gebhart/patrepeval huggingface dataset:
Simultaneous Glycan-Peptide Characterization Using Hydrophilic Interaction Chromatography and Parallel Fragmentation by CID, Higher Energy Collisional Dissociation, and Electron Transfer Dissociation MS Applied to the N-Linked Glycoproteome of Campylobacter jejuni (2010)

Campylobacter jejuni is a gastrointestinal pathogen that is able to modify membrane and periplasmic proteins by the N-linked addition of a 7-residue glycan at the strict attachment motif (D/E)XNX(S/T). Strategies for a comprehensive analysis of the targets of glycosylation, however, are hampered by the resistance of the glycan-peptide bond to enzymatic digestion or β-elimination and have previously concentrated on soluble glycoproteins compatible with lectin affinity and gel-based approaches. We developed strategies for enriching C. jejuni HB93-13 glycopeptides using zwitterionic hydrophilic interaction chromatography and examined novel fragmentation, including collision-induced dissociation (CID) and higher energy collisional (C-trap) dissociation (HCD) as well as CID/electron transfer dissociation (ETD) mass spectrometry. CID/HCD enabled the identification of glycan structure and peptide backbone, allowing glycopeptide identification, whereas CID/ETD enabled the elucidation of glycosylation sites by maintaining the glycan-peptide linkage. A total of 130 glycopeptides, representing 75 glycosylation sites, were identified from LC-MS/MS using zwitterionic hydrophilic interaction chromatography coupled to CID/HCD and CID/ETD. CID/HCD provided the majority of the identifications (73 sites) compared with ETD (26 sites). We also examined soluble glycoproteins by soybean agglutinin affinity and two-dimensional electrophoresis and identified a further six glycosylation sites. This study more than doubles the number of confirmed N-linked glycosylation sites in C. jejuni and is the first to utilize HCD fragmentation for glycopeptide identification with intact glycan. We also show that hydrophobic integral membrane proteins are significant targets of glycosylation in this organism. Our data demonstrate that peptide-centric approaches coupled to novel mass spectrometric fragmentation techniques may be suitable for application to eukaryotic glycoproteins for simultaneous elucidation of glycan structures and peptide sequence.
Synthesis and targeting of insulin-like growth factor-I to the hormone storage granules in an endocrine cell line. (1994)

Export of growth factors is generally believed to be restricted to the constitutive secretory pathway, whereas peptide hormones are typically secreted in a regulated manner. Here we show that insulin-like growth factor (IGF)-I, a growth factor released constitutively from the liver, is synthesized and secreted from the mouse pituitary AtT-20 cell line via the regulated pathway. IGF-I production is 1500-fold less than the peptide hormone ACTH. Secretagogue induces IGF-I secretion in a manner similar to ACTH. Like ACTH, IGF-I is sorted into the regulated pathway >35-fold more efficiently than a constitutively secreted protein. Dense core granules isolated from cells transfected with a human IGF-I cDNA contain both ACTH and human IGF-I. AtT-20 cells also synthesize IGF-binding proteins, and at least one of these is secreted by the regulated pathway. Human IGF-I does not exhibit milieu-induced, concentration-dependent aggregation, in contrast to secretogranin II which sorts by a proposed aggregation mechanism. These data suggest that 1) growth factors are not solely released from tissues via the constitutive pathway, 2) IGF-I may contain information for correct granular targeting, and 3) IGF-I may be sorted by a mechanism distinct from that proposed for the secretogranins.
Optimization of absorption-based optical chemical sensors that employ a single-reflection configuration (2002)

An optimization strategy for a generic absorption-based optical chemical sensor that employs a single-reflection planar configuration is reported. A theoretical model describing the sensor sensitivity is presented and verified experimentally. It is shown that optimum sensitivity is not achieved with an evanescent-wave sensing technique but with a configuration in which the interrogating light propagates within the sensing layer. Moreover, an optimization strategy based on identification of an optimized reflection angle is described. This analysis provides an optimization strategy that is extendable to multimode waveguide platforms. The predictions of the model are used in the design of a prototype LED-based sensor system. The performance of this system is examined, and the results are compared with alternative absorption-based sensor configurations.
Immunohistochemical analysis of CDw52 antigen expression in non-Hodgkin's lymphomas. (1994)

