gebhart/patrepeval huggingface dataset:
Colloidal assemblies on patterned silane layers (2002)

The site-selective assembly of colloidal polymer particles onto laterally patterned silane layers was studied as a model system for the object assembly process at mesoscale dimensions. The structured silane monolayers on silicon oxide substrates were fabricated by a combination of liquid- and gas-phase deposition of different trialkoxysilanes with a photolithographic patterning technique. By using this method various types of surface functionalizations such as regions with amino functions next to areas of the bare silica surface or positively charged regions of a quaternary ammonium silane surrounded by a hydrophobic octadecylsilane film could be obtained. Furthermore, a triethoxysilane with a photoprotected amino group was synthesized, which allowed direct photopatterning after monolayer preparation, leading to free NH(2) groups at the irradiated regions. The different silane monolayer patterns were used to study the surface assembly behavior of carboxylated methacrylate particles by optical and scanning electron microscopy. In dependence of the assembly conditions (different surface functionalizations, pH, and drying conditions), a selective preference of the particles for a specific surface type versus others was found. Site-specific colloid adsorption could be observed also on the photosensitive silane layers after local deprotection with light. From the photosensitive silane and positively charged ammonium silane, molecularly mixed monolayers were prepared, which allowed particle adsorption and photoactivation within the same monolayer as shown by fluorescence labeling.
Transport of Polymeric Nanoparticle Gene Carriers in Gastric Mucus (2004)

Nanoparticle transport through mucosal barriers is often restricted owing to mucoadhesion and the highly viscoelastic nature of mucus gels, which may limit efficient drug and gene delivery. We formulated sub-200 nm particulates from poly(d,l-lactic-co-glycolic) acid (PLGA) and the cationic surfactant dimethyldioctadecylammonium bromide (DDAB). Subsequently, anionic DNA was condensed to the surface to obtain gene carriers with transfection rates 50-fold higher than those of naked DNA in vitro. Using the method of multiple particle tracking (MPT), we measured the transport rates of dozens of individual PLGA-DDAB/DNA nanoparticles in real time in reconstituted pig gastric mucus (PGM) that possessed physiologically relevant rheological properties. The average transport rate of PLGA-DDAB/DNA nanoparticles was 10-fold higher than those of similar size polystyrene nanoparticles. Improved transport rates, stability in mucus, and ability to transfect cells make PLGA-DDAB/DNA nanoparticles candidates for mucosal DNA vaccines and gene therapy.
Carbon Nanotubes with Titanium Nitride as a Low‐Cost Counter‐Electrode Material for Dye‐Sensitized Solar Cells (2010)

Mix and match: The photovoltaic performance of carbon nanotubes with titanium nitride nanoparticles (TiN-CNTs; see picture), which is comparable to that of conventional platinum counter electrodes, is attributed to the ideal combination of the superior electrocatalytic activity of TiN nanoparticles and the high electrical conductivity of CNTs.
CONFORMATIONAL COUPLING IN DNA POLYMERASE FIDELITY (1993)

The fidelity of DNA polymerases is largely attributable to a two-step nucleotide binding mechanism. In the first step, binding contacts are initially made between the template and the incoming dNTP. The selectivity of this ground-state binding is similar in magnitude to the selectivity seen in forming base pairs in solution. In the second step, a change in protein conformation occurs, which leads to rapid incorporation of the dNTP into the growing polymer. This conformational change appears to occur globally in that it is inhibited by mismatches in the dNTP or in any of the three terminal base pairs of the primer/template. The open conformation allows rapid binding of the dNTP from solution, while the closed conformation provides steric checks for the proper Watson-Crick base pair geometry. This conformational change accounts for the extraordinary fidelity of polymerization and also provides selectivity to the exonuclease by inhibiting polymerization over a mismatch in the primer/template. The overall fidelity approaches one error in 10(10) by a combination of selectivity in polymerization (10(5)-10(6)) and in proofreading (10(3)-10(4)). This paradigm provides the theoretical basis for further investigation of the structural basis for fidelity by pointing to the essential elements of the polymerization reaction that need to be examined in order to evaluate active-site-directed mutants of polymerases to test appropriate structure/function relationships.
Vascular Injury During Elevated Glucose can be Mitigated by Erythropoietin and Wnt Signaling (2007)

