gebhart/patrepeval huggingface dataset:
Conformational Mechanics, Adsorption, and Normal Force Interactions of Lubricin and Hyaluronic Acid on Model Surfaces (2008)

Glycoproteins, such as lubricin, and hyaluronic acid (HA) play a prominent role in the boundary lubrication mechanism in diarthrodial joints. Although many studies have tried to elucidate the lubrication mechanisms of articular cartilage, the molecular details of how lubricin and HA interact with cartilage surfaces and mediate their interaction still remain poorly understood. Here we used model substrates, functionalized with self-assembled monolayers terminating in hydroxyl or methyl groups, (1) to determine the effect of surface chemistry on lubricin and HA adsorption using surface plasmon resonance (SPR) and (2) to study normal force interactions between these surfaces as a function of lubricin and HA concentration using colloidal probe microscopy. We found that lubricin is amphiphilic and adsorbed strongly onto both methyl- and hydroxyl-terminated surfaces. On hydrophobic surfaces, lubricin likely adopts a compact, looplike conformation in which its hydrophobic domains at the N and C termini serve as surface anchors. On hydrophilic surfaces, lubricin likely adsorbs anywhere along its hydrophilic central domain and adopts, with increasing solution concentration, an extended tail-like conformation. Overall, lubricin develops strong repulsive interactions when compressing two surfaces into contact. Furthermore, upon surface separation, adhesion occurs between the surfaces as a result of molecular bridging and chain disentanglement. This behavior is in contrast to that of HA, which does not adsorb appreciably on either of the model surfaces and does not develop significant repulsive interactions. Adhesive forces, particularly between the hydrophobic surfaces, are large and not appreciably affected by HA. For a mixture of lubricin and HA, we observed slightly larger adsorptions and repulsions than those found for lubricin alone. Our experiments suggest that this interaction depends on unspecific physical rather than chemical interactions between lubricin and HA. We speculate that in mediating interactions at the cartilage surface, an important role of lubricin, possibly in conjunction with HA, is one of providing a protective coating on cartilage surfaces that maintains the contacting surfaces in a sterically repulsive state.
A new silver staining apparatus and procedure for matrix-assisted laser desorption/ionization-time of flight analysis of proteins after two-dimensional electrophoresis (2001)

We report on a new silver stain especially developed for staining large gels (25 cm x 20 cm) from the Hoefer ISO-DALT system for matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) analysis of proteins. The staining protocol can be summarized as follows: the gels are sensitised in tetrathionate/potassium acetate solution and washed several times in distilled water. After impregnation with silver nitrate, the silver is reduced in the presence of potassium carbonate, thiosulphate and formaldehyde. The staining procedure is stopped with Tris/acetate after which the gels are rinsed and stored in water before spot picking for MALDI-TOF analysis is performed. This protocol has several advantages over existing ones. The gels are stained in a new apparatus that reduces gel handling to a minimum thus also reducing the contamination with keratins to a minimum. The development times in potassium carbonate are very long (up to 40 min) thus improving batch-to-batch reproducibility. Only the surface of the proteins is stained and the silver can be oxidized, thereafter MALDI-TOF can be performed with protein loads as little as 100 micrograms per gel.
Use of Provider Edge to Provider Edge (PE-PE) Generic Routing Encapsulation (GRE) or IP in BGP/MPLS IP Virtual Private Networks (2007)

This document proposes an automated mechanism for establishing tunnels between provider-edge routers in a VPN, but does not provide an automated mechanism for establishing security associations for these tunnels.Without such a mechanism, this document is not appropriate for publication on the Internet standards track.
Preparative synthesis of drug metabolites using human cytochrome P450s 3A4, 2C9 and 1A2 with NADPH-P450 reductase expressed in Escherichia coli (2005)

