gebhart/patrepeval huggingface dataset:
Pt-Ni bilayers on <i>n</i>-type silicon: Metallurgical and electrical behavior (1984)

Silicide formation in the Ni-Pt-Si system has been investigated mainly by megaelectronvolt backscattering spectrometry, glancing-angle x-ray diffraction, and Auger electron spectroscopy as a function of heat treatment (200–850 °C). Schottky-barrier values have been used to identify the kinds of metals present at the silicide/silicon interface. Pt/Ni/Si and Ni/Pt/Si structures have been prepared by e-gun deposition of thin Pt and Ni films on 〈100〉 n-type silicon single crystals. The reaction starts by forming the silicide, Ni2Si or Pt2Si, of the metal in contact with silicon and proceeds until all the inner-metal film has reacted. At about 300 °C for 30 min the outer metal starts to diffuse through the already formed silicide and builds up at the silicon surface. Further annealing enhances the reaction and there is evidence also of silicon diffusion towards the outside layer. At 400 °C for 30 min and in both structures, NiSi starts to form and pushes out the Pt from the silicon surface. The conversion of Ni2Si into NiSi provides the driving force for mass transport. The structures become laterally nonuniform and the changes are difficult to follow. The transformation of Pt2Si into PtSi, at about 500 °C, is accompanied by the transport of Pt through NiSi towards the silicon surface. Most Pt remains in the outside layer and both structures assume the configuration PtSi/NiSi/Si. At higher temperatures PtSi and NiSi intermix and there is no evidence of contribution from the silicon underneath. At 750 °C an almost uniform layer is formed with a Si1(NiPt)1 composition. The barrier height measurements reflect the mass transport in the silicides at the silicide/silicon interface.
Biochemical and Structural Studies of a HECT-like Ubiquitin Ligase from Escherichia coli O157:H7 (2010)

Many microbial pathogens deliver effector proteins via the type III secretion system into infected host cells. Elucidating the function of these effectors is essential for our understanding of pathogenesis. Here, we describe biochemical and structural characterization of an effector protein (NleL) from Escherichia coli O157:H7, a widespread pathogen causing severe foodborne diseases. We show that NleL functionally and structurally mimics eukaryotic HECT E3 ligases and catalyzes formation of unanchored polyubiquitin chains using Lys(6) and Lys(48) linkage. The catalytic cysteine residue forms a thioester intermediate with ubiquitin. The structure of NleL contains two domains, a β-helix domain formed by pentapeptide repeats and a bilobed catalytic domain reminiscent of the N- and C-lobe architecture of HECT E3s. Six structures of NleL observed in two crystal forms revealed a large range of different positions of the C-lobe relative to the N-lobe, indicating that the helix linking the two lobes is extremely flexible. Comparing the structure of NleL with that of the Salmonella homolog SopA showed that the orientation of the C-lobes differ by as much as 108°, suggesting that large movements of the C-lobe may be required to facilitate the transfer of ubiquitin from E2 to the substrate. These results provide critical knowledge toward understanding the molecular mechanism by which pathogens utilize the host ubiquitination system during infection.
Measuring the Mechanical Properties of Living Cells Using Atomic Force Microscopy (2013)

Mechanical properties of cells and extracellular matrix (ECM) play important roles in many biological processes including stem cell differentiation, tumor formation, and wound healing. Changes in stiffness of cells and ECM are often signs of changes in cell physiology or diseases in tissues. Hence, cell stiffness is an index to evaluate the status of cell cultures. Among the multitude of methods applied to measure the stiffness of cells and tissues, micro-indentation using an Atomic Force Microscope (AFM) provides a way to reliably measure the stiffness of living cells. This method has been widely applied to characterize the micro-scale stiffness for a variety of materials ranging from metal surfaces to soft biological tissues and cells. The basic principle of this method is to indent a cell with an AFM tip of selected geometry and measure the applied force from the bending of the AFM cantilever. Fitting the force-indentation curve to the Hertz model for the corresponding tip geometry can give quantitative measurements of material stiffness. This paper demonstrates the procedure to characterize the stiffness of living cells using AFM. Key steps including the process of AFM calibration, force-curve acquisition, and data analysis using a MATLAB routine are demonstrated. Limitations of this method are also discussed.
Two-Port Static Coated Micro Gas Chromatography Column With an Embedded Thermal Conductivity Detector (2011)

