gebhart/patrepeval huggingface dataset:
Nucleotide sequence of cloned cDNA coding for preproricin (1985)

The primary structure of a precursor protein that contains the toxic (A) and galactose-binding (B) chains of the castor bean lectin, ricin, has been deduced from the nucleotide sequence of cloned DNA complementary to preproricin mRNA. A cDNA library was constructed using maturing castor bean endosperm poly(A)-rich RNA enriched for lectin precursor mRNA by size fractionation. Clones containing lectin mRNA sequences were isolated by hybridization using as a probe a mixture of synthetic oligonucleotides representing all possible sequences for a peptide of the ricin B chain. The entire coding sequence of preproricin was deduced from two overlapping cDNA clones having inserts of 1614 and 1049 base pairs. The coding region (1695 base pairs) consists of a 24-amino-acid N-terminal signal sequence (molecular mass 2836 Da) preceding the A chain 267 amino acids, molecular mass 29 399 Da), which is joined to the B chain (262 amino acids, molecular mass 28 517) by a 12-amino-acid linking region (molecular mass 1385 Da).
Targeted destruction of androgen‐sensitive and ‐insensitive prostate cancer cells and xenografts through luteinizing hormone receptors (2001)

Background We have prepared a conjugate of a lytic peptide (hecate) and a 15-amino acid segment of the β-chain of LH to test the concept that this conjugate will target cancer cells expressing LH receptors. Methods Hecate-βLH was added in vitro to cultures of Chinese hamster ovary (CHO) cells with and without LH receptors and to prostate cancer cells in the presence or absence of steroids, follicle-stimulating hormone (FSH), epidermal growth factor (EGF), or βLH. PC-3 xenografts were established in male athymic nude mice and treated once a week for 3 weeks with hecate-βLH via the lateral tail vein. Results The conjugate showed concentration-dependent toxicity for the following prostate cancer cell lines: BRF 41 T β DU145 β PC-3 β LNCaP, according to their LH receptor capacities. Steroid removal reduced sensitivity to the drug in a reversible manner. Hecate-βLH reduced the tumor burden in the nude mice from 60 to 12.5 mg/g body weight. Conclusions We conclude that the hecate-βLH conjugate selectively kills androgen-dependent and-independent prostate cancer cells both in vivo and in vitro; its toxicity depends on the number of LH receptor sites present. Prostate 46:116–125, 2001. © 2001 Wiley-Liss, Inc.
Purification, Cloning and Characterization of Variant LukE‐LukD with Strong Leukocidal Activity of Staphylococcal Bi‐Component Leukotoxin Family (2003)

Staphylococcus aureus produces bi-component leukotoxins composed of non-associated soluble proteins, S and F. Neither S nor F component alone is cytotoxic, but components together are active. These include Panton-Valentine leukocidin (PVL), gamma-hemolysin, LukE-LukD and others. Purification of leukotoxin from Staphylococcus aureus V8 strain (ATCC 27733) which does not have PVL genes, identified an F component with 100% identical to that of PVL in the first twenty-five N-terminal amino acids. Molecular cloning of this toxin obtained 2,595 nucleotides sequences containing two novel open reading frames for S and F. Deduced amino acid sequences of the S and F were respectively 91 and 94% identical to those of LukE and LukD. These were named variant of LukE-LukD (LukEv-LukDv). The activity of the recombinant LukEv-LukDv to rabbit leukocytes was similar to that of recombinant PVL. LukEv-LukDv was hemolytic to rabbit red blood cells although the activity was only 8% of gamma-hemolysin, but PVL was not. These activities were quite different from the LukE-LukD which was reported no hemolytic and poorly cytotoxic to leukocytes compared to PVL. The lukEv-IukDv was found in 87% of clinical isolates of Staphylococcus aureus but lukE-lukD was not detected. These data demonstrate the existence of variant LukE-LukD in V8 strain (ATCC 27733).
Considerations for a new generation of mobile multimedia communication systems (2000)

The simultaneous evolution of mobile communications and multimedia applications points toward a future where both technologies play a significant role in shaping mobile multimedia communication. However, the destiny of mobile communications and, to a great extent, of sophisticated mobile multimedia, heavily depends on the success of the emerging third generation of mobile communication systems.
Inherently phase-stable coherent two-dimensional spectroscopy using only conventional optics (2008)

