gebhart/patrepeval huggingface dataset:
Sample Preparation Methods for Mass Spectrometric Peptide Mapping Directly from 2-DE Gels (2003)

Polyacrylamide gel electrophoresis (PAGE) is probably the most general and widespread protein separation technique. This simple method is used in almost every molecular biology and biochemistry laboratory to monitor protein experiments, including consecutive stages of protein purification. PAGE may even be the final step of a purification protocol. Over the last decade, two-dimensional gel electrophoresis (2-D-PAGE) (1) has been developed, and applied to the separation of crude protein mixtures from organelles, tissues, and whole organisms (2).
Influenza: Propagation, Quantification, and Storage (2006)

Influenza viruses are negative-sense, single-stranded, enveloped RNA viruses belonging to the family Orthomyxoviridae. Three types exist, influenza A, B, and C. All infect humans, but only A and B are major human pathogens. Influenza type A viruses are divided into subtypes based on genetic and antigenic differences in the two surface spike proteins, hemagglutinin (HA) and neuraminidase (NA). The appropriate cell lines to be used for isolation of influenza A or B viruses depend on the clinical information and the host of origin. MDCK cells are the preferred cell line for isolation of human influenza viruses from clinical specimens.
A double‐blind, placebo‐controlled, randomised, clinical study on the effectiveness of collagen peptide on osteoarthritis (2014)

The study demonstrated that collagen peptides are potential therapeutic agents as nutritional supplements for the management of osteoarthritis and maintenance of joint health.
An evidence-based assessment of treatments for cellulite. (2008)

Cellulite, a skin surface change that is nearly ubiquitous in women, is a condition that remains elusive to treatment. In fact, no treatment is completely successful as none are more than mildly and temporarily effective. Despite the lack of evidence to support efficacy, treatment options continue to proliferate. This article will briefly review the currently available data about cellulite treatments including noninvasive devices such as massage, radiofrequency, and laser and light-based treatments; invasive modalities including liposuction, mesotherapy, and subcision; and other treatments including topical creams and carboxy therapy.
A controlled clinical study of metopimazine and perphenazine in treatment of radiation nausea and vomiting (1969)

A total of 252 outpatients receiving radiotherapy were started on a single‐blind placebo medication "for prevention of nausea and vomiting." Those who developed nausea or vomiting participated in a double‐blind study to compare the relative antiemetic efficacy of metopimazine at two dose levels (2.5 mg. and 5.0 mg.) with perphenazine at two dose levels (4.0 mg. and 8.0 mg.) and with inert placebo. The results were analyzed in a variety of ways. The analysis of paired responses in the same patients showed that metopimazine in doses of 10 to 20 mg. per day and perphenazine in doses of 8 to 32 mg. per day were effective antinauseant‐antiemetics significantly super or to placebo but not significantly different from one another. There were no significant differences in side effects among the test medications except for drowsiness, which occurred with a significantly higher frequency in patients receiving the higher dose of perphenazine. A method of population selection was proposed. A preliminary screening of patients by radiotherapists would el:minate from studies of antiemetics a large number of patients unlikely to develop nausea or vomiting after radiotherapy.
The use of recombinant–activated factor VII in von Willebrand disease: a case series (2006)

Spontaneous and surgery-associated bleeding in patients with von Willebrand disease (vWD) cannot always be controlled with desmopressin or replacement therapy. This paper presents results on the use of recombinant-activated factor VII (rFVIIa) in patients with vWD included in the internet registry Haemostasis.com. Twenty-eight reports on the use of rFVIIa in vWD were identified from the database and included in this analysis. The bleeding episodes were classified as mild (n = 7), moderate (n = 16), or severe (n = 2), and were unspecified in three cases. The median dose of rFVIIa administered was 94 microg/kg body weight (40-127.3 microg/kg). Bleeding stopped in 23 of 27 evaluable patients (85%) and markedly decreased in three patients; the total response rate was 96% (26/27 patients). Response did not correlate with the type of vWD, the site or severity of the initial bleed, or the rFVIIa dose. Other replacement therapies were infrequently used, and their use was similar in the 24 h before and after rFVIIa administration. Eighteen patients also received antifibrinolytic treatment, but its impact on response was not recorded. Only one adverse event (mild fever) was observed. These cases suggest a role for rFVIIa as a safe and effective therapy for vWD.
An Alternative Method to Facilitate cDNA Cloning for Expression Studies in Mammalian Cells by Introducing Positive Blue White Selection in Vaccinia Topoisomerase I-Mediated Recombination (2015)

