gebhart/patrepeval huggingface dataset:
A Comprehensive Peptidome Profiling Technology for the Identification of Early Detection Biomarkers for Lung Adenocarcinoma (2011)

The mass spectrometry-based peptidomics approaches have proven its usefulness in several areas such as the discovery of physiologically active peptides or biomarker candidates derived from various biological fluids including blood and cerebrospinal fluid. However, to identify biomarkers that are reproducible and clinically applicable, development of a novel technology, which enables rapid, sensitive, and quantitative analysis using hundreds of clinical specimens, has been eagerly awaited. Here we report an integrative peptidomic approach for identification of lung cancer-specific serum peptide biomarkers. It is based on the one-step effective enrichment of peptidome fractions (molecular weight of 1,000-5,000) with size exclusion chromatography in combination with the precise label-free quantification analysis of nano-LC/MS/MS data set using Expressionist proteome server platform. We applied this method to 92 serum samples well-managed with our SOP (standard operating procedure) (30 healthy controls and 62 lung adenocarcinoma patients), and quantitatively assessed the detected 3,537 peptide signals. Among them, 118 peptides showed significantly altered serum levels between the control and lung cancer groups (p<0.01 and fold change >5.0). Subsequently we identified peptide sequences by MS/MS analysis and further assessed the reproducibility of Expressionist-based quantification results and their diagnostic powers by MRM-based relative-quantification analysis for 96 independently prepared serum samples and found that APOA4 273-283, FIBA 5-16, and LBN 306-313 should be clinically useful biomarkers for both early detection and tumor staging of lung cancer. Our peptidome profiling technology can provide simple, high-throughput, and reliable quantification of a large number of clinical samples, which is applicable for diverse peptidome-targeting biomarker discoveries using any types of biological specimens.
A Novel Method to Generate and Expand Clinical-Grade, Genetically Modified, Tumor-Infiltrating Lymphocytes (2017)

Following the clinical success achieved with the first generation of adoptive cell therapy (ACT) utilizing in vitro expanded tumor-infiltrating lymphocytes (TIL), the second and third generations of TIL ACT are evolving towards the use of genetically-modified TIL. TIL therapy generally involves the transfer of a high number of TIL, ranging from 109 to 1011 cells. One of the technical difficulties in genetically modifying TIL, using a retroviral vector, is the ability to achieve large expansion of transduced TIL, while keeping the technique suitable to a GMP (Good Manufacturing Practices) environment. Consequently, we developed and optimized a novel method for the efficient production of large numbers of GMP-grade, gene-modified TIL for the treatment of patients with ACT. The chemokine receptor CXCR2 was used as the gene of interest for methodology development. The optimized procedure is currently used in the production of gene-modified TIL for two clinical trials for the treatment of metastatic melanoma at MD Anderson Cancer Center.
Identification of the epitopes of calcitonin gene‐related peptide (CGRP) for two anti‐CGRP monoclonal antibodies by 2D NMR (1997)

The interactions between calcitonin gene-related peptide and FAB fragments prepared from two different high-affinity anti-CGRP monoclonal antibodies (CB3 and CD1) have been studied at physiological pH using the ability of 1H NMR to detect selectively regions of dynamic flexibility. The 37-residue peptide retains considerable flexibility in regions of its sequence when bound to both antibodies; in each case, more than half of the residues can be seen to have linewidths little perturbed from those of the free peptide. However the regions where substantial broadening of resonances occur, attributed to substantially reduced motional freedom of the peptide resulting from interactions within the antibody combining site, differ greatly in the two cases. In the complex with CB3 the results indicate that the restricted residues lie exclusively within the C-terminal half of the peptide, and include residues 25 to 32 and the terminal two residues (36 and 37). By contrast, in the complex with CD1, the conformationally restricted residues appear to lie predominantly within the N-terminal half of the CGRP molecule, particularly residues 4-16, although several residues in the middle section of the sequence (22-31) have reduced conformational freedom. These findings, consistent with the results from immunological assays, add considerably to our knowledge of the epitopes.
Transparent luminescent silicone nanocomposites filled with bimodal PDMS-brush-grafted CdSe quantum dots (2012)

