gebhart/patrepeval huggingface dataset:
Optimization of DNA Hybridization Efficiency by pH-Driven Nanomechanical Bending (2012)

The accessibility and binding affinity of DNA are two key parameters affecting the hybridization efficiency in surface-based biosensor technologies. Better accessibility will result in a higher hybridization efficiency. Often, mixed ssDNA and mercaptohexanol monolayers are used to increase the hybridization efficiency and accessibility of surface-bound oligonucleotides to complementary target DNA. Here, no mercaptohexanol monolayer was used. We demonstrate by differential microcantilever deflection measurements at different pH that the hybridization efficiency peaks between pH 7.5 and 8.5. At low pH 4.5, hydration and electrostatic forces led to tensile surface stress, implying the reduced accessibility of the bound ssDNA probe for hybridization. In contrast, at high pH 8.5, the steric interaction between neighboring ssDNA strands was decreased by higher electrostatic repulsive forces, bending the microcantilever away from the gold surface to provide more space for the target DNA. Cantilever deflection scales with pH-dependent surface hybridization efficiency because of high target DNA accessibility. Hence, by changing the pH, the hybridization efficiency is adjusted.
Genetically engineered smooth muscle cells as linings to improve the biocompatibility of cardiovascular prostheses. (1996)

Preliminary studies have shown that SMCs form strong attachments to the surface materials of LVADs and that their proliferation rates could be controlled after transformation with NO synthase under conditions that support production of NO. Therefore, genetically engineered SMCs may provide an improved blood biomaterial interface for cardiovascular prostheses.
Brine Mixing: an Additional Mechanism for Formation of Basin Evaporites (1970)

Experiments using artificial and seawater brines indicate that halite and sylvite can be precipitated by mixing brines of differing stages of evaporation, in addition to the previously recognized mechanisms of direct evaporative crystallization and crystallization by temperature changes. A modification of present geologic models is proposed to show how brine mixing might work in an evaporite basin. Conclusions based on the experiments and their relations to the geologic model are as follows. (1) Salt can precipitate in a marine evaporite basin by mixing brines of different composition and specific gravity. (2) Precipitation may occur without further water loss by evaporation. (3) Precipitation can take place from brines that were undersaturated before mixing. (4) Brine mi ing would cause the most salt to be deposited in the deepest parts of a basin, although nearly all parts of the basin could receive such deposits. (5) Sylvite could be precipitated as a primary mineral. (6) Hopper crystals (cubic and tabular) can form as a result of brine mixing in water of any depth.
pH‐Switchable Water‐Soluble Boron Nitride Nanotubes (2018)

Abstract The first example of aqueous solutions of boron nitride nanotubes (BNNTs) with switchable stability and without use of surfactants is demonstrated. The as‐produced boron nitride nanotubes are both purified and solubilized through an environmentally friendly and scalable approach using water extraction and liquid bromine treatment. This treatment effectively removes elemental boron particles and excess bromine reacts with BNNTs, inducing B−N bond cleavage on the BNNT surface to yield hydroxyl (OH) and amino (NH 2 ) functionalized BNNTs. The resulting functionalized BNNTs form stable aqueous solutions around neutral pH (4 < pH < 8), but readily precipitate in other pH ranges. This switchable solubility is explained in terms of the capability of the functional groups (OH and NH 2 ) to form hydrogen‐bonding networks in water. Further, the solubility differences in selected polar organic solvents have been utilized to prepare functionalized BNNTs with higher purity.
Human GATA-3 trans-activation, DNA-binding, and nuclear localization activities are organized into distinct structural domains. (1994)

