gebhart/patrepeval huggingface dataset:
Functionally Distinct NEAT (NEAr Transporter) Domains within the Staphylococcus aureus IsdH/HarA Protein Extract Heme from Methemoglobin (2008)

The pathogen Staphylococcus aureus uses iron-regulated surface determinant (Isd) proteins to scavenge the essential nutrient iron from host hemoproteins. The IsdH protein (also known as HarA) is a receptor for hemoglobin (Hb), haptoglobin (Hp), and the Hb-Hp complex. It contains three NEAT (NEAr Transporter) domains: IsdH(N1), IsdH(N2), and IsdH(N3). Here we show that they have different functions; IsdH(N1) binds Hb and Hp, whereas IsdH(N3) captures heme that is released from Hb. The staphylococcal IsdB protein also functions as an Hb receptor. Primary sequence homology to IsdH indicates that it will also employ functionally distinct NEAT domains to bind heme and Hb. We have used site-directed mutagenesis and surface plasmon resonance methods to localize the Hp and Hb binding surface on IsdH(N1). High affinity binding to these structurally unrelated proteins requires residues located within a conserved aromatic motif that is positioned at the end of the beta-barrel structure. Interestingly, this site is quite malleable, as other NEAT domains use it to bind heme. We also demonstrate that the IsdC NEAT domain can capture heme directly from Hb, suggesting that there are multiple pathways for heme transfer across the cell wall.
A novel Hsp90 inhibitor to disrupt Hsp90/Cdc37 complex against pancreatic cancer cells (2008)

Pancreatic cancer is an aggressive disease with multiple biochemical and genetic alterations. Thus, a single agent to hit one molecular target may not be sufficient to treat this disease. The purpose of this study is to identify a novel Hsp90 inhibitor to disrupt protein-protein interactions of Hsp90 and its cochaperones for down-regulating many oncogenes simultaneously against pancreatic cancer cells. Here, we reported that celastrol disrupted Hsp90-Cdc37 interaction in the superchaperone complex to exhibit antitumor activity in vitro and in vivo. Molecular docking and molecular dynamic simulations showed that celastrol blocked the critical interaction of Glu33 (Hsp90) and Arg167 (Cdc37). Immunoprecipitation confirmed that celastrol (10 micromol/L) disrupted the Hsp90-Cdc37 interaction in the pancreatic cancer cell line Panc-1. In contrast to classic Hsp90 inhibitor (geldanamycin), celastrol (0.1-100 micromol/L) did not interfere with ATP binding to Hsp90. However, celastrol (1-5 micromol/L) induced Hsp90 client protein degradation (Cdk4 and Akt) by 70% to 80% and increased Hsp70 expression by 12-fold. Celastrol induced apoptosis in vitro and significantly inhibited tumor growth in Panc-1 xenografts. Moreover, celastrol (3 mg/kg) effectively suppressed tumor metastasis by more than 80% in RIP1-Tag2 transgenic mouse model with pancreatic islet cell carcinogenesis. The data suggest that celastrol is a novel Hsp90 inhibitor to disrupt Hsp90-Cdc37 interaction against pancreatic cancer cells.
Single Access Site Laparoscopic Radical Nephrectomy: Initial Clinical Experience (2008)

This represents the initial report of an SAS laparoscopic radical nephrectomy, with intact specimen extraction. Using standard laparoscopic instrumentation, the procedure was performed safely and effectively, with minimal blood loss, and short hospitalization. Additional evaluation and development of this type of approach and instrumentation may allow for further expansion of SAS laparoscopic surgery in the future.
Biomedical Visual Computing: Case Studies and Challenges (2011)

