gebhart/patrepeval huggingface dataset:
In vivo plant flow cytometry: A first proof‐of‐concept (2011)

In vivo flow cytometry has facilitated advances in the ultrasensitive detection of tumor cells, bacteria, nanoparticles, dyes, and other normal and abnormal objects directly in blood and lymph circulatory systems. Here, we propose in vivo plant flow cytometry for the real-time noninvasive study of nanomaterial transport in xylem and phloem plant vascular systems. As a proof of this concept, we demonstrate in vivo real-time photoacoustic monitoring of quantum dot-carbon nanotube conjugates uptake by roots and spreading through stem to leaves in a tomato plant. In addition, in vivo scanning cytometry using multimodal photoacoustic, photothermal, and fluorescent detection schematics provided multiplex detection and identification of nanoparticles accumulated in plant leaves in the presence of intensive absorption, scattering, and autofluorescent backgrounds. The use of a portable fiber-based photoacoustic flow cytometer for studies of plant vasculature was demonstrated. These integrated cytometry modalities using both endogenous and exogenous contrast agents have a potential to open new avenues of in vivo study of the nutrients, products of photosynthesis and metabolism, nanoparticles, infectious agents, and other objects transported through plant vasculature.
NCSA's World Wide Web server: design and performance (1995)

To support continued growth, WWW servers must manage a multigigabyte (in some instances a multiterabyte) database of multimedia information while concurrently serving multiple request streams. This places demands on the servers' underlying operating systems and file systems that lie far outside today's normal operating regime. Simply put, WWW servers must become more adaptive and intelligent. The first step on this path is understanding extant access patterns and responses. The article examines extant Web access patterns with the aim of developing more efficient file-caching and prefetching strategies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An aligned nanofibrous collagen scaffold by electrospinning and its effects on in vitro fibroblast culture (2006)

Fabrication of nanofibrous scaffolds with well-defined architecture mimicking native extracellular matrix analog has significant potentials for many specific tissue engineering and organs regeneration applications. The fabrication of aligned collagen nanofibrous scaffolds by electrospinning was described in this study. The structure and in vitro properties of these scaffolds were compared with a random collagen scaffold. All the collagen scaffolds were first crosslinked in glutaraldehyde vapor to enhance the biostability and keep the initial nano-scale dimension intact. From in vitro culture of rabbit conjunctiva fibroblast, the aligned scaffold exhibited lower cell adhesion but higher cell proliferation because of the aligned orientation of fibers when compared with the random scaffold. And the alignment of the fibers may control cell orientation and strengthen the interaction between the cell body and the fibers in the longitudinal direction of the fibers.
Regulation of cell migration and osteogenic differentiation in mesenchymal stem cells under extremely low fluidic shear stress (2014)

Mesenchymal stem cells (MSCs) are multipotent stem cells predominantly obtained from bone marrow, which are sensitive to mechanical loadings in physiological microenvironment. However, how the MSCs sense and respond to extremely low fluidic shear stress analogous to interstitial flow in vivo is poorly understood. In this work, we present a functional microfluidic device to examine the migration and differentiation behaviors of MSCs in response to multiple orders of physiologically relevant interstitial flow levels. The different magnitudes of fluid flow-induced shear stress were produced by a hydraulic resistance-based microfluidic perfusion system consisting of a microchannel network and a parallel of uniform cell culture chambers. By changing the length and width of the flow-in channels, the multiple magnitudes of low shear stresses could be generated ranging from ∼10−5 to ∼10−2 dyne/cm2. We demonstrated enhanced significant F-actin expression and cell migration in MSCs under applied fluidic shear stress at ∼10−2 dyne/cm2. We also demonstrated a significant osteogenic differentiation under this interstitial level of slow flows from ∼10−2 to ∼10−4 dyne/cm2 in MSCs by analyzing alkaline phosphatase activity and osteopontin staining. Moreover, cytochalasin D and Rho-inhibitor Y-27632 significantly reduced the cytoskeleton F-actin expression and osteogenic differentiation in MSCs, indicating the mediated mechanical responses of MSCs under extremely low fluidic shear stress, possibly as a consequence of Rho-associated kinase pathway. The established microfluidic perfusion system with multiple shear-flow capabilities is simple and easy to operate, providing a flexible platform for studying the responses of diverse types of cells to the multiple interstitial flow levels in a single assay.
Comparison of delayed release 5 aminosalicylic acid (mesalazine) and sulphasalazine in the treatment of mild to moderate ulcerative colitis relapse. (1988)