Impacting a significant portion of the world's population with increasing incidence in minorities, the young, and the physically active, diabetes mellitus (DM) and its complications affect approximately 20 million individuals in the United States and over 100 million individuals worldwide. In particular, vascular disease from DM may lead to some of the most serious complications that can extend into both the cardiac and nervous systems. Unique strategies that can prevent endothelial cell (EC) demise and elucidate novel cellular mechanisms for vascular cytoprotection become vital for the prevention and treatment of vascular DM complications. Here, we demonstrate that erythropoietin (EPO), an agent that has recently been shown to extend cell viability in a number of systems extending beyond hematopoietic cells, prevents EC injury and apoptotic nuclear DNA degradation during elevated glucose exposure. More importantly, EPO employs Wnt1, a cysteine-rich glycosylated protein involved in gene expression, cell differentiation, and cell apoptosis, to confer EC cytoprotection and maintains the integrity of Wnt1 expression during elevated glucose exposure. In addition, application of anti-Wnt1 neutralizing antibody abrogates the protective capacity of both EPO and Wnt1, illustrating that Wnt1 is an important component in the cytoprotection of ECs during elevated glucose exposure. Intimately linked to this cytoprotection is the downstream Wnt1 pathway of glycogen synthase kinase (GSK-3beta) that requires phosphorylation of GSK-3beta and inhibition of its activity by EPO. Interestingly, inhibition of GSK-3beta activity during elevated glucose leads to enhanced EC survival, but does not synergistically improve protection by EPO or Wnt1, suggesting that EPO and Wnt1 are closely tied to the blockade of GSK-3beta activity. Our work exemplifies an exciting potential application for EPO in regards to the treatment of DM vascular disease complications and highlights a previously unrecognized role for Wnt1 and the modulation of the downstream pathway of GSK-3beta to promote vascular cell viability during DM.
The bHLH transcription factor CHF1/Hey2 regulates susceptibility to apoptosis and heart failure after pressure overload (2010)

Cardiac hypertrophy is a common response to hemodynamic stress in the heart and can progress to heart failure. To investigate whether the transcription factor cardiovascular basic helix-loop-helix factor 1/hairy/enhancer of split related with YRPW motif 2 (CHF1/Hey2) influences the development of cardiac hypertrophy and progression to heart failure under conditions of pressure overload, we performed aortic constriction on 12-wk-old male wild-type (WT) and heterozygous (HET) mice globally underexpressing CHF1/Hey2. After aortic banding, WT and HET mice showed increased cardiac hypertrophy as measured by gravimetric analysis, as expected. CHF1/Hey2 HET mice, however, demonstrated a greater increase in the ventricular weight-to-body weight ratio compared with WT mice (P < 0.05). Echocardiographic measurements showed a significantly decreased ejection fraction compared with WT mice (P < 0.05). Histological examination of Masson trichrome-stained heart tissue demonstrated extensive fibrosis in HET mice compared with WT mice. TUNEL staining demonstrated increased apoptosis in HET hearts (P < 0.05). Exposure of cultured neonatal myocytes from WT and HET mice to H(2)O(2) and tunicamycin, known inducers of apoptosis that work through different mechanisms, demonstrated significantly increased apoptosis in HET cells compared with WT cells (P < 0.05). Expression of Bid, a downstream activator of the mitochondrial death pathway, was expressed in HET hearts at increased levels after aortic banding. Expression of GATA4, a transcriptional activator of cardiac hypertrophy, was also increased in HET hearts, as was phosphorylation of GATA4 at Ser(105). Our findings demonstrate that CHF1/Hey2 expression levels influence hypertrophy and the progression to heart failure in response to pressure overload through modulation of apoptosis and GATA4 activity.
A humanized gnotobiotic mouse model of host–archaeal–bacterial mutualism (2006)

