gebhart/patrepeval huggingface dataset:
Wound Healing and Skin Regeneration (2015)

The skin is a complex organ consisting of the epidermis, dermis, and skin appendages, including the hair follicle and sebaceous gland. Wound healing in adult mammals results in scar formation without any skin appendages. Studies have reported remarkable examples of scarless healing in fetal skin and appendage regeneration in adult skin following the infliction of large wounds. The models used in these studies have offered a new platform for investigations of the cellular and molecular mechanisms underlying wound healing and skin regeneration in mammals. In this article, we will focus on the contribution of skin appendages to wound healing and, conversely, skin appendage regeneration following injuries.
Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples (2013)

RNA-Seq is an effective method to study the transcriptome, but can be difficult to apply to scarce or degraded RNA from fixed clinical samples, rare cell populations, or cadavers. Recent studies have proposed several methods for RNA-Seq of low quality and/or low quantity samples, but their relative merits have not been systematically analyzed. Here, we compare five such methods using metrics relevant to transcriptome annotation, transcript discovery, and gene expression. Using a single human RNA sample, we constructed and sequenced ten libraries with these methods and two control libraries. We find that the RNase H method performed best for low quality RNA, and confirmed this with actual degraded samples. RNase H can even effectively replace oligo (dT) based methods for standard RNA-Seq. SMART and NuGEN had distinct strengths for low quantity RNA. Our analysis allows biologists to select the most suitable methods and provides a benchmark for future method development.
Multi-user, multi-display interaction with a single-user, single-display geospatial application (2006)

In this paper, we discuss our adaptation of a single-display, single-user commercial application for use in a multi-device, multi-user environment. We wrap Google Earth, a popular geospatial application, in a manner that allows for synchronized coordinated views among multiple instances running on different machines in the same co-located environment. The environment includes a touch-sensitive tabletop display, three vertical wall displays, and a TabletPC. A set of interaction techniques that allow a group to manage and exploit this collection of devices is presented.
High-Sensitivity Detection of DNA Hybridization on Microarrays Using Resonance Light Scattering (2002)

The application of resonance light scattering (RLS) particles for high-sensitivity detection of DNA hybridization on cDNA microarrays is demonstrated. Arrays composed of ∼2000 human genes (“targets”) were hybridized with colabeled (Cy3 and biotin) human lung cDNA probes at concentrations ranging from 8.3 ng/μL to 16.7 pg/μL. After hybridization, the arrays were imaged using a fluorescence scanner. The arrays were then treated with 80-nm-diameter gold RLS Particles coated with anti-biotin antibodies and imaged in a white light, CCD-based imaging system. At low probe concentrations, significantly more genes were detected by RLS compared to labeling by Cy3. For example, for hybridizations with a probe concentration of 83.3 pg/μL, ∼1150 positive genes were detected using RLS compared to ∼110 positive genes detected with Cy3. In a differential gene expression experiment using human lung and leukemia RNA samples, similar differential expression profiles were obtained for labeling by RLS and fluorescence technologies. The use of RLS Particles is particularly attractive for detection and identification of low-abundance mRNAs and for those applications in which the amount of sample is limited.
Transgenic expression and recovery of biologically active recombinant human insulin from Arabidopsis thaliana seeds (2005)

The increased incidence of diabetes, coupled with the introduction of alternative delivery methods that rely on higher doses, is expected to result in a substantial escalation in the demand for affordable insulin in the future. Limitations in the capacity and economics of production will make it difficult for current manufacturing technologies to meet this demand. We have developed a novel expression and recovery technology for the economical manufacture of biopharmaceuticals from oilseeds. Using this technology, recombinant human precursor insulin was expressed in transgenic plants. Plant-derived insulin accumulates to significant levels in transgenic seed (0.13% total seed protein) and can be enzymatically treated in vitro to generate a product with a mass identical to that of the predicted product, DesB(30)-insulin. The biological activity of this product in vivo and in vitro was demonstrated using an insulin tolerance test in mice and phosphorylation assay performed in a mammalian cell culture system, respectively.
Stackelberg Games and Multiple Equilibrium Behaviors on Networks (2002)