We introduce an inherently phase-stable setup for coherent two-dimensional femtosecond spectroscopy in noncollinear box geometry using only conventional beam splitters, mirrors, and delay stages. Avoiding diffractive optics, pulse shapers, and active phase-locking loops, our spectroscopy setup is simple, robust, and works for ultrabroad bandwidths in all spectral regimes (infrared, visible, and ultraviolet).
Detection of myeloma cells in the peripheral blood by flow cytometry (1996)

Bone marrow plasma cells (PC) from patients with multiple myeloma (MM) express monoclonal cytoplasmic immunoglobulin (clg) light chain, strongly express CD38, and usually lack or dimly express CD45. The detection of malignant plasma cells in the peripheral blood (PB) by immunofluorescence microscopy (IM) distinguishes patients with active MM from those with stable disease. The aim of this study was to learn whether two-color (CD38 and CD45) flow cytometry (FC) on whole blood specimens (WBFC) and three-color FC (CD38, CD45, and anti-kappa or lambda clg) on mononuclear cells could identify circulating PC as well as the standard, more labor intensive IM technique. Split-samples of PB from 73 patients with plasma cell proliferative disorders were examined by both techniques. WBFC detected CD38+ CD45- cells in 94% (33/35) of patients with circulating monoclonal PC detected by IM and three-color FC detected monoclonal CD38+ CD45- cells in 77% (27/35) of these cases. The absolute number of monoclonal PC detected by IM was compared to the FC methods and the Spearman rank correlations were 0.77 with WBFC and 0.80 with three-color FC. This study indicates that WBFC, using antibodies to CD38 and CD45, offers a practical and reliable method to detect and quantify circulating malignant PC in patients with MM.
Genetic Basis for Sleep Regulation and Sleep Disorders (2006)

Sleep disorders arise by an interaction between the environment and the genetic makeup of the individual but the relative contribution of nature and nurture varies with diseases. At one extreme are the disorders with simple Mendelian patterns of inheritance such as familial advanced sleep phase syndrome, and at the other extreme are diseases such as insomnia, which can be associated with a multitude of medical and psychiatric conditions. In this article, we review data on the relative contribution of genetic and environmental factors in the pathogenesis of various sleep disorders. The understanding of many of these disorders has been advanced by the study of sleep and circadian rhythms in model laboratory organisms. We summarize this model system research and how it relates to human sleep disorders. The current challenge in this field is the identification of susceptibility genetic loci for complex diseases such as obstructive sleep apnea. We anticipate such identification will increase our ability to assess risk for disease before symptom onset and by doing so will shift the focus from treatment to prevention of disease.
Molecular recognition : chemical and biochemical problems : the proceedings of an international symposium, University of Exeter, April 1989 (1989)

Molecular recognition and drug design, S.F.Campbell molecular recognition by antibiotics of the Vancomycin group - dimerization of the antibiotics, D.H.Williams and J.P.Waltho NMR approaches to molecular recognition - dihydrofolate reductase, G.C.K.Roberts crystallographic comparison of penicillin-recognizing enzymes, J.R.Knox and J.A.Kelly studies in the beta-lactam area, D.W.Young the interaction of antiviral agents with human rhinovirus-14 capsid protein, G.D.Diana et al protein crystallography, computer graphics and sleeping sickness, W.G.J.Hol et al a conformational approach to the discovery of potent selective neurokinin receptor antagonists, J.R.Brown et al the discovery and design of substrate-based proteinase inhibitors - problems and lessons from the development of renin inhibitors as potential hypotensive drugs, R.J.Arrowsmith et al recent developments in the solid phase synthesis of peptide immunogens, T.Johnson and R.C.Sheppard probing the mechanism of methylaspartase, N.P.Botting and D.Gani structure and dynamics of ligand binding to enzyme receptors, D.J.Osguthorpe et al protein engineering - achievements and prospects, D.M.Blow a program to facilitate the structure-derived design of biologically active molecules, P.A.Bartlett et al host-guest complexation in organic solvents - experimental and theoretical results, W.C.Still et al stereoelectronic effects in molecular recognition, J.Rebek the basis for molecular recognition, P.Kollman design of artificial receptors for biochemically interesting substrates, A.D.Hamilton et al structure-directed synthesis of unnatural products, F.H.Kohnke et al the physical-organic chemistry of surfaces, and its relevance to molecular recognition, G.M.Whitesides and H.Biebuyck.
Phase 1 Study of Aflibercept Administered Subcutaneously to Patients with Advanced Solid Tumors (2009)

