gebhart/patrepeval huggingface dataset:
Sample Zone Dynamics in Peak Mode Isotachophoresis (2008)

We present a theoretical and experimental study of analyte preconcentration via peak mode isotachophoresis (ITP). We perform perturbation analysis of the governing equations that includes electromigration, diffusion, buffer reactions, and nonlinear ionic strength effects. This analysis relaxes the inherent numerical stiffness and achieves a fast solution to the transient sample evolution problem. In this model, we have incorporated a semiempirical relation to capture dispersion phenomenon within ITP interfaces. We also present a simple, closed-form analytical model that identifies key parameters governing the preconcentration dynamics in peak mode ITP. We have validated our models through a detailed experimental study performed in constant current conditions. The relevant governing experiment parameters were varied independently; namely, the leading electrolyte concentration, trailing electrolyte concentration, and current. Through our experimental study, we have identified optimum conditions to achieve high preconcentration ratio and sample accumulation rates. Our approach to the theoretical problem and experimental study provides useful guidelines in optimizing parameters such as detector location, ITP duration, and electrolyte composition in ITP preconcentration and separation assays.
Synthesis of DNA Dumbbells: Chemical vs. Enzymatic Ligation of Self-Complementary Oligonucleotides (1997)

Abstract The chemical (cyanogen bromide) and enzymatic (T4 DNA ligase) ligation of five different self-complementary oligonucleotide sequences which form 14-or 16-base pair dumbbells are described and compared here. A review of both chemical and enzymatic methods is presented; an improved enzymatic method is described as well. While both methods of ligation are effective, chemical ligation may be preferred since it is faster and less costly.
Biochemical Effects of Mercury, Cadmium, and Lead (1972)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Defined Human Pluripotent Stem Cell Culture Enables Highly Efficient Neuroepithelium Derivation Without Small Molecule Inhibitors (2013)

The embryonic neuroepithelium gives rise to the entire central nervous system in vivo, making it an important tissue for developmental studies and a prospective cell source for regenerative applications. Current protocols for deriving homogenous neuroepithelial cultures from human pluripotent stem cells (hPSCs) consist of either embryoid body-mediated neuralization followed by a manual isolation step or adherent differentiation using small molecule inhibitors. Here, we report that hPSCs maintained under chemically defined, feeder-independent, and xeno-free conditions can be directly differentiated into pure neuroepithelial cultures ([mt]90% Pax6(+)/N-cadherin(+) with widespread rosette formation) within 6 days under adherent conditions, without small molecule inhibitors, and using only minimalistic medium consisting of Dulbecco's modified Eagle's medium/F-12, sodium bicarbonate, selenium, ascorbic acid, transferrin, and insulin (i.e., E6 medium). Furthermore, we provide evidence that the defined culture conditions enable this high level of neural conversion in contrast to hPSCs maintained on mouse embryonic fibroblasts (MEFs). In addition, hPSCs previously maintained on MEFs could be rapidly converted to a neural compliant state upon transfer to these defined conditions while still maintaining their ability to generate all three germ layers. Overall, this fully defined and scalable protocol should be broadly useful for generating therapeutic neural cells for regenerative applications.
Angiogenic Effects of Interleukin 8 (CXCL8) in Human Intestinal Microvascular Endothelial Cells Are Mediated by CXCR2 (2003)

