gebhart/patrepeval huggingface dataset:
Identification of a novel serum amyloid A protein in BALB/c mice (1991)

Four serum amyloid A protein (SAA) genes and two SAA gene products, SAA1 and SAA2, were identified in BALB/c mice. Using analytical isoelectric focusing we have identified a quantitatively significant new member of the SAA family and designated it 'SAA5'. This protein has characteristics never before described for any SAA molecule. In the highly conserved region between amino acids 33 and 44, identical in all SAAs from all species examined, SAA5 had four amino acid substitutions. In addition, the induction of SAA5 by lipopolysaccharide had different kinetics from that of the other mouse SAAs. Our data suggest that the mouse SAA gene family is more complex in composition and regulation than previously surmised.
The α-Dystroglycan-β-Dystroglycan Complex (1995)

Aberrant expression of the dystrophin-associated protein complex is thought to underlie the pathogenesis of Duchenne dystrophy, Becker muscular dystrophy, and severe childhood autosomal recessive muscular dystrophy. Recently, our laboratory identified an agrin receptor from Torpedo electric organ postsynaptic membranes. It is a heteromer of 190- and 50-kDa subunits with similarity to two components of the dystrophin-associated protein complex of alpha- and beta-dystroglycan. We now confirm the relationship between the Torpedo agrin receptor and mammalian dystroglycans and provide further information about the structure of the alpha-dystroglycan-beta-dystroglycan complex. The sequences of three peptides from each Torpedo subunit were 69% identical to mammalian dystroglycans. An antiserum to mammalian beta-dystroglycan recognizes the Torpedo 50-kDa polypeptide. Additionally, like alpha-dystroglycan, the 190-kDa agrin receptor subunit binds laminin. Previous studies have indicated that alpha- and beta-dystroglycan arise by cleavage of a precursor protein. Tryptic peptide mapping of both subunits and amino-terminal sequencing of Torpedo beta-dystroglycan indicate a single cleavage site, corresponding to serine 654 of the mammalian dystroglycan precursor. Gel electrophoresis analysis indicates there is at least one intrachain disulfide bond in beta-dystroglycan. These results provide precise primary structures for alpha- and beta-dystroglycan.
A Critical Role of Platelet Adhesion in the Initiation of Atherosclerotic Lesion Formation (2002)

The contribution of platelets to the process of atherosclerosis remains unclear. Here, we show in vivo that platelets adhere to the vascular endothelium of the carotid artery in ApoE(-)(/)(-) mice before the development of manifest atherosclerotic lesions. Platelet-endothelial cell interaction involved both platelet glycoprotein (GP)Ibalpha and GPIIb-IIIa. Platelet adhesion to the endothelium coincides with inflammatory gene expression and preceded atherosclerotic plaque invasion by leukocytes. Prolonged blockade of platelet adhesion in ApoE(-)(/)(-) mice profoundly reduced leukocyte accumulation in the arterial intima and attenuated atherosclerotic lesion formation in the carotid artery bifurcation, the aortic sinus, and the coronary arteries. These findings establish the platelet as a major player in initiation of the atherogenetic process.
Urokinase-Type Plasminogen Activator Is Increased in the Involuting Ventral Prostate of Castrated Rats* (1990)

We have investigated the content of plasminogen activators in the rat ventral prostate during castration. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and zymography demonstrated two major Mr-forms of plasminogen activators that were found to be strongly increased by castration; inclusion of quenching antibodies in the zymography and immunoblotting analysis identified these as urokinase-type plasminogen activator (u-PA) and its Mr 30,000 degradation product, respectively. A third, less abundant form, which was identified as tissue-type plasminogen activator, was also increased by castration. The induction of the plasminogen activators was prevented by treating the rats with 5 alpha-dihydrotestosterone. The increase in u-PA antigen was quantitated by the use of enzyme-linked immunosorbent assay. The increases in u-PA activity and antigen were traced back to a corresponding increase in u-PA messenger RNA (mRNA). By immunohistochemical methods, the u-PA was found to be present in scattered single cells at the surface of the epithelium facing the lumen of the glandular ducts. Such cells were present in control as well as in castrated rats, but their number increased after castration. In addition, after castration, u-PA immunoreactivity appeared in cells throughout the epithelium. These results suggest a role for plasminogen activation in castration-induced involution of the rat ventral prostate, and a role in the normal turnover of the rat ventral prostate epithelium.
Antifibrotic effects of suramin in injured skeletal muscle after laceration (2003)

