gebhart/patrepeval huggingface dataset:
Development of a Protein Chip:  A MS-Based Method for Quantitation of Protein Expression and Modification Levels Using an Immunoaffinity Approach (2004)

Protein chip technology permits analysis of the expression and modification status of numerous targeted proteins within a single experiment, mainly through the use of antibody-based microarrays. Despite recent improvements in these protein chips, their applications are still limited for a variety of reasons, which include technical challenges in fabrication of the antibody chips as well as the very low specificity achieved by current detection methods. We have developed a unique approach for relative and/or absolute quantitation of protein expression and modification based on the capture of epitope peptides on affinity beads, which can be used to develop a mass-spectrometry-based protein chip technology. This new method, which utilizes antibodies immobilized on beads for the capture of target peptides, instead of proteins, eliminates many of the problems previously associated with protein chips. We present here several proof-of-principle experiments examining model peptides by this technique. These experiments show that the method is capable of (i). detecting peptides bound to a single antibody bead, (ii). detecting peptides at low (fmol) levels, (iii). producing MS/MS data of suitable quality for protein identification via database searching or de novo sequencing, (iv). quantitating peptides affinity-bound to antibody beads, (v). specifically detecting target peptides in complex mixtures over wide dynamic ranges, and (vi) is compatible with a microarray format for high-throughput analysis. Because our novel method uses antibody beads instead of a derivatized capture surface, and peptides instead of proteins for affinity capture, it can overcome many of the pitfalls of previous protein chip fabrications. Therefore, this method offers an improved approach to protein chip technology that should prove useful for diagnostics and drug development applications.
Single-Molecule Nanoprobes Explore Defects in Spin-Grown Crystals (2006)

Thin, platelike single crystals of p-terphenyl (PT) doped with terrylene impurity molecules can be prepared by spin-coating from solution. Strikingly, individual terrylene molecules can be observed traveling inside the crystal over distances of several micrometers by using single-molecule fluorescence imaging at room temperature. Analysis of the motion by single-particle tracking and correlation methods indicates that the molecules act as nanoprobes by exploring long, thin crack-like defects with correlated orientations, defects that can be difficult to observe by other means. Apparently, the regions accessible to the moving molecules are in the interior of the crystal and hence are partially protected from oxidation. In addition to the traveling molecules, which photobleach in times on the order of 32 s under continuous irradiation at 2 kW/cm2, two other spatially fixed populations are observed: one with transition dipole oriented along the c-axis of the crystal with a characteristic photobleaching time greater than 32 h, and one with a characteristic photobleaching time of 18 min.
Unobtrusive Estimation of Cardiac Contractility and Stroke Volume Changes Using Ballistocardiogram Measurements on a High Bandwidth Force Plate (2016)

Unobtrusive and inexpensive technologies for monitoring the cardiovascular health of heart failure (HF) patients outside the clinic can potentially improve their continuity of care by enabling therapies to be adjusted dynamically based on the changing needs of the patients. Specifically, cardiac contractility and stroke volume (SV) are two key aspects of cardiovascular health that change significantly for HF patients as their condition worsens, yet these parameters are typically measured only in hospital/clinical settings, or with implantable sensors. In this work, we demonstrate accurate measurement of cardiac contractility (based on pre-ejection period, PEP, timings) and SV changes in subjects using ballistocardiogram (BCG) signals detected via a high bandwidth force plate. The measurement is unobtrusive, as it simply requires the subject to stand still on the force plate while holding electrodes in the hands for simultaneous electrocardiogram (ECG) detection. Specifically, we aimed to assess whether the high bandwidth force plate can provide accuracy beyond what is achieved using modified weighing scales we have developed in prior studies, based on timing intervals, as well as signal-to-noise ratio (SNR) estimates. Our results indicate that the force plate BCG measurement provides more accurate timing information and allows for better estimation of PEP than the scale BCG (r² = 0.85 vs. r² = 0.81) during resting conditions. This correlation is stronger during recovery after exercise due to more significant changes in PEP (r² = 0.92). The improvement in accuracy can be attributed to the wider bandwidth of the force plate. ∆SV (i.e., changes in stroke volume) estimations from the force plate BCG resulted in an average error percentage of 5.3% with a standard deviation of ±4.2% across all subjects. Finally, SNR calculations showed slightly better SNR in the force plate measurements among all subjects but the small difference confirmed that SNR is limited by motion artifacts rather than instrumentation.
Resonant sum-frequency generation (2002)