One of the most basic techniques in biomedical research is cDNA cloning for expression studies in mammalian cells. Vaccinia topoisomerase I-mediated cloning (TOPO cloning by Invitrogen) allows fast and efficient recombination of PCR-amplified DNAs. Among TOPO vectors, a pcDNA3.1 directional cloning vector is particularly convenient, since it can be used for expression analysis immediately after cloning. However, I found that the cloning efficiency was reduced when RT-PCR products were used as inserts (about one-quarter). Since TOPO vectors accept any PCR products, contaminating fragments in the insert DNA create negative clones. Therefore, I designed a new mammalian expression vector enabling positive blue white selection in Vaccinia topoisomerase I-mediated cloning. The method utilized a short nontoxic LacZα peptide as a linker for GFP fusion. When cDNAs were properly inserted into the vector, minimal expression of the fusion proteins in E. coli (harboring lacZΔM15) resulted in formation of blue colonies on X-gal plates. This method improved both cloning efficiency (75%) and directional cloning (99%) by distinguishing some of the negative clones having non-cording sequences, since these inserts often disturbed translation of lacZα. Recombinant plasmids were directly applied to expression studies using GFP as a reporter. Utilization of the P2A peptide allowed for separate expression of GFP. In addition, the preparation of Vaccinia topoisomerase I-linked vectors was streamlined, which consisted of successive enzymatic reactions with a single precipitation step, completing in 3 hr. The arrangement of unique restriction sites enabled further modification of vector components for specific applications. This system provides an alternative method for cDNA cloning and expression in mammalian cells.
Plasmonics of 3-D Nanoshell Dimers Using Multipole Expansion and Finite Element Method (2009)

The spatial and spectral responses of the plasmonic fields induced in the gap of 3-D nanoshell dimers of gold and silver are comprehensively investigated and compared via theory and simulation using the multipole expansion (ME) and the finite element method (FEM) in COMSOL, respectively. The E-field in the dimer gap was evaluated and compared as a function of shell thickness, interparticle distance, and size. The E-field increased with decreasing shell thickness, decreasing interparticle distance, and increasing size, with the error between the two methods ranging from 1 to 10%, depending on the specific combination of these three variables. This error increases several fold with increasing dimer size, as the quasi-static approximation breaks down. A consistent overestimation of the plasmon's fwhm and red shifting of the plasmon peak occurs with FEM, relative to ME, and it increases with decreasing shell thickness and interparticle distance. The size effect that arises from surface scattering of electrons is addressed and shown to be especially prominent for thin shells, for which significant damping, broadening, and shifting of the plasmon band is observed; the size effect also affects large nanoshell dimers, depending on their relative shell thickness, but to a lesser extent. This study demonstrates that COMSOL is a promising simulation environment to quantitatively investigate nanoscale electromagnetics for the modeling and designing of surface-enhanced Raman scattering (SERS) substrates.
Levels of vasodilators (SP, CGRP) and vasoconstrictor (NPY) peptides in early human burns (2001)

An intact nociceptor system of primary afferent sensory nerves is important for the initiation of the inflammatory process and successful tissue repair. Dysfunction of this system could be a contributing factor for delayed wound healing in humans. We examined the levels of vasodilators [substance P (SP), calcitonin gene-related peptide (CGRP)] and a vasoconstrictor peptide [neuropeptide Y (NPY)] in the peripheral blood samples of patients with burns covering from 20 to 75% of body surface area. Thirteen patient samples were obtained immediately on admission (OA), which was within 12 h of the thermal injury, and 24 h post-admission (PA). Enzyme immunoassay techniques were used for the measurement of the neuropeptides. In addition, an inflammatory marker, tumour necrosis factor-alpha (TNF-alpha), and a myofibrillar protein, creatine kinase (CK), were examined and compared with levels in 13 control subjects. CGRP was high OA and the levels were maintained PA (P < 0.05). SP was also significantly high at both sampling times (P < 0.05). Although TNF-alpha and NPY were somewhat higher in the patients' samples than in the control samples, these levels were not statistically significant (P = NS). CK was higher OA (P < 0.01) than PA (P < 0.04), compared to controls. Plasma levels of SP and CGRP increased significantly in patients with thermal injuries. These peptides may yet be another group of neuromodulators playing a significant role in immune, pain, inflammatory and wound healing in burns.
Induction plasmas at low frequencies (1971)