The Campath-1 antibodies showed that CDw52 antigen expression was present in all cases of low grade B cell NHL examined. Immunohistochemical staining in high grade B cell NHL and in T cell NHL was variable. These findings may be relevant to patient selection when considering treatment with Campath-1 antibodies.
MHCflurry: Open-Source Class I MHC Binding Affinity Prediction (2018)

Predicting the binding affinity of major histocompatibility complex I (MHC I) proteins and their peptide ligands is important for vaccine design. We introduce an open-source package for MHC I binding prediction, MHCflurry. The software implements allele-specific neural networks that use a novel architecture and peptide encoding scheme. When trained on affinity measurements, MHCflurry outperformed the standard predictors NetMHC 4.0 and NetMHCpan 3.0 overall and particularly on non-9-mer peptides in a benchmark of ligands identified by mass spectrometry. The released predictor, MHCflurry 1.2.0, uses mass spectrometry datasets for model selection and showed competitive accuracy with standard tools, including the recently released NetMHCpan 4.0, on a small benchmark of affinity measurements. MHCflurry's prediction speed exceeded 7,000 predictions per second, 396 times faster than NetMHCpan 4.0. MHCflurry is freely available to use, retrain, or extend, includes Python library and command line interfaces, may be installed using package managers, and applies software development best practices.
Evidence for a feedback regulated back-up promoter which controls permanent expression of aDictyosteliumgene (1990)

We have previously described the elements of two overlapping promoters regulating differential expression of the Dictyostelium P8A7 gene. One promoter was constitutively active but stimulated during development (S-promoter), while the other (L-promoter) was found to be induced by a variety of stimuli. This effect was mediated by the induction (i-) element. By a series of antisense transformation experiments we here provide evidence that this element is the target of a feedback control circuit. In wild type cells, feedback regulation activates the L-promoter in unfavourable environmental situations when transcription from the S-promoter is insufficient to generate adequate amounts of protein. A model for the function of the feedback loop under natural and experimental conditions is presented.
A novel de-interlacing method based on locally-adaptive Nonlocal-means (2012)

This paper presents an efficient method for video de-interlacing based on Nonlocal-means (NL-means). In the proposed scheme, every interpolated pixel is set to a weighted average of its neighboring pixels. Weights of the pixels are calculated according to the radiometric distance between the surrounding areas of them and the pixel being interpolated. To calculate the weights, we need an estimate of the progressive frames. Therefore, we initially de-interlace frames using a simple and reliable edge-based de-interlacing method. We use steering kernel in NL-means to adapt it locally to the features of the image. Experimental results show the effectiveness of our method.
Lighting a candle in the dark: advances in genetics and gene therapy of recessive retinal dystrophies (2010)

Nonsyndromic recessive retinal dystrophies cause severe visual impairment due to the death of photoreceptor and retinal pigment epithelium cells. These diseases until recently have been considered to be incurable. Molecular genetic studies in the last two decades have revealed the underlying molecular causes in approximately two-thirds of patients. The mammalian eye has been at the forefront of therapeutic trials based on gene augmentation in humans with an early-onset nonsyndromic recessive retinal dystrophy due to mutations in the retinal pigment epithelium-specific protein 65kDa (RPE65) gene. Tremendous challenges still lie ahead to extrapolate these studies to other retinal disease-causing genes, as human gene augmentation studies require testing in animal models for each individual gene and sufficiently large patient cohorts for clinical trials remain to be identified through cost-effective mutation screening protocols.
A phase II trial of nab‐paclitaxel (ABI‐007) and carboplatin in patients with unresectable stage IV melanoma (2010)

The weekly combination of ABI-007 and carboplatin appears to be moderately well tolerated, with promising clinical activity as therapy in patients who are chemotherapy naive and with modest antitumor activity in those previously treated.
Pore-Forming Bacterial Protein Hemolysins (Cytolysins) (1991)

