gebhart/patrepeval huggingface dataset:
Adsorption of Fibrinogen and Lysozyme on Silicon Grafted with Poly(2-methacryloyloxyethyl Phosphorylcholine) via Surface-Initiated Atom Transfer Radical Polymerization (2005)

Surfaces based on grafted poly(2-methacryloyloxyethyl phosphorylcholine) (poly(MPC)) "brushes" with a constant graft density of 0.39 chain/nm2 and chain length from 5 to 200 monomer units were prepared by surface-initiated atom transfer radical polymerization (ATRP) on silicon wafers. The chain length and layer thickness of the poly(MPC) grafts were varied via the ratio of MPC to sacrificial initiator. The surfaces were characterized by water contact angle, XPS, and AFM. The effect of poly(MPC) chain length on fibrinogen and lysozyme adsorption was studied in TBS buffer at pH 7.4. The adsorption of both proteins on the poly(MPC)-grafted surfaces was greatly reduced compared to the unmodified silicon. Adsorption decreased with increasing chain length of the poly(MPC) grafts. Grafts of chain length 200 (MW 59 000) gave adsorption levels of 7 and 2 ng/cm2, respectively, for fibrinogen and lysozyme at 1 mg/mL protein concentration, corresponding to reductions of greater than 98% compared to the unmodified silicon. Adsorption experiments using mixtures of the two proteins showed that the suppression of protein adsorption on the poly(MPC)-grafted surfaces was not strongly dependent on protein size or charge.
Complete 360° circumferential gonioscopic optical coherence tomography imaging of the iridocorneal angle (2015)

Clinically, gonioscopy is used to provide en face views of the ocular angle. The angle has been imaged with optical coherence tomography (OCT) through the corneoscleral limbus but is currently unable to image the angle from within the ocular anterior chamber. We developed a novel gonioscopic OCT system that images the angle circumferentially from inside the eye through a custom, radially symmetric, gonioscopic contact lens. We present, to our knowledge, the first 360° circumferential volumes (two normal subjects, two subjects with pathology) of peripheral iris and iridocorneal angle structures obtained via an internal approach not typically available in the clinic.
Mechanism of Membrane Permeation and Pore Formation by Antimicrobial Peptides (2005)

This chapter contains sections titled: Introduction The Cell Membrane is the Major Binding Site for Most Cationic Antimicrobial Peptides Non-receptor-mediated Interaction of Antimicrobial Peptides with their Target Cells A Receptor-mediated Interaction of Antimicrobial Peptides with their Target Cells Parameters Involved in the Selection of Target Cells by Antimicrobial Peptides The Role of the Composition of the Cell Wall and the Cytoplasmic Membrane The Role of the Peptide Chain and Its Organization The Extent of Hydrophobicity and Distribution of Positively-charged Amino Acids Along the Peptide Chain The Stability of the Amphipathic Structure The Ability of a Peptide to Self-associate in Solution and/or in Membranes Fatty Acid Modification can Compensate for the Hydrophobicity and Amphipathicity of the Peptide Chain The Lethal Event Caused by Antimicrobial Peptides How do Antimicrobial Peptides Damage the Integrity of the Target Cell Membrane? Membrane-imposed Amphipathic Structure Molecular Mechanisms of Membrane Permeation Pore Formation via the Barrel–Stave Model The Carpet Model The Molecular Architecture of the Permeation Pathway Toroidal Pores Channel Aggregates/Hydrophobic Pores Summary and Conclusions References
Optimum element lengths for Yagi-Uda arrays (1975)

An analytical method is developed for the maximization of the directivity of a Yagi-Uda array by adjusting the lengths of the dipole elements. The effects of a finite dipole radius and the mutual coupling between the elements are taken into consideration. Currents in the array elements are approximated by three-term expansions with complex coefficients that convert the governing integral equations into matrix equations. Array directivity is maximized by a perturbation procedure that adjusts the lengths of all array elements simultaneously and that converges very rapidly. This method can be combined with the previously developed spacing-perturbation method to form a double-perturbation procedure and obtain a Yagi-Uda array of nonuniformly spaced elements of unequal lengths. which yields a maximum directivity.
Alteration of Milk Composition Using Molecular Genetics (1989)