The possibility of generating thermal electrodeless plasmas at frequencies below the rf range through the use of magnetic materials has been investigated, both analytically and experimentally. Existing minimum frequency and voltage criteria for the maintenance of quasisteady, tube filling a.c. arcs were combined with the induction law to yield design criteria for a transformer which consists of a conventional iron core and primary but has the secondary replaced by a torus-shaped vessel containing a single plasma turn. The idea has been tested, at a frequency of 9600 Hz, on a small model with an iron core of 100 cm cross section. Glow and arc discharges at pressures up to 600 torr have been generated in argon. Applicability to operation at 60 Hz is discussed.
Cancer stem cell characteristics in retinoblastoma. (2005)

Mouse and human retinoblastoma tumor cells contain a small subpopulation of cells that exhibit a cancer stem cell-like phenotype. Especially significant is the expression of ABCG2 in mouse and human tumor cells, a calcium-sensitive cell surface protein that not only acts to exclude Hoechst dye, but also confers resistance to over 20 different chemotherapeutic agents. These findings point to a heterogeneity in retinoblastoma tumors that may have significant impact on future treatment strategies.
A synthetic tRNA for EF‐Tu mediated selenocysteine incorporation in vivo and in vitro (2015)

Incorporation of selenocysteine (Sec) in bacteria requires a UGA codon that is reassigned to Sec by the Sec-specific elongation factor SelB and a conserved mRNA motif (SECIS element). These requirements severely restrict the engineering of selenoproteins. Earlier, a synthetic tRNASec was reported that allowed canonical Sec incorporation by EF-Tu; however, serine misincorporation limited its scope. We report a superior tRNASec variant (tRNAUTuX) that facilitates EF-Tu dependent stoichiometric Sec insertion in response to UAG both in vivo in Escherichia coli and in vitro in a cellfree protein synthesis system. We also demonstrate recoding of several sense codons in a SelB supplemented cell-free system. These advances in Sec incorporation will aid rational design and directed evolution of selenoproteins.
Preparation of Y-Ba-Cu-O Superconducting Thin Films by the Mist Microwave Plasma Decomposition Method (1989)

Superconducting thin films of the Y-Ba-Cu-O system were prepared on single crystal MgO(100) substrates by a new technique, the mist microwave plasma decomposition method. The onset and zero resistance temperatures occurred at 85 K and 78 K, respectively, for the as-grown film. The lattice constant c 0 estimated from Bragg angles of (00 n ) planes was 11.69 Å.
A CMOS passive mixer with low flicker noise for low-power direct-conversion receiver (2005)

A CMOS passive mixer is designed to mitigate the critical flicker noise problem that is frequently encountered in constituting direct-conversion receivers. With a unique single-balanced passive mixer design, the resulted direct-conversion receiver achieves an ultralow flicker-noise corner of 45 kHz, with 6 dB more gain and much lower power and area consumption than the double-balanced counterpart. CMOS switches with a unique bias-shifting network to track the LO DC offset are devised to reduce the second-order intermodulation. Consequently, the mixer's IIP2 has been greatly enhanced by almost 21 dB from a traditional single-balanced passive mixer. An insertion compensation method is also implemented for effective dc offset cancellation. Fabricated in 0.18 /spl mu/m CMOS and measured at 5 GHz, this passive mixer obtains 3 dB conversion gain, 39 dBm IIP2, and 5 dBm IIP3 with LO driving at 0 dBm. When the proposed mixer is integrated in a direct-conversion receiver, the receiver achieves 29 dB overall gain and 5.3 dB noise figure.
Oxidized alpha2-macroglobulin (alpha2M) differentially regulates receptor binding by cytokines/growth factors: implications for tissue injury and repair mechanisms in inflammation. (1998)

