gebhart/patrepeval huggingface dataset:
Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom‐up proteomics PTM analysis (2015)

MS-based proteomics has become the most utilized tool to characterize histone PTMs. Since histones are highly enriched in lysine and arginine residues, lysine derivatization has been developed to prevent the generation of short peptides (<6 residues) during trypsin digestion. One of the most adopted protocols applies propionic anhydride for derivatization. However, the propionyl group is not sufficiently hydrophobic to fully retain the shortest histone peptides in RP LC, and such procedure also hampers the discovery of natural propionylation events. In this work we tested 12 commercially available anhydrides, selected based on their safety and hydrophobicity. Performance was evaluated in terms of yield of the reaction, MS/MS fragmentation efficiency, and drift in retention time using the following samples: (i) a synthetic unmodified histone H3 tail, (ii) synthetic modified histone peptides, and (iii) a histone extract from cell lysate. Results highlighted that seven of the selected anhydrides increased peptide retention time as compared to propionic, and several anhydrides such as benzoic and valeric led to high MS/MS spectra quality. However, propionic anhydride derivatization still resulted, in our opinion, as the best protocol to achieve high MS sensitivity and even ionization efficiency among the analyzed peptides.
A Novel High Output Resistance Current Source Based on Negative Resistance (2006)

This paper presents a novel scheme for enhancing resistance that utilizes an equivalent negative resistance.Adopting this novel scheme in the proposed current source could remarkably boost its output resistance without requiring increased power supply.Simulation with 0.6μm CMOS process models shows that the output resistance of the novel current source can reach the order of 10~9Ω with a 1.04GHz bandwidth and only 10.6ppm/℃ in the range of -40～145℃.
Tunnel Magnetoresistance above 170% and Resistance–Area Product of 1 Ω (µm)2Attained byIn situAnnealing of Ultra-Thin MgO Tunnel Barrier (2011)

CoFeB/MgO/CoFeB magnetic tunnel junctions (MTJs) prepared by sputtering deposition and in situ annealing exhibited a high magnetoresistance (MR) ratio (above 170%) and an ultra-low resistance–area (RA) product [about 1.0 Ω (µm)2]. The MgO barrier, which was about 1 nm thick, was initially amorphous. In situ annealing of the barrier at 300 °C promoted crystallization of the MgO with (001) orientation, which resulted in the high MR ratio at the ultra-low RA product. The present achievements will enable the development of highly sensitive tunnel magnetoresistive (TMR) read heads for hard disk drives with a recording density of about 1 Tbit/in.2.
The role of retraction in direct nerve injury in total hip replacement (2014)

Iliopsoas can only offer protection to the femoral nerve if the retractor passes deep to the muscle bulk. The anterior retractor should be reinserted if pressure is removed intra-operatively. Vigorous movement of the inferior retractor should be avoided. Cite this article: Bone Joint Res 2014;3:212-6.
ORIGIN OF URINARY EPIDERMAL GROWTH FACTOR IN HUMANS: EXCRETION OF ENDOGENOUS EGF AND INFUSED [131I]‐HUMAN EGF AND KIDNEY HISTOCHEMISTRY (1992)

1. This study examined (i) whether blood-infused epidermal growth factor (EGF) can pass into urine; (ii) whether infused labelled EGF behaves like endogenous plasma immunoreactive EGF; and (iii) which parts of the human nephron show morphological evidence of EGF synthesis? 2. We infused human [131I]-EGF into a volunteer. After 6 min, only 66% of the plasma counts represented intact EGF. At the end of infusion, the T1/2 of EGF was calculated to be 1.6 min. The tail of the curve lasted for at least another 2 h. The total excretion of the labelled EGF was 2.45% of the infused dose and was proportional to the urine volume. 3. After a water load, the excretion of endogenous EGF was, on the contrary, inversely related to urine volume. 4. Immunohistochemically, human kidneys were not stained by monoclonal anti-EGF antibodies but showed positive in situ hybridization for EGF mRNA in the nuclei of glomerular mesangial cells, distal convoluted tubules and collecting tubules. 5. We conclude that human kidneys synthesize EGF and release it into urine. Plasma-derived EGF constitutes under normal conditions only a small part of the urinary EGF. Contrasting volume-dependency of the excretion of endogenous and [131I]-EGF requires further study and cautions against extrapolating results obtained with labelled EGF to physiological conditions.
The maternal and fetal origins of cardiovascular disease. (1992)

interpreted with extreme caution. Hypotheses generated by ecological studies need to be rigorously tested in epidemiological studies based on individuals rather than groups. These are considered in the second part of this review.'5
Majority Logic Gate for Magnetic Quantum-Dot Cellular Automata (2006)