Muscle injuries are very common in traumatology and sports medicine. Although muscle tissue can regenerate postinjury, the healing process is slow and often incomplete; complete recovery after skeletal muscle injury is hindered by fibrosis. Our studies have shown that decreased fibrosis could improve muscle healing. Suramin has been found to inhibit transforming growth factor (TGF)-beta1 expression by competitively binding to the growth factor receptor. We conducted a series of tests to determine the antifibrotic effects of suramin on muscle laceration injuries. Our results demonstrate that suramin (50 microg/ml) can effectively decrease fibroblast proliferation and fibrotic-protein expression (alpha-smooth muscle actin) in vitro. In vivo, direct injection of suramin (2.5 mg) into injured murine muscle resulted in effective inhibition of muscle fibrosis and enhanced muscle regeneration, which led to efficient functional muscle recovery. These results support our hypothesis that prevention of fibrosis could enhance muscle regeneration, thereby facilitating more efficient muscle healing. This study could significantly contribute to the development of strategies to promote efficient muscle healing and functional recovery.
Synthesis and Biological Analysis of Prostate-Specific Membrane Antigen-Targeted Anticancer Prodrugs (2010)

Ligand-targeted therapeutics have increased in prominence because of their potential for improved potency and reduced toxicity. However, with the advent of personalized medicine, a need for greater versatility in ligand-targeted drug design has emerged, where each tumor-targeting ligand should be capable of delivering a variety of therapeutic agents to the same tumor, each therapeutic agent being selected for its activity on a specific patient's cancer. In this report, we describe the use of a prostate-specific membrane antigen (PSMA)-targeting ligand to deliver multiple unrelated cytotoxic drugs to human prostate cancer (LNCaP) cells. We demonstrate that the PSMA-specific ligand, 2-[3-(1, 3-dicarboxy propyl)ureido] pentanedioic acid, is capable of mediating the targeted killing of LNCaP cells with many different therapeutic warheads. These results suggest that flexibility can be designed into ligand-targeted therapeutics, enabling adaptation of a single targeting ligand for the treatment of patients with different sensitivities to different chemotherapies.
Erythropoiesis, serum erythropoietin, and serum IGF-I in rats during accelerated growth (1990)

In this study we have examined the correlation between activity of erythropoiesis and serum concentrations of erythropoietin and insulin-like growth factor I in male and female rats during accelerated growth (day 30-90). We found that fractional incorporation of iron into newly formed red blood cells was linearily correlated with body weight gain. Total iron incorporation into newly formed red blood cells reflecting total daily red cell formation increased almost linearily between day 25 and 80 after birth in both sexes. While serum erythropoietin concentrations decreased in the time interval investigated (25-120 days), serum IGF-I levels increased in both sexes between day 25 and 55. In this period, individual values of total iron incorporation into red blood cells and serum IGF-I concentrations were linearily correlated. Our observations support the concept that IGF-I rather than erythropoietin modulates erythropoiesis during accelerated growth and thus manages a proportional increase in body mass and oxygen transport capacity.
Developmental changes in the ability to synthesize juvenile hormone in vitro by corpora allata from the Eri silkworm, Samia cynthia ricini (Lepidoptera: Saturniidae) (2002)

A radiochemical assay (RCA) has been used for the measurement of juvenile hormone (JH) synthesis in vitro by corpora allata (CA) from the Eri silkworm, Samia cynthia ricini. Using CA from newly emerged female adults for the bioassay, the most suitable incubation conditions were determined. A high rate of JH synthesis was found in medium TC199 at pH 6.5, 30Â°C and 4 mM Ca2+. The time course of JH synthesis showed a steady decrease during the first 6 hours of incubation.Under optimal incubation conditions, CA from the 4th and 5th larval instars, pupae and adults were used for measuring JH synthesis in vitro. The highest rates of JH synthesis were found on the 1st day of both larval stages, and then JH synthesis decreased steadily during the following two days of each instar. From the 4th day of the 5th larval instar to the 2nd day after pupation, CA could still synthesize small amounts of JH. However, from the 3rd day of the pupal stage to 12 hours before adult emergence, no JH release was observed. About 6 hours before emergence, CA of both female and male pharate adults regained the ability to synthesize JH. JH synthesis increased to a maximum shortly after emergence and then decreased again during the following two days. During this period, JH synthesis in vitro by CA from females was always higher than that of males. This is the first report on JH synthesis in vitro by CA from both female and male pharate adults and adults of a lepidopteran species, where the adults do not feed, are relatively short-lived, mate only once, and ovarian maturation and vitellogenesis are completed before emergence.
Multivariate Analysis with Latent Variables: Causal Modeling (1980)

