gebhart/patrepeval huggingface dataset:
Expression of smooth muscle and nonmuscle myosin heavy chains in cultured vascular smooth muscle cells. (1986)

We explored the hypothesis that discrepancies in the literature concerning the nature of myosin expression in cultured smooth muscle cells are due to the appearance of a new form of myosin heavy chain (MHC) in vitro. Previously, we used a very porous sodium dodecyl sulfate gel electrophoresis system to detect two MHCs in intact smooth muscles (SM1 and SM2) which differ by less than 2% in molecular weight (Rovner, A. S., Thompson, M. M., and Murphy, R. A. (1986) Am. J. Physiol. 250, C861-C870). Myosin-containing homogenates of rat aorta cells in primary culture were electrophoresed on this gel system, and Western blots were performed using smooth muscle-specific and nonmuscle-specific myosin antibodies. Subconfluent, rapidly proliferating cultures contained a form of heavy chain not found in rat aorta cells in vivo (NM) with electrophoretic mobility and antigenicity identical to the single unique heavy chain seen in nonmuscle cells. Moreover, these cultures expressed almost none of the smooth muscle heavy chains. In contrast, postconfluent growth-arrested cultures expressed increased levels of the two smooth muscle heavy chains, along with large amounts of NM. Analysis of cultures pulsed with [35S] methionine indicated that subconfluent cells were synthesizing almost exclusively NM, whereas postconfluent cells synthesized SM1 and SM2 as well as larger amounts of NM. Similar patterns of MHC content and synthesis were found in subconfluent and postconfluent passaged cells. These results show that cultured vascular smooth muscle cells undergo differential expression of smooth muscle- and nonmuscle-specific MHC forms with changes in their growth state, which appear to parallel changes in expression of the smooth muscle and nonmuscle forms of actin (Owens, G. K., Loeb, A., Gordon, D., and Thompson, M. M. (1986) J. Cell Biol. 102, 343-352). The reappearance of the smooth muscle MHCs in postconfluent cells suggests that density-related growth arrest promotes cytodifferentiation, but the continued expression of the nonmuscle MHC form in these smooth muscle cells indicates that other factors are required to induce the fully differentiated state while in culture.
Mini‐review: Overcoming tumor‐intrinsic resistance to immune effector function (2004)

In immunological cancer therapy, the current treatment emphasis is on the generation of effector cells that are specific for tumor antigens. However, there is a distressing lack of correlation between the induction of specific immunity in cancer patients and measurable clinical benefit. By studying mouse models of de novo tumorigenesis we are beginning to understand that the tumor itself, in particular the manifestation of a distinct tumor environment, impairs immune effector function; this concept is yet to be applied in human malignancy.
Measuring Frequency Response of a Single-Walled Carbon Nanotube Common-Source Amplifier (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Frequency response function (FRF) showing ac gain from a single-walled carbon nanotube transistor is presented. A top-gated carbon nanotube FET (CNFET) is configured as a common-source amplifier and the FRF of the amplifier is measured. Evidence of unambiguous signal amplification is observed in time domain as well as frequency domain up to a unity voltage gain frequency of approximately 560 kHz. The observed roll-off in frequency is solely due to the <emphasis emphasistype="italic">RC</emphasis> time constant of the measurement apparatus. A specifically designed circuit-compatible SPICE model for the CNFET is used to model both dc and ac characteristic with the same set of physical parameters. Good agreement between measurement and simulation is obtained. For a device without the parasitic load capacitance, we predict an intrinsic unity voltage gain frequency of 29 GHz and a cutoff frequency of <formula formulatype="inline"><tex Notation="TeX">$\sim {50}$</tex></formula> GHz. </para>
The Prediction of Chronicity in Patients With an Acute Attack of Low Back Pain in a General Practice Setting (1995)

The results suggest that, at the earliest stage of low back pain, fear of pain should be identified by clinicians and, where this is severe, pain confrontation should arguably form part of the approach to treatment.
Effects ofEnterococcus faeciumNCIMB 10415 as probiotic supplement on intestinal transport and barrier function of piglets (2006)