We report a simple and effective approach to disperse CdSe quantum dots (QDs) into a high molecular weight silicone matrix and prepare highly transparent luminescent CdSe–silicone nanocomposites. The CdSe QDs were synthesized via a room temperature injection method and were subsequently grafted with organophosphate-terminated poly(dimethyl siloxane) (PDMS) brushes. It was found that the bimodal PDMS-brush-grafted QDs demonstrate a homogeneous dispersion within the high molecular weight silicone matrix, enabling the preparation of thick transparent CdSe–silicone nanocomposites. The good dispersion also benefits the uniformity and long-term stability of the photoluminescence of the CdSe–silicone nanocomposites against thermal annealing. The prepared CdSe–silicone nanocomposites would have potential applications as color-conversion materials on light emitting diodes. This dispersing strategy could be broadly applicable and provides valuable guidelines for dispersing other functional nanoparticles in silicones.
The GuideCane-applying mobile robot technologies to assist the visually impaired (2001)

The GuideCane is a device designed to help blind or visually impaired users navigate safely and quickly among obstacles and other hazards. During operation, the user pushes the lightweight GuideCane forward. When the GuideCane's ultrasonic sensors detect an obstacle, the embedded computer determines a suitable direction of motion that steers the GuideCane and the user around it. The steering action results in a very noticeable force felt in the handle, which easily guides the user without any conscious effort on his/her part.
On the sum rate of channel subspace feedback for multi-antenna broadcast channels (2005)

When a base-station with multiple antennas is transmitting to a single user with one antenna, feeding back the normalized channel vector (channel subsapce feedback) to the transmitter can achieve the same capacity as if the exact channel state information is available at the transmitter. For the multiuser scenario, however, perfect channel knowledge is usually required at the transmitter to obtain the sum rate advantage provided by the multiple transmit antennas. In this paper, we consider the sum rate of a multi-antenna broadcast channel when each user only feeds back the normalized channel vector. We show that in such situation the zero-forcing dirty paper (ZFDP) encoding scheme designed using channel subspace feedback achieves the throughput of full channel knowledge ZFDP encoding without optimal power allocation. It is shown to be asymptotically optimal for high signal-to-noise ratios. The closed-form expression of the ergodic sum rate for an independent Rayleigh fading channel is derived. The throughput performance of the regularized channel inversion technique under channel subspace feedback is also analyzed. We show that channel subspace feedback in the multi-antenna broadcast channel enables the system to achieve most of the sum rate advantage provided by the multiple antennas.
Vip3A, a novel Bacillus thuringiensis vegetative insecticidal protein with a wide spectrum of activities against lepidopteran insects. (1996)

A novel vegetative insecticidal gene, vip3A(a), whose gene product shows activity against lepidopteran insect larvae including black cutworm (Agrotis ipsilon), fall armyworm (Spodoptera frugiperda), beet armyworm (Spodoptera exigua), tobacco budworm (Heliothis virescens), and corn earworm (Helicoverpa zea) has been isolated from Bacillus thuringiensis strain AB88. VIP3-insecticidal gene homologues have been detected in approximately 15% of Bacillus strains analyzed. The sequence of the vip3A(b) gene, a homologue of vip3A(a) isolated from B. thuringiensis strain AB424 is also reported. Vip3A(a) and (b) proteins confer upon Escherichia coli insecticidal activity against the lepidopteran insect larvae mentioned above. The sequence of the gene predicts a 791-amino acid (88.5 kDa) protein that contains no homology with known proteins. Vip3A insecticidal proteins are secreted without N-terminal processing. Unlike the B. thuringiensis 5-endotoxins, whose expression is restricted to sporulation, Vip3A insecticidal proteins are expressed in the vegetative stage of growth starting at mid-log phase as well as during sporulation. Vip3A represents a novel class of proteins insecticidal to lepidopteran insect larvae.
On-Chip Millionfold Sample Stacking Using Transient Isotachophoresis (2006)