INTRODUCTION 419 BASIC CONCEPTS 421 Structural Equations and Path Diagrams 421 Model Specification and Research Design 425 Model Testing 427 Model Modification and Reconfirmation 429 Example: Models of Attitude-Behavior Relations 429
Effect of platelet‐derived growth factor on DNA synthesis and gene expression in bone marrow stromal cells derived from adult and old rats (1995)

The effects of platelet-derived growth factor (PDGF) on DNA synthesis and mRNA expression of osteoblast markers in marrow stromal cells derived from adult (6 months) and old (24 months) rats were examined. Treatment of stromal cells from adult rats with dexamethasone induced the appearance of osteoblast-like cells. PDGF partially also inhibited the differentiation of stromal cells induced by dexamethasone. In cultures of serum-starved stromal cells, PDGF stimulated [3H]-thymidine incorporation into DNA in a dose-dependent manner with a maximum stimulation of 15-fold at 500 ng/ml. By comparison, insulin-like growth factor (IGF-I) has a small effect on [3H]-thymidine incorporation. The effect of PDGF and IGF-I on DNA synthesis was additive. Treatment of the confluent stromal cells from adult rats with PDGF increased the mRNA level of osteopontin fourfold without any significant effect on alkaline phosphatase and type I collagen mRNAs. In contrast, dexamethasone stimulated the mRNA expression of alkaline phosphatase, type I collagen, and osteopontin 2.1-, 2.3-, and 14-fold, respectively. Addition of PDGF to dexamethasone-treated cells failed to induce any further increase in osteopontin expression whereas the expression of alkaline phosphatase and type I collagen was partially reduced. The expression of osteocalcin mRNA was negligible in stromal cells but stimulated several fold by dexamethasone and 1,25(OH)2D3. PDGF inhibited drastically the elevation of osteocalcin mRNA. In contrast, IGF-I stimulated type I collagen expression 100% without any appreciable effect on the expression of osteopontin and alkaline phosphatase. The stimulatory effect of PDGF on osteopontin expression was augmented by IGF-I. Furthermore, PDGF attenuated the stimulatory effect of IGF-I on type I collagen expression. The responses of cultured cells from old rats to growth factors were also examined. PDGF or PDGF plus IGF-I increased [3H]-thymidine incorporation in stromal cells from old rats but to a lesser extent. However, PDGF was equally effective in stimulating osteopontin expression in cells from both adult and old rats. We concluded that PDGF is a potent mitogen but that the response of stromal cells from old rats is impaired. In addition, PDGF stimulates osteopontin expression in stromal cells and this effect is not age dependent.
Plasma interleukin 8 and polymorphonuclear leukocyte elastase concentrations in patients with septic shock. (1995)

We determined the plasma concentrations of interleukin 8 (IL-8), polymorphonuclear leukocyte elastase (PMNE), and endotoxin in patients with septic shock in order to investigate the role of IL-8 and PMNE in the development of septic shock, especially in septic adult respiratory distress syndrome (ARDS). The IL-8 concentration in patients with septic shock was 6.28 +/- 9.00 ng/mL (mean +/- SD, n = 29), which was significantly higher (P < 0.0001) than the concentration in septic patients without shock (0.35 +/- 0.35 ng/mL, n = 40). There was a significant correlation between the IL-8 concentration and the PMNE concentration at the onset of septic shock (r = 0.6916, P < 0.0001). The IL-8 concentration was also significantly correlated with the endotoxin concentration (r = 0.5584, P = 0.0016). There was a significant negative correlation (r = -0.8237, P < 0.0001) between the serum PMNE concentration and the oxygenation index (PaO2/FiO2) at the onset of septic shock. These results indicate that IL-8 and PMNE are produced in large quantities when septic shock occurs, and may play a role in the development of septic ARDS.
Description of a Web-Driven, Problem-Based Learning Environment and Study of the Efficacy of Implementation in Educational Leader Preparation (2001)