Three human cytochrome P450s, 3A4, 2C9 and 1A2, were each co-expressed with NADPH-P450 reductase in Escherichia coli and used in the preparative synthesis of drug metabolites. Low dissolved oxygen (DO) concentration (<1%) during expression was found to be critical for producing active P450s. Control of temperature, pH and glycerol supplementation in 10-L fermentations enhanced enzyme expression 31-86%. Additional improvements were obtained by altering media formulations, resulting in bicistronic expression levels of 890, 1,800 and 1,010 nmol/L for 3A4, 2C9 and 1A2, respectively. The P450 titers achieved in fermentors exceeded those in flask fermentations by 3- to 6-fold in this study and up to 10-fold when compared with previously reported literature. Intact cells and isolated membranes obtained from 10-L fermentations were used to establish an efficient bioconversion system for the generation of metabolites. To demonstrate the utility of this approach, known metabolites of the anabolic steroid testosterone, the anti-inflammatory agent diclofenac and the analgesic agent phenacetin, were generated using 3A4, 2C9 and 1A2, respectively. The reaction conditions were optimized for pH, temperature, DO concentration, use of co-solvent and glucose supplementation. Conversion yields of 29-93% were obtained from 1-L reactions, enabling isolation of 59 mg 6beta-hydroxytestosterone, 110 mg 4'-hydroxydiclofenac and 88 mg acetaminophen.
Inhibition of HIV-1 replication by RNA targeted against the LTR region (2005)

The data provide preliminary evidence of a new class of inhibitory RNAs that can be used to block HIV replication. The results clearly show the importance of the ex vivo antisense effect in the inhibition achieved. A good correlation was found between the in vitro binding efficiency of the inhibitor RNA to the HIV-1 LTR and the inhibition of viral replication.
Robust image-based crack detection in concrete structure using multi-scale enhancement and visual features (2017)

Crack detection is an important technique to evaluate the safety and predict the life of a concrete asset. In order to improve the robustness of the crack detection in complex background, a new crack detection framework based on multi-scale enhancement and visual features is developed. Firstly, to deal with the effect of low contrast, a multi-scale enhancement method using guided filter and gradient information is proposed. Then, the adaptive threshold algorithm is used to obtain the binary image. Finally, the combination of morphological processing and visual features are adopted to purify the cracks. The experimental results with different images of real concrete surface demonstrate the high robustness and validity of the developed technique, in which the average TPR can reach 94.22%.
Transverse momentum dependence of electron and hole tunneling in a full band tight-binding simulation [resonant tunnelling diodes] (2002)

Heterointerfaces, applied bias and built-in potentials break the symmetry of the crystalline lattice in a resonant tunneling diode (RTD) which causes a strong interaction of heavy-, light- and split-off hole bands. This interaction leads to hole transport paths which are significantly more complicated than the paths for electrons. Compared to a direct bandgap electron RTD where most of the carriers are transported straight through the structure (zero transverse momentum) it is shown here that in the hole case most of the holes are transported through the structure at an angle (non-zero transverse momentum) for a wide range of bias points.
Realistic evaluation of the precision and accuracy of instrument calibration systems (1963)

Calibration of ins trumen ts and standards is a refined form of measurement. Meas ur eme nt-of some property of a thing is an operation t hat yields as an end res ult a number t hat indicates how much. of the proper ty t he t hing has. Measuremen t is ordinarily a repeatable oper atIOn, so t hat It IS appropJ'latc to r egard m eas urement a s a production process, t he "product" bein g t he numbers, i .e ., t he measurements, t hat it y ields; a nd to apply to measuremen t processes in t he la borator y the con ce p ts a nd techniques of statistical process control t hat h ave prove d so useful in the quality con trol of indu st ri al production.
不用Windows XP Home版的十大理由——对于商业用户，功能才是王道! (2005)

我看到很多单位——通常是小型企业，在他们的PC上安装了Windows XP Home版。在大多数情况下，这个版本的操作系统都是预装在新的PC上——往往是商务购买的笔记本电脑。这些单位刚开始在购买Windows XP Home版的时候节省了资金，他们猜想这种操作系统既然也是Windows XP，那么应该也能满足需要。
Thymic stromal lymphopoietin (TSLP) is associated with allergic rhinitis in children with asthma (2011)

TSLP SNP rs1837253 is associated with reduced odds for AR in boys with asthma. Our findings support a role for TSLP in the pathogenesis of AR in children with asthma.
The SUMO-Specific Protease SENP5 Is Required for Cell Division (2006)