Oral formulations of 5-aminosalicylic acid (mesalazine) appear less toxic than sulphasalazine. We have therefore compared sulphasalazine, low dose mesalazine and high dose mesalazine in the treatment of mild to moderate relapse of ulcerative colitis. Sixty one patients (32 men, aged 20-78 years) were randomly allocated to sulphasalazine 2 g daily, mesalazine 800 mg daily, or mesalazine 2.4 g daily in a double blind, double dummy, four week trial. Groups were comparable for age, sex, extent of disease, and pretrial sulphasalazine intake. Four patients were unable to complete the study because of treatment failure (two taking sulphasalazine and two high dose mesalazine). A further two patients taking sulphasalazine developed side effects necessitating withdrawal. Within treatment comparisons revealed significant improvement of: sigmoidoscopic grade in the sulphasalazine group; rectal bleeding, sigmoidoscopic and histological grade in the low dose mesalazine group; stool frequency, rectal bleeding and sigmoidoscopic grade in the high dose mesalazine group. Greater improvement in rectal bleeding (p less than 0.05) and sigmoidoscopic appearances (p less than 0.05) occurred in patients taking high dose mesalazine than in those taking sulphasalazine. In two patients taking high dose mesalazine minor rises of plasma creatinine concentrations occurred, suggesting the need to monitor renal function.
Adenovirus Vector-Based Purging of Multiple Myeloma Cells (1998)

Adenoviruses are efficient gene delivery agents for a variety of neoplasms. In the present study, we have investigated the use of adenoviruses for the delivery of the thymidine kinase (tk) gene into multiple myeloma (MM) cells. We first demonstrated that MM cell lines and MM patient cells express both adenovirus receptors as well as the DF3/MUC1 protein, thus providing a rationale for using adenoviruses to selectively deliver genes under the control of the DF3 promoter. By using an adenoviral construct containing beta-galactosidase (beta-gal) gene driven by the DF3 promoter (Ad. DF3-betagal), we demonstrate greater than 80% transduction efficiency in OCI-My5 and RPMI 8226 MM cell lines at a multiplicity of infection of 1 to 100. Importantly, transduction with the tk gene driven by the DF3 promoter (Ad.DF3-tk) followed by treatment with 50 micromol/L ganciclovir (GCV) purged >/=6 log of contaminating OCI-My5 and RPMI 8226 MM cells within bone marrow mononuclear cells. In contrast, normal human hematopoietic progenitor cell number was unaffected under these conditions. Selectivity of DF3/MUC1 promoter was further confirmed, because Ad.DF3-betagal or Ad.DF3-tk did not transduce MUC1-negative HeLa cervical carcinoma cells. In addition, GCV treatment of Ad.DF3-tk-transduced RPMI 8226 MM cells did not induce a significant bystander effect. These findings demonstrate that transduction with Ad vectors using a tumor-selective promoter provides a highly efficient and selective approach for the ex vivo purging of MM cells.
A new series of low molar mass ferroelectric organosiloxanes with unusual electro-optic properties (1993)

Abstract A new series of low molar mass chiral organosiloxanes A*B, C*B and a racemic analogue A(±)B have been synthesised and their mesomorphic and ferroelectric properties investigated. A* and C* denote the mesogenic moiety and B denotes the pentamethyldisiloxane tail. The following organosiloxane materials have been prepared: C8A*B, C10A*B, racemic C10A(±)B and C10C*B, where the C8 or C10 prefix indicates the number of methylene spacers between A* and C* and A* contains a 4-[(S)-2methylbutanoyloxy] and C* contains a chloro chiral end group. C8A*B exhibits only an unstable monotropic mesophase, C10A*B and C10C*B both exhibit one tilted enantiotropic ferroelectric smectic-C mesophase over a broad temperature range, with high tilt angles and high spontaneous polarisation (e.g. C10C*B 28 ° and 150nCcm−2 at 20°C). The achiral siloxane derivative C10A(±)B, exhibits one broad enantiotropic smectic-C phase. Electrooptic measurements on C10A*B and C10C*B indicate that the spontaneous polarisation is only weakly dependent on temperature between 10 °C and the SC* to isotropic transition at 51°C and 55°C, respectively whilst the tilt angles are temperature independent. These results are discussed in comparison with side-chain polymer liquid crystal structures.
A sequential 10-day regimen was better than standard triple therapy for eradicating Helicobacter pylori in older patients (2006)