Advances in genetic technology have made it possible to consider making substantial changes either in the composition of milk or in the production of entirely new products in milk. The technological capabilities that have given rise to the introduction and expression of new genes in animals are discussed. Examples are given of transgenic animals that express foreign proteins in their milk. Advantages of the mammary synthesis of proteins are discussed and potential alterations of milk composition and scenarios for introduction of new proteins are considered. Technological capabilities that either currently exist or are being developed are discussed along with the requirements for making it feasible to utilize the technology on a broad scale in dairy cattle.
Clinical Profile of Pediatric Patients Hospitalized With Respiratory Syncytial Virus Infection (1993)

To update the clinical profile of pediatric patients hospitalized with RSV infection, we retrospectively reviewed the records of 246 children (male:female ratio 1.44:1) admitted during one season to a tertiary-care hospital. The most common admitting diagnoses were bronchiolitis (37.4%), pneumonia (32.5%), and possible septicemia (13%). Median age was 3 months; median length of stay, three days. Twice as many minorities were admitted with RSV infection as all other admissions during the same year. Family history of asthma, while common (35%), did not affect length of stay or complications. Of the 38 (15%) patients requiring intensive care, 29 (76%) underwent ventilation. Patients with underlying cardiopulmonary disease had more complications, were more likely to require intensive care (about 50%), and had significantly longer hospital stays than others. All three patients (1.2%) who died had congenital heart disease. Common risk factors included young age, chronic cardiopulmonary disease, male sex, and possibly family history of asthma. Although the most typical clinical diagnoses remain bronchiolitis and pneumonia, a systemic illness resembling the sepsis syndrome has emerged at our institution as a significant clinical presentation.
Sterilization of Medical Equipment Using Radicals Produced by Oxygen/Water Vapor RF Plasma (2006)

The sterilization of medical equipment was performed using low-pressure RF discharge plasma. Oxygen radicals as oxidizing materials for sterilization were produced from oxygen or water vapor. The generation of atomic oxygen and OH radicals was confirmed using the light emission spectra of the plasma. The pressure in the discharge region was varied periodically during inactivation in order to produce radicals effectively and to penetrate the produced radicals into tiny gaps. Medium sheets for microbial detection indicated that the decimal reduction value of active bacillus was 5 and 8 min using oxygen plasma and water vapor plasma with n e =10 9 cm -3 , respectively. Biological indicators clarified that the sterilization of bacilli spores was successful for a treatment time of 90 min.
Patterning Barriers to Lateral Diffusion in Supported Lipid Bilayer Membranes by Blotting and Stamping (2000)

Two new methods are introduced for patterning fluid lipid bilayer membranes on solid supports. These methods are based on the observation that supported membranes undergo self-limiting lateral expansion when bilayer material is removed from the surface or when it is deposited in a pattern on a surface. Spatially selective (patterned) removal of bilayer material can be achieved by using a poly(dimethylsiloxane) (PDMS) stamp. Following slight lateral expansion into the bilayer-free region created by this blotting process, stable barriers to lateral diffusion are formed. Inspection of the barrier regions indicates that nearly all of the bilayer material is removed, implying that it has been transferred to the stamp. As a consequence, it also proves possible to transfer the lifted material from the stamp onto a fresh surface. The transferred material retains the original pattern from the stamp and is also laterally mobile, and the mobility is confined to the printed region. Alternatively, bilayers assembled on a PDMS stamp can be printed onto fresh surfaces. Together these methods constitute a simple and powerful approach for preparing patterned fluid bilayers in nearly any geometry.
Swift: primary data analysis for the Illumina Solexa sequencing platform (2009)

In this article, we describe Swift, a new tool for performing primary data analysis on the Illumina Solexa Sequencing Platform. Swift is the first tool, outside of the vendors own software, which completes the full analysis process, from raw images through to base calls. As such it provides an alternative to, and independent validation of, the vendor supplied tool. Our results show that Swift is able to increase yield by 13.8%, at comparable error rate.
The irregular Z-buffer (2005)