Posttranslational modification of substrates by the small ubiquitin-like modifier, SUMO, regulates diverse biological processes, including transcription, DNA repair, nucleocytoplasmic trafficking, and chromosome segregation. SUMOylation is reversible, and several mammalian homologs of the yeast SUMO-specific protease Ulp1, termed SENPs, have been identified. We demonstrate here that SENP5, a previously uncharacterized Ulp1 homolog, has SUMO C-terminal hydrolase and SUMO isopeptidase activities. In contrast to other SENPs, the C-terminal catalytic domain of SENP5 preferentially processed SUMO-3 compared to SUMO-1 precursors and preferentially removed SUMO-2 and SUMO-3 from SUMO-modified RanGAP1 in vitro. In cotransfection assays, SENP5 preferentially reduced high-molecular-weight conjugates of SUMO-2 compared to SUMO-1 in vivo. Full-length SENP5 localized to the nucleolus. Deletion of the noncatalytic N-terminal domain led to loss of nucleolar localization and increased de-SUMOylation activity in vivo. Knockdown of SENP5 by RNA interference resulted in increased levels of SUMO-1 and SUMO-2/3 conjugates, inhibition of cell proliferation, defects in nuclear morphology, and appearance of binucleate cells, revealing an essential role for SENP5 in mitosis and/or cytokinesis. These findings establish SENP5 as a SUMO-specific protease required for cell division and suggest that mechanisms involving both the catalytic and noncatalytic domains determine the distinct substrate specificities of the mammalian SUMO-specific proteases.
Breaking good resolutions with ARP/wARP (2003)

New procedures are outlined that enable ARP/wARP to automatically build protein models with diffraction data extending to about 2.5 A. An overview of ongoing research is given and possible future advances are discussed.
Laser separation of carbon isotopes by two-frequency dissociation of Freons (1988)

An experimental investigation was made of the separation of carbon isotopes by selective multiphoton dissociation of CF2HCl, CF2Cl2, and CCl2HF molecules by two-frequency infrared laser radiation. It was found that two-frequency dissociation can substantially improve the parameters of the elementary separation event compared with single-frequency dissociation. In this case, a product highly enriched in 13C was obtained in a single step using laser fields of moderate energy density (less than 1–2 J/cm2). The best parameters of the separation process were achieved using CF2HCl. A final 13C concentration of up to 98% in the products could be achieved for this compound in a single step. When the enrichment was 80%, the energy consumption and the productivity of the separation process utilizing multiphoton dissociation of CF2HCl were ~ 1.9 keV/atom of 13C and ~ 7 g/h of 13C per one 1 kW of average radiation power.
Data-driven systematic parameter identification of an electrochemical model for lithium-ion batteries with artificial intelligence (2021)

Electrochemical models are more and more widely applied in battery diagnostics, prognostics and fast charging control, considering their high fidelity, high extrapolability and physical interpretability. However, parameter identification of electrochemical models is challenging due to the complicated model structure and a large number of physical parameters with different identifiability. The scope of this work is the development of a data-driven parameter identification framework for electrochemical models for lithium-ion batteries in real-world operations with artificial intelligence, i.e., the cuckoo search algorithm. Only current and voltage data are used as input for the multi-objective global optimization of the parameters considering both voltage error between the model and the battery and the relative capacity error between two electrodes. The multi-step identification process based on sensitivity analysis increases the identification accuracy of the parameters with low sensitivity. Moreover, the novel identification process inspired by the training process in machine learning further overcomes the overfitting problem using limited battery data. The data-driven approach achieves a maximum root mean square error of 9 mV and 12.7 mV for the full cell voltage under constant current discharging and real-world driving cycles, respectively, which is only 17.9% and 42.9% of that of the experimental identification approach.
Differential activation of the primary auxin response genes, <i>PS‐IAA4/5</i> and <i>PS‐IAA6,</i> during early plant development (1996)

