gebhart/patrepeval huggingface dataset:
Collagen-Binding Peptidoglycans: A Biomimetic Approach to Modulate Collagen Fibrillogenesis for Tissue Engineering Applications (2009)

The small leucine-rich proteoglycans (SLRPs), prevalent in collagenous tissues, regulate collagen fibrillogenesis and provide a host of biochemical cues critical to tissue function and homeostasis. Incorporating SLRPs may enhance tissue engineering designs that mimic the native extracellular matrix, although SLRPs purified from animal sources bear low yields and lack design control. Consequently, we have designed synthetic peptidoglycans, inspired by the native SLRP decorin, that contain a collagen-binding peptide attached to a glycosaminoglycan (GAG) chain. These peptidoglycans modulate collagen fibrillogenesis and decrease fibril diameter in vitro, similarly to decorin, while maintaining the characteristic D-banded fibrils. Application for tissue engineering is demonstrated as these peptidoglycans are incorporated into collagen gels seeded with smooth muscle cells. Gels formed with peptidoglycans and decorin show a faster rate of gel compaction, and one peptidoglycan uniquely increases elastin production. The peptidoglycan design can be tailored with respect to the peptide sequence and GAG identity and is expected to have versatile application in tissue engineering.
[Changes in the electrophoretic pattern of the venom of the bushmaster (Lachesis muta stenophrys) stored under various conditions]. (1985)

Liquid and lyophilized samples of Lachesis muta venom were stored at different temperatures and for different periods of time, and analyzed by polyacrylamide gel electrophoresis (PAGE) and immunoelectrophoresis. Only slight variations were evident when three pools of freeze-dried venom, that had been kept at -30 degrees C for several months were compared with fresh venom. These results suggest that L. muta venom is not altered drastically when stored under these conditions.
Analysis of oxygen transport in a diffusion‐limited model of engineered heart tissue (2006)

Cardiac tissue engineering has made notable progress in recent years with the advent of an experimental model based on neonatal cardiomyocytes entrapped in collage gels and purified basement membrane extract, known as "engineered heart tissues" (EHTs). EHTs are a formidable display of tissue-level contractile function and cellular-level differentiation, although they suffer greatly from mass transport limitations due to the high density of metabolically active cells and the diffusion-limited nature of the hydrogel. In this report, a mathematical model was developed to predict oxygen levels inside a one-dimensional, diffusion-limited model of EHT. These predictions were then compared to values measured in corresponding experiments with a hypoxia-sensitive stain (pimonidazole). EHTs were cast between two plastic discs, which allowed for mass transfer with the culture medium to occur in only the radial direction. EHTs were cultured for up to 36 h in the presence of pimonidazole, after which time they were snap-frozen, histologically sectioned, and stained for bound pimonidazole. Quantitative image analysis was performed to measure the distance from the culture medium at which hypoxia first occurs under various conditions. As tested by variation of simple design parameters, the trends in oxygen profiles predicted by the model are in reasonable agreement with those obtained experimentally, although a number of ambiguities related to the specific model parameters led to a general overprediction of oxygen concentrations. Based on the sensitivity analysis in the present study, it is concluded that diffusion-reaction models may offer relatively precise predictions of oxygen concentrations in diffusion-limited tissue constructs.
Compensating temperature-induced sensitivity changes in thin film NiFeCo magnetoresistive magnetometers (1986)

The temperature dependence of the sensitivity and resistance of magnetoresistive thin film magnetic sensors has been investigated. Magnetoresistive sensors were fabricated from a range of zero-magnetostrictive NiFeCo alloys with cobalt contents between 0 and 25 wt.%. In the temperature range considered (0 to 60 deg.C) the sensitivity was found to fall and the resistance to rise almost linearly for all of the alloys. The response of the sensor to an externally applied field is proportional to its supply voltage. In the simple case of true complementary correspondence between the temperature coefficients of device resistance and sensitivity a constant-current drive would achieve perfect temperature compensation of sensitivity. For all alloys where the degree of divergence between the temperature-resistance and temperature-sensitivity characteristics is known, electronic control systems incorporating this relationship may be used to provide inherently accurate temperature compensation.
Effects of serum and insulin on the sensitivity of the human breast cancer cell line MCF-7 to estrogen and antiestrogens. (1981)