Source Citation Zullo A, Gatta L, De Francesco V, et al. High rate of Helicobacter pylori eradication with sequential therapy in elderly patients with peptic ulcer: a prospective controlled study. Aliment Pharmacol Ther. 2005;21:1419-24. 15948808
Programmable DNA cleavage in vitro by Cas9 (2013)

The ternary Cas9-crRNA-tracrRNA complex (Cas9t) of the Type II CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) system functions as an Mg2+-dependent RNA-directed DNA endonuclease that locates its DNA target guided by the crRNA (CRISPR RNA) in the tracrRNA-crRNA structure and introduces a double-strand break at a specific site in DNA. The simple modular organization of Cas9t, where specificity for the DNA target is encoded by a small crRNA and the cleavage reaction is executed by the Cas9 endonuclease, provides a versatile platform for the engineering of universal RNA-directed DNA endonucleases. By altering the crRNA sequence within the Cas9t complex, programmable endonucleases can be designed for both in vitro and in vivo applications. Cas9t has been recently employed as a gene-editing tool in various eukaryotic cell types. Using Streptococcus thermophilus Cas9t as a model system, we demonstrate the feasibility of Cas9t as a programmable molecular tool for in vitro DNA manipulations.
Binding of thalidomide to alpha1-acid glycoprotein may be involved in its inhibition of tumor necrosis factor alpha production. (1996)

In addition to its well known sedative and teratogenic effects, thalidomide also possesses potent immunomodulatory and antiinflammatory activities, being most effective against leprosy and chronic graft-versus-host disease. The immunomodulatory activity of thalidomide has been ascribed to the selective inhibition of tumor necrosis factor alpha from monocytes. The molecular mechanism for the immunomodulatory effect of thalidomide remains unknown. To elucidate this mechanism, we synthesized an active photoaffinity label of thalidomide as a probe to identify the molecular target of the drug. Using the probe, we specifically labeled a pair of proteins of 43-45 kDa with high acidity from bovine thymus extract. Purification of these proteins and partial peptide sequence determination revealed them to be alpha1-acid glycoprotein (AGP). We show that the binding of thalidomide photoaffinity label to authentic human AGP is competed with both thalidomide and the nonradioactive photoaffinity label at concentrations comparable to those required for inhibition of production of tumor necrosis factor alpha from human monocytes, suggesting that AGP may be involved in the immunomodulatory activity of thalidomide.
Structural requirements of non-peptide neurotensin receptor antagonists (1996)

Neurotensin has a wide range of pharmacological effects in peripheral tissues and in the central nervous system. The crystal structures of two potent and selective neurotensin receptor antagonists, SR 48692 (I) and SR 48527 (II) have been determined and are reported in this work. By using computational calculations (semiempirical molecular orbital AM1) we studied the conformational properties of those compounds, including an inactive analogue SR 49711 (III) for comparison. Considering the pharmacological properties related to SR 48692 (I) and to optically synthetic analogues SR 48527 (II) and SR 49711 (III), we propose a model of bioactive conformation adopted by those neurotensin receptor antagonists.
Factor XI–Dependent Reciprocal Thrombin Generation Consolidates Blood Coagulation when Tissue Factor Is Not Available (2004)

These findings support the notion that platelet-localized feedback activation of factor XI by thrombin plays an important role in maintaining normal hemostasis as well as in sustaining thrombus formation when the TF pathway is inhibited by tissue factor pathway inhibitor.
Evaluation of preservation methods for improving biogas production and enzymatic conversion yields of annual crops (2011)