Our colons harbor trillions of microbes including a prominent archaeon, Methanobrevibacter smithii. To examine the contributions of Archaea to digestive health, we colonized germ-free mice with Bacteroides thetaiotaomicron, an adaptive bacterial forager of the polysaccharides that we consume, with or without M. smithii or the sulfate-reducing bacterium Desulfovibrio piger. Whole-genome transcriptional profiling of B. thetaiotaomicron, combined with mass spectrometry, revealed that, unlike D. piger, M. smithii directs B. thetaiotaomicron to focus on fermentation of dietary fructans to acetate, whereas B. thetaiotaomicron-derived formate is used by M. smithii for methanogenesis. B. thetaiotaomicron-M. smithii cocolonization produces a significant increase in host adiposity compared with monoassociated, or B. thetaiotaomicron-D. piger biassociated, animals. These findings demonstrate a link between this archaeon, prioritized bacterial utilization of polysaccharides commonly encountered in our modern diets, and host energy balance.
Highly efficient DNA delivery mediated by pH-sensitive immunoliposomes (1989)

We have previously shown that pH-sensitive immunoliposomes can mediate a target-specific delivery of plasmid DNA to tumor cells grown in a mouse model [Wang, C.-Y., & Huang, L. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 7851-7855]. The efficiency of delivery in terms of the target cell transformation frequency has now been characterized for both short- and long-term gene expression in a tissue culture system. Herpes simplex virus thymidine kinase (TK) gene was used as a reporter gene. It was placed under the control of the promoter for the rat phosphoenolpyruvate carboxykinase gene, which contains a cAMP regulatory element. Therefore, the expression of the exogenous gene in the target cell, mouse Ltk- cells, can be regulated by cAMP drugs. The plasmid DNA was encapsulated in liposomes using a detergent dialysis method. The efficiency of gene delivery was optimized with respect to the time course and dose of liposome-associated DNA. The existence of antibody of the liposomes was essential for the maximal level of DNA delivery. Delivery was also dependent on the lipid composition of the liposome. The pH-sensitive lipid composition gave 8-fold higher efficiency than the corresponding pH-insensitive composition. The transformation efficiency of the target cell also depended on the regulation of gene expression; cells incubated with dibutyryl-cAMP and theophylline showed a much higher level of transformation frequency than cells incubated without the drugs. When all liposome and incubation parameters are optimized, the Ltk- cells showed a 47% efficiency for the short-term transformation, and 2% for the long-term transformation.(ABSTRACT TRUNCATED AT 250 WORDS)
Dark Patterns after the GDPR: Scraping Consent Pop-ups and Demonstrating their Influence (2020)

New consent management platforms (CMPs) have been introduced to the web to conform with the EU's General Data Protection Regulation, particularly its requirements for consent when companies collect and process users' personal data. This work analyses how the most prevalent CMP designs affect people's consent choices. We scraped the designs of the five most popular CMPs on the top 10,000 websites in the UK (n=680). We found that dark patterns and implied consent are ubiquitous; only 11.8% meet our minimal requirements based on European law. Second, we conducted a field experiment with 40 participants to investigate how the eight most common designs affect consent choices. We found that notification style (banner or barrier) has no effect; removing the opt-out button from the first page increases consent by 22-23 percentage points; and providing more granular controls on the first page decreases consent by 8-20 percentage points. This study provides an empirical basis for the necessary regulatory action to enforce the GDPR, in particular the possibility of focusing on the centralised, third-party CMP services as an effective way to increase compliance.
Oracle media server (1994)