This paper reports a microfabricated 2×4 cm gas chromatography chip to separate and detect gases in a two-port structure by embedding a microthermal conductivity detector (μTCD) within a separation column. A circular on-chip heater is placed on the backside of the monolithic device enabling temperature programming and consequently faster analysis of the heavier components. A unique process enhanced by reactive ion etching lag (RIE lag) is used to achieve multiple etch depths in silicon and restrict the process flow to just three masks. The silicon substrate contains the separation column, the heater, and the tunnels for the TCD electric feed throughs. A Pyrex wafer containing the TCD elements is anodically bonded to the silicon substrate to seal the structure. Performance of a standalone μTCD fabricated in the same process and integrated in a hybrid fashion is also described. The single-chip design demonstrates successful separation and identification of multi-component gas mixtures with a performance comparable to that obtained through a flame ionization detector connected in series. Further, on-chip temperature programming capability was utilized to elevate the column temperature to 75 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">°</sup> C to exhibit analysis in less than a minute.
NATURALLY OCCURRING β-LACTONES: OCCURRENCE, SYNTHESES AND PROPERTIES. A REVIEW (1995)

(1995). NATURALLY OCCURRING β-LACTONES: OCCURRENCE, SYNTHESES AND PROPERTIES. A REVIEW. Organic Preparations and Procedures International: Vol. 27, No. 3, pp. 305-346.
<title>Application of fluorescence spectroscopy for on-line bioprocess monitoring and control</title> (2001)

12 Modern bioprocess control requires fast data acquisition and in-time evaluation of bioprocess variables. On-line fluorescence spectroscopy for data acquisition and the use of chemometric methods accomplish these requirements. The presented investigations were performed with fluorescence spectrometers with wide ranges of excitation and emission wavelength. By detection of several biogenic fluorophors (amino acids, coenzymes and vitamins) a large amount of information about the state of the bioprocess are obtained. For the evaluation of the process variables partial least squares regression is used. This technique was applied to several bioprocesses: the production of ergotamine by Claviceps purpurea, the production of t-PA (tissue plasminogen activator) by animal cells and brewing processes. The main point of monitoring the brewing processes was to determine the process variables cell count and extract concentration.
Relationship between metabolic syndrome and bone mineral density in the postmenopausal women (2009)

목적: 대사증후군은 복부비만, 고혈압, 지질 대사이상, 공복혈당장애 등에 의한 심혈관계 질환의 위험도가 높아지는 대사 이상이다. 폐경 후 여성에서 대사증후군 및 위험 요소들과 골밀도와의 연관성에 대하여 알아보고자 하였다. 연구 방법: 2006년 1월부터 2007년 12월까지 가톨릭 의과대학 성빈센트병원 산부인과를 방문한 폐경 후 여성 중 대사증후군을 진단받은 여성 66명, 그렇지 않은 여성 85명을 대상으로 하였으며, 대사증후군 및 허리 엉덩이둘레비율, 총 중성지방, HDL 콜레스테롤, 공복 혈당, 혈압 등의 위험 요소들과 골밀도와의 상관관계를 회귀분석 및 ANCOVA를 이용하여 분석하였다. 결과: 대사증후군이 있는 여성에서 그렇지 않은 여성에 비해 요추부 및 대퇴 경부 골밀도의 유의하게 높았으나 나이와 체질량지수를 보정한 뒤에는 유의한 차이는 없었다. HDL 콜레스테롤과 요추부 골밀도와는 통계적으로 유의한 양의 상관관계가 있었으며, 공복혈당과 요추부, 대퇴 경부의 골밀도와 양의 상관관계가 있었다. 복부비만 및 혈압, 총 중성지방과 골밀도와는 유의한 상관관계는 없었다. 대사증후군 위험인자의 양성수와 골밀도와 양의 상관관계를 보였으나 나이와 체질량지수를 보정한 뒤에는 유의한 차이는 없었다. 결론: 대사증후군은 체질량지수의 증가 등으로 골량의 증가 효과를 가질 것으로 생각할 수 있지만 저HDL 콜레스테롤혈증 등의 지질대사에 의해 골량이 감소되며, 체질량지수를 보정할 경우 대사증후군 자체의 골보호 효과는 없는 것으로 생각된다.
A Framework for Annotation of Antigen Specificities in High-Throughput T-Cell Repertoire Sequencing Studies (2019)