The effect of the antiestrogens tamoxifen and nafoxidine on the growth of the human breast cancer cell line MCF-7 is modified by both serum and insulin. Tamoxifen inhibition of the growth of MCF-7 cells in culture is reduced as the concentration of serum in the medium is increased from 0.1% to 5 to 10%. Estradiol does not stimulate cell growth over the same range of serum levels. Insulin changes the sensitivity of MCF-7 cells to both estrogen and antiestrogens. Cells growing in media containing insulin are less sensitive to inhibition by either tamoxifen or nafoxidine than are cells growing in its absence. In addition, higher concentrations of estradiol are required to stimulate the production of plasminogen activator when cells are grown in media containing insulin. This effect of insulin can be accounted for by the finding that insulin lowers the level of estrogen receptor in MCF-7 cells without altering the binding constant for the hormone. Cells grown with insulin have an average of 21,000 +/- 4,700 (S.D.) estrogen binding sites/cell compared to 62,000 +/- 9,700 sites/cell in cells grown in the absence of insulin. This difference in receptor level is sufficient to account for the difference in the concentration of estradiol needed for equivalent induction of plasminogen activator in cultures with or without insulin. These results indicate that the level of estrogen receptor in breast cancer cells can be changed and that the sensitivity of such cells, both to estrogen and to antiestrogens, is altered by changes in the level of estrogen receptor. They also have implications concerning the mechanism by which antiestrogens act to inhibit the growth of mammary tumor cells.
Small aggregates of platelets can be detected sensitively by a flow cytometer equipped with an imaging device: Mechanisms of epinephrine‐induced aggregation and antiplatelet effects of beraprost (2002)

FIC2 is a promising device for detection of platelet aggregates in whole blood, with wide basic and clinical applications.
Optimizing Microphone Arrays for use in Conference Halls (2009)

In conference halls, the question and answer session is often impaired by poor solutions for listening to the audience on the public address system. By using microphone arrays to capture the sound from questions, everyone can hear what the discussion is all about. If a tracking is used as well, these arrays creates an automatic speaker and sound reproduction environment. Because of issues like feedback, delay, and frequency response, a feasibility study on the use of microphone arrays in conference halls has been done. By combining and applying known feedback techniques as well as newly developed methods, this study shows that a $10$ dB louder gain before feedback margin has been achieved and thereby making the automatic sound capture system work. Issues still remain, and many of the feedback techniques used can linearly distort the frequency response and reduce the sound quality. Latency in the processing time has been reduced in this thesis by 20 ms, and the total delay with 15 meters sound travel time and a loudspeaker array is measured to be 58.2 ms. However, according to the Haas effect, the total delay should be below 40 ms to avoid echoes.In this thesis, the best performing setup that gives the loudest maximum stable gain is achieved with a microphone array tilted above the second row to hit in the middle of the audience in an auditorium, loudspeaker arrays mounted high on the front wall programmed to play down towards the audience, a frequency-shifter of -5 Hz, a bandwidth from 500 to 6500 Hz, and a soft equalization along with an automatic tracker for locating the speaker. However, the sound quality difference between a close-up microphone and the microphone array is still present, and the lack of low and middle frequencies in the microphone array makes the microphone array sound a little narrow.
Vascular Endothelial Growth Factor (VEGF) Serum Concentration Changes during Chemotherapy in Patients with Lung Cancer. (2001)

