gebhart/patrepeval huggingface dataset:
Comparative evaluation of label‐free SINQ normalized spectral index quantitation in the central proteomics facilities pipeline (2011)

Normalized spectral index quantification was recently presented as an accurate method of label-free quantitation, which improved spectral counting by incorporating the intensities of peptide MS/MS fragment ions into the calculation of protein abundance. We present SINQ, a tool implementing this method within the framework of existing analysis software, our freely available central proteomics facilities pipeline (CPFP). We demonstrate, using data sets of protein standards acquired on a variety of mass spectrometers, that SINQ can rapidly provide useful estimates of the absolute quantity of proteins present in a medium-complexity sample. In addition, relative quantitation of standard proteins spiked into a complex lysate background and run without pre-fractionation produces accurate results at amounts above 1 fmol on column. We compare quantitation performance to various precursor intensity- and identification-based methods, including the normalized spectral abundance factor (NSAF), exponentially modified protein abundance index (emPAI), MaxQuant, and Progenesis LC-MS. We anticipate that the SINQ tool will be a useful asset for core facilities and individual laboratories that wish to produce quantitative MS data, but lack the necessary manpower to routinely support more complicated software workflows. SINQ is freely available to obtain and use as part of the central proteomics facilities pipeline, which is released under an open-source license.
Dual-Functional Biomimetic Materials:  Nonfouling Poly(carboxybetaine) with Active Functional Groups for Protein Immobilization (2006)

We introduce a dual-functional biocompatible material based on zwitterionic poly(carboxybetaine methacrylate) (polyCBMA), which not only highly resists protein adsorption/cell adhesion, but also has abundant functional groups convenient for the immobilization of biological ligands, such as proteins. The dual-functional properties are unique to carboxybetaine moieties and are not found in other nonfouling moieties such as ethylene glycol, phosphobetaine, and sulfobetaine. The unique properties are demonstrated in this work by grafting a polyCBMA polymer onto a surface or by preparing a polyCBMA-based hydrogel. PolyCBMA brushes with a thickness of 10-15 nm were grafted on a gold surface using the surface-initiated atom transfer radical polymerization method. Protein adsorption was analyzed using a surface plasmon resonance sensor. The surface grafted with polyCBMA very largely prevented the nonspecific adsorption of three test proteins, that is, fibrinogen, lysozyme, and human chorionic gonadotropin (hCG). The immobilization of anti-hCG on the surface resulted in the specific binding of hCG while maintaining a high resistance to nonspecific protein adsorption. Transparent polyCBMA-based hydrogel disks were decorated with immobilized fibronectin. Aortic endothelial cells did not bind to the polyCBMA controls, but appeared to adhere well and spread on the fibronectin-modified surface. With their dual functionality and biomimetic nature, polyCBMA-based materials are very promising for their applications in medical diagnostics, biomaterials/tissue engineering, and drug delivery.
cis-acting elements responsible for interleukin-6 inducible C-reactive protein gene expression. (1990)

To study the mechanism of induction of human C-reactive protein (CRP) gene expression, we have utilized an in vitro liver cell system to analyze the cis-acting DNA sequences located within the 5'-flanking region of human CRP gene. Stable transfection of human hepatoma cells, PLC/PRF/5, by a CRP gene construct containing the 1 kilobase pair of upstream sequence of the CRP gene demonstrated that this region contained the inducible element(s) which regulated human CRP gene transcription. Dissection of this region by 5', 3' and internal deletion constructs of upstream region of the CRP gene fused to a reporter gene, chloramphenicol acetyl transferase, indicated the presence of two inducible elements located proximal to the site of initiation of transcription, two constitutive enhancer-like elements located distal to the promoter, and a negative regulatory region located between the two inducible elements. We had previously shown that a protein factor from monocytes or HTLV1-infected T-cells, was responsible for CRP induction in hepatoma cells. We have found this factor to be synonymous with interleukin-6. By stable and transient transfection assays in hepatoma cells, recombinant interleukin-6 alone was sufficient to activate both inducible elements.
Uncertainty Relations for Shift-Invariant Analog Signals (2009)

