gebhart/patrepeval huggingface dataset:
Stability and CTL activity of N‐terminal glutamic acid containing peptides (2001)

Several cytotoxic T lymphocyte peptide-based vaccines against hepatitis B, human immunodeficiency virus and melanoma were recently studied in clinical trials. One interesting melanoma vaccine candidate alone or in combination with other tumor antigens, is the decapeptide ELA. This peptide is a Melan-A/MART-1 antigen immunodominant peptide analog, with an N-terminal glutamic acid. It has been reported that the amino group and gamma-carboxylic group of glutamic acids, as well as the amino group and gamma-carboxamide group of glutamines, condense easily to form pyroglutamic derivatives. To overcome this stability problem, several peptides of pharmaceutical interest have been developed with a pyroglutamic acid instead of N-terminal glutamine or glutamic acid, without loss of pharmacological properties. Unfortunately compared with ELA, the pyroglutamic acid derivative (PyrELA) and also the N-terminal acetyl-capped derivative (AcELA) failed to elicit cytotoxic T lymphocyte (CTL) activity. Despite the apparent minor modifications introduced in PyrELA and AcELA, these two derivatives probably have lower affinity than ELA for the specific class I major histocompatibility complex. Consequently, in order to conserve full activity of ELA, the formation of PyrELA must be avoided. Furthermore, this stability problem is worse in the case of clinical grade ELA, produced as an acetate salt, like most of the pharmaceutical grade peptides. We report here that the hydrochloride salt, shows higher stability than the acetate salt and may be suitable for use in man. Similar stability data were also obtained for MAGE-3, another N-terminal glutamic acid containing CTL peptide in clinical development, leading us to suggest that all N-terminal glutamic acid and probably glutamine-containing CTL peptide epitopes may be stabilized as hydrochloride salts.
Subsystem pseudopure states (2007)

A critical step in experimental quantum information processing (QIP) is to implement control of quantum systems protected against decoherence via informational encodings, such as quantum error-correcting codes, noiseless subsystems, and decoherence-free subspaces. These encodings lead to the promise of fault-tolerant QIP, but they come at the expense of resource overheads. Part of the challenge in studying control over multiple logical qubits is that QIP testbeds have not had sufficient resources to analyze encodings beyond the simplest ones. The most relevant resources are the number of available qubits and the cost to initialize and control them. Here we demonstrate an encoding of logical information that permits control over multiple logical qubits without full initialization, an issue that is particularly challenging in liquid-state NMR. The method of subsystem pseudopure states will allow the study of decoherence control schemes on up to six logical qubits using liquid-state NMR implementations.
Optimality and Robustness of a Biophysical Decision-Making Model under Norepinephrine Modulation (2009)

The locus ceruleus (LC) can exhibit tonic or phasic activity and release norepinephrine (NE) throughout the cortex, modulating cellular excitability and synaptic efficacy and thus influencing behavioral performance. We study the effects of LC-NE modulation on decision making in two-alternative forced-choice tasks by changing conductances in a biophysical neural network model, and we investigate how it affects performance measured in terms of reward rate. We find that low tonic NE levels result in unmotivated behavior and high levels in impulsive, inaccurate choices, but that near-optimal performance can occur over a broad middle range. Robustness is greatest when pyramidal cells are less strongly modulated than interneurons, and superior performance can be achieved with phasic NE release, provided only glutamatergic synapses are modulated. We also show that network functions such as sensory information accumulation and short-term memory can be modulated by tonic NE levels, and that previously observed diverse evoked cell responses may be due to network effects.
Spatial Multiomics Reveal the Role of Wnt Modulator, Dkk2, in Palatogenesis (2023)