Abstract A Web-driven problem-based learning environment and instructional system was conceived and developed to study the marriage of the problem-based learning instructional method and Web technologies for instructional delivery of educational administration content material. The project described herein was undertaken to examine the efficacy of implementing this new mode of instruction in graduate courses in educational leadership. The ultimate goal of this line of research is to enhance the development of applications of Web technologies to support problem-based learning and improve the efficiency and efficacy of this instructional form in practice across higher education settings. This article describes the prototype software, the rationale and theoretical framework supporting its development, the process and results of research conducted during production and beta-testing, and the educational significance of the project.
Androgens and Bone (2004)

Loss of estrogens or androgens increases the rate of bone remodeling by removing restraining effects on osteoblastogenesis and osteoclastogenesis, and also causes a focal imbalance between resorption and formation by prolonging the lifespan of osteoclasts and shortening the lifespan of osteoblasts. Conversely, androgens, as well as estrogens, maintain cancellous bone mass and integrity, regardless of age or sex. Although androgens, via the androgen receptor (AR), and estrogens, via the estrogen receptors (ERs), can exert these effects, their relative contribution remains uncertain. Recent studies suggest that androgen action on cancellous bone depends on (local) aromatization of androgens into estrogens. However, at least in rodents, androgen action on cancellous bone can be directly mediated via AR activation, even in the absence of ERs. Androgens also increase cortical bone size via stimulation of both longitudinal and radial growth. First, androgens, like estrogens, have a biphasic effect on endochondral bone formation: at the start of puberty, sex steroids stimulate endochondral bone formation, whereas they induce epiphyseal closure at the end of puberty. Androgen action on the growth plate is, however, clearly mediated via aromatization in estrogens and interaction with ERalpha. Androgens increase radial growth, whereas estrogens decrease periosteal bone formation. This effect of androgens may be important because bone strength in males seems to be determined by relatively higher periosteal bone formation and, therefore, greater bone dimensions, relative to muscle mass at older age. Experiments in mice again suggest that both the AR and ERalpha pathways are involved in androgen action on radial bone growth. ERbeta may mediate growth-limiting effects of estrogens in the female but does not seem to be involved in the regulation of bone size in males. In conclusion, androgens may protect men against osteoporosis via maintenance of cancellous bone mass and expansion of cortical bone. Such androgen action on bone is mediated by the AR and ERalpha.
Noninvasive Detection of TMPRSS2:ERG Fusion Transcripts in the Urine of Men with Prostate Cancer (2006)

We recently reported the identification of recurrent gene fusions in the majority of prostate cancers involving the 5' untranslated region of the androgen-regulated gene TMPRSS2 and the ETS family members ERG, ETV1, and ETV4. Here we report the noninvasive detection of these gene fusions in the urine of patients with clinically localized prostate cancer. By quantitative polymerase chain reaction, we assessed the expression of ERG and TMPRSS2:ERG transcripts in urine samples obtained after prostatic massage from 19 patients (11 prebiopsy and 8 pre-radical prostatectomy) with prostate cancer. We observed a strong concordance between ERG overexpression and TMPRSS2:ERG expression, with 8 of 19 (42%) patients having detectable TMPRSS2:ERG transcripts in their urine. Importantly, by fluorescence in situ hybridization, we confirmed the presence or the absence of TMPRSS2:ERG gene fusions in matched prostate cancer tissue samples from three of three patients with fusion transcripts in their urine and from two of two patients without fusion transcripts in their urine. These results demonstrate that TMPRSS2:ERG gene fusions can be detected in the urine of patients with prostate cancer and support larger studies on prospective cohorts for noninvasive detection of prostate cancer.
Adaptive postfiltering for enhancement of noisy speech in the frequency domain (1991)