A theoretical and numerical analysis of doubly or singly resonant sum-frequency generation of two laser beams in an external cavity is presented. The plane-wave equations for three-wave mixing-as applied to Gaussian beams using a Boyd-Kleinman overlap integral-are found to give excellent agreement with 3-D numerical simulations. In many regimes of practical interest, the present theory is also in excellent agreement with earlier work of Kaneda and Kubota. In particular, the generation of 589-nm CW sodium-resonance radiation in lithium triborate using two Nd:YAG lasers is considered. Matching the photon flux of the two laser beams is generally optimal. A suitable choice of input-coupler reflectivities (decreasing as the flux level increases) results in high-efficiency conversion with acceptable tolerance to input flux imbalance.
Macular pigment and risk for age-related macular degeneration in subjects from a Northern European population. (2001)

The two most important risk factors for AMD are associated with a relative absence of MP. These findings are consistent with the hypothesis that supplemental lutein and zeaxanthin may delay, avert, or modify the course of this disease.
Murine Insulin Growth Factor-like (IGFL) and Human IGFL1 Proteins Are Induced in Inflammatory Skin Conditions and Bind to a Novel Tumor Necrosis Factor Receptor Family Member, IGFLR1 (2011)

Psoriasis is a human skin condition characterized by epidermal hyperproliferation and infiltration of multiple leukocyte populations. In characterizing a novel insulin growth factor (IGF)-like (IGFL) gene in mice (mIGFL), we found transcripts of this gene to be most highly expressed in skin with enhanced expression in models of skin wounding and psoriatic-like inflammation. A possible functional ortholog in humans, IGFL1, was uniquely and significantly induced in psoriatic skin samples. In vitro IGFL1 expression was up-regulated in cultured primary keratinocytes stimulated with tumor necrosis factor α but not by other psoriasis-associated cytokines. Finally, using a secreted and transmembrane protein library, we discovered high affinity interactions between human IGFL1 and mIGFL and the TMEM149 ectodomain. TMEM149 (renamed here as IGFLR1) is an uncharacterized gene with structural similarity to the tumor necrosis factor receptor family. Our studies demonstrate that IGFLR1 is expressed primarily on the surface of mouse T cells. The connection between mIGFL and IGFLR1 receptor suggests mIGFL may influence T cell biology within inflammatory skin conditions.
The Patient with Daily Headaches (2005)

The term "chronic daily headache" (CDH) describes a variety of headache types, of which chronic migraine is the most common. Daily headaches often are disabling and may be challenging to diagnose and treat. Medication overuse, or drug rebound headache, is the most treatable cause of refractory daily headache. A pathologic underlying cause should be considered in patients with recent-onset daily headache, a change from a previous headache pattern, or associated neurologic or systemic symptoms. Treatment of CDH focuses on reduction of headache triggers and use of preventive medication, most commonly anti-depressants, antiepileptic drugs, and beta blockers. Medication overuse must be treated with discontinuation of symptomatic medicines, a transitional therapy, and long-term prophylaxis. Anxiety and depression are common in patients with CDH and should be identified and treated. Although the condition is challenging, appropriate treatment of patients with CDH can bring about significant improvement in the patient's quality-of-life.
Modification of the Active Site of Alkaline Phosphatase by Site-Directed Mutagenesis (1986)

The catalytically essential amino acid in the active site of bacterial alkaline phosphatase (Ser-102) has been replaced with a cysteine by site-directed mutagenesis. The resulting thiol enzyme catalyzes the hydrolysis of a variety of phosphate monoesters. The rate-determining step of hydrolysis, however, is no longer the same for catalysis when the active protein nucleophile is changed from the hydroxyl of serine to the thiol of cysteine. Unlike the steady-state kinetics of native alkaline phosphatase, those of the mutant show sensitivity to the leaving group of the phosphate ester.
15-Hydroxyprostaglandin dehydrogenase inactivation as a mechanism of resistance to celecoxib chemoprevention of colon tumors (2009)