Advances in computational geometric modeling, imaging, and simulation let researchers build and test models of increasing complexity, generating unprecedented amounts of data. As recent research in biomedical applications illustrates, visualization will be critical in making this vast amount of data usable; it's also fundamental to understanding models of complex phenomena.
Textual context analysis for information retrieval (1997)

article Free Access Share on Textual context analysis for information retrieval Author: Mark A. Stairmand Centre for Computatioal Linguistics, UMIST, Manchester M60 1QD, UK Centre for Computatioal Linguistics, UMIST, Manchester M60 1QD, UKView Profile Authors Info & Claims ACM SIGIR ForumVolume 31Issue SIDecember 1997 pp 140–147https://doi.org/10.1145/278459.258552Published:01 July 1997Publication History 32citation1,070DownloadsMetricsTotal Citations32Total Downloads1,070Last 12 Months21Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
An Overview of the Strategy and Tactics of Taguchi (1988)

Abstract The methods of Taguchi have received considerable attention in recent years. Part of the attention is due to the success of Genichi Taguchi and his colleagues and part of the attention is due to the mystique and controversy surrounding these methods. In this paper we discuss two separate aspects of the Taguchi method: the strategy of Taguchi and the tactics of Taguchi. The Taguchi tactics involve the specific methods and techniques recommended by Taguchi such as the use of signal-to-noise ratios and the so-called Taguchi designs. We discuss the parameter design strategy of Taguchi for designing and improving products and processes from a statistical point of view. We point out that although there are some apparent flaws in Taguchi's tactics, the basic strategy is a sound one.
QoS-aware multipath-TCP extensions for mobile and multimedia applications (2011)

The increasing number of interfaces using different access technologies in modern devices gives opportunities for enhancing the quality of service (QoS) delivered to multimedia and interactive data transfers involved in mobile and distributed applications. In the modern Internet though, the presence of "middleboxes" (such as NATs, firewalls or proxies) hardly lets applications use any transport protocol but the well-known Transmission Control Protocol (TCP). Currently under standardization at the IETF, the new Multipath-TCP (MPTCP) protocol uses several TCP flows to make use of the multiple interfaces available on the end terminals, thus improving both network availability and QoS, still being capable to cross over middleboxes. Although originally being fully reliable and fully ordered, its two sub-layers architecture gives opportunity to use QoS techniques over fully reliable paths. This paper studies the QoS benefits induced by the implementation of the "partial reliability" concept in MPTCP for interactive video applications based on the codec H.264. Two different mechanisms are thus proposed and experimented with the aim to enhance global quality of video transmission over paths close to 3G networks characteristics. The IETF ns-2 implementation of MPTCP is used for the experimentations and the performances evaluation of the proposed contribution. The Evalvid toolkit over ns-2 is used to measure the QoS benefits expressed in terms of PSNR.
Collaboration using roles (1990)

Abstract Segregation of roles into alternative accounts is a model which provides not only the ability to collaborate but also enables accurate accounting of resources consumed by collaborative projects, protects the resources and objects of such a project, and does not introduce new security vulnerabilities. The implementation presented here does not require users to remember additional passwords and provides a very simple consistent interface.
CD22 EXON 12 deletion as a pathogenic mechanism of human B-precursor leukemia (2010)

Here, we report that primary leukemic cells from infants with newly diagnosed B-precursor leukemia express a truncated and functionally defective CD22 coreceptor protein that is unable to transmit apoptotic signals because it lacks most of the intracellular domain, including the key regulatory signal transduction elements and all of the cytoplasmic tyrosine residues. Expression of this structurally and functionally abnormal CD22 protein is associated with a very aggressive in vivo growth of patients' primary leukemia cells causing disseminated overt leukemia in SCID mice. The abnormal CD22 coreceptor is encoded by a profoundly aberrant mRNA arising from a splicing defect that causes the deletion of exon 12 (c.2208-c.2327) (CD22ΔE12) and results in a truncating frameshift mutation. The splicing defect is associated with multiple homozygous mutations within a 132-bp segment of the intronic sequence between exons 12 and 13. These mutations cause marked changes in the predicted secondary structures of the mutant CD22 pre-mRNA sequences that affect the target motifs for the splicing factors hnRNP-L, PTB, and PCBP that are up-regulated in infant leukemia cells. Forced expression of the mutant CD22ΔE12 protein in transgenic mice perturbs B-cell development, as evidenced by B-precursor/B-cell hyperplasia, and corrupts the regulation of gene expression, causing reduced expression levels of several genes with a tumor suppressor function. We further show that CD22ΔE12-associated unique gene expression signature is a discriminating feature of newly diagnosed infant leukemia patients. These striking findings implicate CD22ΔE12 as a previously undescribed pathogenic mechanism in human B-precursor leukemia.
Monocytes Become Macrophages; They Do Not Become Microglia (1986)