Protein toxins forming pores in biological membranes occur frequently in Gram-positive and Gram-negative bacteria. They kill either bacteria or eukaryotic cells (at most, a few seem to act on both groups of organisms). Most of the toxins affecting eukaryotes have clearly been shown to be related to the pathogenicity of the producing organisms. Toxin formation frequently involves a number of genes which encode the toxin polypeptide as well as proteins for toxin activation and secretion. Regulation of toxin production is usually coupled with that of the synthesis of a number of other virulence factors. Iron is the only known environmental factor that regulates transcription of a number of toxin genes by a Fur repressor-type mechanism, as has been originally described in Escherichia coli. Interestingly, the thiol-activated hemolysins (cytolysins) of Gram-positive bacteria contain a single cysteine which can be replaced by alanine without affecting the cytolytic activity. The Gram-negative hemolysins (cytolysins) are usually synthesized as precursor proteins, then covalently modified to yield an active hemolysin and secreted via specific export systems, which differ for various types of hemolysins.
Viterbi receivers in the presence of severe intersymbol interference (2002)

A method of reducing the number of states in the Viterbi receiver, called PDFE (parallel decision feedback estimation), is described. Four different ISI (intersymbol interference) removal systems and two different TCM (trellis-coded modulation) systems using PDFE are presented and simulated. The simulated channel is a telephone cable operating at high bit rates and causing severe ISI. Gains of between 0.6 and 2.3 dB have been achieved in this severe ISI environment using Viterbi receivers with various proportions of four or 16 states devoted to either ISI mitigation or TCM decoding. With no ISI, the gain of four-state TCM is 3.1 dB and the gain of 16-state TCM is 4.0 dB. The gains of TCM received using PDFE with the severe ISI HDSL (high-rate digital subscriber line) channel are about one half of the gains with no ISI.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Regression of Human Prostate Tumors and Metastases in Nude Mice following Treatment with the Recombinant Oncolytic Vaccinia Virus GLV-1h68 (2010)

Virotherapy using oncolytic vaccinia virus strains is one of the most promising new strategies for cancer therapy. In the current study, we analyzed the therapeutic efficacy of the oncolytic vaccinia virus GLV-1h68 against two human prostate cancer cell lines DU-145 and PC-3 in cell culture and in tumor xenograft models. By viral proliferation assays and cell survival tests, we demonstrated that GLV-1h68 was able to infect, replicate in, and lyse these prostate cancer cells in culture. In DU-145 and PC-3 tumor xenograft models, a single intravenous injection with GLV-1h68 resulted in a significant reduction of primary tumor size. In addition, the GLV-1h68-infection led to strong inflammatory and oncolytic effects resulting in drastic reduction of regional lymph nodes with PC-3 metastases. Our data documented that the GLV-1h68 virus has a great potential for treatment of human prostate carcinoma.
Disconnected operation in the Coda file system (1991)

Disconnected operation is a mode of operation that enables a client to continue accessing critical data during temporary failures of a shared data repository. An important, though not exclusive, application of disconnected operation is in supporting portable computers. In this paper, we show that disconnected operation is feasible, efficient and usable by describing its design and implementation in the Coda File System. The central idea behind our work is that caching of data, now widely used for performance, can also be exploited to improve availability.
Source Code Exploration with Google (2006)

The paper presents a new approach to source code exploration, which is the result of integrating the Google Desktop Search (GDS) engine into the Eclipse development environment. The resulting search engine, named Google Eclipse Search (GES), provides improved searching in Eclipse software projects. The paper advocates for a component-based approach that allows us to develop strong tools, which support various maintenance tasks, by leveraging the strengths of existing frameworks and components. The development effort for such tools is reduced, while customization and flexibility, to fully support user needs, is maintained. GES allows developers to search software projects in a manner similar to searching the Internet or their own desktops. The proposed approach takes advantages of the power of GDS for quick and accurate searching and of Eclipse's extensibility. The paper discusses usage scenarios, advantages, limitations, and possible extensions of the proposed tandem
Development of a Titanium Dioxide-Supported Platinum Catalyst with Ultrahigh Stability for Polymer Electrolyte Membrane Fuel Cell Applications (2009)