The classical Z-buffer visibility algorithm samples a scene at regularly spaced points on an image plane. Previously, we introduced an extension of this algorithm called the irregular Z-buffer that permits sampling of the scene from arbitrary points on the image plane. These sample points are stored in a two-dimensional spatial data structure. Here we present a set of architectural enhancements to the classical Z-buffer acceleration hardware which supports efficient execution of the irregular Z-buffer. These enhancements enable efficient parallel construction and query of certain irregular data structures, including the grid of linked lists used by our algorithm. The enhancements include flexible atomic read-modify-write units located near the memory controller, an internal routing network between these units and the fragment processors, and a MIMD fragment processor design. We simulate the performance of this new architecture and demonstrate that it can be used to render high-quality shadows in geometrically complex scenes at interactive frame rates. We also discuss other uses of the irregular Z-buffer algorithm and the implications of our architectural changes in the design of chip-multiprocessors.
Alternative splicing of RHAMM gene in chinese gastric cancers and its in vitro regulation. (2000)

The expression of mRHAMM variants is closely associated with tumor progression, which may be promoted and modulated by HA.
Purification and Structural and Functional Characterization of FhuA, a Transporter of theEscherichia coliOuter Membrane (1996)

The Escherichia coli outer membrane ferrichrome transporter FhuA was purified chromatographically in a neutral detergent (octyl glucoside or dodecyl maltoside). The amount of dodecyl maltoside bound to the protein (1.2 +/- 0.15 g/g of FhuA) and the Stokes radius of the FhuA-dodecyl maltoside complex (Rs = 4.2 nm) were determined using size exclusion chromatography. Sedimentation equilibrium and velocity experiments indicated that the FhuA preparation was monodisperse and that the protein was monomeric. The value found for the frictional coefficient of the protein-detergent complex (1.18) suggested a globular shape for the complex. Sedimentation experiments gave values for the molecular mass of the FhuA-dodecyl maltoside complex (180 kDa) and for the Stokes radius in complete agreement with those calculated from size exclusion chromatography. The circular dichroism spectrum indicated a 51% beta-sheet content. Functionality of the purified protein was assessed from fluorescence measurements using the DNA probe YO-PRO-1. Interaction of nM concentrations of FhuA with bacteriophage T5 resulted in the release of 90 +/- 8% of the phage DNA. The limiting step in DNA ejection was binding of the phage to its receptor. Release of DNA took place in a few seconds. Ferrichrome (0.8 microM) competed with the phage for binding to FhuA and prevented DNA ejection.
[Towards better understanding of hematolymphoid malignancies--based on the WHO-2008 classification: summary]. (2011)

The revised WHO classification of tumors of hematopoietic and lymphoid tissues (4th edition) was published in 2008. A number of information from molecular biology was introduced, new patterns of classification were proposed, and specific molecular diagnostics and molecular-targeting therapy were introduced in a part of these diseases. In this symposium, four remarkable points of the WHO-2008 classification (myeloproliferative neoplasms and JAK2 mutation, approaches to hypereosinophilic syndromes, morphology of myelodysplastic syndromes, and varied classification of lymphoid malignancies) were presented by the expert speakers, and the better understanding of the revised classification is warranted.
Porcine respiratory coronavirus: molecular features and virus-host interactions. (1993)

Since 1984, a previously unrecognized respiratory coronavirus, causing a mostly unapparent infection, has rapidly and massively spread within the swine population in Europe, and few years later, a virus with similar characteristics has been identified in the USA. The agent, designated PRCV, appears to be derived from the porcine enteric coronavirus TGEV. The aim of the present article is to review comprehensively the state of the knowledge about this new virus and its infection. The review includes the following topics: epizootiology, molecular characterization and antigenic features of PRCV, pathogenesis and clinical aspects, immunity and laboratory diagnosis. The authors' views concerning the impact of the emergence of PRCV on both coronavirus research and swine production are presented in the conclusion.
Dispiroketals in Synthesis (Part 18)1: Regioselective and Enantioselective Protection of Symmetric Polyol Substrates Using an Enantiopure (2S,2’S)-Dimethyl-bis-dihydropyran (1995)

The simultaneous enantioselective differentiation and regioselective protection of a range of acyclic symmetric polyols is investigated. Deprotection of a fully protected derivative leads to an enantiopure dissymmetric diol.
ETHICS AND INFECTIOUS DISEASE1 (2005)