The past several years have witnessed a surge of research investigating various aspects of sparse representations and compressed sensing. Most of this work has focused on the finite-dimensional setting in which the goal is to decompose a finite-length vector into a given finite dictionary. Underlying many of these results is the conceptual notion of an uncertainty principle: a signal cannot be sparsely represented in two different bases. Here, we extend these ideas and results to the analog, infinite-dimensional setting by considering signals that lie in a finitely generated shift-invariant (SI) space. This class of signals is rich enough to include many interesting special cases such as multiband signals and splines. By adapting the notion of coherence defined for finite dictionaries to infinite SI representations, we develop an uncertainty principle similar in spirit to its finite counterpart. We demonstrate tightness of our bound by considering a bandlimited lowpass train that achieves the uncertainty principle. Building upon these results and similar work in the finite setting, we show how to find a sparse decomposition in an overcomplete dictionary by solving a convex optimization problem. The distinguishing feature of our approach is the fact that even though the problem is defined over an infinite domain with infinitely many variables and constraints, under certain conditions on the dictionary spectrum our algorithm can find the sparsest representation by solving a finite-dimensional problem.
The Molecular Biology of Mucosal Field Cancerization of the Head and Neck (2003)

Field cancerization was first described in 1953 as histologically altered epithelium surrounding tumor samples taken from the upper aerodigestive tract. Since then, the term has been used to describe multiple patches of pre-malignant disease, a higher-than-expected prevalence of multiple local second primary tumors, and the presence of synchronous distant tumors within the upper aerodigestive tract. Molecular techniques such as karyotype analysis, microsatellite analysis, p53 mutation screening, and X-chromosome inactivation studies have further refined the relationship among these lesions. While there are differences in the techniques used to identify the clonal origins of the lesions, these studies indicate that there is often lateral clonal spread of pre-malignant or malignant disease, and a significant portion of local second primary tumors are in fact genetically related. Distant second primary tumors found in the esophagus are often not related to concurrent head and neck cancer, whereas synchronous squamous lung tumors with a head and neck primary are often, in fact, metastases, rather than independently arising malignancies. These observations help to explain the high incidence of recurrent disease, despite excision or other therapy--pre-malignant or malignant clones often have the ability to migrate and persist outside of the field of treatment. Therefore, alternative means of prevention or therapy that can affect the entire head and neck region may be of benefit to such patients. Future studies will further refine the relationship among these lesions and perhaps identify key molecular alterations to be used as targets for gene therapy.
Cutting Edge: CTLA-4–B7 Interaction Suppresses Th17 Cell Differentiation (2010)

Th cells that produce IL-17 (Th17 cells) are a distinct subset of Th cells implicated in several autoimmune diseases. Although CD28-B7 interaction has been shown to be involved in Th17 differentiation in vitro, the role of CTLA-4 in controlling Th17 development is completely unknown. We report in this paper that blocking the CTLA-4-B7 interaction potentiates Th17 cell differentiation in vitro and in vivo. Furthermore, blocking CTLA-4-B7 interaction in vivo confers the susceptibility of experimental autoimmune myocarditis to CD28(-/-) mice or increases the severity of experimental autoimmune myocarditis in wild-type mice. The enhanced disease susceptibility is mediated by heightened Th17 responses. With these results, we are the first to demonstrate that CTLA-4-B7 interaction inhibits Th17 differentiation in vitro and in vivo and suppresses Th17-mediated autoimmunity.
Preparation and Formation Mechanism of Silica Microcapsules (Hollow Sphere) by Water/Oil/Water Interfacial Reaction (2004)