This light and electron microscopic autoradiographic study of stab injuries in the spinal cord of mice evaluated the ultrastructural characteristics of cells labeled by incorporation of the thymidine analogue 125I-5-iodo-2'-deoxyuridine (I-UdR), injected one day prior to injury. I-UdR was used instead of tritiated thymidine (H-TdR) because H-TdR can be reutilized and is therefore not a suitable pulse label for long-term studies of cell migration. Using serial thick and thin sections for autoradiography 614 labeled cells were identified. Labeled cells included 545 monocytes/macrophages, 50 lymphocytes, 17 pericytes, one endothelial cell, and one arachnoid cell. No labeled cell had the morphology of microglia. We concluded that macrophages in stab injuries of the spinal cord of mice are derived from blood monocytes. Blood-derived lymphocytes are also involved in the reaction to spinal cord stab injury. Microglia are not blood-derived and are not seen as a transitional form in the differentiation of monocytes to macrophages.
Dendritic cells pulsed with glioma lysates induce immunity against syngeneic intracranial gliomas and increase survival of tumor-bearing mice (2006)

In recent years, the use of dendritic cells (DC), the most powerful antigen presenting cells, has been proposed for the creation of vaccines against gliomas. This approach has been demonstrated to be safe and non-toxic in phase I or I-II trials (2, 3). Immunotherapy plays a central role in the search for new treatments for glioblastoma multiforme (GBM). In particular, several phase I studies have been performed using DC pulsed by GBM proteins as a vaccine for patients with relapsing GBM. The studies demonstrated that DC vaccination is safe and may produce a significant increase in overall survival. As the first step in the preparation of appropriate conditions for a clinical evaluation in Italy, we have performed pre-clinical experiments on immune-competent mice injected intra-cerebrally with syngeneic GL261GBM cells and treated subcutaneously and intra-tumorally with DC loaded with a GL261 homogenate. These results show that vaccination with DC pulsed with a tumor lysate increases considerably survival in mice bearing intracranial glioblastomas and supports the development of DC-based clinical trials for patients with glioblastomas that do not respond to standard therapies.
A Spike-Based Saccadic Recognition System (2007)

The paper presents a spike-based saccadic recognition system that uses a temporal-derivative silicon retina on a pan-tilt unit and an aVLSI multi-neuron classifier with a time-to-first-spike output coding. By using the spike information during the last 150 ms of a saccadic movement, we generate a reliable, sparse stimulus representation of image patches. The paper describes a novel classification scheme where the retinal spikes during this time influence the time-to-first spike of classifier neurons which receive the same constant input current. The preferred pattern of the neuron is stored in the synaptic connectivity between the retina and the classifier neuron. The authors demonstrates the robustness and real-time performance of this recognition scheme on a saccadic system which uses analog VLSI components.
The reactivities and ionization properties of the active-site dithiol groups of mammalian protein disulphide-isomerase (1991)

1. The number of reactive thiol groups in mammalian liver protein disulphide-isomerase (PDI) in various conditions was investigated by alkylation with iodo[14C]acetate. 2. Both the native enzyme, as isolated, and the urea-denatured enzyme contained negligible reactive thiol groups; the enzyme reduced with dithiothreitol contained two groups reactive towards iodoacetic acid at pH 7.5, and up to five reactive groups were detectable in the reduced denatured enzyme. 3. Modification of the two reactive groups in the reduced native enzyme led to complete inactivation, and the relationship between the loss of activity and the extent of modification was approximately linear. 4. Inactivation of PDI by alkylation of the reduced enzyme followed pseudo-first-order kinetics; a plot of the pH-dependence of the second-order rate constant for inactivation indicated that the essential reactive groups had a pK of 6.7 and a limiting second-order rate constant at high pH of 11 M-1.s-1. 5. Since sequence data on PDI show the presence within the polypeptide of two regions closely similar to thioredoxin, the data strongly indicate that these regions are chemically and functionally equivalent to thioredoxin. 6. The activity of PDI in thiol/disulphide interchange derives from the presence of vicinal dithiol groups in which one thiol group of each pair has an unusually low pK and high nucleophilic reactivity at physiological pH.
Corrosion at the Cone/Taper Interface Leads to Failure of Large-diameter Metal-on-metal Total Hip Arthroplasties (2012)