Subcutaneous aflibercept was well tolerated and had manageable side effects. Its favorable pharmacokinetic profile and potential antitumor activity warrants further evaluation.
On the impossibility of approximate obfuscation and applications to resettable cryptography (2013)

The traditional notion of program obfuscation requires that an obfuscation ~Prog of a program Prog computes the exact same function as Prog, but beyond that, the code of ~Prog should not leak any information about Prog. This strong notion of virtual black-box security was shown by Barak et al. (CRYPTO 2001) to be impossible to achieve, for certain unobfuscatable function families. The same work raised the question of approximate obfuscation, where the obfuscated ~Prog is only required to approximate Prog; that is, ~Prog only agrees with Prog with high enough probability on some input distribution.
Abstract 5565: Circulating tumor cells in the peripheral blood and cerebrospinal fluid of patients with central nervous system metastases (2012)

Abstract The enumeration of circulating tumor cells in peripheral blood is a validated method of monitoring disease status in patients with epithelial malignancies involving the breast, colon, prostate, or lung. As cancer therapies improve and aim to decrease metastatic burden, the central nervous system (CNS) is emerging as an important sanctuary site for metastasis. Current surveillance and clinical markers of metastatic disease progression involving the CNS are lacking adequate sensitivity, reproducibility, and specificity. One of these clinical markers is cerebrospinal fluid (CSF) cytology, which lacks clarity, is insensitive, requires high sample volumes and is subject to interpretation bias by the pathologist. To overcome these limitations, we previously adapted the Cellsearch system (Veridex) to isolate and enumerate tumor cells in the CSF of breast or non-small cell lung cancer patients with CNS metastases. We recently reported that the number of cells in the CSF directly correlated with the subject's clinical condition and Karnofsky performance status (KPS) in metastatic breast cancer. Furthermore, imaging of the neuroaxis in these patients revealed disease presence, however, was not indicative of disease burden. A sharp decline in the number of CSF tumor cells (CSFTCs) was universally noted after the onset and maintenance of such ventricular intrathecal chemotherapy. We have continued to follow these patients and have expanded our patient population to include non-small cell lung cancer. This includes a patient that we have followed from a baseline CSFTC count of &amp;gt;10,000 to zero over the course of intrathecal treatment, which as been accompanied by drastically reduced disease by and complete resolution of clinical symptoms. We have also begun to perform concomitant CTC enumeration from peripheral blood in conjunction with CSFTC analysis. Interestingly, while there appears to be no strong correlation between the two subpopulations, tumor cells seemed to be compartmentalized to either the blood or the CSF. Together, the current data indicates that CSFTCs may serve as viable markers for diagnosis and prognostication in the setting of CNS metastases. This novel method of isolating CSFTCs provides a semi-automated platform that greatly increases sensitivity, accuracy and reliability over the standard CSF cytology. Furthermore, this platform enables studies to elucidate the significance and biology of this unique subpopulation of tumor cells, including its relationship with CTCs. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5565. doi:1538-7445.AM2012-5565
Body-on-a-chip simulation with gastrointestinal tract and liver tissues suggests that ingested nanoparticles have the potential to cause liver injury (2014)

