saturation level no further increase in sintered density is obtained for an increase in specific laser energy input. However, the peak density achieved for a given blend varied significantly with the chemical constitution of the alloy, peaking at approximately 9 wt% Si. The tap density of the raw powder mixture (assumed to be representative of bed density) was also a significant factor. Originality/value This is the first study to consider the usefulness of silicon as an alloying element in aluminium alloys to be processed by selective laser sintering. In addition the paper outlines the key factors in optimising processing parameters and powder properties in order to attain sound sinterability for direct laser sintered parts.
Solution-Processed Sintered Nanocrystal Solar Cells via Layer-by-Layer Assembly (2011)

Solar cells made by high temperature and vacuum processes from inorganic semiconductors are at a perceived cost disadvantage when compared with solution-processed systems such as organic and dye-sensitized solar cells. We demonstrate that totally solution processable solar cells can be fabricated from inorganic nanocrystal inks in air at temperature as low as 300 °C. Focusing on a CdTe/ZnO thin-film system, we report solar cells that achieve power conversion efficiencies of 6.9% with greater than 90% internal quantum efficiency. In our approach, nanocrystals are deposited from solution in a layer-by-layer process. Chemical and thermal treatments between layers induce large scale grain formation, turning the 4 nm CdTe particles into pinhole-free films with an optimized average crystallite size of ∼70 nm. Through capacitance-voltage measurements we demonstrate that the CdTe layer is fully depleted which enables the charge carrier collection to be maximized.
An FSM based GUI test automation model (2010)

Graphical User Interfaces (GUIs) constitute a large proportion of today's software and are becoming more and more complex. Testing the correctness of GUIs and their underlying software is paramount for providing quality software products. Manual testing is extremely slow and unacceptably expensive. We present a new technique which enables the process of generating test cases and testing automation, based on an innovative model. Given a GUI based application, the set of GUI states and their running logic is modeled as a finite state machine (FSM). The efficiency of the model is formally analyzed and compared with event flow graph (EFG) model. The results show that our model is more efficient in storage.
A Review on Composite Liposomal Technologies for Specialized Drug Delivery (2011)

The combination of liposomes with polymeric scaffolds could revolutionize the current state of drug delivery technology. Although liposomes have been extensively studied as a promising drug delivery model for bioactive compounds, there still remain major drawbacks for widespread pharmaceutical application. Two approaches for overcoming the factors related to the suboptimal efficacy of liposomes in drug delivery have been suggested. The first entails modifying the liposome surface with functional moieties, while the second involves integration of pre-encapsulated drug-loaded liposomes within depot polymeric scaffolds. This attempts to provide ingenious solutions to the limitations of conventional liposomes such as short plasma half-lives, toxicity, stability, and poor control of drug release over prolonged periods. This review delineates the key advances in composite technologies that merge the concepts of depot polymeric scaffolds with liposome technology to overcome the limitations of conventional liposomes for pharmaceutical applications.
Determination of the GaN/AlN band offset via the (-/0) acceptor level of iron (1994)

A characteristic infrared luminescence spectrum, dominated by a zero-phonon line at 1.30 eV, has been observed on AlN polycrystalline material. It is assigned to the spin-forbidden internal 3d–3d transition 4T1(G)→6A1(S) of Fe3+Al(3d5). By photoluminescence excitation spectroscopy the (-/0) acceptor level of iron in AlN could be located at EV+3.0 eV. The corresponding value for iron in GaN is EV+2.5 eV. From these values, the valence-band offset in AlN/GaN heterojunctions is predicted as ΔEV=0.5 eV, the conduction-band offset as ΔEC=2.3 eV.
The transrepressive activity of peroxisome proliferator-activated receptor alpha is necessary and sufficient to prevent liver fibrosis in mice (2014)

The transrepression activity of PPAR-α on chronic liver inflammation is sufficient to prevent progression of NASH to liver fibrosis. Dissociated PPAR-α agonists, selectively modulating PPAR-α transrepression activity, could thus be an option to prevent NASH and fibrosis progression.
Development of a Multichannel Microfluidic Analysis System Employing Affinity Capillary Electrophoresis for Immunoassay (2001)