Alpha2M binds specifically to TNF-alpha, IL-1beta, IL-2, IL-6, IL-8, basic fibroblast growth factor (bFGF), beta-nerve growth factor (beta-NGF), platelet-derived growth factor (PDGF), and TGF-beta. Since many of these cytokines are released along with neutrophil-derived oxidants during acute inflammation, we hypothesize that oxidation alters the ability of alpha2M to bind to these cytokines, resulting in differentially regulated cytokine functions. Using hypochlorite, a neutrophil-derived oxidant, we show that oxidized alpha2M exhibits increased binding to TNF-alpha, IL-2, and IL-6 and decreased binding to beta-NGF, PDGF-BB, TGF-beta1, and TGF-beta2. Hypochlorite oxidation of methylamine-treated alpha2M (alpha2M*), an analogue of the proteinase/alpha2M complex, also results in decreased binding to bFGF, beta-NGF, PDGF-BB, TGF-beta1, and TGF-beta2. Concomitantly, we observed decreased ability to inhibit TGF-beta binding and regulation of cells by oxidized alpha2M and alpha2M*. We then isolated alpha2M from human rheumatoid arthritis synovial fluid and showed that the protein is extensively oxidized and has significantly decreased ability to bind to TGF-beta compared with alpha2M derived from plasma and osteoarthritis synovial fluid. We, therefore, propose that oxidation serves as a switch mechanism that down-regulates the progression of acute inflammation by sequestering TNF-alpha, IL-2, and IL-6, while up-regulating the development of tissue repair processes by releasing bFGF, beta-NGF, PDGF, and TGF-beta from binding to alpha2M.
Room-Temperature Low-Threshold Surface-Stimulated Emission by Optical Pumping from Al0.1Ga0.9N/GaN Double Heterostructure (1993)

The difference in the refractive index at around λ=0.37 µm between GaN and Al 0.1 Ga 0.9 N is found to be about 0.19. With use of AlGaN/GaN double heterostructures, the threshold power for surface-stimulated emission by optical pumping at room temperature has been markedly decreased to about one-twentieth that of a bulk GaN layer. The mechanism of the stimulated emission in this system is discussed.
Extraction of illusory linear clues in perspectively skewed documents (2005)

The article deals with the recovery of illusory linear clues from perspectively skewed documents, with the purpose of using them for rectification. The computational approach proposed implements the perceptual organization principles implicitly used in textual layouts. The numerous examples provided show that the method is robust and viewpoint and scale invariant.
Local Exchange Trading Systems in the United Kingdom: A Case of Re-Embedding? (1996)

In this paper a recent type of social and economic organization to appear in the United Kingdom—the local exchange trading system—is examined. From comparative research based on interviews with coordinators of six systems the motivation for involvement, the nature of the local money, and the relationship to business and state regulation are explored. The internal coherence of the systems and the relevance of the ‘local’ is assessed. Contextualized by debates on the nature of economics, where the notion of embeddedness of economic life in social relations is gaining ground, the concept of an active ‘re-embedding’ is introduced in order to explore the significance of local exchange trading systems.
Teduglutide for the Treatment of Short Bowel Syndrome (2006)

Data from ongoing clinical trials indicate that teduglutide may have the ability to enhance intestinal absorptive capacity in patients with SBS. Further studies and the completion of Phase III trials are necessary to determine the appropriate dosage and length of treatment for patients with SBS to gain optimal therapeutic benefit from this drug.
General and dramatic glial reaction in Alzheimer brains (1990)