The classical Wardropian principles hypothesize that users either minimize either individual travel cost or overall system cost. In reality, users do not always behave in such a manner; instead there are both competition and cooperation among them, typically when there exist oligopoly Cournot-Nash firms. In this paper, we first formulate a mixed network equilibrium model as variational inequalities (VI) that simultaneously describe the routing behaviors of user equilibrium (UE), system optimum (SO) and Cournot-Nash (CN) players, each player is presumed to make routing decision given knowledge of the routing strategies of other players. To further enhance the system efficiency, we present a Stackelberg game in which the SO player is the leader and the UE and CN players are the followers. The UE and CN players route their flows in a manner of mixed equilibrium given the SO player's routing strategy. In contrast, the SO player, realizing how the UE and CN players will react, routes his flow that will minimize total system travel cost based on the reaction that his choice will produce. The Stackelberg game of network flow routing is formulated as a bilevel mathematical program with equilibrium constraints (MPEC). Using a marginal function approach, the MPEC is transformed into an equivalent, continuously differentiable single-level problem, where the lower level VI is represented by a gap function constraint. The augmented Lagrangian method is then used to solve the Stackelberg game problem.
Identification of the primary collagen-binding surface on human glycoprotein VI by site-directed mutagenesis and by a blocking phage antibody (2003)

Glycoprotein (GP) VI is the major receptor responsible for platelet activation by collagen, but the collagen-binding surface of GPVI is unknown. To address this issue we expressed, from insect cells, the immunoglobulin (Ig)-like ectodomains (residues 1-185) of human and murine GPVI, called hD1D2 and mD1D2, respectively. Both proteins bound specifically to collagen-related peptide (CRP), a GPVI-specific ligand, but hD1D2 bound CRP more strongly than did mD1D2. Molecular modeling and sequence comparison identified key differences between hD1D2 and mD1D2. Ten mutant hD1D2s were expressed, of which 4 had human residues replaced by their murine counterpart, and 6 had replacements by alanine. CRP binding studies with these mutants demonstrated that the exchange of lysine at position 59 for the corresponding murine glutamate substantially reduced binding to CRP. The position of lysine59 on the apical surface of GPVI suggests a mode of CRP binding analogous to that used by the related killer cell Ig-like receptors to bind HLA. This surface was confirmed as critical for collagen binding by epitope mapping of an inhibitory phage antibody against GPVI. This anti-GPVI, clone 10B12, gave dose-dependent inhibition of the hD1D2-collagen interaction. Clone 10B12 inhibited activation of platelets by CRP and collagen in aggregometry and thrombus formation by the latter in whole blood perfusion. Antibody 10B12 showed significantly reduced binding to the hD1D2-E59, and, on that basis, the GPVI:10B12 interface was modeled.
Relationship Between Foam Stability Measured in Static Tests and Flow Behavior of Foams in Porous Media (1984)

ABSTRACT Selection of a suitable foaming agent for mobility control in steam floods requires screening a large number of available surfactants. Many different screening strategies have been reported in the literature for this purpose. Almost all of them rely on some type of foam stability measurement for initial screening. However, the relationship between such foam stability measurements and the flow behavior of foams in porous media under steam flood conditions has not been thoroughly investigated. The objective of this study was to determine whether or not a correlation exists between the foam stability index measured in static tests and the mobility reduction characteristics measured in a porous medium. Foam stability tests were performed under ambient conditions and under conditions of high temperature (200°C) and pressure (6.9 MPa). Foams were generated by injecting nitrogen gas through a gas sparger submerged under the test solution in pressure vessels equipped with glass windows. Subsequent drainage of liquid from the foam as well as rate of decay of the foam volume were then monitored. The mobility control characteristics were measured at 200°C and 6.9 MPa by monitoring the pressure drop across a 30 cm long and 5.7 cm diameter core composed of unconsolidated sand during steady-state flow of foam through the core. Various foams were compared in terms of their mobility reduction factor which represents the ratio of pressure drop across the core at given flow rates of the foaming liquid and gas to the pressure drop obtained at identical flow rates with pure water and gas. The results show that foam stability measurements made under ambient conditions do not provide an indication of how the foam will perform at high temperature. However, foam stability measurements performed at high temperature and pressure are generally a good indicator of the mobility reduction factor. When comparing different concentrations of the same surfactant, the concentration which provided the maximum foam stability also gave the highest value of mobility reduction factor. When comparing different surfactants, a fairly good correlation was found between the foam stability index and the mobility reduction factor.
Recombinant Human Bone Morphogenetic Protein‐2 in Absorbable Collagen Sponge Enhances Bone Healing of Tibial Osteotomies in Dogs (2007)