Silica microcapsules (hollow spheres) were readily prepared by an interfacial reaction using a water/oil/water (W/O/W) emulsion system. A W/O emulsion consisting of an aqueous solution of sodium silicate (WP-1) and an n-hexane solution of Tween 80 and Span 80 (OP) was added to another aqueous solution of a precipitant (WP-2). The reaction of sodium silicate with a precipitant to form silica on this W/O/W emulsion system (WP-1/OP/WP-2) forms the hollow structure spontaneously. Therefore, no core material often utilized in silica hollow sphere fabrication was required in this process. The formation and the particle size of the silica microcapsule depended on the precipitant employed. When NH4HCO3 was used as precipitant, the particle size of the silica microcapsule was successfully controlled by the volume ratio of WP-1/OP/WP-2, the rotation number of the homogenizer, and the concentration of sodium silicate in WP-1. However, this control of the particle size was not achieved when other precipitants such as NH4Cl were used. In the case of NH4HCO3, silica formation takes place at the outer interface between OP and WP-2 on the W/O/W emulsion system. On the other hand, when NH4Cl is utilized, silica is yielded at the inner interface between WP-1 and OP. These differences of reaction mechanisms of sodium silicate among precipitants were important factors in the preparation and properties of microcapsules.
Rethinking the library OS from the top down (2011)

This paper revisits an old approach to operating system construc-tion, the library OS, in a new context. The idea of the library OS is that the personality of the OS on which an application depends runs in the address space of the application. A small, fixed set of abstractions connects the library OS to the host OS kernel, offering the promise of better system security and more rapid independent evolution of OS components. We describe a working prototype of a Windows 7 library OS that runs the latest releases of major applications such as Microsoft Excel, PowerPoint, and Internet Explorer. We demonstrate that desktop sharing across independent, securely isolated, library OS instances can be achieved through the pragmatic reuse of net-working protocols. Each instance has significantly lower overhead than a full VM bundled with an application: a typical application adds just 16MB of working set and 64MB of disk footprint. We contribute a new ABI below the library OS that enables application mobility. We also show that our library OS can address many of the current uses of hardware virtual machines at a fraction of the overheads. This paper describes the first working prototype of a full commercial OS redesigned as a library OS capable of running significant applications. Our experience shows that the long-promised benefits of the library OS approach better protection of system integrity and rapid system evolution are readily obtainable.
Glycine site N-methyl-d-aspartate receptor antagonist 7-CTKA produces rapid antidepressant-like effects in male rats (2013)

Our findings demonstrate that acute 7-CTKA administration produced rapid antidepressant-like effects, indicating that the behavioural response to 7-CTKA is mediated by GSK3β and mTOR signalling function in the mPFC.
Diagnostic and Prognostic Biomarkers in Acute Renal Failure (2008)

Acute kidney injury (AKI) is a process that can lead to renal failure. No biological markers are available for predicting the cause or prognosis of AKI. Tests that can predict which patients will need renal replacement therapy (RRT) are needed. In this chapter, we review the recent literature for proteomic analysis in AKI and identify new candidate markers to predict the need for RRT. We also used artificial neural network (ANN) analysis of urine protein data obtained by two-dimensional gel electrophoresis from 19 patients with acute tubular necrosis to identify a set of proteins that can predict whether a patient will require RRT. Ten patients were randomly selected to train an ANN algorithm. The remaining 9 patients were withheld to serve as an independent validation set. The ANN algorithm correctly predicted the renal prognosis of all 10 patients in the training set. In the validation set, the test correctly predicted the future course of renal failure in 7 of the 9 patients (78% accuracy) including 3 of 4 patients who would require RRT (75% sensitivity) and 4 of 5 who would not (80% specificity). Combinations of urine proteins can be used to predict which patients will require RRT.
Silicide formation at HfO2–Si and ZrO2–Si interfaces induced by Ar+ ion bombardment (2004)

The effect of ion bombardment with Ar+ at several keV energy ranges resulting in silicide formation at HfO2–Si and ZrO2–Si interfaces has been investigated in situ with x-ray photoelectron spectroscopy. The set of spectra recorded during the growth of thin HfO2 and ZrO2 layers on Si(100) was compared to those obtained during subsequent sputtering with an Ar+ beam. It is shown that the Ar+ ion beam affects the MeO2–Si (Me=Hf,Zr) interface at thickness ⩽3nm, inducing the formation of a silicide layer ∼2nm in thickness. The proposed mechanism of silicide formation including the depletion of the interface in oxygen due to its preferential sputtering and subsequent Hf–Si intermixing is corroborated by computer simulations.
Acetaminophen overdose-induced liver injury in mice is mediated by peroxynitrite independently of the cyclophilin d-regulated permeability transition (2011)