Vascular endothelial growth factor (VEGF) is one of the most important angiogenic factors. This study aimed at clarifying the clinical significance of the changes in the serum VEGF (S-VEGF) concentrations in patients with lung cancer during anticancer chemotherapy. Subjects comprised 29 patients with lung cancer (13 adenocarcinomas, 7 squamous cell carcinomas, and 9 small cell carcinomas) who were treated with cisplatin-based chemotherapy. S-VEGF was measured by ELISA. We compared the S-VEGF concentrations between the responders and nonresponders to anticancer chemotherapy. S-VEGF concentrations before treatment of the chemotherapy (pretreatment S-VEGF concentrations) were correlated with the number of WBC, neutrophil count, monocyte count and platelet count but not the lymphocyte count. The mean pretreatment S-VEGF concentrations in responders and those in nonresponders were not significantly different, 509.7 pg/ml in the former and 382.8 pg/ml in the latter, respectively., The S-VEGF concentrations in the responders decreased to a mean of 356.0 pg/ml and 304.1 pg/ml during and at the end of therapy, respectively while those in the nonresponders increased to a mean of 474.2 pg/ml and 598.4 pg/ml during and at the end of therapy. The S-VEGF concentration changes in the responders were significantly different from those in the nonresponders (p = .006). The S-VEGF concentration may relate to tumor burden, however it may not be a good marker for tumor burden, because it can be influenced by various factors such as neutrophil which increases during infection. A decrease in S-VEGF concentrations may improve neoangiogenesis and the immune response, and may correlate with improvements in the quality of life and survival of patients.
Towards efficient feature interaction handling (2002)

One of the primary objectives behind the IN is to facilitate rapid provisioning of new services. The phenomena of service interaction is regarded as one of the major obstacles to this objective. In order to assure short time-to-market without compromising service quality, service providers have to implement efficient methods for detecting interactions already in the early phases of service creation. So far, unfortunately, the question of efficiency received very little attention from the research community dealing with service interaction. We present an approach called filtering which may improve the efficiency of interaction detection for IN services. The filtering approach aims at reducing the problem space (i.e. the number of service feature combinations to be considered) prior to an extensive interaction analysis. We motivate the proposed approach, introduce the idea of a service usage model (SUM), and explain its semantics and application. We also discuss formalisation of the SUM with Petri nets. The formalisation is introduced step-by-step on the basis of the service examples already given. Possible extensions of the original SUM are presented. Finally, the pro and cons of the proposed approach as well as some areas for future work are discussed.
Low-fluence vs. standard fluence hair removal: A contralateral control non-inferiority study (2011)

Lower fluence diode laser, delivered under conditions of vacuum and using larger spot sizes, can provide significant hair reduction.
Preoperative Skin Conditioning: Extracellular Matrix Clearance and Skin Bed Preparation, A New Paradigm (2019)

This paper introduces the concept of "skin bed preparation" prior to surgical procedures. Following the theory of chronic wound bed preparation and adapting the skin model to one of chronic wound changes related to extrinsic and intrinsic factors, a topical formulation aimed at recycling the extracellular matrix (ECM) from accumulated waste products is evaluated and discussed. The clearance of these products and stimulation of new replacements has the potential to change the regenerative milieu of the skin so that when procedures are carried out, cellular signaling and cross-talk at the dermal level are improved and healing is optimized. By introducing a combination of peptides and other synergistic active agents, a sequence of clearance, regeneration, and remodeling is initiated. This is confirmed and validated by a series of biopsies and clinical studies that demonstrate changes in the ECM as early as 2 to 3 weeks after application. Clinical studies related to resurfacing procedures show accelerated healing and improved symptomatic relief compared with standard of care by preconditioning the skin 2 weeks prior to the procedure. A similar approach is suggested as a potential advantage for invasive surgical procedures based on similar scientific principles elucidated on in the text.
Complexity management for video encoders (2002)

Computational complexity is an important performance constraint for software-only video CODECs. The aim of this research is to develop a video coding system with variable, controllable computational complexity. Adaptive algorithms for DCT and motion estimation are proposed separately to reduce complexity of each function and maintain it at target level. An integrated approach to video CODEC complexity management is also addressed. This work will have potential benefit for a wide range of computation-constrained or power-constrained multimedia applications.
Expression of Ly-6, a marker for highly malignant murine tumor cells, is regulated by growth conditions and stress (1998)