Bioethics apparently suffers from a misdistribution of research resources analogous to the '10/90' divide in medical research. Though infectious disease should be recognized as a topic of primary importance for bioethics, the general topic of infectious disease has received relatively little attention from the discipline of bioethics in comparison with things like abortion, euthanasia, genetics, cloning, stem cell research, and so on. The fact that the historical and potential future consequences of infectious diseases are almost unrivalled is one reason that the topic of infectious disease warrants more attention from bioethicists. The 'Black Death' eliminated one third of the European population during the 14th Century; the 1989 flu killed between 20 and 100 million people; and, in the 20th Century smallpox killed perhaps three times more people than all the wars of that period. In the contemporary world, epidemics (AIDS, multi-drug resistant turberculosis, and newly emerging infectious diseases such as SARS) continue to have dramatic consequences. A second reason why the topic of infectious disease deserves further attention is that it raises difficult ethical questions of its own. While infected individuals can threaten the health of other individuals and society as a whole, for example, public health care measures such as surveillance, isolation, and quarantine can require the infringement of widely accepted basic human rights and liberties. An important and difficult ethical question asks how to strike a balance between the utilitarian aim of promoting public health, on the one hand, and libertarian aims of protecting privacy and freedom of movement, on the other, in contexts involving diseases that are--to varying degrees--contagious, deadly, or otherwise dangerous. Third, since their burden is most heavily shouldered by the poor (in developing countries), infectious diseases involve issues of justice--which should be a central concern of ethics. I conclude by providing sociological and historical explanations of why the topic of infectious disease has not already received more attention from bioethicists.
10-Year Follow-up of Intensive Glucose Control in Type 2 Diabetes (2008)

Despite an early loss of glycemic differences, a continued reduction in microvascular risk and emergent risk reductions for myocardial infarction and death from any cause were observed during 10 years of post-trial follow-up. A continued benefit after metformin therapy was evident among overweight patients. (UKPDS 80; Current Controlled Trials number, ISRCTN75451837.)
A randomized phase II study of FOLFOX or FOLFIRI.3 as second-line therapy in patients with advanced pancreatic cancer previously treated with gemcitabine-based chemotherapy (2009)

4618 Background: Only few clinical trials have been conducted in patients with advanced pancreatic cancer after failure of first-line gemcitabine-based chemotherapy. We conducted a randomized phase II trial of modified FOLFOX vs. modified FOLFIRI.3 as second-line regimen for the patients with gemcitabine refractory pancreatic cancer ( NCT00786006 ). Methods: Patients with advanced pancreatic adenocarcinoma previously treated with gemcitabine were randomly assigned to FOLFOX or FOLFIRI.3 stratifying by age (≤ 65 vs. &gt;65), performance status (0–1 vs. 2) and prior response to gemcitabine (PR/SD vs. PD). FOlFIRI.3 regimen consisted of Irinotecan 70 mg/m 2 (over 60 min) D1, leucovorin 400 mg/m 2 (over 2h) D1, 5-FU 2000 mg/m 2 (over 46 hours) from D1, then irinotecan 70 mg/m 2 (over 60 min) at the end of the 5-FU infusion every two week. FOLFOX regimen is composed of oxaliplatin 85 mg/m 2 (over 120 min) D1, LV 400 mg/m 2 D1, 5-FU 2,000 mg/m 2 (over 46 hours) every two week. The primary end-point was 6-month overall survival (P 0 =20%) and Simon-Wittes-Ellenberg design was used to calculate the sample size (29 evaluable patients for each treatment arm). Results: From January 2007 to December 2008, sixty patients were enrolled and randomized to FOLFOX (N=30) or FOLFIRI.3 (N=30). Baseline characteristics were well balanced between each arm; median age 56 (35–60) vs. 56 yo (37–73); ECOG PS 0/1/2, 5/24/1 vs. 5/25/0; prior response to gemcitabine-based chemotherapy PR/SD/PD 10/13/7 vs. 10/11/9. With a median follow-up period of 6.0 months (95% CI, 4.7–7.3) the median overall survival was 4.0 months in both group (HR=0.95, 95% CI 0.52–1.75) with 6-month survival rates of 25% and 20%, respectively. The median PFS was 1.4 months for FOLFOX and 1.9 months for FOLFIRI.3 (HR=1.11, 95% CI, 0.64–1.92). Disease control (PR+SD) was achieved in 20% (5/25 in FOLFOX) and 28% (7/25 in FOLFIRI.3) of patients with measurable disease. The incidences of grade 3/4 toxicities were similar in both groups. Conclusions: Both FOLFOX and FOLFIRI.3 were tolerated with manageable toxicity, offering modest activity as second-line treatment of patients with advanced or metastatic pancreatic cancer, previously treated with gemcitabine. No significant financial relationships to disclose.
Sequence analysis and DNA-protein interactions within the 5' flanking region of the Ca2+/calmodulin-dependent protein kinase II alpha-subunit gene. (1990)