A six-channel microfluidic immunoassay device with a scanned fluorescence detection system is described. Six independent mixing, reaction, and separation manifolds are integrated within one microfluidic wafer, along with two optical alignment channels. The manifolds are operated simultaneously and data are acquired using a singlepoint fluorescence detector with a galvano-scanner to step between separation channels. A detection limit of 30 pM was obtained for fluorescein with the scanning detector, using a 7.1-Hz sampling rate for each of the reaction manifolds and alignment channels (57-Hz overall sampling rate). Simultaneous direct immunoassays for ovalbumin and for anti-estradiol were performed within the microfluidic device. Mixing, reaction, and separation could be performed within 60 s in all cases and within 30 s under optimized conditions. Simultaneous calibration and analysis could be performed with calibrant in several manifolds and sample in the other manifolds, allowing a complete immunoassay to be run within 30 s. Careful chip conditioning with methanol, water, and 0.1 M NaOH resulted in peak height RSD values of 3-8% (N = 5 or 6), allowing for cross-channel calibration. The limit of detection (LOD) for an anti-estradial assay obtained in any single channel was 4.3 nM. The LOD for the cross-channel calibration was 6.4 nM. Factors influencing chip and detection system design and performance are discussed in detail.
소프트웨어공학 : 프로젝트 인도율 그룹 분할 방법을 이용한 소프트웨어 개발노력 추정 (2002)

소프트웨어 개발시 중요하게 제기되는 문제점으로 소프트웨어 생명주기의 초기단계에서 개발에 투입될 노력과 비용을 추정하는 능력이다. 측정된 소프트웨어 규모인 기능점수 (FP, Function Point)로부터 프로젝트 개발에 소요되는 노력과 비용을 추정하는 회귀모델들이 제안되었다. 그러나 이들 제안된 모델들은 사용한 표본의 크기가 작고, 과거에 개발된 프로젝트를 대상으로 하고 있다. 1990년대에 개발된 789개 소프트웨어 개발 프로젝트들에 투입된 개발노력에 이들 모델을 적용한 결과 결정계수 가 0.53 이하로 데이터의 변동을 설명하였다. 본 논문은 프로젝트 인도율 (PDR)을 이용하여 동질성을 갖는 그룹으로 분류하여 개발노력을 추정하는 모델을 제안하였다. 제안된 모델은 랜덤한 잔차 분포를 갖고 있고, 대부분의 PDR 범위에서 0.99 이상의 결정계수로 데이터의 변동을 설명하였다.
Development and Implantation of a Minimally Invasive Wireless Subretinal Neurostimulator (2009)

A wirelessly operated, minimally invasive retinal prosthesis was developed for preclinical chronic implantation studies in Yucatan minipig models. The implant conforms to the outer wall of the eye and drives a microfabricated polyimide stimulating electrode array with sputtered iridium oxide electrodes. This array is implanted in the subretinal space using a specially designed ab externo surgical technique that fixes the bulk of the prosthesis to the outer surface of the sclera. The implanted device is fabricated on a host polyimide flexible circuit. It consists of a 15-channel stimulator chip, secondary power and data receiving coils, and discrete power supply components. The completed device is encapsulated in poly(dimethylsiloxane) except for the reference/counter electrode and the thin electrode array. In vitro testing was performed to verify the performance of the system in biological saline using a custom RF transmitter circuit and primary coils. Stimulation patterns as well as pulse strength, duration, and frequency were programmed wirelessly using custom software and a graphical user interface. Wireless operation of the retinal implant has been verified both in vitro and in vivo in three pigs for more than seven months, the latter by measuring stimulus artifacts on the eye surface using contact lens electrodes.
CD40 Ligation Ablates the Tolerogenic Potential of Lymphoid Dendritic Cells (2001)

The outcome of dendritic cell (DC) presentation of P815AB, a tolerogenic tumor/self peptide, depends on a balance between the respective immunogenic and tolerogenic properties of myeloid (CD8 alpha(-)) and lymphoid (CD8 alpha(+)) DC. We have previously shown that CD8(-) DC can be primed by IL-12 to overcome inhibition by the CD8(+) subset and initiate immunogenic presentation in vivo when the two types of peptide-pulsed DC are cotransferred into recipient hosts. IFN-gamma enhances the inhibitory activity of CD8(+) DC on Ag presentation by the other subset, blocking the ability of IL-12-treated CD8(-) DC to overcome suppression. We report here that CD40 ligation on lymphoid DC ablated their inhibitory function on Ag presentation as well as IFN-gamma potentiation of the effect. CD40 modulation of IFN-gamma action on lymphoid DC involved a reduction in IFN-gamma R expression and tryptophan-degrading ability. This effect was accompanied in vitro by an impaired capacity of the CD40-modulated and IFN-gamma-treated DC to initiate T cell apoptosis. In vivo, not only did CD40 triggering on lymphoid DC abrogate their tolerogenic activity, but it also induced the potential for immunogenic presentation of P815AB. Importantly, a pattern similar to P815AB as well as CD40 modulation of lymphoid DC function were observed on testing reactivity to NRP, a synthetic peptide mimotope recognized by diabetogenic CD8(+) T cells in nonobese diabetic mice.
Gene transfer of Fas ligand induces tumor regression <i>in vivo</i> (1997)

