gebhart/patrepeval huggingface dataset:
Formation of Novel D-Ring and E-Ring Isoprostane-like Compounds (D4/E4-Neuroprostanes) in Vivo from Docosahexaenoic Acid (2000)

Free radical-mediated oxidant injury and lipid peroxidation have been implicated in a number of neural disorders. We have reported that bioactive prostaglandin D2/E2-like compounds, termed D2/E2-isoprostanes, are produced in vivo by the free radical-catalyzed peroxidation of arachidonic acid. Docosahexaenoic acid, in contrast to arachidonic acid, is the most abundant unsaturated fatty acid in brain. We therefore questioned whether D/E-isoprostane-like compounds (D4/E4-neuroprostanes) are formed from the oxidation of docosahexaenoic acid. Levels of putative D4/E4-neuroprostanes increased 380-fold after oxidation of docosahexaenoic acid in vitro from 15.2 +/- 6.3 to 5773 +/- 1024 ng/mg of docosahexaenoic acid. Subsequently, chemical approaches and liquid chromatography electrospray ionization tandem mass spectrometry definitively identified these compounds as D4/E4-neuroprostanes. We then explored the formation of D4/E4-neuroprostanes from a biological source, rat brain synaptosomes. Basal levels of D4/E4-neuroprostanes were 3.8 +/- 0.6 ng/mg of protein and increased 54-fold after oxidation (n = 4). We also detected these compounds in fresh brain tissue from rats at levels of 12.1 +/- 2.4 ng/g of brain tissue (n = 3) and in human brain tissue at levels of 9.2 +/- 4.1 ng/g of brain tissue (n = 4). Thus, these studies have identified novel D/E-ring isoprostane-like compounds that are derived from docosahexaenoic acid and that are formed in brain in vivo. The fact that they are readily detectable suggests that ongoing oxidative stress is present in the central nervous system of humans and animals. Further, identification of these compounds provides a rationale for examining their role in neurological disorders associated with oxidant stress.
Systemic Diseases in Association with Microbial Species in Oral Biofilm from Elderly Requiring Care (2003)

The coexistence of Pseudomonas spp. and C. albicans in elderly with 10-19 teeth is a potential indicator of high risk for pneumonia and heart disease. Therefore, attention to oral hygiene and professional care for removing the indicators may diminish the occurrence of systemic disease in the elderly requiring systemic care.
PKC-δ inhibitors sustain self-renewal of mouse embryonic stem cells under hypoxiain vitro (2010)

Under hypoxia, mouse embryonic stem cells (mESCs) lose their self-renewal activity and display an early differentiated morphology mediated by the hypoxia-inducible factor-1 alpha (HIF-1 alpha). Previous studies have demonstrated that PKC-delta is activated by hypoxia and increases the protein stability and transcriptional activity of HIF-1 alpha in human cancer cells. Furthermore, activation of PKC-delta mediates cardiac differentiation of ESCs and hematopoietic stem cells. However, the role of PKC-delta in hypoxia-induced early differentiation of mESCs remains largely unknown. Here, we show the inhibition of PKC-delta activity prevents the early differentiation of mESCs under hypoxia using PKC-delta inhibitors, GF 109203X and rottlerin. Reduction of PKC-delta activity under hypoxia effectively decreased HIF-1 alpha protein levels and substantially recovered the expression of LIF-specific receptor (LIFR) and phosphorylated-STAT3 in mESCs. Furthermore, PKC-delta inhibitors aid to sustain the expression of self-renewal markers and suppress the expression of early differentiation markers in mESCs under hypoxia. Taken together, these results suggest that PKC-delta inhibitors block the early differentiation of mESCs via destabilization of HIF-1 alpha under hypoxia.
mCAL: A New Approach for Versatile Multiplex Action of Cas9 Using One sgRNA and Loci Flanked by a Programmed Target Sequence (2016)