Many studies report positive effects of probiotic supplementation on the performance and health of piglets. The intention of this study was to describe the effects of Enterococcus faecium NCIMB 10415 on the transport and barrier functions of pig small intestine to improve our understanding of the underlying mechanisms of this probiotic. Ussing chamber studies were conducted with isolated jejunal epithelia of piglets at the age of 14, 28, 35 and 56 days. Jejunal tissues of the control group were compared with epithelia of piglets that had received a diet supplemented with the probiotic Enterococcus faecium NCIMB 10415. Transport properties (absorption and secretion) of the epithelia were examined by mucosal addition of glucose or L-glutamine or by serosal addition of PGE2. Electrophysiology of the epithelia was continuously recorded and the change in short circuit current (Isc) was determined. Paracellular permeability was measured by measuring the flux rates of mannitol. The increase of Isc caused by mucosal addition of glucose was, at all glucose concentrations, higher in the probiotic group compared with the control group. However, the difference (up to 100% of the control) was not significant. The increase of Isc after the mucosal addition of L-glutamine (12mmol/l) was higher in the tissues of the probiotic group but did not reach significance. Serosal PGE2 induced a significantly higher increase of Isc in tissues of the probiotic group at the age of 28 days. No consistent differences were observed in mannitol transport rates between the feeding groups. Significant age-dependent alterations of absorptive and secretory properties of the jejunal epithelium were observed; these were independent of the treatment. A probiotic supplementation seems to influence transport properties of small intestine epithelium. The increased absorption of glucose could be interpreted as a positive effect for the animal.
Bone Marrow-Derived Mesenchymal Stem Cells Prevent the Loss of Niemann-Pick Type C Mouse Purkinje Neurons by Correcting Sphingolipid Metabolism and Increasing Sphingosine-1-phosphate (2010)

Niemann-Pick type C (NP-C) disease exhibits neuronal sphingolipid storage and cerebellar Purkinje neuron (PN) loss. Although it is clear that PNs are compromised in this disorder, it remains to be defined how neuronal lipid storage causes the PN loss. Our previous studies have shown that bone marrow-derived mesenchymal stem cells (BM-MSCs) transplantation prevent PN loss in NP-C mice. The aim of the present study was therefore to examine the neuroprotective mechanism of BM-MSCs on PNs. We found that NP-C PNs exhibit abnormal sphingolipid metabolism and defective lysosomal calcium store compared to wild-type mice PNs. BM-MSCs promote the survival of NP-C PNs by correction of the altered calcium homeostasis, restoration of the sphingolipid imbalance, as evidenced by increased sphingosine-1-phosphate levels and decreased sphingosine, and ultimately, inhibition of apoptosis pathways. These effects suggest that BM-MSCs modulate sphingolipid metabolism of endogenous NP-C PNs, resulting in their survival and improved clinical outcome in mice.
Effect of DETOX as an adjuvant for melanoma vaccine (1995)

The identification of effective adjuvants is critical for tumor vaccine development. Towards this end, we examined whether the immunogenicity of a melanoma vaccine could be potentiated by DETOX™, an adjuvant consisting of monophosphoryl lipid A (MPL) and purified mycobacterial cell-wall skeleton (CWS). Nineteen patients with resected stage III melanoma were immunized with a polyvalent melanoma antigen vaccine (40 μg) admixed with DETOX™, q3 wks × 4. Seven patients received vaccine + low-dose DETOX™ (10 μg MPL + 100 μg CWS) and 12 received vaccine + high-dose DETOX™ (20 μg MPL + 200 μg CWS). A non-randomized control group of 35 patients was treated similarly with 40 μg vaccine + alum. One week after the fourth vaccine immunization, melanoma antibodies were increased over baseline in 77 (100%) patients treated with vaccine + low-dose DETOX™, 812 (67%) patients treated with vaccine + high-dose DETOX, and in 419 (21%) of vaccine + alum patients. For the entire DETOX group, the antibody response rate was 1519 (79%) compared 419 (21%) in the alum group (p < 0.001). In contrast, a strong delayed-type hypersensitivity (DTH) response (≥ 15 mm increase in DTH response over baseline) was induced in 50% of the entire DETOX™ group versus in 47% of the alum group. Median disease-free (DF) survival for the entire DETOX™ group was 17.8 months compared with 32.1 months in the alum group (p < 0.05). In conclusion, DETOX™ markedly potentiated antibody but had little effect on DTH responses to melanoma vaccine immunization. It did not appear to improve disease-free survival in comparison to alum in this non-randomized study.
Crystal structure of Cmr2 suggests a nucleotide cyclase‐related enzyme in type III CRISPR‐Cas systems (2012)