A novel frequency-domain adaptive postfilter for enhancement of noisy speech is presented. The postfilter suppresses the noise in spectral valleys and allows more noise in the formant regions where it is masked by the speech signal. First, the authors perform an LPC (linear predictive coding) analysis of the noisy speech and calculate its log magnitude spectrum. After identifying the formants and spectral valleys, the log magnitude spectrum is modified to obtain the postfilter frequency response. This response has local maxima of equal magnitude at the formant frequencies. Experimental results show that this novel frequency-domain approach results in enhanced speech of better perceptual quality than obtained by a time-domain method. The proposed method is especially efficient in eliminating high frequency noise and in preserving the weaker, high frequency formants in sonorant sounds.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Development of High-Sensitivity Ion Trap Ion Mobility Spectrometry Time-of-Flight Techniques:  A High-Throughput Nano-LC-IMS-TOF Separation of Peptides Arising from a Drosophila Protein Extract (2003)

A linear octopole trap interface for an ion mobility time-of-flight mass spectrometer has been developed for focusing and accumulating continuous beams of ions produced by electrospray ionization. The interface improves experimental efficiencies by factors of approximately 50-200 compared with an analogous configuration that utilizes a three-dimensional Paul geometry trap (Hoaglund-Hyzer, C. S.; Lee, Y. J.; Counterman, A. E.; Clemmer, D. E. Anal. Chem. 2002, 74, 992-1006). With these improvements, it is possible to record nested drift (flight) time distributions for complex mixtures in fractions of a second. We demonstrate the approach for several well-defined peptide mixtures and an assessment of the detection limits is given. Additionally, we demonstrate the utility of the approach in the field of proteomics by an on-line, three-dimensional nano-LC-ion mobility-TOF separation of tryptic peptides from the Drosophila proteome.
Towards safe human robot collaboration - Risk assessment of intelligent automation (2020)

Automation and robotics are two enablers for developing the Smart Factory of the Future, which is based on intelligent machines and collaboration between robots and humans. Especially in final assembly and its material handling, where traditional automation is challenging to use, collaborative robot (cobot) systems may increase the flexibility needed in future production systems. A major obstacle to deploy a truly collaborative application is to design and implement a safe and efficient interaction between humans and robot systems while maintaining industrial requirements such as cost and productivity. Advanced and intelligent control strategies is the enabler when creating this safe, yet efficient, system, but is often hard to design and build.This paper highlights and discusses the challenges in meeting safety requirements according to current safety standards, starting with the mandatory risk assessment and then applying risk reduction measures, when transforming a typical manual final assembly station into an intelligent collaborative station. An important conclusion is that current safety standards and requirements must be updated and improved and the current collaborative modes defined by the standards community should be extended with a new mode, which in this paper is refereed to the deliberative planning and acting mode.
ALK-1 Protein Expression and ALK Gene Rearrangements Aid in the Diagnosis of Inflammatory Myofibroblastic Tumors of the Female Genital Tract (2012)

This is the first report, to our knowledge, of ALK gene rearrangements in inflammatory myofibroblastic tumors in the female genital tract. If a myxoid background is appreciated in a spindle cell lesion of the female genital tract, especially if inflammatory cells are present, anaplastic lymphoma kinase-1 staining along with fluorescence in situ hybridization studies, for ALK gene rearrangements, may aid in distinguishing inflammatory myofibroblastic tumors from their malignant mimics.
Gate Work Function and Contact Engineering in Nanoscale Vertical Pillar Transistor for DRAM Cell Transistors (2007)

In this work, p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> /n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> gate structure is applied to vertical pillar transistor (VPT) for DRAM cell transistor to reduce gate induced drain leakage (GIDL) current. The VPT performance with contact structure and source/drain (S/D) geometry connected to cell capacitor node was investigated.
A Diagnostic Test for Prostate Cancer From Gene Expression Profiling Data (2004)

We describe and validate a new gene ratio based test for the diagnosis of prostate cancer, which was developed from the analysis of extensive gene profiling data for the diagnosis of prostate cancer. This test can be easily adapted to the clinical arena without the need for complex computer software or hardware. We anticipate that the gene ratio based diagnosis of prostate cancer using fine needle aspirations could serve as a useful adjunct to standard histopathological techniques.