Abstract Genome editing exploiting CRISPR/Cas9 has been adopted widely in academia and in the biotechnology industry to manipulate DNA sequences in diverse organisms. Molecular engineering of Cas9 itself and its guide RNA, and the strategies for using them, have increased efficiency, optimized specificity, reduced inappropriate off-target effects, and introduced modifications for performing other functions (transcriptional regulation, high-resolution imaging, protein recruitment, and high-throughput screening). Moreover, Cas9 has the ability to multiplex, i.e., to act at different genomic targets within the same nucleus. Currently, however, introducing concurrent changes at multiple loci involves: (i) identification of appropriate genomic sites, especially the availability of suitable PAM sequences; (ii) the design, construction, and expression of multiple sgRNA directed against those sites; (iii) potential difficulties in altering essential genes; and (iv) lingering concerns about “off-target” effects. We have devised a new approach that circumvents these drawbacks, as we demonstrate here using the yeast Saccharomyces cerevisiae. First, any gene(s) of interest are flanked upstream and downstream with a single unique target sequence that does not normally exist in the genome. Thereafter, expression of one sgRNA and cotransformation with appropriate PCR fragments permits concomitant Cas9-mediated alteration of multiple genes (both essential and nonessential). The system we developed also allows for maintenance of the integrated, inducible Cas9-expression cassette or its simultaneous scarless excision. Our scheme—dubbed mCAL for “Multiplexing of Cas9 at Artificial Loci”—can be applied to any organism in which the CRISPR/Cas9 methodology is currently being utilized. In principle, it can be applied to install synthetic sequences into the genome, to generate genomic libraries, and to program strains or cell lines so that they can be conveniently (and repeatedly) manipulated at multiple loci with extremely high efficiency.
An Animal Model of Type A Cystinuria Due to Spontaneous Mutation in 129S2/SvPasCrl Mice (2014)

Cystinuria is an autosomal recessive disease caused by the mutation of either SLC3A1 gene encoding for rBAT (type A cystinuria) or SLC7A9 gene encoding for b0,+AT (type B cystinuria). Here, we evidenced in a commonly used congenic 129S2/SvPasCrl mouse substrain a dramatically high frequency of kidney stones that were similar to those of patients with cystinuria. Most of 129S2/SvPasCrl exhibited pathognomonic cystine crystals in urine and an aminoaciduria profile similar to that of patients with cystinuria. In addition, we observed a heterogeneous inflammatory infiltrate and cystine tubular casts in the kidney of cystinuric mice. As compared to another classical mouse strain, C57BL/6J mice, 129S2/SvPasCrl mice had an increased mortality associated with bilateral obstructive hydronephrosis. In 129S2/SvPasCrl mice, the heavy subunit rBAT of the tetrameric transporter of dibasic amino acids was absent in proximal tubules and we identified a single pathogenic mutation in a highly conserved region of the Slc3a1 gene. This novel mouse model mimicking human disease would allow us further pathophysiological studies and may be useful to analyse the crystal/tissue interactions in cystinuria.
Study and application on product design system orienting to optimal utilization of material resources (2006)

产品设计在生产系统在材料资源消费起一个明确的作用。学习从产品设计的观点生产系统的材料资源的最佳的利用因此是重要的。这篇论文第一定义产品设计的概念，然后，在设计目的分析以后，作者与三个分系统建议产品设计的一个目标系统：结构的系统，功能的系统，和技术系统。最后，建筑上的金属结构企业上的一个产品设计系统在金属结构企业考虑到材料资源的大消费被开发并且使用。系统在改进企业的材料资源的全面的最佳的使用率上得到了明显的效果，减少设计周期，改进企业的管理。
A review of ion projection lithography (1998)