CRISPR RNAs (crRNAs) mediate sequence-specific silencing of invading viruses and plasmids in prokaryotes. The crRNA-Cmr protein complex cleaves complementary RNA. We report the crystal structure of Pyrococcus furiosus Cmr2 (Cas10), a component of this Cmr complex and the signature protein in type III CRISPR systems. The structure reveals a nucleotide cyclase domain with a set of conserved catalytic residues that associates with an unexpected deviant cyclase domain like dimeric cyclases. Additionally, two helical domains resemble the thumb domain of A-family DNA polymerase and Cmr5, respectively. Our results suggest that Cmr2 possesses novel enzymatic activity that remains to be elucidated.
Surface emitting semiconductor laser array: Its advantage and future (1989)

In this paper we review the research progress of surface emitting lasers. A two-dimensional arrayed configuration of surface emitting lasers will open up a new era of the semiconductor laser, since it provides high power capability, parallel optical processing, and vertical optical interconnection of circuit boards. We present experimental results on vertical cavity surface emitting semiconductor lasers. In order to reduce the threshold current, some improvements have been made on the laser reflector and a circular buried heterostructure has been introduced to confine injection current more effectively. The microcavity structure, which is 7 μm long and 6 μm in diameter, yields a threshold of 6 mA. A possibility of realizing an extremely low threshold current surface emitting laser device and a densely packed two-dimensional array are suggested.
Glycolipids from sponges, II. Glycosyl ceramide composition of the marine sponge Agelas longissima (1995)

Abstract A specimen of the marine sponge Agelas longissima was analyzed for glycosphingolipids. Three cerebrosides 1a ‐ 3a were isolated, each as a mixture of homologs. The structure of the new glycosphingolipid 1a was elucidated by extensive NMR studies of its peracetate derivative and chemical analysis. Compound 2a , previously isolated from another specimen of A. longissima , exhibits in the new specimen a remarkably different alkyl chain composition.
Interlaboratory Study on Differential Analysis of Protein Glycosylation by Mass Spectrometry: The ABRF Glycoprotein Research Multi-Institutional Study 2012 (2013)

One of the principal goals of glycoprotein research is to correlate glycan structure and function. Such correlation is necessary in order for one to understand the mechanisms whereby glycoprotein structure elaborates the functions of myriad proteins. The accurate comparison of glycoforms and quantification of glycosites are essential steps in this direction. Mass spectrometry has emerged as a powerful analytical technique in the field of glycoprotein characterization. Its sensitivity, high dynamic range, and mass accuracy provide both quantitative and sequence/structural information. As part of the 2012 ABRF Glycoprotein Research Group study, we explored the use of mass spectrometry and ancillary methodologies to characterize the glycoforms of two sources of human prostate specific antigen (PSA). PSA is used as a tumor marker for prostate cancer, with increasing blood levels used to distinguish between normal and cancer states. The glycans on PSA are believed to be biantennary N-linked, and it has been observed that prostate cancer tissues and cell lines contain more antennae than their benign counterparts. Thus, the ability to quantify differences in glycosylation associated with cancer has the potential to positively impact the use of PSA as a biomarker. We studied standard peptide-based proteomics/glycomics methodologies, including LC-MS/MS for peptide/glycopeptide sequencing and label-free approaches for differential quantification. We performed an interlaboratory study to determine the ability of different laboratories to correctly characterize the differences between glycoforms from two different sources using mass spectrometry methods. We used clustering analysis and ancillary statistical data treatment on the data sets submitted by participating laboratories to obtain a consensus of the glycoforms and abundances. The results demonstrate the relative strengths and weaknesses of top-down glycoproteomics, bottom-up glycoproteomics, and glycomics methods.
Risk of Cardiovascular Events in a Randomized Placebo-Controlled, Double-Blind Trial of Difluoromethylornithine plus Sulindac for the Prevention of Sporadic Colorectal Adenomas (2009)