Pharmacologic inhibitors of the prostaglandin-synthesizing COX-2 oncogene prevent the development of premalignant human colon adenomas. However, resistance to treatment is common. In this study, we show that the adenoma prevention activity of the COX-2 inhibitor celecoxib requires the concomitant presence of the 15-hydroxyprostaglandin dehydrogenase (15-PGDH) tumor suppressor gene, and that loss of 15-PGDH expression imparts resistance to celecoxib's anti-tumor effects. We first demonstrate that the adenoma-preventive activity of celecoxib is abrogated in mice genetically lacking 15-PGDH. In FVB mice, celecoxib prevents 85% of azoxymethane-induced tumors >1 mm in size, but is essentially inactive in preventing tumor induction in 15-PGDH-null animals. Indeed, celecoxib treated 15-PGDH null animals develop more tumors than do celecoxib naive WT mice. In parallel with the loss of tumor prevention activity, celecoxib-mediated suppression of colonic PGE(2) levels is also markedly attenuated in 15-PGDH-null versus WT mice. Finally, as predicted by the murine models, humans with low colonic 15-PGDH levels also exhibit celecoxib resistance. Specifically, in a colon adenoma prevention trial, in all cases tested, individuals who developed new adenomas while receiving celecoxib treatment were also found as having low colonic 15-PGDH levels.
Comparison of two glucoamylases from Hormoconis resinae (1990)

Two extracellular glucoamylases (EC 3.2.1.3), glucoamylase P and glucoamylase S, were purified to homogeneity from the culture medium of Hormoconis resinae (ATCC 20495; formerly Cladosporium resinae) by a new method. Their apparent molecular masses (71 kDa glucoamylase P; 78 kDa glucoamylase S) and catalytic properties agreed well with those previously reported in the literature. Heat inactivation studies suggested that the high debranching (1,6-glycosidic) activity of glucoamylase P preparations (measured with pullulan) may reside in the same protein molecule as its 1,4-glycosidic activity (measured with soluble starch). Although glucoamylase S had virtually no debranching activity, it cross-reacted with polyclonal antibodies raised against glucoamylase P, and the two enzymes had very similar amino acid compositions. However, peptide mapping and amino-terminal sequencing studies of the peptides showed that the two enzymes have different sequences and must be encoded by different genes.
PlayAnywhere (2005)

We introduce PlayAnywhere, a front-projected computer vision-based interactive table system which uses a new commercially available projection technology to obtain a compact, self-contained form factor. PlayAnywhere's configuration addresses installation, calibration, and portability issues that are typical of most vision-based table systems, and thereby is particularly motivated in consumer applications. PlayAnywhere also makes a number of contributions related to image processing techniques for front-projected vision-based table systems, including a shadow-based touch detection algorithm, a fast, simple visual bar code scheme tailored to projection-vision table systems, the ability to continuously track sheets of paper, and an optical flow-based algorithm for the manipulation of onscreen objects that does not rely on fragile tracking algorithms.
Efficient methods for attachment of thiol specific probes to the 3′-ends of synthetic oligodeoxyribonucleotides (1987)

Methodology is described for the synthesis of DNA oligomers containing a free 3'-thiol group which can be selectively crosslinked with a wide variety of probes. This chemistry is compatible with both phosphotriester and phosphoramidite solid phase chemistry. Moreover, the sulphydryl group is introduced into the 3'-nucleoside solid support linkage prior to oligonucleotide synthesis. Consequently, no additional coupling steps are required after oligonucleotide synthesis, and isolation of the 3'-thiol oligonucleotide requires only one additional deprotection step. Cross-linking of the thiol-containing oligonucleotide to a fluorescent probe was carried out with high selectivity, in high yield, and under mild conditions.
Management of Children With Autism Spectrum Disorders (2007)