We describe the operation of, and demonstrate logic functionality in, networks of physically coupled, nanometer-scale magnets designed for digital computation in magnetic quantum-dot cellular automata (MQCA) systems. MQCA offer low power dissipation and high integration density of functional elements and operate at room temperature. The basic MQCA logic gate, that is, the three-input majority logic gate, is demonstrated.
Fusion Cell Vaccination of Patients with Metastatic Breast and Renal Cancer Induces Immunological and Clinical Responses (2004)

Our findings demonstrate that fusion cell vaccination of patients with metastatic breast and renal cancer is a feasible, nontoxic approach associated with the induction of immunological and clinical antitumor responses.
New Real-Time Quantitative PCR Procedure for Quantification of Bifidobacteria in Human Fecal Samples (2004)

The application of a real-time quantitative PCR method (5' nuclease assay), based on the use of a probe labeled at its 5' end with a stable, fluorescent lanthanide chelate, for the quantification of human fecal bifidobacteria was evaluated. The specificities of the primers and the primer-probe combination were evaluated by conventional PCR and real-time PCR, respectively. The results obtained by real-time PCR were compared with those obtained by fluorescent in situ hybridization, the current gold standard for intestinal microbiota quantification. In general, a good correlation between the two methods was observed. In order to determine the detection limit and the accuracy of the real-time PCR procedure, germfree rat feces were spiked with known amounts of bifidobacteria and analyzed by both methods. The detection limit of the method used in this study was found to be about 5 x 10(4) cells per g of feces. Both methods, real-time PCR and fluorescent in situ hybridization, led to an accurate quantification of the spiked samples with high levels of bifidobacteria, but real-time PCR was more accurate for samples with low levels. We conclude that the real-time PCR procedure described here is a specific, accurate, rapid, and easy method for the quantification of bifidobacteria in feces.
Efficient generation of Rosa26 knock-in mice using CRISPR/Cas9 in C57BL/6 zygotes (2016)

Altogether, our protocols and resources support the fast and direct generation of new Rosa26 knock-in alleles and of Cas9-mediated in vivo gene editing in the widely used C57BL/6 inbred strain.
Improved Inhibitors of Glucosylceramide Synthase (1999)

Previous work has led to the identification of inhibitors of glucosylceramide synthase, the enzyme catalyzing the first glycosylation step in the synthesis of glucosylceramide-based glycosphingolipids. These inhibitors have two identified sites of action: the inhibition of glucosylceramide synthase, resulting in the depletion of cellular glycosphingolipids, and the inhibition of 1-O-acylceramide synthase, resulting in the elevation of cell ceramide levels. A new series of glucosylceramide synthase inhibitors based on substitutions in the phenyl ring of a parent compound, 1-phenyl-2-palmitoylamino-3-pyrrolidino-1-propanol (P4), was made. For substitutions of single functional groups, the potency of these inhibitors in blocking glucosylceramide synthase was primarily dependent upon the hydrophobic and electronic properties of the substituents. An exponential relationship was found between the IC50 of each inhibitor and the sum of derived hydrophobic (pi) and electronic (sigma) parameters. This relationship demonstrated that substitutions that increased the electron-donating characteristics and decreased the lipophilic characteristics of the homologues enhanced the potency of these compounds in blocking glucosylceramide formation. A novel compound was subsequently designed and observed to be even more active in blocking glucosylceramide formation. This compound, D-threo-4'-hydroxy-P4, inhibited glucosylceramide synthase at an IC50 of 90 nM. In addition, a series of dioxane substitutions was designed and tested. These included 3',4'-methylenedioxyphenyl-, 3',4'-ethylenedioxyphenyl-, and 3'4'-trimethylenedioxyphenyl-substituted homologues. D-threo-3', 4'-Ethylenedioxy-P4-inhibited glucosylceramide synthase was comparably active to the p-hydroxy homologue. 4'-Hydroxy-P4 and ethylenedioxy-P4 blocked glucosylceramide synthase activity at concentrations that had little effect on 1-O-acylceramide synthase activity. These novel inhibitors resulted in the inhibition of glycosphingolipid synthesis in cultured cells at concentrations that did not significantly raise intracellular ceramide levels or inhibit cell growth.
Nucleation and Crystallization Kinetics of Hydrated Amorphous Lactose Above the Glass Transition Temperature (1999)