Multiple genetic and environmental etiologies contribute to the pathogenesis of cleft palate, which constitutes the most common among the inherited disorders of the craniofacial complex. Insights into the molecular mechanisms regulating osteogenic differentiation and patterning in the palate during embryogenesis are limited and needed for the development of innovative diagnostics and cures. This study utilized the <i>Pax9</i><sup>-/-</sup> mouse model with a consistent phenotype of cleft secondary palate to investigate the role of <i>Pax9</i> in the process of palatal osteogenesis. While prior research had identified upregulation of Wnt pathway modulators <i>Dkk1</i> and <i>Dkk2</i> in <i>Pax9</i><sup>-/-</sup> palate mesenchyme, limitations of spatial resolution and technology restricted a more robust analysis. Here, data from single-nucleus transcriptomics and chromatin accessibility assays validated by <i>in situ</i> highly multiplex targeted single-cell spatial profiling technology suggest a distinct relationship between <i>Pax9+</i> and osteogenic populations. Loss of <i>Pax9</i> results in spatially restricted osteogenic domains bounded by <i>Dkk2</i>, which normally interfaces with <i>Pax9</i> in the mesenchyme. These results suggest that Pax9-dependent Wnt signaling modulators influence osteogenic programming during palate formation, potentially contributing to the observed cleft palate phenotype.
Hakata Antigen, a New Member of the Ficolin/Opsonin p35 Family, Is a Novel Human Lectin Secreted into Bronchus/Alveolus and Bile (1999)

Hakata antigen was first reported as a serum protein that reacted with an autoantibody from patients with systemic lupus erythematosus. Recently, it has been found that Hakata antigen is a new member of the ficolin/opsonin p35 family, which is a distinct lectin family, on the basis of homology of structures and the common characteristic of possessing lectin activity. In this study we analyzed the tissue distribution of Hakata antigen. Hakata antigen mRNA and protein were generated in the lung and liver. In the lung, Hakata antigen was produced by both ciliated bronchial epithelial cells and Type II alveolar epithelial cells and was secreted into the bronchus and alveolus. In the liver, Hakata antigen was produced by bile duct epithelial cells and hepatocytes and was also secreted into the bile duct. These results demonstrate that Hakata antigen is a unique lectin protein that exists not only in serum but also in bronchus/alveolus and bile, and indicate that Hakata antigen plays a role in bronchus/alveolus and bile under physiological conditions.
Treatment of recent hepatitis C virus infection in a predominantly injection drug user cohort: the ATAHC Study (2009)

Haber, Paul (Australia); Hellard, Margaret; Matthews, Gail V.; Grebely, Jason; Petoumenos, Kathy; Yeung, Barbara; Marks, Pip; van Beek, Ingrid; McCaughan, Geoff; White, Peter A.; Ffrench, Rosemary; Rawlinson, William; Lloyd, Andrew; Kaldor, John; Dore, Gregory J. for the ATAHC Study Group
S1872 Purely Endoscopic Appendectomy Using Double Balloon Endolumenal Interventional Platform (2020)

INTRODUCTION: Appendectomy traditionally performed through open or laparoscopic surgery and requires incisions (or punctures) of anterior abdominal wall causing post-surgical pain, risk of postoperative incisional hernias, restricting physical activity and delaying return to work post appendectomy. Previously reported Natural Orifice Translumenal Endoscopic Surgery (NOTES) appendectomy required incision of gastric or vaginal wall for advancement of the endoscope into peritoneal cavity with subsequent risk of intraperitoneal infection, adhesions and dyspareunia. A new double balloon endolumenal interventional platform (DBEIP) consists of a flexible overtube with 2 manually inflatable balloons, one behind the endoscope tip, the other with the ability to be advanced beyond the scope tip. Aim of the presentation: To describe purely endoscopic appendectomy using DBEIP. CASE DESCRIPTION/METHODS: The patient is a 51-year old women referred for endoscopic removal of cecal submucosal lesion. Colonoscope preloaded with DBEIP was advanced into the cecum. Submucosal mass was visualized in the cecum. Endoscopic ultrasound demonstrated hyperechoic lesion originating from submucosal layer. Circumferential incision around the lesion was performed. The lesion was attached with 2 endoscopic clips to a suture-loop mounted on fore- balloon of the DBEIP and pulled into colonic lumen. The lesion was carefully dissected from surrounding tissues. At this point it became evident that lesion originated inside the appendix. Using multidirectional dynamic retraction the appendix was pulled into cecum and removed en bloc. DBEIP served as a conduit to remove colonoscope and then to deliver endoscopic suturing device into the cecum. Full-thickness defect post appendectomy was completely closed with 2 continuous sutures. The patient had no pain post procedure and was discharged home from endoscopy unit on oral antibiotics. She restarted her regular physical activity and returned to work the morning after appendectomy. DISCUSSION: Purely endoscopic appendectomy using DBEIP is technically feasible, does not require advancement of the endoscope into the peritoneal cavity and abolishes incisions/punctures of the abdominal wall, eradicating the risk of post-surgical incisional hernias and intraperitoneal adhesions. Endoscopic appendectomy eliminates pain post appendectomy and need for hospital admission, enables early return to work and regular physical activity and can become a valuable alternative to surgical/laparoscopic/NOTES appendectomy.Figure 1.: Double balloon endolumenal interventional platform (DBEIP).Figure 2.: Endoscopic appendectomy - appendix is pulled into the cecum and dissected with hook knife.Figure 3.: Resected appendix.
Compact and low-noise quartz-enhanced photoacoustic sensor for sub-ppm ethylene detection in atmosphere (2018)