Although optical lithography has been extended to far smaller dimensions than was predicted 15 years ago, there are definite physical barriers to extending it to the minimum dimensions of 70 nm that are projected to be required 15 years from now. Both focused, point electron beams and ion beams have been used to write dimensions in resist well below 20 nm, albeit at speeds far too slow for production lithography. Projection systems, which employ a mask and, in effect, produce a large array of beams, can provide both small minimum dimensions and high throughput. Ions are particularly well suited for this because they suffer little or no scattering in the resist, the linewidth is not a strong function of dose (good process latitude), and the resist sensitivity is relatively independent to resist thickness or ion energy. IMS in Vienna, Austria has built two generations of ion projection lithography systems which have demonstrated many of the features needed for high throughput lithography. In these systems a stencil mask is irradiated with a uniform beam of light ions, H+, H2+, or He+, and the transmitted pattern is demagnified (by 10× to 3×) and focused on a resist covered wafer at energies in the 70–150 keV range. So far, minimum dimensions down to 70 nm line-space pairs have been demonstrated, drift has been eliminated with a “pattern lock” servo system, and field distortion of less than 0.15 μm over 8×8 mm has been measured in agreement with calculations. Based on these achievements a new generation ion lithography machine has been designed which uses 3× demagnification and will expose a 20×20 mm field at 0.12 μm minimum dimensions with less than 10 nm of distortion introduced by the ion optics. Global and stochastic space charge effects have been modeled and, in some cases, measured with the existing machines. Stochastic space charge effects will not cause unacceptable blur in the new design if the total ion current is kept below 3 μA. At this total current the time to expose one chip is still of order 0.5 s so that the calculated throughput is about 70 wafers (200 mm) per hour. Ion sources with low energy spread (∼2 eV) have been developed and will provide uniform illumination of the mask. Stencil mask fabrication on membranes of 2.5-μm-thick silicon has been developed. Distortion of the pattern cut in the membrane due to stress relief has been modeled, and with proper mask design can be kept below 20 nm (6.7 nm on the wafer). According to calculations and measurements mask distortion due to ion beam heating can be reduced to a negligible level if a radiation cooling cylinder is used. As a result of the building and evaluation of the existing machines and the design of the next generation, significant progress has been made in ion projection lithography which we will review in this article. The next step in the development of ion projection lithography is being conducted by the MEDEA program in Europe, which will develop a full field processing tool.
The effectiveness of the aquaflex gel pad in the transmission of acoustic energy. (1996)

I believe gel pads are a practical choice for clinical applications of ultrasound over uneven surfaces. The reusable gel pads offer the clinician a convenient and reliable method for delivering ultrasound energy to the patient. I believe it is preferable to use the gel pad with ultrasound gel directly applied to the patient and at the sound head-gel pad interface as opposed to using the traditional water bath immersion method.
BLAST: at the core of a powerful and diverse set of sequence analysis tools (2004)

Basic Local Alignment Search Tool (BLAST) is one of the most heavily used sequence analysis tools available in the public domain. There is now a wide choice of BLAST algorithms that can be used to search many different sequence databases via the BLAST web pages (http://www.ncbi.nlm.nih.gov/BLAST/). All the algorithm-database combinations can be executed with default parameters or with customized settings, and the results can be viewed in a variety of ways. A new online resource, the BLAST Program Selection Guide, has been created to assist in the definition of search strategies. This article discusses optimal search strategies and highlights some BLAST features that can make your searches more powerful.
The involvement of BDNF, NGF and GDNF in aging and Alzheimer's disease (2015)

Aging is a normal physiological process accompanied by cognitive decline. This aging process has been the primary risk factor for development of aging-related diseases such as Alzheimer's disease (AD). Cognitive deficit is related to alterations of neurotrophic factors level such as brain-derived neurotrophic factor (BDNF), nerve growth factor (NGF) and glial cell-derived neurotrophic factor (GDNF). These strong relationship between aging and AD is important to investigate the time which they overlap, as well as, the pathophysiological mechanism in each event. Considering that aging and AD are related to cognitive impairment, here we discuss the involving these neurotrophic factors in the aging process and AD.
How to Set Up a Digital Learning Co-Laboratory for Chinese Studies Between the Universities of America and China (2005)

similar curricula exist in the universities of america and china in the fields of chinese economics ancient china and chinese archaeology and university libraries in america and china hold strong chinese collections that support research and teaching in these fields this paper proposes settingtl up a digital t learningZD co laboratory for chinese studies between america and china in order to enhance exchange for research and teaching in these fields and to increase the sharing of collections between the teachers and students of chinese studies in both countries the paper describes how to establish this digital learning co laboratory including the construction of resources the system framework and functions how to resolve digital copyright issues and the extensibility of this co laboratory
Tailored Porous Materials (1999)

Tailoring of porous materials involves not only chemical synthetic techniques for tailoring microscopic properties such as pore size, pore shape, pore connectivity, and pore surface reactivity, but also materials processing techniques for tailoring the meso- and the macroscopic properties of bulk materials in the form of fibers, thin films, and monoliths. These issues are addressed in the context of five specific classes of porous materials: oxide molecular sieves, porous coordination solids, porous carbons, sol−gel-derived oxides, and porous heteropolyanion salts. Reviews of these specific areas are preceded by a presentation of background material and review of current theoretical approaches to adsorption phenomena. A concluding section outlines current research needs and opportunities.
Cyclodextrin Induces Calcium-Dependent Lysosomal Exocytosis (2010)