We quantified glial fibrillary acidic protein (GFAP) using immunoblot techniques and anti-GFAP, in unfractionated homogenates of different brain regions from Alzheimer's disease (AD) patients. The amount of GFAP was significantly higher than in brains from controls and other neurodegenerative disorders (mean of 11 times), even in brain regions usually free of AD lesions such as caudate nucleus, thalamus, cerebellum, or brainstem. This dramatic increase of GFAP is not simply reflective of the astrocytic gliosis usually observed near the neurofibrillary tangles and senile plaques but more likely represents an astrocytic reaction in the whole brain corresponding to an overproduction or an accumulation of GFAP. The significance of such an increase is unknown, but it might be a key element in the pathogenesis of AD.
ChemInform Abstract: Chiral Magnesium(II)‐Catalyzed Asymmetric Ring‐Opening of Meso‐Aziridines with Primary Alcohols. (2014)

Abstract An efficient catalytic system is found for the asymmetric ring‐opening of meso‐aziridines with different nucleophiles, e.g. aniline, water, and methanol.
PILAR is a novel modulator of human T-cell expansion (2008)

Robust T-cell responses without autoimmunity are only possible through a fine balance between activating and inhibitory signals. We have identified a novel modulator of T-cell expansion named proliferation-induced lymphocyte-associated receptor (PILAR). Surface PILAR is markedly up-regulated on CD4 and, to a lesser extent, on CD8 T cells on T-cell receptor engagement. In absence of CD28 costimulation, PILAR signaling through CD161 supports CD3 antibody-dependent and antigen-specificT-cell proliferation by increasing the expression of antiapoptotic Bcl-xL and induces secretion of T helper type 1 cytokines. These effects are abrogated by PILAR blockade with specific antibodies, which decrease surface levels of CD28. In contrast, PILAR induces apoptotic death on naive and early activated T cells if CD161 engagement is blocked. PILAR is expressed by approximately 7% to 10% of CD4 T cells in 2 samples of inflammatory synovial fluid, suggesting a potential role in the pathogenesis of joint inflammation. In addition, in the ovarian cancer microenvironment, effector T cells express PILAR, but not CD161, although expression of both can be augmented ex vivo. Our results indicate that PILAR plays a central role in modulating the extent of T-cell expansion. Manipulation of PILAR signaling may be important for treatment of autoimmune diseases and cancer.
835. Studies in the synthesis of cortisone. Part XV. Improvements in the conversion of hecogenin into 3β : 12β-diacetoxy-5α : 25D-spirostan-11-one and a study of the isomeric 11 : 12-ketols (1956)

J. Elks, G. H. Phillipps, T. Walker and L. J. Wyman, J. Chem. Soc., 1956, 4330 DOI: 10.1039/JR9560004330
Specific Expression of Activation-induced Cytidine Deaminase (AID), a Novel Member of the RNA-editing Deaminase Family in Germinal Center B Cells (1999)

We have identified a novel gene referred to as activation-induced deaminase (AID) by subtraction of cDNAs derived from switch-induced and uninduced murine B lymphoma CH12F3-2 cells, more than 80% of which switch exclusively to IgA upon stimulation. The amino acid sequence encoded by AID cDNA is homologous to that of apolipoprotein B (apoB) mRNA-editing enzyme, catalytic polypeptide 1 (APOBEC-1), a type of cytidine deaminase that constitutes a catalytic subunit for the apoB mRNA-editing complex. In vitro experiments using a glutathione S-transferase AID fusion protein revealed significant cytidine deaminase activity that is blocked by tetrahydrouridine and by zinc chelation. However, AID alone did neither demonstrate activity in C to U editing of apoB mRNA nor bind to AU-rich RNA targets. AID mRNA expression is induced in splenic B cells that were activated in vitro or by immunizations with sheep red blood cells. In situ hybridization of immunized spleen sections revealed the restricted expression of AID mRNA in developing germinal centers in which modulation of immunoglobulin gene information through somatic hypermutation and class switch recombination takes place. Taken together, these findings suggest that AID is a new member of the RNA-editing deaminase family and may play a role in genetic events in the germinal center B cell.
Endocannabinoids and liver disease – review (2005)

Endocannabinoids appear to be involved in several aspects of acute and chronic liver disease, including vascular changes, modulation of inflammatory process and neurological function, Further research may provide new insights into the pathophysiology of liver disease, as well as a basis for novel treatment modalities.