We present a simple and robust isotachophoresis (ITP) method that can be integrated with microchip-based capillary electrophoresis (CE) devices to achieve millionfold sample stacking. We performed an experimental parametric study to show the effects of initial sample ion concentration, leading ion concentration, and trailing ion concentration on ITP stacking. We also discuss the usefulness and limitations of a simple one-dimensional nondispersive model and a scaling analysis for dispersion rate. We found that a single-column ITP configuration together with electroosmotic flow suppression and high leading ion concentration provide high-performance ITP and can be integrated readily with CE separation. We demonstrated detection of trace of 100 fM Alexa Fluor 488 (signal-to-noise ratio of 11) with a concentration increase of a factor of 2 × 106. Application of our ITP/CE protocol to the stacking and separation of negatively charged fluorescent tracers (Alexa Fluor 488 and bodipy) resulted in a concentration increase of 6.4 × 104 and a signal increase of 4.5 × 105. The ITP/CE protocol can be performed with a standard microchannel cross design or simple flow control. The method can be implemented with available off-the-shelf chip systems using off-the-shelf voltage control systems and buffer chemistries.
Trabeculectomy With Intraoperative 5-Fluorouracil (1998)

* BACKGROUND AND OBJECTIVE: To investigate the outcome and complication rates of trabeculectomy following the combined use of intraoperative, topical 5-fluorouracil (5-FU) and low-dose, postoperative subconjunctival 5-FU injections. * PATIENTS AND METHODS: Forty-one eyes of 41 patients with advanced, medically uncontrolled glaucoma underwent trabeculectomy with intraoperative episcleral application of 5-FU (50 mg/ml for 5 minutes). A variable number of subconjunctival 5-FU injections were administered postoperatively at the discretion of the operating surgeon. * RESULTS: Six-, 12-, and 15-month life-table success rates (5 mm Hg ≤ intraocular pressure [IOP ≤ 21 mm Hg) were 100%, 97%, and 83%, respectively. Mean postoperative IOP was 12.1 ± 4.3 mm Hg. An average of 2.2 ± 1.6 (range 0 to 7) supplemental subconjunctival 5-FU injections were administered postoperatively. Corneal epithelial erosions developed in 7 (17%) of the eyes. Five of 7 patients who underwent subsequent surgical procedures maintained successful control of IOP at an average of 11.0 ± 4.8 (range 5 to 16) months after the secondary surgery. * CONCLUSION: Trabeculectomy with intraoperative 5-FU is effective in controlling IOP while possibly minimizing the need for frequent postoperative injections and the occurrence of corneal epitheliopathy. [Ophthalmic Surg Lasers 1998;29:552-561.]
Automatic identification of cochlear implant electrode arrays for post-operative assessment (2011)

Cochlear implantation is a procedure performed to treat profound hearing loss. Accurately determining the postoperative position of the implant in vivo would permit studying the correlations between implant position and hearing restoration. To solve this problem, we present an approach based on parametric Gradient Vector Flow snakes to segment the electrode array in post-operative CT. By combining this with existing methods for localizing intra-cochlear anatomy, we have developed a system that permits accurate assessment of the implant position in vivo. The system is validated using a set of seven temporal bone specimens. The algorithms were run on pre- and post-operative CTs of the specimens, and the results were compared to histological images. It was found that the position of the arrays observed in the histological images is in excellent agreement with the position of their automatically generated 3D reconstructions in the CT scans.
Post-transcriptional control of immune responses via RNA binding proteins (2018)