We report on the development of a gas sensor system based on quartz-enhanced photoacoustic spectroscopy (QEPAS) for the detection of trace levels of ethylene using a quantum cascade laser operating at ~ 10.3 &mu;m. To realize a compact sensor architecture, a dedicated acoustic detection module was designed and implemented. The module includes a QEPAS spectrophone, composed of a quartz tuning fork, a micro-resonator tube and a low-noise pre-amplifier chip for the signal readout. The volume of the ADM is ~30 cm<sup>3</sup>. A minimum detection limit of 30 part-per-billion in concentration was obtained with a data acquisition time of 10 s.
Synthesis and glycosidase inhibition of N-substituted derivatives of 1,4-dideoxy-1,4-imino-d-mannitol (DIM) (2019)

N-Substituted derivatives of 1,4-dideoxy-1,4-imino-d-mannitol (DIM), the pyrrolidine core of swainsonine, have been synthesized efficiently and stereoselectively from d-mannose with 2,3:5,6-di-O-isopropylidene DIM (10) as a key intermediate. These N-substituted derivatives include N-alkylated, N-alkenylated, N-hydroxyalkylated and N-aralkylated DIMs with the carbon number of the alkyl chain ranging from one to nine. The obtained 33 N-substituted DIM derivatives were assayed against various glycosidases, which allowed a systematic evaluation of their glycosidase inhibition profiles. Though N-substitution of DIM decreased their α-mannosidase inhibitory activities, some of the derivatives showed significant inhibition of other glycosidases.
Conformational Heterogeneity in Antibody-Protein Antigen Recognition (2014)

Specific, high affinity protein-protein interactions lie at the heart of many essential biological processes, including the recognition of an apparently limitless range of foreign proteins by natural antibodies, which has been exploited to develop therapeutic antibodies. To mediate biological processes, high affinity protein complexes need to form on appropriate, relatively rapid timescales, which presents a challenge for the productive engagement of complexes with large and complex contact surfaces (∼600-1800 Å(2)). We have obtained comprehensive backbone NMR assignments for two distinct, high affinity antibody fragments (single chain variable and antigen-binding (Fab) fragments), which recognize the structurally diverse cytokines interleukin-1β (IL-1β, β-sheet) and interleukin-6 (IL-6, α-helical). NMR studies have revealed that the hearts of the antigen binding sites in both free anti-IL-1β Fab and anti-IL-6 single chain variable exist in multiple conformations, which interconvert on a timescale comparable with the rates of antibody-antigen complex formation. In addition, we have identified a conserved antigen binding-induced change in the orientation of the two variable domains. The observed conformational heterogeneity and slow dynamics at protein antigen binding sites appears to be a conserved feature of many high affinity protein-protein interfaces structurally characterized by NMR, suggesting an essential role in protein complex formation. We propose that this behavior may reflect a soft capture, protein-protein docking mechanism, facilitating formation of high affinity protein complexes on a timescale consistent with biological processes.
Interactive region segmentation for manga (2016)

Manga (Japanese comics) are popular all over the world, and are created digitally. In this paper, we propose an interactive segmentation method tailored for manga. The proposed method enables annotators to select areas in manga efficiently. Our experimental results showed that the proposed framework works better than Adobe Photoshop CC, which is the most widely used commercial image editing software.
Bio-Oil Co-Processing with Refinery Streams (2023)

The project seeks to accelerate the adoption of co-processing biomass-derived feedstocks with petroleum streams in operating petroleum refineries to produce biogenic-carbon-containing fuels.
Conditional Mutagenesis in Drosophila (2009)