The crystallization kinetics of amorphous lactose in the presence and absence of seed crystals were investigated at 57.5% relative humidity. Isothermal crystallization studies were conducted gravimetrically in an automated vacuum moisture balance at several temperatures between 18 and 32 degrees C. The crystallization rate constants were then determined from Johnson-Mehl-Avrami (JMA) treatment and isothermal activation energies were obtained from Arrhenius plots. Based on microscopic observations, a reaction order of 3 was used for JMA analysis. The nonisothermal activation energies were determined by differential scanning calorimetry using Kissinger's analysis. Isothermal activation energies for amorphous lactose with and without seed crystals were 89.5 (+/-5.6) kJ/mol and 186.5 (+/-17.6) kJ/mol, respectively. Nonisothermal activation energies with and without seed crystals were 71 (+/-7.5) kJ/mol and 80.9 (+/-8.9) kJ/mol, respectively. The similarity of the isothermal and nonisothermal activation energies for the sample with seeds suggested that crystallization was occurring by growth from a fixed number of preexisting nuclei. Markedly different isothermal and nonisothermal activation energies in the absence of seeds suggested a site-saturated nucleation mechanism, and therefore allowed calculation of an activation energy for nucleation of 317 kJ/mol.
Spin-glass models of neural networks (1985)

Two dynamical models, proposed by Hopfield and Little to account for the collective behavior of neural networks, are analyzed. The long-time behavior of these models is governed by the statistical mechanics of infinite-range Ising spin-glass Hamiltonians. Certain configurations of the spin system, chosen at random, which serve as memories, are stored in the quenched random couplings. The present analysis is restricted to the case of a finite number p of memorized spin configurations, in the thermodynamic limit. We show that the long-time behavior of the two models is identical, for all temperatures below a transition temperature ${T}_{c}$. The structure of the stable and metastable states is displayed. Below ${T}_{c}$, these systems have 2p ground states of the Mattis type: Each one of them is fully correlated with one of the stored patterns. Below T\ensuremath{\sim}0.46${T}_{c}$, additional dynamically stable states appear. These metastable states correspond to specific mixings of the embedded patterns. The thermodynamic and dynamic properties of the system in the cases of more general distributions of random memories are discussed.
The Potential of Antiangiogenic Therapy in Non–Small Cell Lung Cancer (2007)

The long-term prognosis for patients with advanced non-small cell lung cancer (NSCLC) remains poor despite the availability of several cytotoxic chemotherapy regimens. The use of targeted therapies, particularly those against the key mediator of angiogenesis vascular endothelial growth factor (VEGF), has the potential to improve outcomes for NSCLC patients. Bevacizumab, a recombinant humanized monoclonal anti-VEGF antibody, is the most clinically advanced antiangiogenic agent in NSCLC. In a phase III study, bevacizumab showed significantly improved overall and progression-free survival when used in combination with standard first-line chemotherapy in patients with advanced NSCLC. Bevacizumab was generally well tolerated in patients with NSCLC; however, tumor-related bleeding adverse events have been noted in some patients, predominantly those with squamous cell histology or centrally located tumors. Several small-molecule VEGF receptor tyrosine kinase inhibitors have also shown promise in phase I and II trials in NSCLC. This review summarizes the most important findings of angiogenesis inhibitors in NSCLC and discusses the potential for the use of these novel agents in different settings of NSCLC.
Diffusion of arylpropionate non‐steroidal anti‐inflammatory drugs into the cerebrospinal fluid: a quantitative structure–activity relationship approach (2004)