Currently, most data accessed on large servers is structured data stored in traditional databases. Networks are LAN based and clients range from simple terminals to powerful workstations. The user is corporate and the application developer is an MIS professional.With the introduction of broadband communications to the home and better than 100-to-1 compression techniques, a new form of network-based computing is emerging. Structured data is still important, but the bulk of data becomes unstructured: audio, video, news feeds, etc. The predominant user becomes the consumer. The predominant client device becomes the television set. The application developer becomes the storyboard developer, director, or the video production engineer.The Oracle Media Server supports access to all types of conventional data stored in Oracle relational and text databases. In addition, we have developed a real-time stream server that supports storage and playback of real-time audio and video data. The Media Server also provides access to data stored in file systems or as binary large objects (images, executables, etc.)The Oracle Media Server provides a platform for distributed client-server computing and access to data over asymmetric real-time networks. A service mechanism allows applications to be split such that client devices (set-top boxes, personal digital assistants, etc.) can focus on presentation, while backend services running in a distributed server complex, provide access to data via messaging or lightweight RPC (Remote Procedure Call).
Glutathione depletion as a determinant of sensitivity of human leukemia cells to cyclophosphamide. (1986)

The role of glutathione (GSH) as a determinant of cellular sensitivity to the cytotoxic and DNA-damaging effects of cyclophosphamide (CP) was studied in a dual culture system of rat hepatocytes and K562 human chronic myeloid leukemia cells, which have elevated aldehyde dehydrogenase activity with a corresponding insensitivity to activated CP. Exposure of K562 cells to 50 microM DL-buthionine-S,R-sulfoximine for 24 h resulted in a depletion of cellular GSH content to 10% of control values without toxicity. Subsequent 1-h exposure of GSH-depleted cells to activated cyclophosphamide, obtained by incubation of CP with suspension cultures of rat hepatocytes, resulted in a 5-fold potentiation of the cytotoxicity of CP. Alkaline elution analysis of cellular DNA demonstrated that the level of apparent interstrand cross-linking was 3 to 4 times higher in GSH-depleted cells than in nondepleted cells. GSH-depleted cells were, in addition, more sensitive to induction of DNA single strand breaks than nondepleted cells. Depletion of GSH content did not increase cellular sensitivity to the cytotoxicity of phosphoramide mustard. Preincubation of K562 cells with 1 mM cysteine for 4 h resulted in an approximately 60% increase in cellular GSH content, which was accompanied by decreased sensitivity to the cytotoxicity of hepatocyte-activated CP. Exposure of nondepleted cells to clinically relevant concentrations of hepatocyte-activated CP resulted in depletion of cellular GSH content. Replenishment of GSH content in these cells was relatively slow following CP exposure. Acrolein was highly effective at depleting cellular GSH content, whereas phosphoramide mustard had no effect on cellular GSH content. The depletion of GSH by intracellularly released acrolein may be important in the mechanism of cytotoxicity of CP.
A microcontroller system for investigating the catch effect: Functional electrical stimulation of the common peroneal nerve (2005)

Correction of drop foot in hemiplegic gait is achieved by electrical stimulation of the common peroneal nerve with a series of pulses at a fixed frequency. However, during normal gait, the electromyographic signals from the tibialis anterior muscle indicate that muscle force is not constant but varies during the swing phase. The application of double pulses for the correction of drop foot may enhance the gait by generating greater torque at the ankle and thereby increase the efficiency of the stimulation with reduced fatigue. A flexible controller has been designed around the Odstock Drop Foot Stimulator to deliver different profiles of pulses implementing doublets and optimum series. A peripheral interface controller (PIC) microcontroller with some external circuits has been designed and tested to accommodate six profiles. Preliminary results of the measurements from a normal subject seated in a multi-moment chair (an isometric torque measurement device) indicate that profiles containing doublets and optimum spaced pulses look favourable for clinical use.
Microfabricated multilayer parylene‐C stencils for the generation of patterned dynamic co‐cultures (2008)