Recently developed molecular methods allow large-scale profiling of T-cell receptor (TCR) sequences that encode for antigen specificity and immunological memory of these cells. However, it is well-known that the even unperturbed TCR repertoire structure is extremely complex due to the high diversity of TCR rearrangements and multiple biases imprinted by VDJ rearrangement process. The latter gives rise to the phenomenon of "public" TCR clonotypes that can be shared across multiple individuals and non-trivial structure of the TCR similarity network. Here, we outline a framework for TCR sequencing data analysis that can control for these biases in order to infer TCRs that are involved in response to antigens of interest. We apply two previously published methods, ALICE and TCRNET, to detect groups of homologous TCRs that are enriched in samples of interest. Using an example dataset of donors with known HLA haplotype and CMV status, we demonstrate that by applying HLA restriction rules and matching against a database of TCRs with known antigen specificity, it is possible to robustly detect motifs of epitope-specific responses in individual repertoires. We also highlight potential shortcomings of TCR clustering methods and demonstrate that highly expanded TCRs should be individually assessed to get the full picture of antigen-specific response.
Glutamine transporter in crypts compensates for loss of villus absorption in bovine cryptosporidiosis (2001)

Cryptosporidium parvum infection represents a significant cause of diarrhea in humans and animals. We studied the effect of luminally applied glutamine and the PG synthesis inhibitor indomethacin on NaCl absorption from infected calf ileum in Ussing chambers. Infected ileum displayed a decrease in both mucosal surface area and NaCl absorption. Indomethacin and glutamine or its stable derivative alanyl-glutamine increased the net absorption of Na(+) in infected tissue in an additive manner and to a greater degree than in controls. Immunohistochemical and Western blot studies showed that in control animals neutral amino acid transport system ASC was present in villus and crypts, whereas in infected animals, ASC was strongly present only on the apical border of crypts. These results are consistent with PGs mediating the altered NaCl and water absorption in this infection. Our findings further illustrate that the combined use of a PG synthesis inhibitor and glutamine can fully stimulate Na(+) and Cl(-) absorption despite the severe villous atrophy, an effect associated with increased expression of a Na(+)-dependent amino acid transporter in infected crypts.
Failure analysis of heavy truck trailer axles (1998)

A combined analytical/experimental approach was utilized to analyse failures of steel axles in a fleet of refrigeration semi-trailers equipped with dual rear axle air-ride suspensions. Experimental data were used in combination with an analytical model to identify the cause of the axle failures, estimate time to failure, and evaluate the relative effectiveness of proposed design changes to minimize future axle failures. The centrepieces of the program were finite element and fracture mechanics models of the axles. Experiments conducted in support of the analytical models consisted of: (1) field and laboratory inspection of failed axles to determine failure mode and the size of pre-existing flaws; (2) full scale trailer road testing to determine the service load spectrum; (3) fatigue tests on laboratory specimens to determine material properties; and, (4) full scale axle fatigue testing to calibrate and verify the ability of the analytical methods to predict axle lifetimes, and also to evaluate empirically the effect of design and manufacturing process changes. Focus is on the analytical models. Two potential solutions were evaluated, including an axle reinforcing jacket, and replacement of the original axle with a thicker walled axle. The analytical models were a vital tool in determining that both of these solutions effectively extend axle lives so that they have adequate design margins.
<i>Candida</i>biofilms on implanted biomaterials: a clinically significant problem (2006)

In recent years there has been an increasing appreciation that microbial biofilms are ubiquitous, which has resulted in a number of studies on infectious diseases from a biofilm perspective. Biofilms are defined as structured microbial communities that are attached to a surface and encased in a matrix of exopolymeric material. A wide range of biomaterials used in clinical practice have been shown to support colonization and biofilm formation by Candida spp., and the increase in Candida infections in the last decades has almost paralleled the increase and widespread use of a broad range of medical implant devices, mainly in populations with impaired host defenses. Formation of Candida biofilms has important clinical repercussions because of their increased resistance to antifungal therapy and the ability of cells within biofilms to withstand host immune defenses. Further recognition and understanding of the role of Candida biofilms in human infection should help in the clinical management of these recalcitrant infections.
Hydrosilylation catalysis by an earth alkaline metal silyl: synthesis, characterization, and reactivity of bis(triphenylsilyl)calcium (2014)