GATA-3 is a zinc finger transcription factor which is expressed in a highly restricted and strongly conserved tissue distribution pattern in vertebrate organisms, specifically, in a subset of hematopoietic cells, in cells within the central and peripheral nervous systems, in the kidney, and in placental trophoblasts. Tissue-specific cellular genes regulated by GATA-3 have been identified in T lymphocytes and the placenta, while GATA-3-regulated genes in the nervous system and kidney have not yet been defined. We prepared monoclonal antibodies with which we could dissect the biochemical and functional properties of human GATA-3. The results of these experiments show some anticipated phenotypes, for example, the definition of discrete domains required for specific DNA-binding site recognition (amino acids 303 to 348) and trans activation (amino acids 30 to 74). The signaling sequence for nuclear localization of human GATA-3 is a property conferred by sequences within and surrounding the amino finger (amino acids 249 to 311) of the protein, thereby assigning a function to this domain and thus explaining the curious observation that this zinc finger is dispensable for DNA binding by the GATA family of transcription factors.
Pemphigoid, pemphigus and desmoplakin as antigenic markers of differentiation in normal and tumorigenic mouse keratinocyte lines (1989)

The expression of differentiation stages in a murine epidermal cell transformation model has been investigated as a basis for studies of chemically-induced differentiation. Antibodies in sera of patients with the autoimmune diseases bullous pemphigoid and pemphigus vulgaris exhibit specific reactivity to antigenic determinants of basal and spinous cells, respectively, in sections of mouse and human epidermis. In addition, spinous cells in epidermis are reactive with a mouse monoclonal antibody to desmoplakin, a desmosomal component immunologically distinct from pemphigus. These antibodies were used to identify and attempt to quantify keratinocyte subpopulations in culture based on differentiation stage. Epidermal cell lines were cultured under conditions which favour proliferation (0.02 to 0.04 mM extracellular Ca2+, i.e. low Ca2+ conditions) or differentiation (0.1 mM to 1.4 mM Ca2+), as previously shown using primary cultures of mouse keratinocytes. Two independently-derived normal keratinocyte lines demonstrated Ca2(+)-dependent reactivity with pemphigoid and pemphigus antiserum, like that which has been observed in primary cultures. Furthermore, a Ca2+ and time-dependent reactivity with the three antisera was also observed in a papilloma cell line (derived from one of the normal cell lines after treatment in vitro with 7,12-dimethylbenz[alpha]anthracene). Papilloma cells cultured under conditions of low extracellular Ca2+ were comprised of three subpopulations: cells reactive only with pemphigoid anti-serum, cells reactive only with desmoplakin antibody. However, like the normal cell lines, papilloma cells underwent a transition to predominantly a spinous cell population (i.e. reactive with pemphigus and desmoplakin antibody) in response to extracellular Ca2+. A slower loss of pemphigoid antibody reactivity was noted in papilloma cells, consistent with an abnormal regulation of differentiation. The attempt to characterize these dynamic transitions from basal to spinous cell subpopulations in culture was considered to be prerequisite for the use of the model to investigate differentiation-inducing agents in carcinoma therapy.
SPsort: How to Sort a Terabyte Quickly (1999)

In December 1998, a 488 node IBM RS/6000 SP * sorted a terabyte of data (10 billion 100 byte records) in 17 minutes, 37 seconds. This is more than 2.5 times faster than the previous record for a problem of this magnitude. The SPsort program itself was custom-designed for this benchmark, but the cluster, its interconnection hardware, disk subsystem, operating system, file system, communication library, and job management software are all IBM products. The system sustained an aggregate data rate of 2.8 GB/s from more than 6 TB of disks managed by the GPFS global shared file system during the sort. Simultaneous with these transfers, 1.9 GB/s of local disk I/O and 5.6 GB/s of interprocessor communication were also sustained. Introduction The speed of sorting has long been used as a measure of computer systems I/O and communication performance. In 1985, an article in Datamation magazine proposed a sort of one million records of 100 bytes each, with random 10 bytes keys, as a useful measu...
Multiple Liver Metastases of Breast Cancer: Report of a Case Successfully Treated with Hormone--Cytokine--Chemotherapy (1999)