A quantitative structure-activity relationship (QSAR) analysis of a series of arylpropionic acid non-steroidal anti-inflammatory drugs (NSAIDs) has been performed to determine which physicochemical properties of these compounds are involved in their diffusion into the cerebrospinal fluid (CSF). The penetration of eight arylpropionic acid derivatives into CSF was studied in male Wistar rats. After intraperitoneal administration of each compound (5 mg/kg), blood and CSF samples were collected at different times (0.5, 1, 3 and 6 h). The fraction unbound to plasma protein was determined using ultrafiltration. The areas under the curve of the free plasma (AUCF) and CSF (AUCCSF) concentrations were calculated according to the trapezoidal rule. The overall drug transit into CSF was estimated by the ratio RAUC (AUCCSF : AUCF). The lipophilicity was expressed as the chromatographic capacity factor (log kIAM) determined by high-performance liquid chromatography on an immobilized artificial membrane (IAM) column. A significant parabolic relationship was sought between lipophilicity (log kIAM) and the capacity of diffusion across the blood-brain barrier (log RAUC) (r = 0.928; P < 0.01). The arylpropionic acid NSAIDs exhibiting a lipophilicity value between 1.1 and 1.7 entered the CSF easily (RAUC > 1). The molecular weight (MW) was included in this parabolic relationship by means of a multiple regression analysis. This physicochemical parameter improved the correlation (r = 0.976; P < 0.005). Based on our findings, diffusion of arylpropionic acid NSAIDs into CSF appears to depend primarily on their lipophilicity and MW.
Algorithmic Self-Assembly of DNA Sierpinski Triangles (2004)

Algorithms and information, fundamental to technological and biological organization, are also an essential aspect of many elementary physical phenomena, such as molecular self-assembly. Here we report the molecular realization, using two-dimensional self-assembly of DNA tiles, of a cellular automaton whose update rule computes the binary function XOR and thus fabricates a fractal pattern--a Sierpinski triangle--as it grows. To achieve this, abstract tiles were translated into DNA tiles based on double-crossover motifs. Serving as input for the computation, long single-stranded DNA molecules were used to nucleate growth of tiles into algorithmic crystals. For both of two independent molecular realizations, atomic force microscopy revealed recognizable Sierpinski triangles containing 100-200 correct tiles. Error rates during assembly appear to range from 1% to 10%. Although imperfect, the growth of Sierpinski triangles demonstrates all the necessary mechanisms for the molecular implementation of arbitrary cellular automata. This shows that engineered DNA self-assembly can be treated as a Turing-universal biomolecular system, capable of implementing any desired algorithm for computation or construction tasks.
Preliminary Ideas on Designing an Unmanned Aerial Vehicle Based on Coanda Effect (2013)

The final goal of this research is to develop a safe and inexpensive flying vehicle. In this paper, only some preliminary ideas on the design of an unmanned aerial vehicle, based on Coandă effect, will be presented. These ideas are concerning the optimization of the aerodyne body profile.
Log-based directory resolution in the Coda file system (2002)

A key problem in optimistic replication, namely, using semantic knowledge of objects to resolve concurrent updates from multiple partitions, is addressed. The authors describe how the Coda file system resolves partitioned updates to directories. The central result is that logging of updates is a simple yet efficient and powerful technique for directory resolution in Unix file systems. Measurements show that the time for resolution is typically less than 10% of the time for performing the original set of partitioned updates. Analysis based on file traces indicates that a log size of 2 MB per hour of partition should be ample for typical services.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Common factor 1 is a transcriptional activator which binds in the c-myc promoter, the skeletal alpha-actin promoter, and the immunoglobulin heavy-chain enhancer. (1991)

Ubiquitously expressed transcription factors play an integral role in establishing and regulating patterns of gene transcription. Common factor 1 (CF1) is a ubiquitously expressed DNA-binding protein previously identified in our laboratory. We show here that CF1 recognizes sites in several diverse transcription elements, and we demonstrate the ability of the c-myc CF1 site to activate transcription of a basal promoter in both B cells and fibroblasts.
Development of an Ultrafine Grained Ferrite in a Low C-Mn Steel Intensely Deformed under Hot Torsion (2004)