Angiogenesis plays a critical role in metastasis and tumor growth. Human tumors, including colorectal adenocarcinoma, secrete angiogenic factors, inducing proliferation and chemotaxis of microvascular endothelial cells, eventually leading to tumor neovascularization. The chemokine interleukin 8 (IL-8; CXCL8) exerts potent angiogenic properties on endothelial cells through interaction with its cognate receptors CXCR1 and CXCR2. As CXCR1 and CXCR2 expression is differentially regulated in tissue-specific endothelial cells and effects of IL-8 on intestinal endothelial cells are not defined, we characterized the potential IL-8-induced angiogenic mechanisms in primary cultures of human intestinal microvascular endothelial cells (HIMEC) and IL-8 receptor expression in human intestinal microvessels. CXCR1 and CXCR2 expression on HIMEC were defined using reverse transcriptase-PCR, immunohistochemistry, flow cytometry, and Western blot analysis. IL-8-induced downstream signaling events were assessed using immunoblot analysis and immunofluorescence. The angiogenic effects of IL-8 on HIMEC were determined using proliferation and chemotaxis assays. HIMEC responded to IL-8 with rapid stress fiber assembly, chemotaxis, enhanced proliferation, and phosphorylation of extracellular signal-regulated protein kinase 1/2 (ERK 1/2). HIMEC express CXCR2, but not CXCR1. Neutralizing antibodies to CXCR2 diminished IL-8-induced chemotaxis and stress fiber assembly. Specific inhibitors of ERK 1/2 and phosphoinositide 3-kinase abrogated endothelial tube formation and IL-8-induced chemotaxis in HIMEC. IL-8 elicits angiogenic responses in microvascular endothelial cells isolated from human intestine by engaging CXCR2. We confirmed tissue expression of CXCR2 in human intestinal microvessels. Supported by the notion that malignant colonic epithelial cells overexpress IL-8, CXCR2 blockade may be a novel target for anti-angiogenic therapy in colorectal adenocarcinoma.
Botulinum toxin for focal hyperhidrosis: technical considerations and improvements in application (1998)

Journal Article Botulinum toxin for focal hyperhidrosis: technical considerations and improvements in application Get access M. Naumann, M. Naumann Departments of Neurology and Dermatology, Bayerische Julius‐Maximilians‐Universität Würzburg, Josef‐Schneider‐Straße 11, 97080 Würzburg, Germany Search for other works by this author on: Oxford Academic Google Scholar I. Bergmann, I. Bergmann Departments of Neurology and Dermatology, Bayerische Julius‐Maximilians‐Universität Würzburg, Josef‐Schneider‐Straße 11, 97080 Würzburg, Germany Search for other works by this author on: Oxford Academic Google Scholar U. Hofmann, U. Hofmann Departments of Neurology and Dermatology, Bayerische Julius‐Maximilians‐Universität Würzburg, Josef‐Schneider‐Straße 11, 97080 Würzburg, Germany Search for other works by this author on: Oxford Academic Google Scholar H. Hamm, H. Hamm Departments of Neurology and Dermatology, Bayerische Julius‐Maximilians‐Universität Würzburg, Josef‐Schneider‐Straße 11, 97080 Würzburg, Germany Search for other works by this author on: Oxford Academic Google Scholar K. Reiners K. Reiners Departments of Neurology and Dermatology, Bayerische Julius‐Maximilians‐Universität Würzburg, Josef‐Schneider‐Straße 11, 97080 Würzburg, Germany Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 139, Issue 6, 1 December 1998, Pages 1123–1124, https://doi.org/10.1046/j.1365-2133.1998.2576k.x Published: 01 December 1998
Inhibition of Src Homology 2 Domain-Containing Protein Tyrosine Phosphatase Substrate-1 Reduces the Severity of Collagen-Induced Arthritis (2008)

Administration of a monoclonal antibody for SHPS-1 reduced the severity of arthritis in CIA mice. Regulation of biological functions of SHPS-1 may be a novel and potent strategy to treat patients with rheumatoid arthritis.
The dosage requirements for immunological paralysis by soluble proteins. (1968)

The quantitative dose requirements for induction of paralysis by BSA in mice has been the subject of further study. Parallel studies have been made with lysozyme, ovalbumin, diphtheria toxoid and ribonuclease, in which similar paralysing and immunizing procedures were used, and similar direct binding tests applied to measurement of the response. In normal adults all the antigens tested induced high-zone paralysis and concomitant immunization, but BSA alone induced low-zone paralysis. With irradiation, with courses of injection commencing at birth, and with paralysis-maintaining treatment, all the antigens tested induced paralysis in a zone quantitatively similar to the low zone detectable in normal adults with BSA. Neither irradiation, treatment with cortisol, nor thymectomy affected the rate of induction of paralysis in the low zone. On the other hand the minimum dose required for immunization varied markedly from one antigen to another.