Pediatricians have an important role not only in early recognition and evaluation of autism spectrum disorders but also in chronic management of these disorders. The primary goals of treatment are to maximize the child's ultimate functional independence and quality of life by minimizing the core autism spectrum disorder features, facilitating development and learning, promoting socialization, reducing maladaptive behaviors, and educating and supporting families. To assist pediatricians in educating families and guiding them toward empirically supported interventions for their children, this report reviews the educational strategies and associated therapies that are the primary treatments for children with autism spectrum disorders. Optimization of health care is likely to have a positive effect on habilitative progress, functional outcome, and quality of life; therefore, important issues, such as management of associated medical problems, pharmacologic and nonpharmacologic intervention for challenging behaviors or coexisting mental health conditions, and use of complementary and alternative medical treatments, are also addressed.
Recent advances in in vivo applications of intein-mediated protein splicing (2014)

Intein-mediated protein splicing has become an essential tool in modern biotechnology. Fundamental progress in the structure and catalytic strategies of cis- and trans-splicing inteins has led to the development of modified inteins that promote efficient protein purification, ligation, modification and cyclization. Recent work has extended these in vitro applications to the cell or to whole organisms. We review recent advances in intein-mediated protein expression and modification, post-translational processing and labeling, protein regulation by conditional protein splicing, biosensors, and expression of trans-genes.
Radioactive tracer techniques in the sequencing of glycoprotein oligosaccharides (1991)

Complete sequencing of the oligosaccharide units of glycoproteins can be performed by conventional physical techniques if nanomole quantities of pure molecules are available. However, isolation of sufficient quantities of a glycoprotein may not be technically feasible (e.g., the analysis of biosynthetic intermediates, or rare molecules). Alternatively, partial structural analyses may answer the biological question at hand. In both instances, radioactive sugars can be used to metabolically label the oligosaccharide units of a glycoprotein, permitting substantial structural characterization. Several aspects of this approach are discussed in this overview, including selection of the labeled precursor, maximization of uptake and incorporation, determinants of the specificity of labeling, and general principles for the release and structural analysis of labeled oligosaccharides. Particular advantages include simplicity, ease of use without sophisticated instrumentation, and the fact that purification to radiometric homogeneity is sufficient. Radioactive tracer techniques cannot replace conventional approaches to sequencing oligosaccharides. However, they do provide a rapid, relatively simple approach to obtaining considerable information from limited amounts of material. For molecules such as short-lived biosynthetic intermediates, there is no substitute for these techniques. This approach has been responsible for the initial identification and characterization of many novel oligosaccharides of biological interest.
Surface Coating from Phosphonate Ionic Liquid Electrolyte for the Enhancement of the Tribological Performance of Magnesium Alloy (2015)

A chronoamperometric method has been applied for the growth of a surface coating on AZ31B magnesium alloy, using the imidazolium alkylphosphonate room-temperature ionic liquid 1-ethyl-3-methylimidazolium ethylphosphonate ([EMIM][EtPO3H]) as electrolyte. A surface coating layer is obtained after 4 h under a constant voltage bias of -0.8 V with respect to the standard electrode. The coating nucleation and growth process correlates well with a 3D progressive mechanism. X-ray photoelectron spectrometry (XPS) analysis of [EMIM][EtPO3H] shows new P 2p and O 1s peaks after its use as electrolyte, as a consequence of reaction between the phosphonate anion and the magnesium substrate. Angle-resolved XPS (ARXPS) analysis of [EMIM][EtPO3H] did not show any change in the composition of the surface before and after chronoamperometry, since the sampling depth (1.5 nm at the highest emission angle) is larger than the cation and anion sizes (ca. 7 and 5 Å, respectively). Characterization of the coating was made by scanning electron microscopy (SEM), focussed ion beam SEM, energy dispersive X-ray spectroscopy, XPS, and ARXPS. FIB-SEM shows that the coating presents a mean thickness of 374 (±36) nm and contains magnesium and aluminum phosphates. Linear reciprocating tribological tests under variable load show that the presence of the coating can reduce friction coefficients of the coated AZ31B against steel up to 32% and wear rates up to 90%, with respect to the uncoated alloy.
Bladder cancer: allelic deletions at and around the retinoblastoma tumor suppressor gene in relation to stage and grade. (2000)