These findings suggest that in modular cone/taper connections, friction of the MoM articulations may cause failure of the cone/taper interface leading to galvanic corrosion and loosening. It is unclear whether the design of this MoM system provides sufficient stability at the taper.
The Adaptive Lasso and Its Oracle Properties (2006)

The lasso is a popular technique for simultaneous estimation and variable selection. Lasso variable selection has been shown to be consistent under certain conditions. In this work we derive a necessary condition for the lasso variable selection to be consistent. Consequently, there exist certain scenarios where the lasso is inconsistent for variable selection. We then propose a new version of the lasso, called the adaptive lasso, where adaptive weights are used for penalizing different coefficients in the ℓ1 penalty. We show that the adaptive lasso enjoys the oracle properties; namely, it performs as well as if the true underlying model were given in advance. Similar to the lasso, the adaptive lasso is shown to be near-minimax optimal. Furthermore, the adaptive lasso can be solved by the same efficient algorithm for solving the lasso. We also discuss the extension of the adaptive lasso in generalized linear models and show that the oracle properties still hold under mild regularity conditions. As a byproduct of our theory, the nonnegative garotte is shown to be consistent for variable selection.
The quantitative relationship of urinary peptide hydroxyproline excretion to collagen degradation (1969)

To determine the quantitative relationship of urinary hydroxyproline peptide excretion to collagen breakdown, known quantities of radioactive hydroxyproline peptides were administered to unlabeled animals and excertion of radioactivity in respiratory carbon dioxide, urine, and feces was measured. The major routes of excretion of collagen peptide metabolites were respiratory carbon dioxide (75%) and urine, as hydroxyproline-containing peptides (25%). Since the predominant urine hydroxyproline peptide linkage is proly-hydroxyproline, L-prolyl-L-hydroxyproline-(3)H was administered to unlabeled animals. Greater than 80% of the administered dipeptide was excreted in urine, suggesting that this peptide linkage is not hydrolyzed to a significant extent in vivo. These data suggest that urinary hydroxyproline excretion is a "fairly" sensitive indicator of collagen breakdown and can be used at the clinical level to quantitate changes in collagen breakdown.
Molecular detection and identification of enteroviruses using enzymatic amplification and nucleic acid hybridization (1990)

Analysis of enteroviral genomes has revealed that the 5' nontranslated region is highly conserved, providing consensus sequences for the design of oligonucleotides which should anneal to most, if not all, human enteroviral RNAs. We designed and used a pair of such generic primers to enzymatically amplify cDNA from coxsackievirus group B types 1 through 6, poliovirus types 1 through 3, 4 coxsackievirus A types, and 29 echoviruses. The polymerase chain reaction (PCR) products generated with these enteroviral primers were analyzed by agarose gel electrophoresis, Southern blotting, or slot blot hybridization. A genotype-specific PCR was used to detect coxsackievirus B3, to the exclusion of other enteroviruses, by using a coxsackievirus B3 genome-specific primer pair that was derived from sequences coding for part of a capsid protein. A technique is demonstrated by which individual genotypes, for which no sequence information is known, can be identified by high-criterion hybridization analysis following amplification with generic enterovirus PCR primers.
Effect of Partial Incision of the Zona Pellucida by Piezo-Micromanipulator for In Vitro Fertilization Using Frozen-Thawed Mouse Spermatozoa on the Developmental Rate of Embryos Transferred at the 2-Cell Stage (2002)