Most genes function at multiple stages of metazoan development, in dividing and nondividing cells. Generating mouse conditional knock-outs (cKO), where a gene can be eliminated in a temporally and spatially controlled manner, is a valuable technique because it allows study of gene function at any stage of life. In contrast and despite the development of many other powerful genetic tools, cKO has thus far been lacking in Drosophila. We combined several recent molecular and genetic technical advances in an approach termed integrase-mediated approach for gene knock-out (IMAGO). IMAGO allows the replacement of any genomic sequence, such as a gene, with another desired sequence, including cKO alleles that can be used to create positively marked mutant cells. IMAGO should also be applicable to other genetic model organisms.
Immobilization can improve the stability of hybridoma antibody productivity in serum‐free media (1990)

Hybridoma cells (S3H5/gamma2bA2) were cultivated in spinner flasks with 1% serum media and serum-free media. Monoclonal antibody productivity was maintained in 1% serum media. However, cells in serum-free media showed a decrease in antibody productivity, and it completely disappeared in IMDM-based low protein medium. This loss of antibody productivity was not observed when the cells were immobilized in alginate beads. In fact, immobilization enhanced the specific MAb productivity.
Glomerular Function and Structural Integrity Depend on Hyaluronan Synthesis by Glomerular Endothelium (2019)

Endothelial loss of hyaluronan results in disturbed glomerular endothelial stabilization. Glomerular endothelial hyaluronan is a previously unrecognized key component of the extracelluar matrix that is required for glomerular structure and function and lost in diabetic nephropathy.
Forced Convective Heat Transfer Characteristics of Rotating Drum with Fin Array (2002)

A non-dimensional correlating equation for the forced convective heat transfer from a rotating drum with fin array to air is proposed to improve the cooling performance of the Permanent Magnet Type Eddy Current Retarder. It is assumed that the forced convective heat transfer consists of that for the cavity flow along the circumference of the drum, and of that for the channel flow passing through the space between the fines. Two correlations proposed by the other researchers are adopted to evaluate the each heat transfer coefficient in the equation. The complex characteristics of the heat transfer are correlated with the mean error of 9.9%.
Curli Loci of Shigella spp (2000)

An unstable chromosomal element encoding multiple antibiotic resistance in Shigella flexneri serotype 2a was found to include sequences homologous to the csg genes encoding curli in Escherichia coli and Salmonella enterica serovar Typhimurium. As curli have been implicated in the virulence of serovar Typhimurium, we investigated the csg loci in all four species of Shigella. DNA sequencing and PCR analysis showed that the csg loci of a wide range of Shigella strains, of diverse serotypes and different geographical distributions, were almost universally disrupted by deletions or insertions, indicating the existence of a strong selective pressure against the expression of curli. Strains of enteroinvasive E. coli (EIEC), which share virulence traits with Shigella spp. and cause similar diseases in humans, also possessed insertions or deletions in the csg locus or were otherwise unable to produce curli. Since the production of curli is a widespread trait in environmental isolates of E. coli, our results suggest that genetic lesions that abolish curli production in the closely related genus Shigella and in EIEC are pathoadaptive mutations.
Dense image registration and deformable surface reconstruction in presence of occlusions and minimal texture (2015)

Deformable surface tracking from monocular images is well-known to be under-constrained. Occlusions often make the task even more challenging, and can result in failure if the surface is not sufficiently textured. In this work, we explicitly address the problem of 3D reconstruction of poorly textured, occluded surfaces, proposing a framework based on a template-matching approach that scales dense robust features by a relevancy score. Our approach is extensively compared to current methods employing both local feature matching and dense template alignment. We test on standard datasets as well as on a new dataset (that will be made publicly available) of a sparsely textured, occluded surface. Our framework achieves state-of-the-art results for both well and poorly textured, occluded surfaces.
Microfluidic Integration of Parallel Solid-Phase Liquid Chromatography (2013)

We report the development of a fully integrated microfluidic chromatography system based on a recently developed column geometry that allows for robust packing of high-performance separation columns in poly(dimethylsiloxane) microfluidic devices having integrated valves made by multilayer soft lithography (MSL). The combination of parallel high-performance separation columns and on-chip plumbing was used to achieve a fully integrated system for on-chip chromatography, including all steps of automated sample loading, programmable gradient generation, separation, fluorescent detection, and sample recovery. We demonstrate this system in the separation of fluorescently labeled DNA and parallel purification of reverse transcription polymerase chain reaction (RT-PCR) amplified variable regions of mouse immunoglobulin genes using a strong anion exchange (AEX) resin. Parallel sample recovery in an immiscible oil stream offers the advantage of low sample dilution and high recovery rates. The ability to perform nucleic acid size selection and recovery on subnanogram samples of DNA holds promise for on-chip genomics applications including sequencing library preparation, cloning, and sample fractionation for diagnostics.
Human gamete fusion can bypass beta1 integrin requirement (1998)