Bis(triphenylsilyl)calcium [Ca(SiPh3)2(thf)] obtained in high yield as a crystalline ether adduct catalyzes the hydrosilylation of activated C-C double bonds efficiently and regioselectively.
Estrogen Regulation of Thecal Cell Steroidogenesis and Differentiation: Thecal Cell-Granulosa Cell Interactions* (1990)

Estrogen regulation of thecal cell steroidogenesis and differentiation was investigated with cells from ovarian antral follicles. Bovine theca interna cells were isolated and cultured in serum-free conditions to evaluate the effects of estradiol on thecal cell production of androstenedione, testosterone, and progesterone. Estradiol increased thecal cell androgen production throughout a 6-day culture period; however, the basal and stimulated levels of androgen production diminished after day 3 of culture. Androstenedione accumulation was approximately 10-fold greater than that of testosterone. In contrast to the stimulatory effects that estradiol had on androgen production, estradiol suppressed progesterone production throughout the 6-day culture period. Comparison of the effects of estradiol and hCG on thecal cells from small (less than 5 mm), medium (5-10 mm), and large (greater than 10 mm) antral follicles demonstrated that estradiol stimulated androgen production to a greater extent than hCG with cells from all of these stages of follicle development. Estradiol stimulation of androstenedione was greater in theca from small follicles than in theca from medium or large follicles. In contrast, suppressive effects of estradiol on progesterone were most apparent on thecal cells from medium and large follicles and less apparent on theca from small follicles. Estradiol stimulated androstenedione production in a dose-dependent fashion, with a minimum effective concentration of 10(-9) M and a maximum effective concentration of 10(-7)-10(-6) M. Concentrations greater than 10(-6) M estradiol resulted in a decline in the stimulatory response and may be important in the preovulatory follicle to suppress thecal cell androgen production and initiate the process of luteinization. Progesterone production was slightly stimulated by 10(-9) M estradiol, whereas higher concentrations (10(-7)-5 x 10(-6) M) resulted in a dose-dependent suppression of progesterone production. Interestingly, combined treatment of thecal cells with estradiol and hCG resulted in a greater than additive stimulation of androstenedione production, and estradiol decreased the ability of hCG to stimulate progesterone production. Observations demonstrate that estradiol can dramatically alter thecal cell production of steroids and support a hypothesis that steroid-mediated interactions between granulosa and thecal cells play an important role in regulating cellular function within follicles. The data provide evidence that a local feedback loop may exist in ovarian follicles, where androgens produced by thecal cells are used as a substrate for granulosa cell aromatization into estrogens, which, in turn, may feed back to stimulate thecal cell production of androgens.(ABSTRACT TRUNCATED AT 400 WORDS)
Age-associated mitochondrial oxidative decay: Improvement of carnitine acetyltransferase substrate-binding affinity and activity in brain by feeding old rats acetyl- <scp>l</scp> - carnitine and/or <i>R</i> -α-lipoic acid (2002)

We test whether the dysfunction with age of carnitine acetyltransferase (CAT), a key mitochondrial enzyme for fuel utilization, is due to decreased binding affinity for substrate and whether this substrate, fed to old rats, restores CAT activity. The kinetics of CAT were analyzed by using the brains of young and old rats and of old rats supplemented for 7 weeks with the CAT substrate acetyl-l-carnitine (ALCAR) and/or the mitochondrial antioxidant precursor R-alpha-lipoic acid (LA). Old rats, compared with young rats, showed a decrease in CAT activity and in CAT-binding affinity for both substrates, ALCAR and CoA. Feeding ALCAR or ALCAR plus LA to old rats significantly restored CAT-binding affinity for ALCAR and CoA, and CAT activity. To explore the underlying mechanism, lipid peroxidation and total iron and copper levels were assayed; all increased in old rats. Feeding old rats LA or LA plus ALCAR inhibited lipid peroxidation but did not decrease iron and copper levels. Ex vivo oxidation of young-rat brain with Fe(II) caused loss of CAT activity and binding affinity. In vitro oxidation of purified CAT with Fe(II) inactivated the enzyme but did not alter binding affinity. However, in vitro treatment of CAT with the lipid peroxidation products malondialdehyde or 4-hydroxy-nonenal caused a decrease in CAT-binding affinity and activity, thus mimicking age-related change. Preincubation of CAT with ALCAR or CoA prevented malondialdehyde-induced dysfunction. Thus, feeding old rats high levels of key mitochondrial metabolites can ameliorate oxidative damage, enzyme activity, substrate-binding affinity, and mitochondrial dysfunction.
Analysis and Improvement of Authenticatable Ring Signcryption Scheme. (2008)