The 5' flanking region of the brain Ca2+/calmodulin-dependent protein kinase II alpha-subunit gene was identified and characterized. A total of 430 bases was sequenced upstream from the translation initiation codon, and the site of transcription initiation was located at -149 or -147 bases as determined by primer extension and S1 nuclease protection analysis, respectively. TATA and CAAT boxes were absent from their standard positions; however, the 5' flanking region was rich in G + C and contained a GGGCG and a TATATAA sequence 76 and 160 bases upstream from the transcription initiation site, respectively. Moreover, the sequence CAACGG was found 85 and 146 bases upstream from this site, indicating presumptive binding sites for the Myb protein. Gel-mobility shift assays revealed that a 120-base-pair fragment, which included the G + C-rich, TATA, and CAACGG sequences bound nuclear proteins specifically. DNA-protein complexes with similar gel mobilities were obtained with nuclear extracts from rat forebrain or cerebellum and from neonatal or adult brains. Extracts from rat liver, kidney, and spleen generated specific DNA-protein complexes with different electrophoretic mobilities, suggesting the occurrence of different nuclear proteins that bind to 5' regulatory elements of the Ca2+/calmodulin-dependent kinase II alpha-subunit gene.
Manufacturing of recombinant adeno-associated viral vectors for clinical trials (2016)

The ability to elicit robust and long-term transgene expression in vivo together with minimal immunogenicity and little to no toxicity are only a few features that make recombinant adeno-associated virus (rAAV) vectors ideally suited for many gene therapy applications. Successful preclinical studies have encouraged the use of rAAV for therapeutic gene transfer to patients in the clinical setting. Nevertheless, the use of rAAV in clinical trials has underscored the need for production and purification systems capable of generating large amounts of highly pure rAAV particles. To date, generating vector quantities sufficient to meet the expanding clinical demand is still a hurdle when using current production systems. In this chapter, we will provide a description of the current methods to produce clinical grade of rAAV under current good manufacturing practice (cGMP) settings.
Longitudinal Assessment of Negative Symptoms in Schizophrenia/Schizoaffective Patients, Other Psychotic Patients, and Depressed Patients (2001)

This study assessed differences in negative symptom presentation between schizophrenia/schizoaffective, other psychotic, and depressed patients over a 10-year followup period. One hundred fifty individuals with schizophrenia or schizoaffective disorders (SZ/SZAF), other psychotic disorders (OP), and depressed patients (DP) were assessed at index hospitalization, then reassessed at 4.5-year, 7.5-year, and 10-year followups. SZ/SZAF patients significantly differed from DP patients in frequency and persistence of negative symptoms but were not significantly different from the OP group. Negative symptoms were not associated with depression in any diagnostic group. Dosage, but not simple use, of conventional antipsychotic medications was related to severity of symptoms in the SZ/SZAF group. Although negative symptoms were typically most severe and most common in the SZ/SZAF subjects in comparison to the DP patients, there were few statistically significant differences in the phenomenology of negative symptoms between the OP and SZ/SZAF groups. The data are consistent with a model that identifies negative symptoms as common to mental illnesses generally, with particularly high rates in psychotic illnesses.
Haploid Plants from Pollen Grains (1969)

A method is presented by which hundreds of haploid plants of various species of Nicotiana can be raised from pollen grains. Stamens should be excised when pollen grains have been individualized, but are still uninucleate and free of starch. When grown in vitro on a relatively simple medium, some pollen grains proliferate into embryo-liké, structures which develop in stages similar to those of zygotic embryos. The plantlets mature and flower profusely, but do not set seed.