A significant decrease in performance was observed for commercial Pt/C due to electrochemical oxidation of the carbon support and subsequent detachment and agglomeration of Pt particles. The Pt/TiO(2) cathode catalyst exhibited excellent fuel cell performance and ultrahigh stability under accelerated stress test conditions and can be considered as a promising alternative for improving the reliability and durability of PEMFCs.
A carbon nanotube bearing and Stodola rotor (2008)

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 2008.
Kinetics of Visual Pigment Regeneration in Excised Mouse Eyes and in Mice with a Targeted Disruption of the Gene Encoding Interphotoreceptor Retinoid-Binding Protein or Arrestin (1999)

Photoisomerization of 11-cis-retinal to all-trans-retinal and reduction to all-trans-retinol occur in photoreceptor outer segments whereas enzymatic esterification of all-trans-retinol, isomerization to 11-cis-retinol, and oxidation to 11-cis-retinal occur in adjacent cells. The processes are linked into a visual cycle by intercellular diffusion of retinoids. Knowledge of the mechanistic aspects of the visual cycle is very limited. In this study, we utilize chemical analysis of visual cycle retinoids to assess physiological roles for components inferred from in vitro experiments and to understand why excised mouse eyes fail to regenerate their bleached visual pigment. Flash illumination of excised mouse eyes or eyecups, in which regeneration of rhodopsin does not occur, produced a block in the visual cycle after all-trans-retinal formation; constant illumination of eyecups produced a block in the cycle after all-trans-retinol formation; and constant illumination of whole excised eyes resulted in a block of the cycle after formation of all-trans-retinyl ester. These blocks emphasize the role of cellular metabolism in the visual cycle. Interphotoreceptor retinoid-binding protein (IRBP) has been postulated to play a role in intercellular retinoid transfer in the retina; however, the rates of recovery of 11-cis-retinal and of regeneration of rhodopsin in the dark in IRBP-/- mice were very similar to those found with wild-type (wt) mice. Thus, IRBP is necessary for photoreceptor survival but is not essential for a normal rate of visual pigment turnover. Arrestin forms a complex with activated rhodopsin, quenches its activity, and affects the release of all-trans-retinal in vitro. The rate of recovery of 11-cis-retinal in arrestin-/- mice was modestly delayed relative to wt, and the rate of rhodopsin recovery was approximately 80% of that observed with wt mice. Thus, the absence of arrestin appeared to have a minor effect on the kinetics of the visual cycle.
Human facial illustrations (2004)

We present a method for creating black-and-white illustrations from photographs of human faces. In addition an interactive technique is demonstrated for deforming these black-and-white facial illustrations to create caricatures which highlight and exaggerate representative facial features. We evaluate the effectiveness of the resulting images through psychophysical studies to assess accuracy and speed in both recognition and learning tasks. These studies show that the facial illustrations and caricatures generated using our techniques are as effective as photographs in recognition tasks. For the learning task we find that illustrations are learned two times faster than photographs and caricatures are learned one and a half times faster than photographs. Because our techniques produce images that are effective at communicating complex information, they are useful in a number of potential applications, ranging from entertainment and education to low bandwidth telecommunications and psychology research.
Activation of the Sphingomyelin Cycle Through the Low-Affinity Neurotrophin Receptor (1994)

The role of the low-affinity neurotrophin receptor (p75NTR) in signal transduction is undefined. Nerve growth factor can activate the sphingomyelin cycle, generating the putative-lipid second messenger ceramide. In T9 glioma cells, addition of a cell-permeable ceramide analog mimicked the effects of nerve growth factor on cell growth inhibition and process formation. This signaling pathway appears to be mediated by p75NTR in T9 cells and NIH 3T3 cells overexpressing p75NTR. Expression of an epidermal growth factor receptor-p75NTR chimera in T9 cells imparted to epidermal growth factor the ability to activate the sphingomyelin cycle. These data demonstrate that p75NTR is capable of signaling independently of the trk neurotrophin receptor (p140trk) and that ceramide may be a mediator in neurotrophin biology.
Phase II Trial of Carboxyamidotriazole in Patients With Relapsed Epithelial Ovarian Cancer (2003)