The plant growth hormone auxin typified by indoleacetic acid (IAA) transcriptionally activates early genes in pea, PS-IAA4/5 and PS-IAA6, that are members of a multigene family encoding short-lived nuclear proteins. To gain first insight into the biological role of PS-IAA4/5 and PS-IAA6, promoter-beta-glucuronidase (GUS) gene fusions were constructed and their expression during early development of transgenic tobacco seedlings was examined. The comparative analysis reveals spatial and temporal expression patterns of both genes that correlate with cells, tissues, and developmental processes known to be affected by auxin. GUS activity in seedlings of both transgenic lines is located in the root meristem, sites of lateral root initiation and in hypocotyls undergoing rapid elongation. In addition, mutually exclusive cell-specific expression is evident. For instance, PS-IAA4/5-GUS but not PS-IAA6-GUS is expressed in root vascular tissue and in guard cells, whereas only PS-IAA6-GUS activity is detectable in glandular trichomes and redistributes to the elongating side of the hypocotyl upon gravitropic stimulation. Expression of PS-IAA4/5 and PS-IAA6 in elongating, dividing, and differentiating cell types indicates multiple functions during development. The common and yet distinct activity patterns of both genes suggest a combinatorial code of spatio-temporal co-expression of the various PS-IAA4/5-like gene family members in plant development that may mediate cell-specific responses to auxin.
Characterization of the rat mas oncogene and its high-level expression in the hippocampus and cerebral cortex of rat brain. (1988)

The human mas oncogene was originally detected by its ability to transform NIH 3T3 cells. We previously showed that the protein encoded by this gene is unique among cellular oncogene products in that it has seven hydrophobic potential transmembrane domains and shares strong sequence similarity with a family of hormone-receptor proteins. We have now cloned the rat homolog of the mas oncogene, determined its DNA sequence, and examined its expression in various rat tissues. A comparison of the predicted sequences of the rat and human mas proteins shows that they are highly conserved, except in their hydrophilic amino-terminal domains. Our examination of the expression of mas, determined by RNA-protection studies, indicates that high levels of mas RNA transcripts are present in the hippocampus and cerebral cortex of the brain, but not in other neural regions or in other tissues. This pattern of expression and the similarity of mas protein to known receptor proteins suggest that mas encodes a receptor that is involved in the normal neurophysiology and/or development of specific neural tissues.
<i>Drosophila</i>Mcm10 Interacts with Members of the Prereplication Complex and Is Required for Proper Chromosome Condensation (2003)

Mcm10 is required for the initiation of DNA replication in Saccharomyces cerevisiae. We have cloned MCM10 from Drosophila melanogaster and show that it complements a ScMCM10 null mutant. Moreover, Mcm10 interacts with key members of the prereplication complex: Mcm2, Dup (Cdt1), and Orc2. Interactions were also detected between Mcm10 and itself, Cdc45, and Hp1. RNAi depletion of Orc2 and Mcm10 in KC cells results in loss of DNA content. Furthermore, depletion of Mcm10, Cdc45, Mcm2, Mcm5, and Orc2, respectively, results in aberrant chromosome condensation. The condensation defects observed resemble previously published reports for Orc2, Orc5, and Mcm4 mutants. Our results strengthen and extend the argument that the processes of chromatin condensation and DNA replication are linked.
Optimizing delay tests at the memory boundary (2015)

Delay faults on the inputs and outputs of memories embedded in an integrated circuit are difficult to cover efficiently in manufacturing test. A complicated approach, separate from standard digital logic tests or memory built-in self-test, is needed to target these faults and further improve manufacturing quality. This paper discusses some of the challenges of implementing this approach and the design-for-test changes we made to the memories and to the surrounding logic to address these challenges. Our optimized method for testing the boundaries of repaired memories is presented. Our implementation has been validated and is included in our standard manufacturing test suite. It improves tests for delay faults on the memory functional boundary by minimizing the capture of unknown data, simplifying the test sequences, and testing different memory types in parallel. Results from five 32nm industry parts show that our method enables entirely automatic generation of a compact set of high-coverage test patterns for any integrated circuit design.
A New Wavelet-Based Algorithm for Compression of Emg Signals (2007)

Despite the growing interest in the transmission and storage of electromyographic signals for long periods of time, only a few studies dealt with the compression of these signals. In this article we propose a novel algorithm for EMG signal compression using the wavelet transform. For EMG signals acquired during isometric contractions, the proposed algorithm provided compression factors ranging from 50 to 90%, with an average PRD ranging from 1.4 to 7.5%. The proposed method uses a new scheme for normalizing the wavelet coefficients. The wavelet coefficients are quantized using dynamic bit allocation, which is carried out by a Kohonen Neural Network. After the quantization, these coefficients are encoded using an arithmetic encoder. The compression results using the proposed algorithm were compared to other algorithms based on the wavelet transform. The proposed algorithm had a better performance in compression ratio and fidelity of the reconstructed signal.
Acetyl Coenzyme A Carboxylase System of Escherichia coli (1974)