The ability of BSA to induce low-zone paralysis in normal adults can, therefore, be attributed to the failure of low doses of this antigen to immunize. The consistency of paralysis threshold, in contrast to the variability for immunization, is interpreted as evidence of an additional step of complexity involved in immunization that is not required for paralysis.
Three-dimensional TCAD Process and Device Simulations (2006)

Shrinking feature sizes, novel device designs as well as stress engineering increase the need for three- dimensional process and device simulations. We present several application examples for full 3D process and device simulations using Sentaurus TCAD, including a 3D NMOSFET with shallow trench isolations (STI), a PMOSFET device with SiGe pockets for stress engineering (similar to the structure presented in Ref. [1]) and a Omega-FinFET (similar to structures presented in Refs. [2,3]). TCAD simulations of the full process flow as well as of the electrical device characteristics are performed. We also show examples of 3D oxidation simulations with Sentaurus Process.
Manipulation of OCT4 Levels in Human Embryonic Stem Cells Results in Induction of Differential Cell Types (2007)

To fully understand self-renewal and pluripotency and their regulation in human embryonic stem cells (hESCs), it is necessary to generate genetically modified cells and analyze the consequences of elevated and reduced expression of genes. Genes expressed in hESCs using plasmid vectors, however, are subject to silencing. Moreover, hESCs have a low plating efficiency when dissociated to single cells, making creation of subcloned lines inefficient. In addition to overexpression experiments, it is important to perform loss-of-function studies, which can be achieved rapidly using RNA interference (RNAi). We report stable long-term expression of enhanced green fluorescent protein (eGFP) in hESCs using a lentiviral vector, and establishment of an eGFP-expressing subline (RG6) using manual dissection. To demonstrate the efficacy of RNAi in hESCs, an RNAi expression vector was used to achieve reduced expression of eGFP in hESCs. To evaluate the role of OCT4 in the regulation of hESC self-renewal and differentiation, a vector expressing a hairpin RNA targeting endogenous expression of OCT4 was constructed. In a novel experiment in hESCs, the OCT4 cDNA sequence was cloned into an expression vector to allow for the transient upregulation of OCT4 in hESCs. The ability to manipulate levels of OCT4 above and below enodogenous levels allows the determination of OCT4 function in hESCs. Specifically, reduced expression of OCT4 in hESCs promoted upregulation of markers indicative of mesoderm and endoderm differentiation, and elevated levels of OCT4 in hESCs promoted upregulation of markers indicative of endoderm derivatives. Thus, both upregulation and downregulation of Oct4 in hESCs results in differentiation, but with patterns distinct from parallel experiments in mice.
Online Monitoring of Controlled Radical Polymerization:  Nitroxide-Mediated Gradient Copolymerization (2004)

A comprehensive characterization of the controlled radical copolymerization of styrene and n-butyl acrylate comonomers is obtained by using a recently introduced method termed automatic continuous online monitoring of polymerization reactions (ACOMP). By simultaneously monitoring and combining signals from a continuously diluted reactor stream, light scattering, viscosity, differential refractive index, and UV absorption were used, in a model-independent fashion, to follow the weight-average molecular weight Mw, weight-average intrinsic viscosity [η]w, the concentrations of each comonomer, and hence also the evolution of the average instantaneous and cumulative compositions along the chains as comonomers were consumed. The “composition profile” along the chain will largely influence the copolymer properties, and it is suggested that gradient copolymers might also be termed “profiled copolymers”, which then includes di- and multiblock polymers. Invoking the Mayo−Lewis model allowed sequence length averages and reactivity ratios to be computed. It is believed that the use of ACOMP with gradient copolymerization will lead to a better understanding of underlying kinetics and mechanisms and eventually lead to the ability to control the composition profile formation during the polymerization reaction.
The antibiotic ADEP reprogrammes ClpP, switching it from a regulated to an uncontrolled protease (2009)

A novel class of antibiotic acyldepsipeptides (designated ADEPs) exerts its unique antibacterial activity by targeting the peptidase caseinolytic protease P (ClpP). ClpP forms proteolytic complexes with heat shock proteins (Hsp100) that select and process substrate proteins for ClpP-mediated degradation. Here, we analyse the molecular mechanism of ADEP action and demonstrate that ADEPs abrogate ClpP interaction with cooperating Hsp100 adenosine triphosphatases (ATPases). Consequently, ADEP treated bacteria are affected in ClpP-dependent general and regulatory proteolysis. At the same time, ADEPs also activate ClpP by converting it from a tightly regulated peptidase, which can only degrade short peptides, into a proteolytic machinery that recognizes and degrades unfolded polypeptides. In vivo nascent polypeptide chains represent the putative primary target of ADEPactivated ClpP, providing a rationale for the antibacterial activity of the ADEPs. Thus, ADEPs cause a complete functional reprogramming of the Clp-protease complex.
Assembly of 1D Nanostructures into Sub‐micrometer Diameter Fibrils with Controlled and Variable Length by Dielectrophoresis (2003)