These data support the concept that an overdose of APAP results in liver injury that is refractory to pharmacological inhibition or genetic depletion of CypD and that peroxynitrite-mediated cell injury predominates in the absence of CypD.
Genetic basis of minicell formation in Escherichia coli K-12 (1984)

Hfr- and P1-mediated genetic transfer experiments failed to confirm the presence of a " minA " gene in Escherichia coli K-12, leading to the conclusion that mutation at a single locus, the minB locus, is sufficient to cause minicell production in this species.
Isolation and characterization of Pseudomonas pseudomallei flagellin proteins (1994)

Flagellin proteins from several different strains of Pseudomonas pseudomallei have been isolated and purified to homogeneity by mechanical shearing and differential centrifugation techniques. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis yielded flagellin monomer protein bands with an estimated M(r) of 43,400. No lipopolysaccharide contamination of the purified protein preparations was detectable by silver staining of flagellin displayed on polyacrylamide gels and by Western immunoblotting with P. pseudomallei antilipopolysaccharide monoclonal antibody. NH2-terminal amino acid sequence analysis of the flagellin protein of P. pseudomallei 319a revealed significant homology with flagellins from Proteus mirabilis, Bordetella bronchiseptica, and Pseudomonas aeruginosa PAK. Rabbit polyclonal antiserum raised against the 319a flagellin protein reacted with 64 of 65 P. pseudomallei strains tested. The polyclonal antiserum proved effective in inhibiting the motility of these organisms in motility agar plates. Passive immunization studies demonstrated that 319a flagellin-specific antiserum was capable of protecting diabetic rats from challenge with a heterologous P. pseudomallei strain.
Human Cardiovascular and Metabolic Response to Acute, Severe Isovolemic Anemia (1998)

Acute isovolemic reduction of blood Hb concentration to 50 g/L in conscious healthy resting humans does not produce evidence of inadequate systemic TO2, as assessed by lack of change of VO2 and plasma lactate concentration. Analysis of Holter readings suggests that at this Hb concentration in this resting healthy population, myocardial ischemia would occur infrequently.
Smokeless tobacco and premalignant and malignant lesions of the oral cavity. (1991)

The paper compares the prevalence of oral carcinoma and dysplasia in smokeless tobacco users and non users. A total of 3205 subjects were studied. Of the smokeless tobacco users, 1.96 percent had oral carcinoma compared with 0.36 percent of non-users. The prevalence of oral dysplasia in the users' group was 14.4 percent as compared with 6.85 percent in the group of non-users.
Procainamide inhibits DNA methyltransferase in a human T cell line. (1991)

Procainamide, a widely used antiarrythmic, causes DNA hypomethylation in the human T cell line Jurkat, but the mechanism is unknown. We report that procainamide inhibits the DNA methyltransferase catalyzed transfer of methyl groups from S-adenosylmethionine to DNA, but has no effect on other known regulators of DNA methylation. Our results suggest that procainamide could inhibit cellular DNA methylation by inhibiting DNA methyltransferase activity.
Cytokine blockers in psoriatic arthritis (2001)

The cellular events underlying the pathogenesis of psoriatic arthritis (PsA) and psoriasis have not yet been fully elucidated. Nevertheless, some clues to these conditions are beginning to emerge. In particular, a growing body of data supports the role of proinflammatory cytokines, such as tumour necrosis factor (TNF), in the pathophysiology of PsA and psoriasis. Raised levels of these cytokines are found in the joints of patients with PsA, as well as in psoriatic skin lesions. Physiotherapy, non-steroidal anti-inflammatory agents, corticosteroids, and disease modifying antirheumatic agents, such as methotrexate, are the most commonly used treatments for PsA. However, the data supporting the effectiveness of these treatments are limited, and disease resolution is usually incomplete. This study examined the effects of etanercept, a TNF inhibitor, in patients with PsA. Etanercept treatment was well tolerated and resulted in significant improvement in the signs and symptoms of PsA and in psoriatic skin lesions. Infliximab, another TNF inhibitor, has also been shown to be effective in patients with PsA. Such studies confirm the importance of proinflammatory cytokines in PsA, and hold out hope for patients who require new options for the treatment of their disease.
Biodegradable and Renal Clearable Inorganic Nanoparticles (2015)