Nonsteroidal anti-inflammatory drugs (NSAID) have been associated with adverse cardiovascular (CV) outcomes in cancer prevention and other clinical trials. A recent meta-analysis suggested that baseline CV risk is associated with NSAID-associated adverse CV events. We evaluated the effect of baseline CV risk on adverse CV events in a phase III trial of difluoromethylornithine (DFMO) plus the NSAID sulindac versus placebo in preventing colorectal adenomas. Trial data were analyzed to determine baseline CV risk. CV toxicity outcomes were then assessed overall and excluding high CV-risk patients. Baseline CV risk scores were evenly distributed within our overall trial population of 184 placebo (low risk, 27%; moderate risk, 34%; high risk, 39%) and 191 DFMO/sulindac (low risk, 30%; moderate risk, 29%; high risk, 41%) patients. In patients with a high baseline CV risk, the number of adverse CV events was greater among DFMO/sulindac (n = 9) than among placebo (n = 3) patients. Excluding patients with a high baseline CV risk, the numbers of adverse CV events were similar in the DFMO/sulindac (n = 7) and placebo (n = 6) arms. A high CV risk score at baseline may confer an increased risk of CV events associated with treatment with DFMO/sulindac, and a low baseline score may not increase this risk. These results have implications for future NSAID-based cancer prevention clinical trials.
Optical properties and mechanofluorochromism of new BODIPY dyes based on the pyridine–pyrimidine hybrid structure (2017)

A new family of BODIPY dyes (PPB1-4) based on the pyridine-pyrimidine hybrid structure has been synthesized. These dyes show high cyan fluorescence in hexane with quantum yields (Φ<sub>f</sub>) ranging from 0.33 to 0.90. Interestingly, moderate fluorescence of PPB1-4 is observed in the solid state (Φ<sub>f</sub>, 0.11-0.26). X-ray structure analysis demonstrates that H-aggregation should be responsible for the red-shifted and quenched emission in the solid state. Moreover, PPB1-4 show high contrast and reversible mechanochromic fluorescence based on the proposed mechanism of mechanical stimuli triggered dimer dissolution and formation. In addition, rewritable mechanochromic fluorescence recording media fabricated with PPB4 have been successfully achieved.
Extracellular matrix remodelling: the role of matrix metalloproteinases (2003)

Matrix metalloproteinases (MMPs) are a growing family of metalloendopeptidases that cleave the protein components of the extracellular matrix and thereby play a central role in tissue remodelling. For many years following their discovery, MMPs were believed to function primarily as regulators of ECM composition and to facilitate cell migration simply by removing barriers such as collagen. It is becoming increasingly clear, however, that MMPs are implicated in the functional regulation of a host of non-ECM molecules that include growth factors and their receptors, cytokines and chemokines, adhesion receptors and cell surface proteoglycans, and a variety of enzymes. MMPs therefore play an important role in the control of cellular interactions with and response to their environment in conditions that promote tissue turnover, be they physiological, such as normal development, or pathological, such as inflammation and cancer. This review summarizes some of the recent discoveries that have shed new light on the role of MMPs in physiology and disease.
Reduced Cardiotoxicity of Doxorubicin Delivered on a Weekly Schedule (1983)

Endomyocardial biopsy was done 119 times in 98 patients receiving doxorubicin therapy once every 3 weeks and 41 times in 27 patients receiving doxorubicin therapy weekly. Factors contributing to the degree of anthracycline-induced endomyocardial injury were evaluated. Neither age, sex, type of malignancy, concomitant use of other chemotherapeutic agents including cyclophosphamide, nor history of cardiac disease or hypertension influenced the extent of the endomyocardial injury. The dose of doxorubicin (p = 0.0001) and the schedule (weekly versus 3 weekly) (p = 0.0020) independently predicted the degree of endomyocardial damage in multivariate analyses. Previous cardiac irradiation had borderline significance (p = 0.074) in predicting endomyocardial damage in this analysis. Doxorubicin therapy administered on a weekly schedule is associated with less anthracycline-induced cardiac damage than is doxorubicin therapy delivered in the conventional, 3-weekly schedule.
Osteoarthritis and obesity in the general population. A relationship calling for an explanation. (1988)