After a long bone fracture, dogs may face a long recovery period before full return of limb function. rhBMP-2, in association with good fracture fixation principles, may enhance bone healing in dogs with diaphyseal fractures.
Digital LAMP in a sample self-digitization (SD) chip (2012)

This paper describes the realization of digital loop-mediated DNA amplification (dLAMP) in a sample self-digitization (SD) chip. Digital DNA amplification has become an attractive technique to quantify absolute concentrations of DNA in a sample. While digital polymerase chain reaction is still the most widespread implementation, its use in resource-limited settings is impeded by the need for thermal cycling and robust temperature control. In such situations, isothermal protocols that can amplify DNA or RNA without thermal cycling are of great interest. Here, we accomplished the successful amplification of single DNA molecules in a stationary droplet array using isothermal digital loop-mediated DNA amplification. Unlike most (if not all) existing methods for sample discretization, our design allows for automated, loss-less digitization of sample volumes on-chip. We demonstrated accurate quantification of relative and absolute DNA concentrations with sample volumes of less than 2 μl. We assessed the homogeneity of droplet size during sample self-digitization in our device, and verified that the size variation was small enough such that straightforward counting of LAMP-active droplets sufficed for data analysis. We anticipate that the simplicity and robustness of our SD chip make it attractive as an inexpensive and easy-to-operate device for DNA amplification, for example in point-of-care settings.
Catalytic pyrolysis of several kinds of bamboos over zeolite NaY (2005)

The catalytic pyrolysis of four kinds of bamboo, Neosinocalamus affinis, Pubescens, Bambusa rigida and Dendrocalamus latiflorus, was performed in a fixed bed reactor in an inert atmosphere of nitrogen at 773 K and 873 K for 10 h using zeolite NaY as catalyst. For Neosinocalamus affinis and Pubescens, the influence of pyrolysis temperature on the product distribution was also studied over the temperature range of 573–873 K at an interval of 50 K. As the pyrolysis temperature increases, the yield of gaseous products increases, while the yield of liquid products goes through a maximum value, and the amount of residue reduces. For the four kinds of samples, the liquid yield at 873 K increases to 64.1–68.8 wt% in the presence of NaY catalyst, in compared to that of 19.7–53.3 wt% from direct pyrolysis. In addition, the non-catalytic liquid contains numerous species including mainly carboxylic, carbonylic, lactonic, phenolic and furan compounds, while the catalytic liquid contains markedly reduced number of species composed mainly of carboxylic and carbonylic compounds, of which acetic acid is the major component. Scanning Electron Microscopy (SEM), X-Ray Diffraction (XRD) and X-ray Photoelectron Spectroscopy (XPS) were used to characterize the catalysts before and after use at 873 K. The results show that during the pyrolysis the NaY catalyst interacts with the primary pyrolysis intermediates of bamboos and thus leads to in situ reconstruction involving the impairment of [111] and [220] planes, and the enhancement of the [311] plane.
Alternative O-Glycosylation/O-Phosphorylation of the Murine Estrogen Receptor β (2000)

Estrogen receptor beta, a homologue to estrogen receptor alpha, is a new member of the steroid hormone receptor family. Recently, we documented that estrogen receptor alpha, like other transcription factors, is modified by O-linked N-acetylglucosamine (O-GlcNAc), a ubiquitous transitory posttranslational modification on nuclear and cytoplasmic proteins. Here, we report that estrogen receptor beta is alternatively modified by either O-GlcNAc or O-phosphate. Lectin chromatography of in vitro translated protein first suggested that murine estrogen receptor beta (mER-beta) is O-GlcNAcylated. Structural characterization of the carbohydrate moieties on mER-beta, overexpressed in insect Sf9 cells, confirmed the presence of O-GlcNAc. mER-beta, overexpressed in mammalian cells, is also O-GlcNAcylated. The major site of O-GlcNAc on mER-beta from Sf9 cells is Ser(16) near the N-terminus. Concomitant analyses also documented the O-phosphorylation of mER-beta at Ser(16). MALDI-TOF mass spectrometry showed alternative occupancy of this locus by these two abundant and dynamic posttranslational modifications. The localization of a major O-GlcNAc/O-phosphate site in proximity of the transactivation domain and as part of a PEST region (target sequences for rapid protein degradation) on mER-beta suggests that these modifications may play a role in regulating estrogen receptor beta transactivation and turnover.
Inhibition of tumor-specific cytotoxic T-lymphocyte responses by transforming growth factor beta 1. (1992)