Abstract Methylation of enzymatically synthesized carboxy-d-biotin yields 1'-N-methoxycarbonyl-d-biotin methyl ester, a fact which earlier led to the conclusion that the site of carboxylation of biotin was the 1'-N position. However, as pointed out by Bruice and Hegarthy ((1970) Proc. Nat. Acad. Sci. U.S.A. 65, 805) this structural assignment is equivocal for if carboxylation were to occur at the ureido-O, methylation would facilitate intramolecular O to N migration of the (methoxycarbonyl) group and lead to the same derivative, 1'-N-methoxycarbonyl-d-biotin methyl ester. In the present investigation definitive evidence was obtained which indicates that the ureido-N of biotin is in fact the site of carboxylation. Carboxy-d-biotins generated enzymatically by the biotin carboxylase or carboxyltransferase components of the Escherichia coli acetyl-CoA carboxylase system and tested immediately have stability properties indistinguishable from that of 1'-N-carboxy-d-biotin; first-order decarboxylation rates over the pH range 5 to 9 are identical for the enzymatic products and the authentic carboxybiotin derivative. Specificity studies reveal that the carboxylate terminus of the valeric acid side chain of biotin renders this molecule a poor model substrate for the E. coli carboxyltransferase; it accounts as well for the inability of this enzyme to utilize 1'-N-carboxy-d-biotin as a carboxyl donor substrate. Thus, derivatives lacking the side chain carboxylate function, e.g. biotinol and biotinyl acetate, which are excellent carboxyl acceptor substrates, were used as precursors for the synthesis of enzymatically active 1'-N carboxy derivatives. The carboxyltransferase-catalyzed reaction of [3-14C]malonyl-CoA and d-biotinyl acetate yields a product which after methylation and chromatography has properties identical with 1'-N-methoxycarbonyl-d-biotinyl acetate. Alkaline hydrolysis of the labeled compound yielded putative 1'-N-[14C]carboxy-dbiotinol which serves as a substrate for E. coli carboxyltransferase. 1'-N-Methoxycarbonyl-d-biotinyl acetate was chemically synthesized from d-biotinyl acetate and methylchloroformate under conditions known to effect 1'-N-acylation of a related d-biotin derivative. The product was characterized by chemical, mass spectral, and nuclear magnetic resonance (proton and 13C NMR) analyses; 13C NMR spectra indicated methoxycarbonyl substitution at the 1'-N, rather than the ureido-O, of the imidazolidone ring. Alkaline hydrolysis of 1'-N-methoxycarbonyl-d-biotinyl acetate yields a product, 1'-N-carboxy-d-biotinol, which served efficiently as a carboxyl donor substrate for carboxyltransferase-catalyzed transcarboxylation to acetyl-CoA giving rise to malonyl-CoA. These results and the fact that authentic 1'-N-carboxy-d-biotin also is a substrate for biotin carboxylase-catalyzed net ATP formation from ADP and Pi indicate that the 1'-ureido-N position of biotin is the enzymatic site of carboxylation.
Circulating serum sVCAM-1 concentration in advanced ovarian cancer patients: correlation with concentration in ascites (2013)

This is the first study demonstrating that serum concentrations of sVCAM-1 in advanced ovarian cancer patients correlate with sVCAM-1 concentrations in ascites, thus expressing the biologic potential of malignant disease to metastasis, rather than systemic inflammation. Higher serum and ascites sVCAM-1 concentrations might have predictive potential for different biologic behaviour.
Both Primary and Secondary Abdominal Compartment Syndrome can be Predicted Early and are Harbingers of Multiple Organ Failure (2003)

Primary and secondary ACS have similar demographics, injury severity, time to decompression from hospital admit, and bad outcome. 2 degrees ACS is an earlier ICU event preceded by more crystalloid administration. With appropriate monitoring both could be accurately predicted upon ICU admission.