Cyclodextrins (CDs) have long been used to manipulate cellular cholesterol levels both in vitro and in vivo, but their direct effects at a cellular level are not well characterized. Recently, CDs have garnered much interest because of their ability to clear stored cholesterol from Niemann Pick Type C (NPC) cells and markedly prolong the life of NPC1 disease mice. Here, we investigate the hypothesis that treatment with 2-hydroxypropyl- β-cyclodextrin (HPB-CD) stimulates lysosomal exocytosis in a calcium-enhanced manner. We propose that this exocytosis is the mechanism by which HPB-CD ameliorates the endolysosomal cholesterol storage phenotype in NPC cells. These findings have significant implications for the use of HPB-CD in biochemical assays and data interpretation as well as for their use for the treatment for NPC and other disorders.
Gain-flattened optical-fiber amplifiers with a hybrid Er-doped-fiber configuration for WDM transmission (1995)

In wavelength-division-multiplexing (WDM) transmission systems in the 1.55-μm wavelength band, gain nonuniformity of erbium-doped-fiber amplifiers (EDFAs) is one of the most important problems. Several techniques1−4 for equalizing the nonuniform EDFA gain have been proposed, but problems remain in the reliability and the complexity of such EDFA configurations. On the other hand, it has been suggested4 that short and highly pumped erbium-doped fiber (EDF) exhibits excellent gain flatness. However, amplification efficiency or output signal power is heavily sacrificed by reducing the EDF length.
Three-periodic nets and tilings: regular and quasiregular nets (2002)

Regular nets are defined as those with symmetry that requires the coordination figure to be a regular polygon or polyhedron. It is shown that this definition leads to five regular 3-periodic nets. There is also one quasiregular net with a quasiregular coordination figure. The natural tiling of a net and its associated essential rings are also defined, and it is shown that the natural tilings of the regular nets have the property that there is just one kind of vertex, one kind of edge, one kind of ring and one kind of tile, i.e. transitivity 1111. The quasiregular net has two kinds of natural tile and transitivity 1112.
Oligonucleotide Adjuvants for T Helper 1 (Th1)–specific Vaccination (1997)

sufficient to eliminate malignant cells. By increasing endogenous IFN- synthesis, therapeutic Th1 vaccines could promote recovery from chronic viral or parasitic infections.
Kinetics of Blood Coagulation Factor Xaα Autoproteolytic Conversion to Factor Xaβ (1996)

Autoproteolysis of blood coagulation factor Xa (FXa) results in the excision of a 4-kDa fragment (beta-peptide) from the intact subform, factor Xaalpha (FXaalpha), to yield factor Xabeta (FXabeta). In the preceding paper, we showed that generation of FXabeta leads to expression of a plasminogen binding site. FXabeta may consequently participate in fibrinolysis; therefore, the timing of subform conversion compared with thrombin production is important. In the current study we evaluated the kinetics of FXabeta generation, which showed that autoproteolysis of FXaalpha followed a second order mechanism where FXaalpha and FXabeta behaved as identical enzymes. Rate constants of 9 and 172 M-1 s-1 were derived, respectively, in the absence and presence of FXaalpha binding to procoagulant phospholipid. Under identical conditions the latter is estimated to be 6 orders of magnitude slower than thrombin generation by prothrombinase. Since heparin binding and prothrombin recognition have been previously attributed to a region of FXaalpha proximal to the beta-peptide, functional comparisons were conducted using homogeneous and stabilized preparations of FXaalpha and FXabeta. Comparisons included 1) the recognition of small substrates; 2) the rate of interaction with antithrombin/heparin; 3) the assembly of prothrombinase; and 4) the activation of prothrombin by prothrombinase. Although the beta-peptide neighbors a probable functional region in FXaalpha, conversion to FXabeta was not observed to influence these functions. The data support a model where FXaalpha is predominantly responsible for thrombin generation and where slow conversion to FXabeta coordinates coagulation and the initiation of fibrinolysis at sites of prothrombinase assembly.
The New England Maternal PKU Project: identification of at-risk women. (1988)