The prognosis of patients with hepatic metastasis from breast cancer is usually extremely poor. We present the case of a 39-year-old Japanese woman diagnosed with multiple liver metastasis from breast cancer. A novel approach consisting of hormone-cytokine-chemotherapy with an arterial infusion therapy was carried out. Computed tomography and ultrasonography revealed that the multiple liver metastases were reduced with remaining calcification. Tumor markers decreased rapidly. Complete regression was achieved after these treatments. To date, there has been no relapse during the 8-year follow-up period. These results suggest that the hormone-cytokine-chemotherapy might be a rational modality of treatment against multiple metastatic breast cancer.
Genomics and evolution of protein phosphatases (2017)

Genomic analysis provides a global catalog of phosphatases, a key component of cell signaling.
Obesity, diabetes, and neoplasia in yellow <i>A</i> <sup>vy</sup> /‐ mice: ectopic expression of the <i>agouti</i> gene (1994)

The viable yellow A(vy) mutation results in a mottled yellow mouse that is obese, slightly larger than its nonyellow sibs, and more susceptible to tumor formation in those tissues sensitized by the strain genome. The mutation exhibits variable expressivity resulting in a continuum of coat color phenotypes, from clear yellow to pseudoagouti. The mouse agouti protein is a paracrine signaling molecule that induces hair follicle melanocytes to switch from the synthesis of black pigment to yellow pigment. Molecular cloning studies indicate that the obesity and growth effects of the A(vy) mutation result from ectopic expression of the normal agouti gene product. This review seeks to summarize the current state of knowledge regarding the obesity, stimulation of somatic growth, and enhancement of tumor formation caused by the A(vy) mutation, and to interpret these pleiotropic effects in terms of the normal function of the agouti protein.
Synthetic Carbohydrate-Based Antitumor Vaccines (2008)

Our laboratory has a longstanding program devoted to the preparation and immunological evaluation of fully synthetic carbohydrate-based antitumor vaccine constructs. We present herein a brief historical account of the evolution of this research program, and describe key achievements, including the synthesis of the Globo-H-KLH construct, which is currently in clinical trials. Remarkable advances in carbohydrate and glycopeptide assembly techniques have allowed for the synthesis of increasingly sophisticated, structurally complex vaccine constructs. In this setting, we have successfully accomplished the synthesis of a highly complex unimolecular pentavalent vaccine construct, in which five prostate and breast cancer-associated carbohydrate antigens are displayed on a single polypeptide backbone.
Overexpression of plasminogen activator inhibitor type‐1 in senescent fibroblasts from normal subjects and those with Werner syndrome (1994)

We previously reported that plasminogen activator inhibitor type-1 (PAI-1) mRNA was present at higher steady-state levels in prematurely senescent fibroblasts derived from a subject with Werner syndrome (WS) compared to early passage (EP) fibroblasts from an age-matched normal subject (Murano et al., 1991, Mol. Cell. Biol. 11:3905-3914). To explore the generally of this phenomenon with respect to chronological age of donor (in vivo aging) and the late-passage (LP) or senescent phase of the fibroblast replicative lifespan, we assayed PAI-1 mRNA in cells and PAI-1 antigen in medium conditioned by 20 normal fibroblast strains at EP and LP and six WS strains during their curtailed replicative lifespans. The lowest accumulations of PAI-1 were found in medium conditioned by fetal and newborn cells with a shallow but progressive rise seen in postnatal cells from normal donors of increasing chronological age. With few exceptions, normal LP fibroblasts showed increased PAI-1 accumulations in medium compared to their EP counterparts. Conditioned medium from four of the six WS strains showed PAI-1 accumulations that were significantly higher than the media of any normal controls at EP and LP. PAI-1 mRNa levels were generally commensurate with the cumulative amount of PAI-1 in the medium but the frequent exceptions indicate that translational and post-translational mechanisms also regulate PAI-1 output. The augmentation in PAI-1 output of fibroblasts as a direct function of chronological age and during in vitro senescence suggests that PAI-1 may play an important role in the reduced capacity for wound healing and the increasing tendency to thrombogenesis and atherogenesis seen during biological aging and in particular in persons with Werner syndrome.
Technology Update: Leveraging Subsurface Insight, Screening, and Diversion Technology in Refracturing (2016)