A dielectrophoresis method for manipulation, alignment, and assembly of 1D nanostructures is reported. Processed carbon nanotubes dispersed in water are assembled into micro‐electrodes and fibrils of variable and controllable length from ∼ 1 μm to over 1 cm (see Figure). The method allows of parallel fabrication, and the fibrils could find applications as probes for scanning probe microscopes, electrodes, and conducting wires.
Large-Scale Adaptive Hitchhiking Upon High Recombination in Drosophila simulans (2003)

Natural selection is expected to leave a characteristic footprint on neighboring nucleotide variation through the effects of genetic linkage. The size of the region affected is proportional to the strength of selection and greatly reduced with the recombinational distance from the selected site. Thus, the genomic footprint of selection is generally believed to be restricted to a small DNA stretch in normal and highly recombining regions. Here, we study the effect of selection on linked polymorphism (hitchhiking effect) by surveying nucleotide variation across a highly recombining approximately 88-kb genomic fragment in an African population of Drosophila simulans. We find a core region of up to 38 kb with a major haplotype at intermediate frequency. The extended haplotype structure that gradually vanishes until disappearing is unusual for a highly recombining region. Both the presence in the structured genomic domain of a single major haplotype depleted of variability and the detected spatial pattern of variation along the approximately 88-kb fragment are incompatible with neutral predictions in a panmictic population. A major role of demographic effects could also be discarded. The observed pattern of variation clearly provides evidence that directional selection has acted recently on this region, sweeping out variation around a strongly adaptive mutation. Our findings suggest a major role of positive selection in shaping DNA variability even in highly recombining regions.
Ping-Pong-Pang Instrumentation Amplifier (2010)

This thesis describes the implementation of a Precision Instrumentation Amplifier using a Current Feedback Instrumentation Amplifier topology (CFIA). CFIAs are attractive for sensor readout, because of their high CMRR and their ability to interface with ground-referenced sensors. Several chopping and auto-zeroing techniques have been developed to reduce the offset and 1/f noise of such amplifiers to the ?V level. As a result, their dominant source of error is now gain error, which is limited by mismatch to at best 0.1%. This paper describes a CFIA that applies dynamic element matching (DEM) to achieve a gain error of less than 0.04%. Moreover, it presents the first silicon implementation of the ping-pong-pang (PPP) auto-zeroing scheme, which enables a 3.5× reduction in power consumption and 2.5× improvement in gain error as compared to state-of-the-art ping-pong auto-zeroed CFIAs.
Simulating Cut-to-Length Harvesting Operations in Appalachian Hardwoods (2005)

Abstract Cut-to-length (CTL) harvesting systems involving small and large harvesters and a forwarder were simulated using a modular computer simulation model. The two harvesters simulated were a modified John Deere 988 tracked excavator with a single grip sawhead and a Timbco T425 based excavator with a single grip sawhead. The forwarder used in the simulations was a Valmet 524 machine with 2.4-meter log bunks. Production rates and costs were examined for a wide range of even-age oak forest stand conditions. The simulation results suggest that when the tree’s DBH is less than 26 cm, harvesting using the Timbco T425 is about 30% more expensive than using the John Deere 988. However, if the tree is larger than 26 cm of DBH, the unit cost of the Timbco T425 was about 8% less than that of the John Deere 988. The balanced John Deere 988 CTL system was 31% more productive and 8% more expensive than the balanced Timbco T425 CTL system in the 20 to 36 cm DBH range. General regression equations were developed for estimating the productivity and cost for the range of conditions simulated. The results should be valuable to managers, planners, and loggers considering the use of CTL systems in this region.
Immune suppression by neutrophils and granulocytic myeloid-derived suppressor cells: similarities and differences (2013)