The Fas-Fas ligand (FasL) system plays an important role in the induction of lymphoid apoptosis and has been implicated in the suppression of immune responses. Herein, we report that gene transfer of FasL inhibits tumor cell growth in vivo. Although such inhibition is expected in Fas+ tumor cell lines, marked regression was unexpectedly observed after FasL gene transfer into the CT26 colon carcinoma that does not express Fas. Infection by an adenoviral vector encoding FasL rapidly eliminated tumor masses in the Fas+ Renca tumor by inducing cell death, whereas the elimination of Fas- CT26 cells was mediated by inflammatory cells. Analysis of human malignancies revealed Fas, but not FasL, expression in a majority of tumors and susceptibility to FasL in most Fas+ cell lines. These findings suggest that gene transfer of FasL generates apoptotic responses and induces potent inflammatory reactions that can be used to induce the regression of malignancies.
Photodynamic Alteration of the Surface Receptor Expression Pattern of Murine Splenic Dendritic Cells (1999)

The photosensitizer benzoporphyrin-derivative monoacid ring A (BPD-MA, verteporfin), in combination with visible light irradiation, a clinical procedure termed photodynamic therapy (PDT), has immunomodulatory activity in various mouse models. We studied the impact of BPD-MA and light upon DBA/2 mouse splenic dendritic cells (DC), a potent antigen-presenting cell (APC) type. DC treated with nanomolar amounts of BPD-MA and 690 nm wavelength light had a reduced capacity to stimulate the proliferation of alloreactive T cells. Treatment with BPD-MA and light reduced DC levels of major histocompatibility (MHC) Class I and II antigens, intercellular adhesion molecule-1 (ICAM-1, CD54), the costimulatory B7-1 (CD80) and B7-2 (CD86) molecules, leucocyte common antigen CD45, the apoptosis-regulating Fas (CD95) receptor and the integrin CD11c. In contrast, DC expression of leucocyte function-associated-1 (LFA-1, CD11a), Mac-1 (CD11b), integrin beta2 chain (CD18) and the DEC-205 receptor increased, while CD40 levels were relatively unchanged 24 h after the treatment. MHC Class I and ICAM-1 levels decreased to 40% of control levels within 2 h following the photodynamic treatment. In the absence of light, BPD-MA did not affect DC receptor levels. Changes in DC receptor levels produced by BPD-MA and red light were similar to those produced by ultraviolet B light irradiation. The photodynamic treatment of activated splenic B cells, a separate APC class, had little effect upon receptor expression, except that MHC Class II levels were moderately decreased 24 h later. Changes in DC receptor expression may contribute to the immunomodulatory action of PDT.
Epitaxial growth of CeO2 layers on silicon (1990)

CeO2 layer was epitaxially grown for the first time on both (111) and (100) silicon substrates by vacuum evaporation. Characterization using Rutherford backscattering and reflection high-energy electron diffraction proved that a CeO2 layer on (111) Si has considerably good crystalline quality, whereas that on (100)Si contains a large amount of crystallographic defects, especially in the vicinity of the CeO2/Si interface. Auger electron spectroscopy analysis showed a uniform concentration distribution of Ce and O throughout the epitaxial layer.
Interactive properties of calmodulin (1988)

Research Article| February 01 1988 Interactive properties of calmodulin J A Cox J A Cox Department of Biochemistry, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva 4, Switzerland Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1988) 249 (3): 621–629. https://doi.org/10.1042/bj2490621 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation J A Cox; Interactive properties of calmodulin. Biochem J 1 February 1988; 249 (3): 621–629. doi: https://doi.org/10.1042/bj2490621 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. © 1988 London: The Biochemical Society1988 Article PDF first page preview Close Modal You do not currently have access to this content.
Effect of ultrasound on mobility in osteoarthritis of the knee. A randomized clinical trial (1992)

Ultrasound increases soft tissue extensibility and may be an effective adjunct in the treatment of knee contractures secondary to connective tissue shortening. A randomized clinical trial was conducted to determine the effectiveness of ultrasound in relieving stiffness and pain in patients (age mean = 67.5 years, SD = 13.0) who had osteoarthritis (OA) and a chronic knee contracture. Subjects received 12 treatments of exercise preceded by either ultrasound (n = 34) or sham ultrasound (n = 35) and a blinded evaluation at baseline, after treatment, and 2 months after treatment. MANCOVA controlling for baseline scores showed that there were no significant differences in knee active range of motion (ROM) (goniometry) or pain (visual analogue scale) between experimental and control groups. Possible explanations for the no difference finding involve dosage issues, muscle shortening, transiency of effects, and the effects of exercise. Paired t-tests revealed that both groups significantly improved (p less than 0.05) in active ROM, pain, and gait velocity, and maintained improvement for at least 2 months. Although ultrasound may not contribute to the management of patients with chronic knee stiffness and OA, benefits of the exercise program and increased activity secondary to program participation probably influenced the overall improvement.