Cryopreservation of mouse spermatozoa is widely used, although considerable strain differences in fertilization rates using frozen-thawed mouse spermatozoa have been described. The C57BL/6 mouse strain is a very widely used for establishment of transgenic mice, but the fertilization rate associated with the use of cryopreserved C57BL/6 spermatozoa is very low compared with rates for other inbred strains. We have recently solved this difficulty by in vitro fertilization (IVF) in combination with partial zona pellucida dissection (PZD). However, this technique requires culture of fertilized eggs with PZD in vitro up to morula or blastocyst stage before transfer into the uterus because blastomeres are lost after transfer into the oviduct because of the relatively large artificial slit in the zona pellucida. To overcome this problem, we performed a partial zona pellucida incision by using a piezo-micromanipulator (ZIP) for IVF with frozen-thawed mouse spermatozoa. The blunt end of the micropipette touched the surface of the zona pellucida of the oocytes, and piezo pulses were used to incise the zona pellucida while the pipette was moved along by the surface of zona pellucida. The length of the incision was pir/6 microm. When cumulus-free ZIP and PZD oocytes were inseminated with frozen-thawed genetically modified C57BL/6J spermatozoa, the fertilization rates of ZIP and PZD oocytes were 52% and 48%, respectively. After embryo transfer at the 2-cell stage, 18% and 2% of the transferred embryos with ZIP and PZD developed to term, respectively. This difference was significant (P < 0.05). When ZIP and PZD zygotes were cultured to blastocyst stage and subsequently transferred to uterine horns of recipient animals, the difference between ZIP and PZD zygotes for development rate to full term was not significant. Our results indicate that ZIP is an effective alternative technique for IVF using cryopreserved mouse spermatozoa and subsequent embryo transfer.
ADEPT: a computer program for prediction of protein antigenic determinants (1993)

ADEPT, a program that can be used for prediction of protein antigenic determinants from the amino acid sequence alone for the cases of humoral and cellular immune response, is described. Most methods presently utilized for this purpose are implemented in the program along with some original parameters for the case of humoral immune response. There is also a possibility to combine several methods for the case of humoral immune response, which provides a means to create new predictive methods. ADEPT also includes a literature-derived database of proteins in the SWISS-PROT standard with experimentally determined antigenic determinants, so the predictive ability of new methods can be assessed within the program and corresponding statistical information is calculated. ADEPT may be useful for solving vamious tasks involving the delineation of antigenic regions on proteins or characterization of peptide fragments, arising, for examnple, in protein engineering (e.g. selection of protein portions most suitable for insertion of peptide sequences that are antigenically active or possessing other desired characteristics), and in particular for construction of vaccines containing B- and/or T-cell epitopes, as well as for other problems of medico-biological research.
A microfabricated electrical SPLITT system (2005)

A growing need for methods to analyze and prepare monodisperse nanoparticles on an industrial scale exists and may be solved by the application of split flow thin fractionation (SPLITT) at the microscale. Microfluidic systems of this type have the ability to separate nanoparticles with high precision in a continuous manner. A miniaturized SPLITT system can be fabricated using standard microfabrication technologies, works in a continuous mode, and can be used as a sample preparation instrument in a micro-total-analysis-system (micro-TAS). In this paper, a miniaturized electrical SPLITT system, which separates particles continuously based on electrophoretic mobility, has been characterized. The advantages of miniaturization have been elucidated. The various aspects of the micro SPLITT system discussed in this paper can be broadly classified into: micro SPLITT system design, fluidics modeling to refine the splitter arrangements, and experimental characterization of the SPLITT system. The design of the micro SPLITT system has been elucidated focusing on the two designs that were implemented. Fluid modeling, used to arrive at a new SPLITT design, was done using a commercially available CFD package to investigate behavior of the fluid in the microchannel with various splitter arrangements. Testing was done with nanoparticles of varying diameter and electrophoretic mobilities to verify the modeling results and demonstrate functionality of the SPLITT system. Particles eluted from both outlets of the SPLITT system were characterized using AFM and SEM to verify the function of the system.