Inhibition of the retinoblastoma tumor suppressor gene (RB) is probably important in the pathogenesis of urinary bladder cancer. Little information is available concerning allelic loss on 13q11 to 13q32 and its relation to grade and stage. In a population-based study, freshly frozen tissue was collected from all new cases of urinary bladder cancer in the Stockholm region during 1995-1996. Here we report the occurrence of loss of heterozygosity (LOH) at seven sites in 13q11 to 13q32 as analyzed in 236 cases by a fluorescent multiplex PCR-based on tumor DNA and peripheral blood. For each site, about 30% of the cases were not informative because of homozygosity. Replication errors were detected in 4% (17 cases). LOH was found in 21 (at 13q11-12.1) to 32% (at 13q14.3 in RB) of the informative cases. A correlation was found between the prevalence of LOH at all observed loci and stage and grade, respectively, and it was statistically significant for 13q14.3. LOH at RB was found in Ta as well as grade 1 tumors. Also, a statistically significant correlation was found between the number of loci with LOH at 13q and tumor stage and grade, respectively. Typically an altered RB function is related to the expected clinical course of urinary bladder cancer, but allelic loss including the gene also occurs in low grade and low stage tumors. An altered RB function probably is not necessary for a malignant transformation of urothelial cells. The causal direction of the relation between the quantity of the deleted DNA and tumor aggressiveness is not clear.
Low threshold CW operation of circular-grating surface-emitting DBR lasers using MQW and a self-aligned process (1994)

In this letter, we present the first room temperature continuous wave operation of circular-grating surface-emitting DBR lasers. The structure is an InGaAs/GaAs strained multiquantum-well. A modified fabrication process with a better control on the steps is used. A CW threshold current as low as 26 mA at a lasing wavelength of about 977 mm are reported. This is the first demonstration of CW operation for these lasers in any material system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Early Detection of Graft Failure Using the Blood Metabolic Profile of a Liver Recipient (2007)

In this case report we describe the blood metabolic profile ("metabolomics") by nuclear magnetic resonance (NMR) spectroscopy and principle component analysis (PCA) from a patient who underwent two consecutive liver transplantations. The first graft from a living-related donor failed and was followed by a second successful transplant from a deceased donor. Using quantitative high-resolution H-NMR spectroscopy, 48 endogenous metabolites were analyzed in whole blood samples at baseline and different time points after each transplantation. From 48 analyzed metabolites, six metabolites were identified by PCA as metabolic markers consistent with a non-functional liver after first transplantation. Importantly, this distinctive metabolic profile was present as early as two hours after first transplant surgery when no other variable or conventional laboratory tests indicated poor graft function. This article reports the potential usefulness of quantitative H-NMR based metabolomics to diagnose early graft dysfunction in liver transplantation.
Classification of small cell lung cancer and pulmonary carcinoid by gene expression profiles. (1999)

Small cell lung cancer is a common type of lung cancer that is generally classified within the spectrum of neuroendocrine lung neoplasms. Using high-density cDNA arrays, we profiled gene expression of small cell lung cancers and compared these expression profiles to those of normal bronchial epithelial cells and pulmonary carcinoids, which are classified as benign neuroendocrine tumors. We found the overall expression profiles of two small cell lung cancer cell lines, two microdissected tissue samples of primary small cell lung cancer, and cultured bronchial epithelial cells to be relatively similar to one another, with an average Pearson correlation coefficient for these comparisons of 0.63. However, we found the expression profiles of small cell lung cancers (and bronchial epithelial cells) to be surprisingly dissimilar to those of two samples of pulmonary carcinoid tumors, with an average correlation coefficient for these comparisons of 0.20. We then compared the pulmonary carcinoid expression profiles to those of two samples of infiltrating astrocytic brain cancers (oligodendroglioma and high-grade astrocytoma) and found similarity of gene expression among these four samples (average correlation coefficient, 0.57). These gene expression profiles suggest that small cell lung cancers are closely related to (and possibly derived from) epithelial cells, and that pulmonary carcinoids are related to neural crest-derived brain tumors. More generally, our results suggest that broad profiles of gene expression may reveal similarities and differences between tumors that are not apparent by traditional morphological criteria.