The use of energy crops and agricultural residues is expected to increase to fulfil the legislative demands of bio-based components in transport fuels. Ensiling methods, adapted from the feed sector, are suitable storage methods to preserve fresh crops throughout the year for, for example, biogas production. Various preservation methods, namely ensiling with and without acid addition for whole crop maize, fibre hemp and faba bean were investigated. For the drier fibre hemp, alkaline urea treatment was studied as well. These treatments were also explored as mild pretreatment methods to improve the disassembly and hydrolysis of these lignocellulosic substrates. The investigated storage treatments increased the availability of the substrates for biogas production from hemp and in most cases from whole maize but not from faba bean. Ensiling of hemp, without or with addition of formic acid, increased methane production by more than 50% compared to fresh hemp. Ensiling resulted in substantially increased methane yields also from maize, and the use of formic acid in ensiling of maize further enhanced methane yields by 16%, as compared with fresh maize. Ensiled faba bean, in contrast, yielded somewhat less methane than the fresh material. Acidic additives preserved and even increased the amount of the valuable water-soluble carbohydrates during storage, which affected most significantly the enzymatic hydrolysis yield of maize. However, preservation without additives decreased the enzymatic hydrolysis yield especially in maize, due to its high content of soluble sugars that were already converted to acids during storage. Urea-based preservation significantly increased the enzymatic hydrolysability of hemp. Hemp, preserved with urea, produced the highest carbohydrate increase of 46% in enzymatic hydrolysis as compared to the fresh material. Alkaline pretreatment conditions of hemp improved also the methane yields. The results of the present work show that ensiling and alkaline preservation of fresh crop materials are useful pretreatment methods for methane production. Improvements in enzymatic hydrolysis were also promising. While all three crops still require a more powerful pretreatment to release the maximum amount of carbohydrates, anaerobic preservation is clearly a suitable storage and pretreatment method prior to production of platform sugars from fresh crops.
Rapid Homogeneous-Phase Sonogashira Coupling Reactions Using Controlled Microwave Heating (2001)

A microwave-enhanced, rapid and efficient homogeneous-phase version of the Sonogashira reaction is presented. It has been applied to the coupling of aryl iodides, bromides, triflates, and aryl chloride, as well as pyridine and thiophene derivatives with trimethylsilylacetylene. Excellent yields (80-95%) for substrates containing a large variety of substituents in different positions are obtained in 5-25 min.
The Functions of Human Papillomavirus Type 11 E1, E2, and E2C Proteins in Cell-free DNA Replication (1995)

We examined the functions of human papillomavirus type 11 (HPV-11) E1 and E2 proteins purified from Sf9 cells infected with recombinant baculoviruses in cell-free HPV-11 origin (ori) replication. The E1 protein binds specifically to a wild type but not to a mutated sequence in the ori spanning nucleotide position 1. It also has a relatively strong affinity for nonspecific DNA. A neutralizing antiserum directed against the amino-terminal one-third of the E1 protein totally abolishes initiation and elongation, suggesting that it functions as an initiator and a helicase at the replication fork. An antiserum against the carboxyl-terminal portion of E1 protein abolished replication only when added prior to initiation. Thus this portion of E1 is hidden in the replication complexes. The HPV-11 E2 protein appears not to be essential for elongation, but it must be present in the preinitiation complex for the E1 protein to recruit host DNA replication machinery to the ori. E2 antiserum added after preincubation in the absence of the cell extracts totally abolished replication. An identical conclusion is also reached for the bovine papillomavirus type 1 E2 protein. Finally, the HPV-11 E2C protein lacking the transacting domain of the full-length E2 protein partially inhibits E2-dependent ori replication.
Breathing Abnormalities During Sleep (1983)

The purpose of this communication is to review obstructive and central breathing abnormalities that may occur during sleep, such as obstructive sleep apnea, and Cheyne-Stokes respiration. Emphasis is placed on noninvasive monitoring of the breathing pattern and intrapleural pressure swings by respiratory and surface inductive plethysmography, respectively, which establish the diagnosis of these abnormal breathing patterns.
Characterization of Oxidative Enzymes Involved in the Biosynthesis of Benzylisoquinoline Alkaloids in Opium Poppy (Papaver somniferum) (2015)