Ly-6E.1 is highly expressed in murine tumor cells with a high malignancy phenotype and may serve as a marker for such a phenotype. In this study, we examined the effects of various growth conditions and stress on the expression levels of Ly-6E.1 by tumor cells. Previous preliminary results have shown that murine DA3 mammary tumor cells expressing high levels of Ly-6E.1 (Ly-6(hi)) are more highly tumorigenic than the same tumor cells expressing low levels of this membrane protein (Ly-6(lo)). In this study, we demonstrate that mice bearing Ly-6(hi) DA3 tumors have a significantly higher burden of spontaneous pulmonary metastasis than mice bearing Ly-6(lo) DA3 tumors. Furthermore, the survival time of the former mice was significantly shorter than that of the latter ones. We further show that certain other members of the Ly-6 gene family such as Ly-6C.1 and Ly-6G.1 are coregulated with Ly-6E.1. This was shown to occur with respect to both DA3 cells as well as A3 tumor cells which are of fibroblast origin. However, these 2 cells differ with respect to regulation of Sca-2 (TSA1, another member of the Ly-6 family) expression on these cells. Levels of Sca-2 on A3 cells appear to be coregulated with Ly-6E.1 (i.e., Ly-6(hi) A3 cells express high levels of Sca-2 and Ly-6(lo) A3 cells express low levels of Sca-2). These 2 Ly-6 proteins were, however, not coregulated on DA3 cells. Both Ly-6(hi) as well as Ly-6(lo) DA3 cells express equal levels of Sca-2. Levels of Thy-1, another glycosylphosphatidylinositol (GPI)-anchored protein expressed by A3 tumor cells, were equally expressed by both Ly-6(hi) and Ly-6(lo) A3 tumor cells. Levels of Ly-6 (but not those of CD44) on A3 tumor cells were upregulated on cells from dense cultures but were not influenced by the position of the cells in the cell cycle. Stress conditions such as serum starvation or heat shock upregulated the expression of Ly-6 by the 2 types of tumor cells but did not induce apoptosis in these cells. The kinetics of the stress-dependent upregulation of Ly-6 expression differed, however, between the epithelial and fibroblastic tumor cells.
Folate receptor overexpression is associated with poor outcome in breast cancer (2007)

The high affinity folate receptor is a membrane-associated glycoprotein that is preferentially expressed in cancers of epithelial origin and rarely expressed in normal cells. We examined its expression pattern in breast cancer, utilizing a tissue microarray containing samples from 63 invasive breast cancers from women with divergent clinical outcomes. Thirty-three women comprised the poor outcome group with a median time to recurrence of 1.9 years. Thirty women, the good outcome group, were free of recurrence for a minimum of 7 years after diagnosis. The intensity of folate receptor staining was strongly correlated with outcome. There were two summary categories of staining intensity: weak (n = 42) or strong (n = 21). In the strong staining group, 17 of 21 women (81%) have recurred and their median survival is 2.4 years. In the weak staining group, 16 of 42 women (38%) have recurred. Their median survival is not estimable. After adjustment for tumor size, nodal status, ER status, adjuvant therapy, histology and tumor grade, strong staining for the folate receptor remained significantly associated with poor outcome, p < 0.001. Our work requires validation in a larger cohort, but supports the possibility of using folate receptor-targeted approaches in the management of breast cancer.
Thrombospondin-1 stimulates platelet aggregation by blocking the antithrombotic activity of nitric oxide/cGMP signaling (2007)

Platelet alpha-granules constitute the major rapidly releasable reservoir of thrombospondin-1 in higher animals. Although some fragments and peptides derived from thrombospondin-1 stimulate or inhibit platelet aggregation, its physiologic function in platelets has remained elusive. We now show that endogenous thrombospondin-1 is necessary for platelet aggregation in vitro in the presence of physiologic levels of nitric oxide (NO). Exogenous NO or elevation of cGMP delays thrombin-induced platelet aggregation under high shear and static conditions, and exogenous thrombospondin-1 reverses this delay. Thrombospondin-1-null murine platelets fail to aggregate in response to thrombin in the presence of exogenous NO or 8Br-cGMP. At physiologic concentrations of the NO synthase substrate arginine, thrombospondin-1-null platelets have elevated basal cGMP. Ligation of CD36 or CD47 is sufficient to block NO-induced cGMP accumulation and mimic the effect of thrombospondin-1 on aggregation. Exogenous thrombospondin-1 also reverses the suppression by NO of alphaIIb/beta3 integrin-mediated platelet adhesion on immobilized fibrinogen, mediated in part by increased GTP loading of Rap1. Thrombospondin-1 also inhibits cGMP-mediated activation of cGMP-dependent protein kinase and thereby prevents phosphorylation of VASP. Thus, release of thrombospondin-1 from alpha-granules during activation provides positive feedback to promote efficient platelet aggregation and adhesion by overcoming the antithrombotic activity of physiologic NO.
A Critical Site in the Core of the CCR5 Chemokine Receptor Required for Binding and Infectivity of Human Immunodeficiency Virus Type 1 (1999)