Since alpha6beta1 integrin has been shown to function as a sperm adhesion receptor in the mouse, we investigated the potential role of beta1 integrin in the gamete fusion process in humans. The expression of beta1 integrin was morphologically analysed by indirect immunofluorescence and confocal microscopy. A homogeneous and intense staining was detected at the plasma membrane, and in some subcortical vesicles of germinal vesicle stage oocytes (GV). Beta1 almost disappeared from oolemma and cytoplasm of metaphase I (MI) oocytes, but was re-expressed as asymmetrical patches at the plasma membrane of metaphase II stage oocytes (MII). A functional fusion assay based on Hoechst or calcein-AM dye transfer from one gamete to the other showed that maturing oocytes were able to fuse with an increasing number of spermatozoa (11-22 from GV to MII respectively), and that fused spermatozoa co-localized with beta1 integrin patches. Human gamete fusion was only partially inhibited either by RGD-containing peptide (GRGDTP), or by blocking anti-human beta1 integrin monoclonal antibody (DE9), with a maximum of 50% inhibition. Despite the combined addition of GRGDTP and blocking mouse anti-human beta1 integrin DE9 in the assay, a complete inhibition of fusion could not be achieved. A mouse polyclonal antibody raised against human oocyte membranes was more potent in inhibiting the fusion. Since beta1 integrin expression at the plasma membrane was not correlated to oocyte fusibility, and since it was only partially inhibited by DE9 and/or RGD peptide, we suggest that human gamete fusion can bypass the beta1 requirement. Beta1 integrin certainly participates in human gamete fusion by acting in co-operation with multiple integrin/disintegrin couples or another cofactor, not yet identified.
Supplementary Figure S9 from Evolution of Castration-Resistant Prostate Cancer in ctDNA during Sequential Androgen Receptor Pathway Inhibition (2023)

&lt;p&gt;Supplementary Figure S9 shows the correlation between serum prostate-specific antigen (PSA) levels and plasma circulating tumor DNA fraction.&lt;/p&gt;
Moving object segmentation using depth and optical flow in car driving sequences (2016)

Segmentation of moving objects in a scene is difficult for non-stationary cameras, and especially challenging in the presence of fast and unstable egomotion, e.g., as encountered with car-mounted cameras or wearable devices. Based on an analysis of motion vanishing points of the scene and estimated depth, a geometric model that relates extracted 2D motion to a 3D motion field relative to the camera is derived. Observing that the 3D motion field is piece-wise smooth, a constrained optimization problem that considers group sparsity is formulated to recover the 3D motion field from the 2D motion. The recovered 3D motion field is then clustered to provide the segmentation of moving objects. Experiments are performed using the KITTI Vision Benchmark Suite and demonstrate that the proposed framework provides a dense segmentation of moving objects that is robust to the challenging conditions inherent with car driving sequences.
Searching for Non-Gaussian Signals in the BOOMERANG 2003 CMB Maps (2007)

We analyze the BOOMERANG 2003 (B03) 145 GHz temperature map to constrain the amplitude of a non-Gaussian, primordial contribution to CMB fluctuations. We perform a pixel-space analysis restricted to a portion of the map chosen in view of high-sensitivity, very low foreground contamination and tight control of systematic effects. We set up an estimator based on the three Minkowski functionals which relies on high-quality simulated data, including non-Gaussian CMB maps. We find good agreement with the Gaussian hypothesis and derive the first limits based on BOOMERANG data for the nonlinear coupling parameter fNL as -300 &lt; fNL &lt; 650 at 68% CL and -800 &lt; fNL &lt; 1050 at 95% CL.
Production Cross Section of Intermediate Bosons by Neutrinos in the Coulomb Field of Protons and Iron (1961)

Received 13 November 1961DOI:https://doi.org/10.1103/PhysRevLett.7.429©1961 American Physical Society