In the last years, several studies concerning ultra refinement of ferrite grains have been conducted using different experimental techniques (ECAP, ARB, HPT). The aim of all investigations was to provide an optmized relationship between mechanical properties and microstructure of steels. The present work, likewise, deals with strain induced dynamic transformation of ferrite. Samples of low C-Mn steel were intensely deformed in hot torsion aiming at the production of ultrafine grains of ferrite thereby enhancing the mechanical properties when compared to hot rolled products. After soaking during 5min at 900°C, the samples were quenched and then reheated and submitted to hot torsion deformation at temperatures of 700 and 740°C. The torsion schedule consisted of 7 isothermal passes leading to a total strain of ≈1, generating an ultrafine microstructure with grain sizes of the order of 1µm. The shape of stress-strain curves so obtained suggested that ferrite refinement occurred by dynamic recrystallization. The various constituents present in the microstructure as well as ferrite grain size and morphology were examined by optical and scanning electron microscopy. Microhardness tests were performed to evaluate mechanical properties.
Manipulating the Tumor Microenvironment Ex Vivo for Enhanced Expansion of Tumor-Infiltrating Lymphocytes for Adoptive Cell Therapy (2014)

Our results highlight a previously unrecognized concept in TIL ACT that the tumor microenvironment can be dynamically regulated in the initial tumor fragment cultures to regulate the types of T cells expanded and their functional characteristics.
Elevated plasma chitotriosidase activity in various lysosomal storage disorders (1995)

Recently a striking elevation of the activity of chitotriosidase, an endo beta-glucosaminidase distinct from lysozyme, was found in plasma from patients with Gaucher type I disease (McKusick 230800). Plasma chitotriosidase originates from activated macrophages and this elevation is secondary to the basic defect in Gaucher disease. To investigate the specificity of this phenomenon, we have investigated 24 different lysosomal storage diseases. In 11 different diseases increased chitotriosidase activity in plasma was found (in 28% of the patients). None of these diseases showed elevations as high as in Gaucher disease. Chitotriosidase was not significantly elevated in plasma from 20 different non-lysosomal enzymopathies or in plasma from patients with infectious diseases associated with hepatomegaly. The results show that marked elevation of chitotriosidase activity in plasma appears to be specific for Gaucher disease. The data further suggest that elevated levels of chitotriosidase activity in plasma from patients with unexplained diseases may be indicative for a lysosomal disorder.
[Biochemical markers of bone turnover. New aspect. Dialysis and bone metabolic marker]. (2009)

Disturbances in mineral metabolism and bone disease are common complications of chronic kidney disease (CKD). There is increasing evidence suggesting that these disorders in mineral and bone metabolism are associated with increased risk for cardiovascular calcification, morbidity, and mortality, especially among those who undergo maintenance dialysis. It is very important for dialysis patients to assess the mineral and bone abnormalities. Although bone biopsy is necessary to diagnosis of renal osteodystrophy in CKD-mineral and bone disorder (CKD-MBD) classification system, this technique is not recommended of routine evaluation for this bone disease. Bone metabolic markers, such as bone specific alkaline phosphatase and tartrate-resistant acid phosphatase isoform 5b, may be useful clinical indicator of bone turnover in CKD-MBD.
Reactivation of DNA viruses in association with histone deacetylase inhibitor therapy: a case series report (2009)

Histone deacetylase inhibitors are a class of anti-neoplastic agents that induce growth arrest, differentiation, and/or apoptotic cell death of transformed cells in vitro and in vivo. A phase II study exploring the efficacy of romidepsin, an histone deacetylase inhibitor, in patients with cutaneous or peripheral T-cell lymphomas was initiated at the National Cancer Institute. To date, over 120 patients with T-cell lymphoma have been treated on a multi-institutional phase II trial of romidepsin. Reactivation of latent DNA viruses including EBV, HBV, and VZV is well described as a consequence of the immune suppression associated with systemic chemotherapy. The incidence of viral reactivation in patients treated with histone deacetylase inhibitors is not yet known. We report the observation of EBV-associated illnesses in 2 patients and the reactivation of HBV in an additional patient treated with romidepsin. These cases may represent reactivation of DNA viruses due to histone deacetylase inhibitor induced immunosuppression, or direct promotion of viral replication via histone deacetylase inhibitor induced chromatin remodeling, or, alternatively, may be related to the underlying disease process. These observations suggest that vigilance for DNA virus reactivation is needed to quantify the risk in patients treated with histone deacetylase inhibitors.