Young women with phenylketonuria (PKU) are at risk for bearing children with mental retardation, microcephaly, heart defects, and low birthweight. These effects may be prevented if a low phenylalanine diet is maintained prior to and throughout pregnancy. This report describes the procedures of the New England Regional Maternal PKU Project for identifying and locating this population of at-risk women. Newborn screening records, routine umbilical cord blood screening, and PKU Clinic records provided most of the identifying information. We identified 235 women with hyperphenylalaninemia, ages 12 to 44 years. Of these, 183 had PKU or atypical PKU while 52 had non-PKU mild hyperphenylalaninemia. The 235 women represent 88 per cent of the expected number of women with hyperphenylalaninemia in New England. We identified more than the expected number of those with PKU but only 57 per cent of the expected number with mild hyperphenylalaninemia. Developing a national registry, as well as screening women who utilize birth control clinics or prenatal clinics, may be helpful. Implementing routine umbilical cord blood screening programs may be beneficial in efforts to identify women with hyperphenylalaninemia who have had a child and may want more children in the future.
Systematic enhancement of in-field critical current density with rare-earth ion size variance in superconducting rare-earth barium cuprate films (2004)

Enhanced in-field critical current densities (Jc’s) have been obtained in epitaxial superconducting (RE1,RE2)Ba2Cu3O7−x (RE1=rare-earthion 1, and RE2=rare earth ion 2) films grown on both single crystal and buffered metallic substrates. For a constant average RE ionic radius (equal to that of yttrium), there is a systematic dependence of the in-field Jc on the RE ion size variance, with a small, but nonzero, variance being optimum. Compared to the standard YBa2Cu3O7−x composition, a factor of two improvement in Jc(75.5K) is reproducibly observed at 0.2T(‖c) for the composition Dy1∕3Ho2∕3Ba2Cu3O7−x on both single crystal and buffered-metallic substrates. Angular dependent magnetic field studies and transmission electron microscopy indicate the presence of additional pointlike random defects.
Controllable gas-liquid phase flow patterns and monodisperse microbubbles in a microfluidic T-junction device (2006)

This letter describes the gas-liquid phase flow patterns and the mechanism of generation of monodisperse microbubbles in a T-junction microfluidic device using the crossflowing shear-rupturing technique. The bubble size is ranged from 100 to 500μm. The air phase states as isolate air slugs, “pearl necklaces,” periodic isolate bubbles, zig-zag bubble patterns, and multiple-bubble layer can be observed in the wider measured channel. The bubble size relates with the continuous phase flow velocity and viscosity as Vb∝1∕(μcuc), while being almost independent of surface tension γ and air phase flow rate Qg, for the conditions used in this work. The bubble formation mechanism by using the crossflowing shear-rupturing technique is different from the hydrodynamic flow focusing and both geometry-dominated breakup techniques. Our system provides independent control of both the size and volume fraction of dispersed bubbles.
Association of Borderline Oxacillin-Susceptible Strains ofStaphylococcus aureuswith Surgical Wound Infections (1998)

Staphylococcus aureus isolates which produce type A staphylococcal beta-lactamase have been associated with wound infections complicating the use of cefazolin prophylaxis in surgery. To further evaluate this finding, 215 wound isolates from 14 cities in the United States were characterized by antimicrobial susceptibility and beta-lactamase type and correlated with the preoperative prophylactic regimen. Borderline-susceptible S. aureus isolates of phage group 5 (BSSA-5), which produce large amounts of type A beta-lactamase and exhibit borderline susceptibility to oxacillin, comprised a greater percentage of the 120 wound isolates associated with cefazolin prophylaxis than they did of the 95 isolates associated with other prophylactic regimens (25% versus 12.6%, respectively; P < 0.05). In contrast, methicillin-resistant S. aureus isolates were distributed evenly between the two groups (8.3% versus 11.6%, respectively). In vitro assays demonstrated that cefazolin was hydrolyzed faster by BSSA-5 strains than by other beta-lactamase-producing, methicillin-susceptible strains (1.54 versus 0.50 microg/min/10(8) CFU, respectively; P < 0.0001). These data demonstrate that BSSA-5 strains are a distinct subpopulation of methicillin-susceptible S. aureus which frequently cause deep surgical wound infections. Cefazolin use in prophylaxis is a risk factor for BSSA-5 infection.