Technology Update A challenging commodity price environment has forced operators to seek methods for sharply lowering recovery cost per barrel of oil equivalent (BOE) in unconventional plays. Some reduced costs have resulted from the overcapacity of global services. Other reductions have resulted from declining industry activity, which has increased the availability of personnel and led to a renewed focus on maximizing drilling and completion (D&C) process efficiency. A portion of the recovery cost reduction has resulted directly from incremental technical innovations and process improvements that were difficult to achieve when operators and service companies were concerned chiefly with D&C execution. Older processes were designed to maximize early production, whereas a number of newer technologies focus on maximizing net present value (NPV). High NPV is most often achieved by reducing uncertainty and manipulating the cost portion of the NPV equation, especially when the commodity price and/or discount rate is uncontrollable. D&C portfolios have primarily contained a mix of delineation wells and development wells. Delineation wells have a higher cost per BOE but a higher potential for accelerating reserve recovery. Development wells have a lower cost per BOE but a lower potential for accelerating recovery. This mix of wells is appropriate for periods when margins are high enough to cover the associated D&C costs. However, the loss of such margins in a low-price environment has prompted adjustments to lower the average cost per BOE. One strategy for lowering that cost is to increase the percentage of refractured wells in a portfolio. Typically, the cost per BOE of refracturing is substantially lower than that of drilling and completing delineation or development wells. Recently, the development and implementation of effective stimulation diversion techniques and greater focus on candidate screening have narrowed the window of uncertainty in executing refracturing operations in horizontal wells. These improvements have reduced the economic risk of these operations and created further incentive to shift portfolio strategies toward refracturing. Taking advantage of refracturing opportunities in a portfolio involves four steps. Screen the best candidate properties, based on reservoir quality and the potential to exceed the original completion quality. Design the optimal refracture treatment to place new conductive fractures where desired and reconnect existing ones. Execute the refracture treatment for coverage of all selected lateral areas, using the latest processes, techniques, and materials. Diagnose the refracture performance and optimize the refracture design for analogous properties, using state-of-the- art diagnostic tools. This article primarily discusses the candidate selection process.
Soaring on the Wings of Pride (2004)

This essay treats the meaning and significance of Martin Luther King Jr.'s life and message for South Africans over the last decade and in the future. Attempts are made to relate King to questions concerning South Africa's Government of National Unity, to underscore his significance for the mounting crusade for gender equality, to explore his meaning for South Africa during the administrations of Presidents Nelson Mandela and Thabo Mbeki, and to explain how his ideas can influence South Africa's continuing transformation in the twenty-first century.
Better Access to Information about Clinical Trials (2000)

Access to information about clinical trials is important to researchers, health care professionals, and patients. Many have argued for the establishment of clinical trials registries, citing their substantial benefits. Although some registries do exist, it has been difficult to create comprehensive, easily accessible systems. This paper briefly reviews existing registries, discusses the challenges in building registries, and reviews some of their benefits. The paper concludes with a description of a new, extensive Web-based registry called ClinicalTrials.gov (http://clinicaltrials. gov/), which was developed at the National Institutes of Health (NIH) by the National Library of Medicine as a result of recent legislation calling for a comprehensive, publicly accessible registry of clinical trials. The first version of the system became available in late February 2000 and contains information about approximately 5000 trials. The first release contains primarily NIH-sponsored trials, and new trials are regularly added to the system. Subsequent versions will contain information about trials sponsored by other federal agencies and by the private sector. The system was developed in accordance with basic informatics principles, including adherence to standards, usability considerations, and iterative testing and evaluation.
Atomic commitment for integrated database systems (2002)