CAI is a potential agent for additional study in the stabilization of relapsed ovarian cancer. Given a limited toxicity profile, it may have utility as a maintenance therapeutic agent for this disease.
Statistical path selection for at-speed test (2008)

Process variations make at-speed testing significantly more difficult. They cause subtle delay changes that are distributed rather than the localized nature of a traditional fault model. Due to parametric variations, different paths can be critical in different parts of the process space, and the union of such paths must be tested to obtain good process space coverage. This paper proposes a novel branch-and-bound algorithm that elegantly and efficiently solves the hitherto open problem of statistical path tracing. The resulting paths are used for at-speed structural testing. A new Test Quality Metric (TQM) is proposed and paths which maximize this metric are selected. After chip timing has been performed, the path selection procedure is extremely efficient. Path selection for a multi-million gate chip design can be completed in a matter of seconds.
Ethylene Biosynthesis and Signaling Networks (2002)

Despite its simple two-carbon structure, the olefin ethylene is a potent modulator of plant growth and development ([Ecker, 1995][1]). The plant hormone ethylene is involved in many aspects of the plant life cycle, including seed germination, root hair development, root nodulation, flower senescence
Aesthetics, Ideology, and Social Commitment in the Prose Fiction of Ousmane Sembene (1993)

The prose fiction of Ousmane Sembene is very easy to comprehend on the surface but it is, in fact, profoundly complex. There is a remarkable consistency in his work: a preoccupation with the struggles of the working poor and the unemployed; and also with the exploitation and oppression of a relentless capitalism that seriously threatens the social and cultural structures ofsociety as well as the inner recesses of the mind. There is also a consistent aesthetic context in his work, in which African artistic principles underlie and undermine the limitations of French forms of expression, since these forms do not always provide the author with the semantic, linguistic, and symbolic tools he needs.
The tac promoter: a functional hybrid derived from the trp and lac promoters. (1983)

Two hybrid promoters that are functional in Escherichia coli have been constructed. These hybrid promoters, tacI and tacII, were derived from sequences of the trp and the lac UV5 promoters. In the first hybrid promoter (tacI), the DNA upstream of position -20 with respect to the transcriptional start site was derived from the trp promoter. The DNA downstream of position -20 was derived from the lac UV5 promoter. In the second hybrid promoter (tacII), the DNA upstream of position -11 at the Hpa I site within the Pribnow box was derived from the trp promoter. The DNA downstream of position -11 is a 46-base-pair synthetic DNA fragment that specifies part of the hybrid Pribnow box and the entire lac operator. It also specifies a Shine-Dalgarno sequence flanked by two unique restriction sites (portable Shine-Dalgarno sequence). The tacI and the tacII promoters respectively direct transcription approximately 11 and 7 times more efficiently than the derepressed parental lac UV5 promoter and approximately 3 and 2 times more efficiently than the trp promoter in the absence of the trp repressor. Both hybrid promoters can be repressed by the lac repressor and both can be derepressed with isopropyl beta-D-thiogalactoside. Consequently, these hybrid promoters are useful for the controlled expression of foreign genes at high levels in E. coli. In contrast to the trp and the lac UV5 promoters, the tacI promoter has not only a consensus -35 sequence but also a consensus Pribnow box sequence. This may explain the higher efficiency of this hybrid promoter with respect to either one of the parental promoters.
Naphthalen-1-yl-(4-pentyloxynaphthalen-1-yl)methanone:  A Potent, Orally Bioavailable Human CB1/CB2Dual Agonist with Antihyperalgesic Properties and Restricted Central Nervous System Penetration (2007)

Selective activation of peripheral cannabinoid CB1 receptors has the potential to become a valuable therapy for chronic pain conditions as long as central nervous system effects are attenuated. A new class of cannabinoid ligands was rationally designed from known aminoalkylindole agonists and showed good binding and functional activities at human CB1 and CB2 receptors. This has led to the discovery of a novel CB1/CB2 dual agonist, naphthalen-1-yl-(4-pentyloxynaphthalen-1-yl)methanone (13), which displays good oral bioavailability, potent antihyperalgesic activity in animal models, and limited brain penetration.