Neutrophils are essential effector cells in the host defense against invading pathogens. Recently, novel neutrophil functions have emerged in addition to their classical anti-microbial role. One of these functions is the suppression of T cell responses. In this respect, neutrophils share similarities with granulocytic myeloid-derived suppressor cells (G-MDSCs). In this review, we will discuss the similarities and differences between neutrophils and G-MDSCs. Various types of G-MDSCs have been described, ranging from immature to mature cells shaping the immune response by different immune suppressive mechanisms. However, all types of G-MDSCs share distinct features of neutrophils, such as surface markers and morphology. We propose that G-MDSCs are heterogeneous and represent novel phenotypes of neutrophils, capable of suppressing the immune response. In this review, we will attempt to clarify the differences and similarities between neutrophils and G-MDSCs and attempt to facilitate further research.
Anticancer and Antioxidant Properties of Terpinolene in Rat Brain Cells (2013)

Terpinolene (TPO) is a natural monoterpene present in essential oils of many aromatic plant species. Although various biological activities of TPO have been demonstrated, its neurotoxicity has never been explored. In this in vitro study we investigated TPO's antiproliferative and/or cytotoxic properties using the 3-(4,5-dimethylthiazol-2-yl)-2,5 diphenyltetrazolium bromide (MTT) test, genotoxic damage potential using the single-cell gel electrophoresis (SCGE), and oxidative effects through total antioxidant capacity (TAC) and total oxidative stress (TOS) in cultured primary rat neurons and N2a neuroblastoma cells. Dose-dependent effects of TPO (at 10 mg L(-1), 25 mg L(-1), 50 mg L(-1), 100 mg L(-1), 200 mg L(-1), and 400 mg L(-1)) were tested in both cell types. Significant (P<0.05) decrease in cell proliferation were observed in cultured primary rat neurons starting with the dose of 100 mg L(-1) and in N2a neuroblastoma cells starting with 50 mg L(-1). TPO was not genotoxic in either cell type. In addition, TPO treatment at 10 mg L(-1), 25 mg L(-1), and 50 mg L(-1) increased TAC in primary rat neurons, but not in N2a cells. However, at concentrations above 50 mg L(-1) it increased TOS in both cell types. Our findings clearly demonstrate that TPO is a potent antiproliferative agent for brain tumour cells and may have potential as an anticancer agent, which needs to be further studied.
Langmuir-Blodgett film pyroelectric heat sensors (1994)

Copolysiloxane - eicosylamine polar molecular assemblies, built up using the alternate layer Langmuir-&#13;\nBlodgett (LB) film deposition technique, have been shown to possess very high quasi-static pyroelectric&#13;\ncoefficients compared to other LB film systems. Indeed, values around 10 pCm-2K-1 at 303K represent a level&#13;\nof activity which is nearly 30% of that exhibited by commercially available polyvinylidenedifluoride (PVF2)&#13;\npyroelectric heat sensors. Data are presented in this paper to demonstrate the reproducibility of the&#13;\npyroelectric response and its temperature dependence. Furthermore, preliminary studies of the dielectric&#13;\nbehaviour of these polar films have shown that the low frequency ( ~ 5 0H0z )d ielectric loss is about 0.01 but a&#13;\ndielectric relaxa t i p occurs at around 4 kHz.
Radio‐immunotargeting in experimental animal models of intraperitoneal cancer (1992)

The field of immunotargeting, and the challenges met when this technique is applied in experimental animals or in patients, are reviewed. Even with highly specific monoclonal antibodies, non-specific uptake in normal tissues and high background level of unbound radioactivity in blood and extravascular body fluids remain significant problems. Further experimental work in animal model systems is needed to bring this technique from the state of being an experimental method, with limited clinical application, to a routine diagnostic or therapeutic method. Different animal models are available, and their potential for elucidation of the various methodological problems in radio-immunotargeting are discussed in the present paper. In our laboratory, two intraperitoneal models were devised, having relevance for gynecologic and other forms of intraperitoneal malignancies. These models were elaborated with special emphasis on the possibility for exact measurement of important parameters in immunotargeting reactions. In the first model, hybridoma cells are inoculated intraperitoneally to mimic intraperitoneal carcinomatosis, and the monoclonal antibody produced by the hybridoma is used as serum tumor marker. In the second model the tumor cells are contained within intraperitoneally implanted micropore chambers, resembling a localized tumor. An artificial tumor like this allows control with the antigen load in the target, and measurement of the concentration of the injected antibody in the fluid within the target.