Benzylisoquinoline alkaloids (BIAs) are a large group of nitrogen-containing specialized metabolites. Opium poppy (Papaver somniferum) is an important pharmaceutical plant and has been cultivated for thousands of years for its analgesic constituents: the morphinan BIAs codeine and morphine. In addition, opium poppy produces other BIAs with biological activities, such as the vasodilator papaverine, the potential anti-cancer drug noscapine and the antimicrobial agent sanguinarine. The objective of this work was to identify and characterize oxidative enzymes involved in BIA biosynthesis, with a specific focus on cytochromes P450 (P450s). The biosynthesis of sanguinarine from (S)-reticuline requires four P450s. Our first objective was to identify these unidentified P450s in opium poppy. Our approach was based on the coordinated induction of all sanguinarine biosynthetic enzyme transcripts and proteins in elicited opium poppy cell suspension cultures. Using data from a previous microarray study, we identified 12 uncharacterized inducible P450s. Recombinant expression in Saccharomyces cerevisiae revealed that 4 of these enzymes (CYP719A20, CYP719A25, CYP82N3 and CYP82N4) were involved in sanguinarine biosynthesis. Unexpectedly, in planta silencing using virus-induced gene silencing showed that plants suppressed in these P450s transcripts have significantly increased levels of sanguinarine and dihydrosanguinarine. Many changes in the accumulation of sanguinarine biosynthetic intermediates were also detectable. In CYP82N3- and CYP82N4-silenced plants, we detected a significant accumulation of some alkaloids in roots and a significant reduction of some of these in latex. Previous silencing of the penultimate step in morphine biosynthesis, codeinone reductase (COR), showed a dramatic decrease in morphinan alkaloids, as well as a significant increase in reticuline, the central BIA branch point intermediate. A search for similar enzymes that may be co-silenced revealed a P450 reductase fusion. Further in vitro and in planta characterization showed that this enzyme is responsible for the final unidentified and first committed steps in morphine biosynthesis, the epimerization of (S)-reticuline. Papaver rhoeas, which does not accumulate morphinan alkaloids, possesses this enzyme as two polypeptides. The significance of this difference remains to be studied. We were also able to identify a paralog of COR which can catalyze the isomerization of many morphinans, potentially opening new routes to manufacture novel opiates.
Snapshot 3D Optical Coherence Tomography System using Image Mapping Spectrometer (2012)

A snapshot 3-Dimensional Optical Coherence Tomography system was developed using Image Mapping Spectrometry. This proof-of-concept system can give depth information at different spatial positions within one integration time to reduce motion artifact and enhance throughput.
Cellular location of heat-labile enterotoxin in Escherichia coli (1984)

We demonstrated that both the A and B subunits of heat-labile enterotoxin from Escherichia coli are located in the periplasm. The toxin was shown to form aggregates in Tris-EDTA buffers which are routinely used for isolating membranes. The aggregates pellet upon centrifugation, and this may explain why several previous investigators have concluded that enterotoxin is associated with membranes.
Effects of 12-O-Tetradecanoylphorbol-13-acetate (TPA) in Combination with Paclitaxel (Taxol) on Prostate Cancer LNCaP Cells Cultured In vitro or Grown as Xenograft Tumors in Immunodeficient Mice (2006)

TPA and paclitaxel in combination had a stronger inhibitory effect on the growth of LNCaP cells in culture or as xenograft tumors in immunodeficient mice than either agent alone. Clinical trials with TPA alone or in combination with paclitaxel in patients with prostate cancer may be warranted.
Pore Size Analysis of Activated Carbons from Argon and Nitrogen Porosimetry Using Density Functional Theory (2000)

We present isotherms calculated from density functional theory for the adsorption of argon in model slit-shaped carbon pores at 77 K. The model isotherms are used to interpret experimental argon uptake measurements and to obtain the pore size distributions of several porous carbons. A similar set of density functional theory isotherms, previously reported for nitrogen adsorption on carbon slit pores at 77 K, are used to determine pore size distributions for the same set of carbons. The pore size distribution maxima, mean pore widths, and specific pore volumes measured using the two different probe gases are all found to agree to within approximately 8% on average. Some of the differences in the pore size distributions obtained from argon and nitrogen porosimetry may be attributable to quadrupolar interactions of the nitrogen molecules with functional groups on the carbon surface.
Viewstamped Replication Revisited (2012)

This paper presents an updated version of Viewstamped Replication, a replication technique that handles failures in which nodes crash. It describes how client requests are handled, how the group reorganizes when a replica fails, and how a failed replica is able to rejoin the group. The paper also describes a number of important optimizations and presents a protocol for handling reconfigurations that can change both the group membership and the number of failures the group is able to handle. 1