The association between obesity and osteoarthritis (OA), was studied by analysis of data from an epidemiologic survey of a population of 1071 men and 1097 women in The Netherlands. A total of 20 joints and groups of joints were investigated. OA was clearly associated with obesity in the most frequently affected joints, weight bearing as well as nonweight bearing. This association was less strong for severely affected joints than for mildly affected joints. This pattern was neither compatible with a generalized (metabolic) abnormality nor with weight induced mechanical "wear-and-tear". OA is a heterogeneous condition and some site specific associations with obesity are strong, thus there is scope for prevention by weight reduction for some sites.
Increasing Leakoff Pressure With New Class of Drilling Fluid (2002)

Abstract A new class of drilling fluid has been developed and proved to be extremely effective in increasing the leakoff pressure in permeable formations. A simple laboratory test is described to assess the limits of potential increase of leakoff pressure in the field. This paper describes some fundamental issues regarding fracture and leakoff pressures for well construction purposes and then shows how the increase in leakoff pressure can be achieved with the use of this new drilling fluid. Some case histories are presented in which the fluid has proven to increase the leakoff pressure effectively, and a comparison is made with drilling fluids traditionally used, highlighting the limitations of the current fluids to effectively deliver what the industry really needs. Several applications are presented in which an increase in leakoff pressure can hugely reduce the costs and risks of the wells.
Searching for More Effective Agents and Conditions for the RAFT Polymerization of MMA:  Influence of Dithioester Substituents, Solvent, and Temperature (2005)

A series of tertiary dithiobenzoates differently substituted on the phenyl group (Z) were synthesized in order to investigate the RAFT-mediated polymerization of MMA. The chain-transfer agent 2-cyanoprop-2-yl dithiobenzoate, although an excellent RAFT agent for polymerization of MMA, does not yield a very narrow polydispersed polymer at low conversion. The introduction of electron-withdrawing substituents on the dithiobenzoate aromatic ring improves the activity of the chain-transfer agent narrowing the molecular weight distribution, especially in the first 2 h of the process; conversely, electron-donating substituents deteriorate the performance of the process in the early stages. Substituents on the dithiobenzoate that, for reasons of steric hindrance reduce the conjugation of the phenyl with the CS double bond of the dithiogroup, diminish the effectiveness of the chain-transfer agent. The nature of the leaving group (R) also has a strong influence on the process: the substitution of 2-cyanoprop-2-yl with the bulkier 2-cyano-4-methylpent-2-yl as leaving group improves remarkably the MMA polymerization, especially in the early stages. The solvent effect on MMA RAFT polymerization using benzene, acetonitrile, and DMF was also investigated. The lower propagation rate constant of MMA in benzene gives rise to reduced rates of polymerization but narrower polydispersities of the polymer, especially at low conversions. The RAFT polymerizations of MMA were carried out at 60 and 90 °C to assess the temperature dependence of the process. The higher temperature increases both the rate of polymerization and the transfer constant of the RAFT agent, resulting in lower polydispersities at a given conversion. Ab initio calculations confirmed the observed experimental results.
Principles of magnetic resonance imaging : a signal processing perspective (2000)

Since its inception in 1971, magnetic resonance imaging (MRI) has developed into a premier tool for anatomical and functional imaging. This textbook provides a clear and comprehensive treatment of MR image formation principles from a signal processing perspective. Coverage includes: mathematical fundamentals; signal generation and detection principles; signal characteristics; signal localization principles; image reconstruction techniques; image contrast mechanisms; image resolution, noise and artifacts; fast-scan imaging; constrained reconstruction; and spatial information encoding. The text contains comprehensive examples and homework problems. It should give students of biomedical engineering, biophysics, chemistry, electrical engineering and radiology a systematic, in-depth understanding of MRI principles.
Recent advances in three‐dimensional multicellular spheroid culture for biomedical research (2008)

Many types of mammalian cells can aggregate and differentiate into 3-D multicellular spheroids when cultured in suspension or a nonadhesive environment. Compared to conventional monolayer cultures, multicellular spheroids resemble real tissues better in terms of structural and functional properties. Multicellular spheroids formed by transformed cells are widely used as avascular tumor models for metastasis and invasion research and for therapeutic screening. Many primary or progenitor cells on the other hand, show significantly enhanced viability and functional performance when grown as spheroids. Multicellular spheroids in this aspect are ideal building units for tissue reconstruction. Here we review the current understanding of multicellular spheroid formation mechanisms, their biomedical applications, and recent advances in spheroid culture, manipulation, and analysis techniques.