Co-culturing different cell types can be useful to engineer a more in vivo-like microenvironment for cells in culture. Recent approaches to generating cellular co-cultures have used microfabrication technologies to regulate the degree of cell-cell contact between different cell types. However, these approaches are often limited to the co-culture of only two cell types in static cultures. The dynamic aspect of cell-cell interaction, however, is a key regulator of many biological processes such as early development, stem cell differentiation, and tissue regeneration. In this study, we describe a micropatterning technique based on microfabricated multilayer parylene-C stencils and demonstrate the potential of parylene-C technology for co-patterning of proteins and cells with the ability to generate a series of at least five temporally controlled patterned co-cultures. We generated dynamic co-cultures of murine embryonic stem cells in culture with various secondary cell types that could be sequentially introduced and removed from the co-cultures. Our studies suggested that dynamic co-cultures generated by using parylene-C stencils may be applicable in studies investigating cellular interactions in controlled microenvironments such as studies of ES cell differentiation, wound healing and development.
UIDs as internal names in a distributed file system (1982)

The use of UIDs as internal names in an operating system for a local network is discussed. The use of internal names in other distributed systems is briefly surveyed. For this system, UIDs were chosen because of their intrinsic location independence and because they seemed to lend themselves to a clean structure for the operating system nucleus. The problems created by UIDs were: generating UIDs; locating objects; supporting multiple versions of objects; replicating objects; and losing objects. Some solutions to these problems are presented; for others, no satisfactory solution has yet been implemented.
Dormant tumor cells develop cross-resistance to apoptosis induced by CTLs or imatinib mesylate, via methylation of SOCS1 (2006)

Proc Amer Assoc Cancer Res, Volume 47, 2006

4881 

.In tumor dormancy, tumor cells perist in the host for a long time but do not grow. In the BCR/ABL DA1-3b mouse model of acute myeloid leukemia, dormant tumor cells may persist in the host in a state of equilibrium with the CD8+ CTL-mediated immune response, by actively inhibiting T-cells. Dormant tumor cells also show a progressive decrease of SOCS1 gene expression and a deregulation of the JAK/STAT pathway, due to methylation of SOCS1 gene promoter. Dormant tumor cells were more resistant to apoptosis induced by specific CTLs but resistance decreased when SOCS1 expression was restored by demethylation or gene transfer. AG490 JAK2 inhibitor decreased the resistance of dormant tumor cells to CTLs, but MG132 proteasome inhibitor was effective only in SOCS1-transfected cells. Thus, SOCS1 regulation of the JAK/STAT pathways contributes to the resistance of tumor cells to CTL-mediated killing. Resistance of dormant tumor cells to apoptosis was also observed when induced by irradiation, cytarabine, or imatinib mesylate, but was reduced by SOCS1 gene transfer. Thus, tumor cells that remain dormant for long periods in the host in spite of a specific CTL immune response may deregulate their JAK/STAT pathways and develop cross-resistance to various treatments. These data suggest new possible therapeutic targets to eradicate dormant tumor cells.
Separation and purification of the hemagglutinins from Bordetella pertussis (1983)

The role of the filamentous hemagglutinin (FHA) and the lymphocytosis-promoting factor hemagglutinin (LPF) in pertussis pathogenesis and immunity is the subject of active investigation. To be certain of their role as protective antigens, the hemagglutinins must be pure and free of each other. This report describes procedures to separate and purify FHA and LPF from the culture supernatant of stationary cultures of Bordetella pertussis Tohama, using hydroxylapatite, haptoglobin-Sepharose, and Sepharose CL-6B filtration chromatography. Purified FHA contained less than 0.002% active LPF assayed by histamine-sensitizing activity, and both hemagglutinins contained less than 0.01% of each other based on antigenic activity measured by an enzyme-linked immunosorbent assay, using affinity chromatography-purified antibody to each hemagglutinin. LPF and FHA were also shown to be antigenically distinct by immunodiffusion and were judged to be highly purified proteins by polyacrylamide gel electrophoresis. In addition, the purification procedures yielded milligram amounts of each hemagglutinin with very good recovery of starting activities.