The use of nanoparticles in medical applications is highly anticipated, and at the same time little is known about how these nanoparticles affect human tissues. Here we have simulated the oral uptake of 50 nm carboxylated polystyrene nanoparticles with a microscale body-on-a-chip system (also referred to as multi-tissue microphysiological system or micro Cell Culture Analog). Using the 'GI tract-liver-other tissues' system allowed us to observe compounding effects and detect liver tissue injury at lower nanoparticle concentrations than was expected from experiments with single tissues. To construct this system, we combined in vitro models of the human intestinal epithelium, represented by a co-culture of enterocytes (Caco-2) and mucin-producing cells (TH29-MTX), and the liver, represented by HepG2/C3A cells, within one microfluidic device. The device also contained chambers that together represented the liquid portions of all other organs of the human body. Measuring the transport of 50 nm carboxylated polystyrene nanoparticles across the Caco-2/HT29-MTX co-culture, we found that this multi-cell layer presents an effective barrier to 90.5 ± 2.9% of the nanoparticles. Further, our simulation suggests that a larger fraction of the 9.5 ± 2.9% nanoparticles that travelled across the Caco-2/HT29-MTX cell layer were not large nanoparticle aggregates, but primarily single nanoparticles and small aggregates. After crossing the GI tract epithelium, nanoparticles that were administered in high doses estimated in terms of possible daily human consumption (240 and 480 × 10(11) nanoparticles mL(-1)) induced the release of aspartate aminotransferase (AST), an intracellular enzyme of the liver that indicates liver cell injury. Our results indicate that body-on-a-chip devices are highly relevant in vitro models for evaluating nanoparticle interactions with human tissues.
Type 1 diabetes (poster) (2012)

info:eu-repo/semantics/published
Location of the Pteroylpolyglutamate-binding Site on Rabbit Cytosolic Serine Hydroxymethyltransferase (2003)

Serine hydroxymethyltransferase (SHMT; EC 2.1.2.1) catalyzes the reversible interconversion of serine and glycine with transfer of the serine side chain one-carbon group to tetrahydropteroylglutamate (H(4)PteGlu), and also the conversion of 5,10-methenyl-H(4)PteGlu to 5-formyl-H(4)PteGlu. In the cell, H(4)PteGlu carries a poly-gamma-glutamyl tail of at least 3 glutamyl residues that is required for physiological activity. This study combines solution binding and mutagenesis studies with crystallographic structure determination to identify the extended binding site for tetrahydropteroylpolyglutamate on rabbit cytosolic SHMT. Equilibrium binding and kinetic measurements of H(4)PteGlu(3) and H(4)PteGlu(5) with wild-type and Lys --> Gln or Glu site mutant homotetrameric rabbit cytosolic SHMTs identified lysine residues that contribute to the binding of the polyglutamate tail. The crystal structure of the enzyme in complex with 5-formyl-H(4)PteGlu(3) confirms the solution data and indicates that the conformation of the pteridine ring and its interactions with the enzyme differ slightly from those observed in complexes of the monoglutamate cofactor. The polyglutamate chain, which does not contribute to catalysis, exists in multiple conformations in each of the two occupied binding sites and appears to be bound by the electrostatic field created by the cationic residues, with only limited interactions with specific individual residues.
A Valve-less Planar Pump In Silicon (2005)

A planar double chamber pump fabricated in silicon anodically bonded to glass and based on the diffuser/nozzle pump principle is presented. The diffuser/nozzle elements have a depth of 24 - 48 /spl mu/m and a neck width of 88 - 104/spl mu/m. The pump chamber diameter is 6 mm. Pump cavities and diffuser/nozzle elements are etched with an isotropic HNA-etch in the silicon. Pumps with three different diffuser lengths are compared reaching a maximum pump capacity of 230 /spl mu/min and a maximum pump pressure of 1.7 in H20 at a resonance frequency of 1318 Hz for methanol.
Structure of Minimal Non-Commutative Zero-Insertive Rings (1998)

To date, the decellularized scaffold has been widely explored as a source of biological scaffolds for regenerative medicine. However, the acellular matrix derived from natural tissues and organs has a lot of defects, including the limited amount of autogenous tissue and surgical complication such as risk of blood loss, wound infection, pain, shock, and functional damage in the donor part of the body. In this study, we prepared acellular matrix using adipose-derived stem cell (ADSC) sheets and evaluate the cellular compatibility and immunoreactivity. The ADSC sheets were fabricated and subsequently decellularized using repeated freeze-thaw, Triton X-100 and SDS decellularization. Oral mucosal epithelial cells were seeded onto the decellularized ADSC sheets to evaluate the cell replantation ability, and silk fibroin was used as the control. Then, acellular matrix was transplanted onto subcutaneous tissue for 1 week or 3 weeks; H&E staining and immunohistochemical analysis of CD68 expression and quantitative real-time PCR (qPCR) were performed to evaluate the immunogenicity and biocompatibility. The ADSC sheet-derived ECM scaffolds preserved the three-dimensional architecture of ECM and retained the cytokines by Triton X-100 decellularization protocols. Compared with silk fibroin in vitro, the oral mucosal epithelial cells survived better on the decellularized ADSC sheets with an intact and consecutive epidermal cellular layer. Compared with porcine small intestinal submucosa (SIS) in vivo, the homogeneous decellularized ADSC sheets had less monocyte-macrophage infiltrating in vivo implantation. During 3 weeks after transplantation, the mRNA expression of cytokines, such as IL-4/IL-10, was obviously higher in decellularized ADSC sheets than that of porcine SIS. A Triton X-100 method can achieve effective cell removal, retain major ECM components, and preserve the ultrastructure of ADSC sheets. The decellularized ADSC sheets possess good recellularization capacity and excellent biocompatibility. This study demonstrated the potential suitability of utilizing acellular matrix from ADSC sheets for soft tissue regeneration and repair.
Effects of tumor necrosis factor-related apoptosis-inducing ligand alone and in combination with chemotherapeutic agents on patients' colon tumors grown in SCID mice. (2002)