Cytokines are critical mediators of immune responses caused by infection with pathogens. Proinflammatory cytokines are produced by innate immune cells upon sensing of pathogens by Toll-like receptors (TLRs). The expression of proinflammatory cytokines is controlled at the transcriptional and post-transcriptional levels. Post-transcriptional control of cytokine mRNAs is critical for preventing excess and persistent production of cytokines by degrading them via a set of RNA binding proteins (RBPs) recognizing cis-elements present in the mRNA 3'-untranslated region. Among RBPs, Roquin recognizes stem-loop structures present in mRNAs encoding inflammatory proteins and degrades them by recruiting a CCR4-NOT deadenylase complex to its target mRNAs. Roquin-mutant mice spontaneously develop autoimmunity by elevated expression of ICOS on T cells and enhanced production of TNF in innate immune cells. We identified Regnase-1 (also known as Zc3h12a) as an endonuclease essential for degradation of inflammation-related mRNAs such as Il6 induced by TLR stimuli in innate immune cells. Regnase-1 is also critical for suppressing activation of T cells and maintenance of immune homeostasis in mice. We found that Regnase-1 and Roquin regulate an overlapping set of mRNAs via a common stem-loop structure. However, Regnase-1 and Roquin function in distinct subcellular locations: ribosome/endoplasmic reticulum and processing-body/stress granules, respectively. Moreover, Regnase-1 specifically degrades translationally active mRNAs depending on UPF1, a helicase essential for the nonsense-mediated mRNA decay. Regnase-1 and Roquin control early and late phase of inflammation, respectively. Interestingly, Regnase-1 recognizes inflammatory mRNAs undergoing pioneer rounds of translation, which is triggered by the phosphorylation of UPF1 by a kinase SMG1. Taken together, our findings reveal that differential regulation of immune-related mRNAs by two RNA binding proteins, Regnase-1 and Roquin, depends on their translation status and enables elaborate control of inflammation. We have recently discovered that Regnase-1 is expressed not only in the immune cells, but also in airway epithelial cells (AECs). Regnase-1 controls distinct sets of genes in AECs and T cells, Regnase-1 orchestrates AEC- and immune cell-mediated host defense against pulmonary bacterial infection. These results underscore the importance of post-transcriptional regulation in coordinating immune reactions.
On the Track to Silica-Supported Tungsten Oxo Metathesis Catalysts: Input from 17O Solid-State NMR (2013)

The grafting of an oxo chloro trisalkyl tungsten derivative on silica dehydroxylated at 700 °C was studied by several techniques that showed reaction via W-Cl cleavage, to afford a well-defined precatalyst for alkene metathesis. This was further confirmed by DFT calculations on the grafting process. (17)O labeling of the oxo moiety of a series of related molecular and supported tungsten oxo derivatives was achieved, and the corresponding (17)O MAS NMR spectra were recorded. Combined experimental and theoretical NMR studies yielded information on the local structure of the surface species. Assessment of the (17)O NMR parameters also confirmed the nature of the grafting pathway by ruling out other possible grafting schemes, thanks to highly characteristic anisotropic features arising from the quadrupolar and chemical shift interactions.
Dendritic cells process exogenous viral proteins and virus‐like particles for class I presentation to CD8+ cytotoxic T lymphocytes (1996)

Previous reports have indicated that both dendritic cells and macrophages have the ability to induce cytotoxic T lymphocyte (CTL) and T helper (Th) cell responses in vivo. Dendritic cells process exogenous antigens conventionally for presentation on major histocompatibility complex (MHC) class II molecules. However, unconventional processing of exogenous antigens in vitro for presentation on MHC class I molecules is still an open question. In this study, we report that a cloned dendritic cell line (D2SC/1) is able to present cell debris-associated exogenous viral proteins to MHC class I-restricted CTL in vitro. The dendritic cell line was very efficient in processing recombinant lymphocytic choriomeningitis virus nucleoprotein (LCMV NP) and presenting the class I-restricted epitope to CTL primed in vivo. Peritoneal macrophages could also process the recombinant LCMV NP for subsequent MHC class I presentation, but were less efficient compared to the dendritic cells. Furthermore, recombinant yeast-derived virus-like particles carrying the HIV-1 V3 loop (V3-VLP), which are protenaceous and do not contain any lipid, were also found to be efficiently processed by the dendritic cell line for presentation of the class I-restricted epitope. These results clearly indicate that viral proteins, in particulate form or associated with cell debris, are processed by dendritic cells for CTL induction.
Monoclonal antibodies specific for the alpha subunit of the Escherichia coli DNA polymerase III holoenzyme. (1984)

We have established three murine hybridoma cell lines that secrete monoclonal antibodies directed specifically against the alpha subunit of the DNA polymerase III holoenzyme of Escherichia coli. All three antibodies have been purified and identified to be of the IgM class. competition binding assays indicate that these antibodies bind to at least two distinct but adjacent or interacting sites. An immunoblot assay has been developed that permits quantitation of alpha in crude extracts. These assays agree with previous determinations of the number of polymerase molecules present/cell and indicate that the size of alpha is the same in both the crude and pure form. Anti-alpha IgM can be used with fixed Staphylococcus aureus, cells and anti-IgM to specifically precipitate alpha.
Third‐generation Blood Pumps With Mechanical Noncontact Magnetic Bearings (2006)