Transforming growth factor beta (TGF-beta) is a potent immunosuppressive cytokine that is produced by neoplastic and normal cells. It has not been demonstrated directly, however, that TGF-beta can inhibit antigen-specific T-cell responses to tumor cells in vitro. We show here that generation of antitumor cytotoxic T-lymphocyte (CTL) activity in mixed-lymphocyte tumor cultures of splenocytes from DBA/2 mice immunized with the syngeneic P815 mastocytoma + Corynebacterium parvum was consistently and profoundly inhibited when 0.675 to 10 ng/ml of TGF-beta were added on Day 0 of culture. TGF-beta added on Day 1 or later had little or no effect. In contrast to the results with P815 immune mice, mixed-lymphocyte tumor cultures established with splenocytes from P815 tumor-bearing hosts showed variable degrees of inhibition by TGF-beta, depending on the stage of the ongoing in vivo immune response. Addition of recombinant murine tumor necrosis factor alpha (1,000 or 10,000 units/ml) partially reversed inhibition of CTL responses by TGF-beta, while recombinant interleukin 2 nearly completely reversed the suppression. These data indicate that one level at which TGF-beta may act to inhibit mixed-lymphocyte tumor cultures is that of cytokine production. To determine whether TGF-beta also has any direct effect on CTL, P815-specific CTL clones derived from tumor-bearing host mice were utilized. We found that proliferation of rested CTL clones in response to tumor cells + interleukin 2 was inhibited by 5 ng/ml of TGF-beta, while the interleukin 2-dependent reactivation of cytolytic activity was not affected by TGF-beta. In contrast to rested CTL, when TGF-beta was added to cultures of previously activated CTL, proliferation was not inhibited. These data demonstrate that TGF-beta has profound inhibitory effects on the in vitro generation of effector CTL from tumor-specific murine splenocytes, and this inhibition may be an indirect result of suppressed cytokine production as well as a direct antiproliferative effect on CTL.
Clozapine therapy in refractory affective disorders: polarity predicts response in long-term follow-up. (1994)

Clozapine is an efficacious and well-tolerated therapy for refractory affective illness. Manic symptomatology predicts a more favorable response than depression.
Cloning of a cDNA Encoding Porcine Brain Natriuretic Peptide (1989)

Complimentary DNA (cDNA) clones encoding porcine brain natriuretic peptide (BNP) were isolated from a porcine atrial cDNA library. The longest of the cDNA clones (1507 nucleotides) apparently originated from an unprocessed messenger RNA, since the nucleotide sequence encoding BNP-26 was interrupted by an intron of 554 nucleotides. A partial cDNA clone representing processed BNP mRNA was prepared by polymerase chain reaction. A comparison of the sequence of these two cDNAs reveals the presence of an additional intron within the sequence encoding the BNP precursor. The identification of these introns suggests that the BNP gene structure differs from the atrial natriuretic peptide gene in the location of intron 2. BNP mRNA encodes a propeptide of 131 amino acids, including a signal peptide domain (25 amino acids) and a prohormone domain (106 amino acids). Like atrial natriuretic peptide, the bioactive BNP sequence is localized at the carboxyl terminus of the prohormone. Although the carboxyl-terminal peptide sequences of porcine atrial natriuretic peptide and BNP are well conserved, there is relatively little homology within their propeptide regions.
CEO 이미지의 브랜드적 가치에 관한 연구: CEO 이미지의 구성 요소 및 기업 가치에 미치는 영향을 중심으로 (2004)