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) has been reported to induce apoptosis in a variety of malignant cell lines, but it shows little or no toxicity in most normal cells. We examined the response of three human colon tumors to TRAIL alone and in combination with chemotherapy, using SCID mice engrafted with intact patient surgical specimens. These tumors, taken from fresh surgical specimens, contained the heterogeneous tumor cell population characteristic of patient tumors and showed differential sensitivity to TRAIL alone. We also investigated the effect of TRAIL in combination with chemotherapy, using one tumor that showed moderate sensitivity to TRAIL alone. Combining TRAIL with either 5-fluorouracil (5-FU) or CPT-11 (irinotecan hydrochloride) produced a greatly enhanced antitumor effect over that of either agent alone, with 50% of the animals achieving complete tumor regression with a combination of TRAIL and CPT-11. By histological analysis, tumors treated with TRAIL plus either 5-FU or CPT-11 were seen to consist mainly of connective tissue and fibrotic areas with only a few scattered tumor cells encapsulated in the connective tissue. Several markers were assessed to investigate the basis for the observed therapeutic effect, and significant induction of apoptosis was observed in tumors treated with curative combinations. Cytoplasmic and cell surface expression of the TRAIL receptors DR4 and DR5 was observed in this patient's tumor by immunohistochemistry. Tumors treated with CPT-11 showed increased membrane expression of DR5, suggesting that CPT-11 may increase sensitivity to TRAIL by up-regulation of DR5. These results obtained in a relevant preclinical model support the idea that the use of TRAIL in combination with either 5-FU or CPT-11 may be an effective strategy in controlling human colon cancer.
Magnetic Resonance and Ultrasound Contrast Media (1990)

From the Pittsburgh NMR Institute, Pittsburgh, Pennsylvania. Wolf G. Magnetic resonance and ultrasound contrast media. Invest Radiol 1990;25:S12-S13.
Glycomyces sambucus sp. nov., an endophytic actinomycete isolated from the stem of Sambucus adnata Wall (2007)

An actinomycete, designated strain E71(T), was isolated from the stem of Sambucus adnata Wall, a Chinese medicinal plant, and subjected to a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence showed that the organism was a member of the genus Glycomyces, and formed a distinct phyletic line distantly related to recognized species of the genus Glycomyces. Morphological and chemotaxonomic data supported the affiliation of strain E71(T) to the genus Glycomyces. A number of physiological properties and a unique menaquinone profile allowed differentiation of the strain from related Glycomyces species. It is therefore proposed that strain E71(T) represents a novel species of the genus Glycomyces, for which the name Glycomyces sambucus sp. nov. is proposed. The type strain is E71(T) (=CGMCC 4.3147(T)=DSM 45047(T)).
Passive pulse shaping by spectral narrowing of picosecond pulses (1981)

Synchronizing a picosecond laser pulse with a nanosecond one would be useful in laser fusion research. Amplitude modulation of a picosecond spectrum makes this possible; this passive technique has already been studied by C. Froehly and demonstrated by B. Colombeau. It is shown here that this kind of pulse shaper is usable on a power laser chain. Starting from a 40-psec pulse, several pulse shapes with durations up to 640- and 40-psec rise time have been obtained at different power levels. Efficiency and signal to noise ratio of the system have been studied. The diffraction-limited beam has been amplified in a power laser chain.