A systematic discussion of atomic commitment for heterogeneous database systems is presented. An analysis is given of two alternative protocols for atomic commitment: commitment of local transaction after or before the global commit or abort decision is made. The impact of the protocols on recovery and concurrency control is shown. Atomicity, consistency, isolation, and durability properties are achieved for global transactions. It is demonstrated that commitment before fits best to multilevel transactions. In this case, the commitment protocol causes no additional overhead and a higher degree of concurrency can be achieved.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Thermal shutdown characteristics of insulating materials used in lithium ion batteries (2010)

The lithium ion (Li-ion) battery market has undergone tremendous growth since its conception in 1990. Projections have indicated that the Li-ion battery market in the United States will top $9 billion in the next 3 years. Several factors including technical innovation, increased use of sophisticated consumer electronic gadgets and surge in high efficiency power sources for industrial applications have been the key in propelling the market demand for these products. Despite the positive trends, safety concerns related to the use of Li-ion batteries remain and may impact the market growth in future. Product recalls due to rechargeable batteries overheating and thereby posing a fire hazard to consumers have occurred as recently as April 2010. Research efforts have been undertaken to develop new separator materials with increased dimensional and thermal stability at high temperatures to make the Li-ion batteries safer for use. The separator is an electrically insulating polymer material that is engineered to have pores that allow lithium ions to shuttle back and forth between the battery's electrodes during the charge and discharge cycles. This paper presents an introduction to separator materials used in commercially available Li-ion batteries and a discussion of their thermal shutdown characteristics.
Chromosome engineering of Escherichia coli for constitutive production of salvianic acid A (2017)

The plasmid-free and inducer-free strain for SAA production was developed by targeted integration of the constitutive expression of SAA biosynthetic genes into E. coli chromosome. Our work provides the industrial potential for constitutive production of SAA by the indel microbial cell factory and also sets an example of further producing other valuable natural and unnatural products.
Purification and characterization of protein H, the major porin of Pasteurella multocida (1993)

Protein H (B. Lugtenberg, R. van Boxtel, D. Evenberg, M. de Jong, P. Storm, and J. Frik, Infect. Immun. 52:175-182, 1986) is the major polypeptide of the outer membrane of Pasteurella multocida, a bacterium pathogenic for humans and animals. We have purified this protein to homogeneity by size exclusion chromatography after selective extraction with surfactants and demonstrated its pore-forming ability after reincorporation into planar lipid bilayers. In these experiments, the current through the pores was a linear function of the applied voltage in the range of -50 to +50 mV. Voltages beyond +/- 50 mV tended to partially close the channels, giving rise to apparent negative resistances. These observations suggest that protein H channels are probably not voltage regulated in vivo. With the patch clamp technique, single-channel conductance fluctuations of 0.33 nS were recorded in 1 M KCl. Electrophoretic and circular dichroism analyses showed that protein H forms homotrimers stable in sodium dodecyl sulfate at room temperature, with a high content of beta-sheet secondary structure. Upon boiling, the trimers were fully dissociated into monomers with an increase of alpha helix and irregular structure, at the expense of beta sheets. The apparent molecular mass of fully denatured monomers ranged between 37 and 41.8 kDa, depending on the electrophoretic system used for analysis. The trimeric arrangement of protein H was confirmed by image analysis of negatively stained, two-dimensional crystal arrays. This morphological study revealed, in agreement with electrophoretical data, a trimeric structure with an overall diameter of 7.7 nm. Each monomer appeared to contain a pore with an average diameter of 1 nm. Quantitative comparisons revealed that the amino acid composition (hydropathy index of -0.40) and the N-terminal sequence (determined over 36 residues) of protein H are similar to those of bacterial general porins, notably porin P2 of Haemophilus influenzae. We conclude from this set of structural and functional data that protein H of P. multocida is a pore-forming protein related to the superfamily of the nonspecific bacterial porins.
Cover Picture: Impact of surface recombination on efficiency of III‐nitride light‐emitting diodes (Phys. Status Solidi RRL 6/2016) (2016)

No abstract is available for this article.