This article reviews third-generation blood pumps, focusing on the magnetic-levitation (maglev) system. The maglev system can be categorized into three types: (i) external motor-driven system, (ii) direct-drive motor-driven system, and (iii) self-bearing or bearingless motor system. In the external motor-driven system, Terumo (Ann Arbor, MI, U.S.A.) DuraHeart is an example where the impeller is levitated in the axial or z-direction. The disadvantage of this system is the mechanical wear in the mechanical bearings of the external motor. In the second system, the impeller is made into the rotor of the motor, and the magnetic flux, through the external stator, rotates the impeller, while the impeller levitation is maintained through another electromagnetic system. The Berlin Heart (Berlin, Germany) INCOR is the best example of this principle where one-axis control combination with hydrodynamic force achieves high performance. In the third system, the stator core is shared by the levitation and drive coil to make it as if the bearing does not exist. Levitronix CentriMag (Zürich, Switzerland), which appeared recently, employs this concept to achieve stable and safe operation of the extracorporeal system that can last for a duration of 14 days. Experimental systems including HeartMate III (Thoratec, Woburn, MA, U.S.A.), HeartQuest (WorldHeart, Ottawa, ON, Canada), MagneVAD (Gold Medical Technologies, Valhalla, NY, U.S.A.), MiTiHeart (MiTi Heart, Albany, NY, U.S.A.), Ibaraki University's Heart (Hitachi, Japan) and Tokyo Medical and Dental University/Tokyo Institute of Technology's disposable and implantable maglev blood pumps are also reviewed. In reference to second-generation blood pumps, such as the Jarvik 2000 (Jarvik Heart, New York, NY, U.S.A.), which is showing remarkable achievement, a question is raised whether a complicated system such as the maglev system is really needed. We should pay careful attention to future clinical outcomes of the ongoing clinical trials of the second-generation devices before making any further remarks. What is best for patients is the best for everyone. We should not waste any efforts unless they are actually needed to improve the quality of life of heart-failure patients.
Geographic location tags on digital images (2003)

We describe an end-to-end system that capitalizes on geographic location tags for digital photographs. The World Wide Media eXchange (WWMX) database indexes large collections of image media by several pieces of metadata including timestamp, owner, and critically, location stamp. The location where a photo was shot is important because it says much about its semantic content, while being relatively easy to acquire, index, and search.The process of building, browsing, and writing applications for such a database raises issues that have heretofore been un- addressed in either the multimedia or the GIS community. This paper brings all of these issues together, explores different options, and offers novel solutions where necessary. Topics include acquisition of location tags for image media, data structures for location tags on photos, database optimization for location-tagged image media, and an intuitive UI for browsing a massive location-tagged image database. We end by describing an application built on top of the WWMX, a lightweight travelogue-authoring tool that automatically creates appropriate context maps for a slideshow of location-tagged photographs.
Integrating human factors with system development methods: an overview of a structured human factors method (1992)

The typical involvement of human factors (HF) only at the evaluation stage of system development often results in poor realisation of HF contributions. By emulating the characteristics of SADMs, a structured HF method that covers the system design cycle is developed. Since the method complies with the requirements of a SADM it is expected to inherit the desirable characteristics of SADMs (e.g. the benefits of systematic analysis and design). Also, by recruiting existing national schemes of SADMs, the communication of HF design products to software engineers is also facilitated. In addition, structured integration of software engineering and HF design could be achieved effectively by integrating a particular SADM with the described structure HF method. To this end, the explicit characteristics of both methods would support the identification of design inter-dependencies between the disciplines. The relevance (e.g. scope and timeliness) and applicability (e.g. format and granularity) of HF inputs with respect to the system design cycle are thus ensured. Consequently, an improved uptake of HF may be expected to accrue.
Contribution of damage-associated molecular patterns to transfusion-related acute lung injury in cardiac surgery. (2014)

No evidence was found that HMGB1 and sRAGE contribute to the development of TRALI. S100A12 is associated with duration of cardiopulmonary bypass, pulmonary inflammation, hypoxia and prolonged mechanical ventilation and may contribute to acute lung injury in cardiac surgery patients.