Like the CCR5 chemokine receptors of humans and rhesus macaques, the very homologous (approximately 98-99% identical) CCR5 of African green monkeys (AGMs) avidly binds beta-chemokines and functions as a coreceptor for simian immunodeficiency viruses. However, AGM CCR5 is a weak coreceptor for tested macrophage-tropic (R5) isolates of human immunodeficiency virus type 1 (HIV-1). Correspondingly, gp120 envelope glycoproteins derived from R5 isolates of HIV-1 bind poorly to AGM CCR5. We focused on a unique extracellular amino acid substitution at the juncture of transmembrane helix 4 (TM4) and extracellular loop 2 (ECL2) (Arg for Gly at amino acid 163 (G163R)) as the likely source of the weak R5 gp120 binding and HIV-1 coreceptor properties of AGM CCR5. Accordingly, a G163R mutant of human CCR5 was severely attenuated in its ability to bind R5 gp120s and to mediate infection by R5 HIV-1 isolates. Conversely, the R163G mutant of AGM CCR5 was substantially strengthened as a coreceptor for HIV-1 and had improved R5 gp120 binding affinity relative to the wild-type AGM CCR5. These substitutions at amino acid position 163 had no effect on chemokine binding or signal transduction, suggesting the absence of structural alterations. The 2D7 monoclonal antibody has been reported to bind to ECL2 and to block HIV-1 binding and infection. Whereas 2D7 antibody binding to CCR5 was unaffected by the G163R mutation, it was prevented by a conservative ECL2 substitution (K171R), shared between rhesus and AGM CCR5s. Thus, it appears that the 2D7 antibody binds to an epitope that includes Lys-171 and may block HIV-1 infection mediated by CCR5 by occluding an HIV-1-binding site in the vicinity of Gly-163. In summary, our results identify a site for gp120 interaction that is critical for R5 isolates of HIV-1 in the central core of human CCR5, and we propose that this site collaborates with a previously identified region in the CCR5 amino terminus to enable gp120 binding and HIV-1 infections.
Alteration of the nucleoside triphosphate (NTP) catalytic domain within Escherichia coli recA protein attenuates NTP hydrolysis but not joint molecule formation. (1993)

The hydrolysis of the nucleoside triphosphates, such as ATP or GTP, plays a central role in a variety of biochemical processes; but, in most cases, the specific mechanism of energy transduction is unclear. DNA strand exchange promoted by the Escherichia coli recA protein is normally associated with ATP hydrolysis. However, we advanced the idea that the observed ATP hydrolysis is not obligatorily linked to the exchange of DNA strands (Menetski, J. P., Bear, D. G., and Kowalczykowski, S. C. (1990) Proc. Natl. Acad. Sci. U. S. A. 87, 21-25); instead, ATP binding resulting in an allosteric transition to an active form of the recA protein is sufficient. In this paper, we extend this conclusion by introducing a mutation within a highly conserved region of the recA protein that, on the basis of sequence similarity, is proposed to interact with the pyrophosphate moiety of a bound NTP molecule. The conservative substitution of an arginine for the invariant lysine at position 72 reduces NTP hydrolysis by approximately 600-850-fold. This mutation does not significantly alter the capacity of the mutant recA (K72R) protein either to bind nucleotide cofactors and single-stranded DNA or to respond allosterically to nucleotide cofactor binding. Despite the dramatic attenuation in NTP hydrolysis, the recA (K72R) protein retains the ability to promote homologous pairing and extensive exchange of DNA strands (up to 1.5 kilobase pairs). These results both identify a component of the catalytic domain for NTP hydrolysis and demonstrate that the recA protein-promoted pairing and exchange of DNA strands mechanistically require the allosteric transition induced by NTP cofactor binding, but not the energy educed from NTP hydrolysis.