Personalized treatment plans for cancer therapy have been at the forefront of oncology research for many years. With the advent of many novel nanoplatforms, this goal is closer to realization today than ever before. Inorganic nanoparticles hold immense potential in the field of nano-oncology, but have considerable toxicity concerns that have limited their translation to date. In this review, an overview of emerging biologically safe inorganic nanoplatforms is provided, along with considerations of the challenges that need to be overcome for cancer theranostics with inorganic nanoparticles to become a reality. The clinical and preclinical studies of both biodegradable and renal clearable inorganic nanoparticles are discussed, along with their implications.
Neuropathology of some hereditary conditions affecting central and peripheral nervous system. (2002)

Neuropathology plays a crucial role in the phenotypic individualization of hereditary disorders affecting the central and peripheral nervous system even if molecular genetics represents the most essential step in describing the genotypes. The neuropathological description of phenotypes and genotypes can be used for refining clinical skills and understanding many clinical, neurophysiological and neuroradiological features. It contributes to the diagnosis of such disorders. The use of immunohistochemical techniques in combination with molecular genetics improves also our knowledge of their pathogenesis and might participate to the future development of therapeutic strategies. We discuss new features of spino-cerebellar ataxia (SCA) type 7 and of a recently identified SCA17 in order to illustrate the significance of the neuronal intranuclear inclusions (NIIs) described in various CAG/polyglutamine repeat expansion diseases. In the field of the peripheral neuropathies we present data on a newly described autosomal recessive Charcot-Marie-Tooth disease (CMT4F) with mutations in the periaxin gene. We document a dysjunction between myelin loops and axolemma with disappearance of the septate-like junctions or transverse bands. The significance of this dysjunction is not yet elucidated. We hope to show by these examples that the combination of classical and new neuropathological methods is useful in the study of hereditary disorders of the nervous system.
Influence of DNA Target Melting Behavior on Real-Time PCR Quantification (2000)

Before a primer system is used for precise quantitative real-time PCR, the dependence of the quantification results on the positions of reaction tubes in the thermocycler should be tested. Our data indicate that amplification efficiencies, especially in the first cycles, depend not only on the priming efficiencies of the primers and the melting temperature of the amplicon, but also on the melting behavior of the amplicon's genomic vicinity. Complete denaturation of genomic DNA is necessary to maximize precision of quantitative PCR. Higher denaturation temperatures in the initial cycles or boiling of DNA before the PCR can improve the accuracy of quantification in some cases.
Droplet-interface-bilayer assays in microfluidic passive networks (2015)

Basic biophysical studies and pharmacological processes can be investigated by mimicking the intracellular and extracellular environments across an artificial cell membrane construct. The ability to reproduce in vitro simplified scenarios found in live cell membranes in an automated manner has great potential for a variety of synthetic biology and compound screening applications. Here, we present a fully integrated microfluidic system for the production of artificial lipid bilayers based on the miniaturisation of droplet-interface-bilayer (DIB) techniques. The platform uses a microfluidic design that enables the controlled positioning and storage of phospholipid-stabilized water-in-oil droplets, leading successfully to the scalable and automated formation of arrays of DIBs to mimic cell membrane processes. To ensure robustness of operation, we have investigated how lipid concentration, immiscible phase flow velocities and the device geometrical parameters affect the system performance. Finally, we produced proof-of-concept data showing that diffusive transport of molecules and ions across on-chip DIBs can be studied and quantified using fluorescence-based assays.