Abstract. Ring signcryption is an anonymous signcryption which allows a user to anonymously signcrypt a message on behalf of a set of users including himself. In an ordinary ring signcryption scheme, even if a user of the ring generates a signcryption, he also cannot prove that the signcryption was produced by himself. In 2008, Zhang, Yang, Zhu, and Zhang solve the problem by introducing an identity-based authenticatable ring signcryption scheme (denoted as the ZYZZ scheme). In the ZYZZ scheme, the actual signcrypter can prove that the ciphertext is generated by himself, and the others cannot authenticate it. However, in this paper, we show that the ZYZZ scheme is not secure against chosen plaintext attacks. Furthermore, we propose an improved scheme that remedies the weakness of the ZYZZ scheme. The improved scheme has shorter ciphertext size than the ZYZZ scheme. We then prove that the improved scheme satisfies confidentiality, unforgeability, anonymity and authenticatability. Keywords: Identity-based cryptography, bilinear pairings, ring signcryption, ring signature. 1
ChemInform Abstract: Electrochemical Decarboxylation of L‐Threonine and Oligopeptide Derivatives with Formation of N‐Acyl‐N,O‐acetals: Preparation of Oligopeptides with Amide or Phosphonate C‐Terminus. (1989)

Abstract N‐protected di‐, tri‐ or tetrapeptides such as the dipeptides (I) undergo an anodic oxidative substitution of the ‐COOH by an ‐O‐Me group to give the N‐acyl N,O‐acetals (III).
<title>Nonscanned ladar imaging and applications</title> (1993)

A scannerless laser detection and ranging (LADAR) system is presently in development for applications at Sandia National Laboratories. This LADAR design eliminates the need for a mechanical laser beam scanner which is often the system component that limits the use of laser radars for many applications. Range to the target scene is determined in this approach by measuring the phase shift of the intensity modulation on the received optical return compared to the reference. The approach used in this LADAR is unique because the method used to detect this phase shift is an array of time integrating detectors that also records the image of the target scene. An analytical model is presented that describes the LADAR system performance. Applications of this LADAR system also are reviewed. They include terminal guidance of advanced conventional munitions, perimeter surveillance of secure facilities, mapping potholes/cracks in the U.S. highway system for improved maintenance scheduling, active collision avoidance of commercial/private vehicles, robotic vision integrated into advanced manufacturing concepts, and a novel airborne multi-sensor system containing LADAR, SAR, and LIDAR to locate and measure the thickness of ocean oil spills.
Systematic Analysis of the Content of 502 Polyphenols in 452 Foods and Beverages: An Application of the Phenol-Explorer Database (2010)

Considerable information on polyphenol content in foods is scattered in up to 1000 peer-reviewed publications and is therefore not easily exploited. Over 60000 food composition data have been collected from this literature and stored in the new Phenol-Explorer database ( www.phenol-explorer.eu ). Thirty-seven thousand data were selected after evaluation and aggregated separately according to 5 categories of analytical methods to generate mean content values for 502 compounds (glycosides, esters, or aglycones) in 452 foods. These data are exploited here in a first systematic analysis of the content in foods of these 502 polyphenols. These data will be useful for epidemiologists to determine polyphenol intake and associations with health and diseases in populations and for food scientitsts and food manufacturers to develop new products with optimized properties.
A Novel Feedforward Compensation Canceling Input Filter-Regulator I nteraction (1983)

The interaction between the input filter and the control loop of switching regulators often results in detrimental effects, such as loop instability, degradation of transient response, and audiosusceptibility, etc. The concept of pole-zero cancellation is employed to mitigate some of these detrimental effects and is implemented using a novel feedforward loop, in addition to existing feedback loops of a buck regulator. Experimental results are presented which show excellent correlation with theory.