이 연구의 목적은 CEO 이미지의 구성 요소들을 파악하고, 이러한 CEO 이미지의 구성 요소들이 기업 가치 및 회사에 대한 해도에 미치는 영향과 그 상대적 중요도를 규명하는 것이다. 구체적으로 우리나라의 PR 실무자들을 대상으로 심층 인터뷰와 설문 조사를 병행하여 CEO 이미지의 구성 요소들을 파악하고, 계층적 회귀 분석을 통하여 CEO 이미지의 구성 요소들이 기업 가치 및 PR 실무자들의 회사에 대한 태도에 미치는 영향을 살펴 보았다. 연구 결과 CEO 이미지는 14개의 구성 요소들을 포함하여 네 가지의 유형으로 분류되었다. 이 네 가지 유형에는 CEO 능력, 자질, 성품, 그리고 외적 조건들이 포함되는 것으로 나타났다. 계층적 회귀 분석 결과 17개의 예측 변인들 가운데 9개의 요인들이 기업 가치와 통계적으로 유의미한 관계를 갖는 것으로 나타났으며, 8개는 PR 실무자들의 회사에 대한 태도와 통계적으로 유의미한 관계를 갖는 것으로 나타냈과. 이 가운데 외모는 기업 가치에 대해 가장 강력한 예측 변인으로 나타였으며, 조직 융화 능력은 PR 실무자들의 회사에 대한 태도에 대해 가장 강력한 예측 변인으로 나타났다. 그리고 총 14개의 CEO 이미지 구성 요소들 가운데 경영 능력, 조직 융화 능력, 결단력, 그리고 신뢰성의 네 개 변인들은 기업 가치와 회사에 대한 태도 모두에 대해 통계적으로 유의미한 관계를 갖는 것으로 나타났다. 따라서 PR 실무자들은 CEO의 브랜드 가치를 제고하고 기업 가치 및 직원들의 회사에 대한 긍정적인 태도를 높이기 위하여 이들 CEO 이미지 구성 요소들을 중심으로 CEO 이미지를 체계적으로 관리하고 강화해 나가야 할 것이다.
Amphipathic DNA Polymers Exhibit Antiherpetic Activity In Vitro and In Vivo (2008)

Phosphorothioated oligonucleotides have a sequence-independent antiviral activity as amphipathic polymers (APs). The activity of these agents against herpesvirus infections in vitro and in vivo was investigated. The previously established sequence-independent, phosphorothioation-dependent antiviral activity of APs was confirmed in vitro by showing that a variety of equivalently sized homo- and heteropolymeric AP sequences were similarly active against herpes simplex virus type 1 (HSV-1) infection in vitro compared to the 40mer degenerate parent compound (REP 9), while the absence of phosphorothioation resulted in the loss of antiviral activity. In addition, REP 9 demonstrated in vitro activity against a broad spectrum of other herpesviruses: HSV-2 (50% effective concentration [EC(50)], 0.02 to 0.06 microM), human cytomegalovirus (EC(50), 0.02 to 0.13 microM), varicella zoster virus (EC(50), <0.02 microM), Epstein-Barr virus (EC(50), 14.7 microM) and human herpesvirus types 6A/B (EC(50), 2.9 to 10.2 microM). The murine microbicide model of genital HSV-2 was then used to evaluate in vivo activity. REP 9 (275 mg/ml) protected 75% of animals from disease and infection when provided 5 or 30 min prior to vaginal challenge. When an acid-stable analog (REP 9C) was used, 75% of mice were protected when treated with 240 mg/ml 5 min prior to infection (P < 0.001), while a lower dose (100 mg/ml) protected 100% of the mice (P < 0.001). The acid stable REP 9C formulation also provided protection at 30 min (83%, P < 0.001) and 60 min (50%, P = 0.07) against disease. These observations suggest that APs may have microbicidal activity and potential as broad-spectrum antiherpetic agents and represent a novel class of agents that should be studied further.
GLUT‐1 and CAIX as intrinsic markers of hypoxia in carcinoma of the cervix: Relationship to pimonidazole binding (2003)

The presence of hypoxia in tumours results in the overexpression of certain genes, which are controlled via the transcription factor HIF-1. Hypoxic cells are known to be radioresistant and chemoresistant, thus, a reliable surrogate marker of hypoxia is desirable to ensure that treatment may be rationally applied. Recently, the HIF-1-regulated proteins Glut-1 and CAIX were validated as intrinsic markers of hypoxia by comparison with pO(2) measured using oxygen electrodes. We compare the expression of Glut-1 and CAIX with the binding of the bioreductive drug hypoxia marker pimonidazole. Pimonidazole was administered to 42 patients with advanced carcinoma of the cervix, 16 hr before biopsy. Sections of single or multiple biopsies were then immunostained for Glut-1 and CAIX, and the area of staining scored by eye, using a "field-by-field" semi-quantitative averaging system. Using 1 biopsy only, Glut-1 (r = 0.54, p = <0.001) correlated with the level of pimonidazole binding, and Glut-1 and CAIX expression also correlated significantly (r = 0.40, p = <0.009). Thus, our study has shown that HIF-1 regulated genes have potential for future use as predictors of the malignant changes mediated by hypoxia, and warrant further investigation as indicators of response to cancer therapy.