gebhart/patrepeval huggingface dataset:
CD4+ and CD8+ T-Cell Skewness in Classic Kaposi Sarcoma (2012)

It is widely accepted that a deranged immune system plays a key role in the onset and evolution of classic Kaposi sarcoma (CKS). Nevertheless, the usage of the T-cell receptor (TCR) β-variable (BV) chain repertoire expressed by peripheral blood lymphocytes in patients with CKS is still unknown. With the aim of providing some further insights into the complex role of the immune system in CKS pathogenesis, we performed an extensive analysis of the TCR BV repertoire in both CD4(+) and CD8(+) T cells in 30 human herpesvirus 8-positive Sardinian patients with CKS and an equal number of age-matched healthy controls. We used a panel of monoclonal antibodies covering approximately 70% of human BV subfamilies and third complementarity determining region (CDR3) spectratyping. Patients with CKS showed an increased frequency of BV expansions in both CD4(+) and CD8(+) lymphocytes, with no prevalent clones. On spectratyping analysis, most of the 720 BV CDR3 profiles obtained from both CD4(+) and CD8(+) T cells in patients with CKS were skewed. In particular, the surprising increase of BV skewing observed in CD4(+) lymphocytes mimics the pattern of progressive TCR BV narrowing described in responses to persistent viral antigen stimulations. Our findings support the hypothesis that CKS evolution is associated with inadequate activation rather than impairment of the immune system.
Motif-Raptor: a cell type-specific and transcription factor centric approach for post-GWAS prioritization of causal regulators (2021)

Supplementary data are available at Bioinformatics online.
Placental immunomodulator ferritin, a novel immunoregulator, suppresses experimental arthritis (2003)

Human PLIF and C48 were shown to exert cross-species immunosuppressive activity in vitro. The in vivo suppression of articular inflammation in the experimental models of ZIA and AIA was the result of treatment with the antiinflammatory human C48. These results suggest that treatment with C48 may offer an effective immunotherapeutic means of controlling inflammatory polyarthritis.
Self-Assembly of Heteroleptic [Cu(dipyrrinato)(hfacac)] Complexes Directed by Fluorine−Fluorine Interactions (2005)

Heteroleptic copper(II) complexes were synthesized from three different meso-substituted pyridyl- and quinoline-dipyrrinato ligands (3-pyrdpm, 3-quindpm, and 4-quindpm). Metal complexes were prepared with both acetylacetonate (acac) and hexafluoroacetylactonate (hfacac) ancillary ligands. The complexes undergo a self-complementary self-assembly process upon crystallization to generate a range of solid-state topologies including one-dimensional coordination polymers and discrete hexameric rings. The self-assembly of these molecular aggregates is driven by metal-ligand bonding, but is also modulated by fluorine-fluorine interactions. Perfluorination of the spectator ligand tends to generate more compact structures, which is attributed to aggregation of the perfluoromethyl groups. The results presented here demonstrate that fluorine-fluorine contacts can be used to modulate supramolecular structures in the solid state.
A major antigen from Mycobacterium tuberculosis which is homologous to the heat shock proteins groES from E.coli and the htpA gene product of Coxiella burneti (1988)

Journal Article A major antigen from Mycobacterium tuberculosis which is homologous to the heat shock proteins groES from E.coli and the htpA gene product of Coxiella burneti Get access Paul N. Baird, Paul N. Baird Department of Medical Microbiology, London Hospital Medical CollegeTurner St., London, E1 2AD, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Lucinda M.C. Hall, Lucinda M.C. Hall Department of Medical Microbiology, London Hospital Medical CollegeTurner St., London, E1 2AD, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Anthony R.M. Coates Anthony R.M. Coates Department of Medical Microbiology, London Hospital Medical CollegeTurner St., London, E1 2AD, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 18, 26 September 1988, Page 9047, https://doi.org/10.1093/nar/16.18.9047 Published: 26 September 1988 Article history Received: 15 August 1988 Published: 26 September 1988
Scalable Real-Time Flock Detection (2016)

Smart Cities services and applications can generate massive amounts of data to be processed in real-time, including the ones regarding moving objects. The ability to handle fast streams of data, especially detecting movements of groups of objects, is of paramount importance for the advance of such services. In this paper, we address the challenge of scalability for real-time detection trajectories of flocks, in the context of smart cities. The Bitmap Disk Filtering (BitDF) is an scalable algorithm capable of handling large-scale datasets. Performance evaluation results shows that, when compared to the current state-of-the- art algorithm, BitDF can reduce 99% of the processing time while not affecting accuracy. We prove the efficiency of BitDF by performing evaluation with both real and synthetic large datasets. BitDF is then very suitable to meet the requirements of real-time applications for a variety of trajectory-based applications.
Mechanical failure of the Mobi-C implant for artificial cervical disc replacement: report of 4 cases (2020)

Cervical spondylosis is one of the most commonly treated conditions in neurosurgery. Increasingly, cervical disc replacement (CDR) has become an alternative to traditional arthrodesis, particularly when treating younger patients. Thus, surgeons continue to gain a greater understanding of short- and long-term complications of arthroplasty. Here, the authors present a series of 4 patients initially treated with Mobi-C artificial disc implants who developed postoperative neck pain. Dynamic imaging revealed segmental kyphosis at the level of the implant. All implants were locked in the flexion position, and all patients required reoperation. This is the first reported case series of symptomatic segmental kyphosis after CDR.
Protein induced lipid demixing in homogeneous membranes (2021)

Specific lipid environments are necessary for the establishment of protein signaling platforms in membranes, yet their origin has been highly debated. We present a continuum, exactly solvable model of protein induced local demixing of lipid membranes. The coupling between a local composition and a local thickness of the membrane induces lipid domains around inclusions with hydrophobic mismatch, even for temperatures above the miscibility critical point of the membrane. The model qualitatively explains the experimentally observed formation of lipid domains induced by anchoring of reconstituted actin in flat supported lipid bilayers.
Delayed Reimplantation Arthroplasty for Candidal Prosthetic Joint Infection: A Report of 4 Cases and Review of the Literature (2002)

Fungal prosthetic joint infection (PJI) is rare, with Candida species being the most frequently reported pathogen in the medical literature. The risk of relapse following delayed reimplantation arthroplasty for candidal PJI is unknown. We describe 4 new cases and summarize 6 previously reported cases of candidal PJI treated with delayed reimplantation arthroplasty. Ninety percent of the patients received antifungal therapy. Eight patients received amphotericin B either alone or in combination with other antifungals. One patient received fluconazole alone. The median duration of time from resection arthroplasty to reimplantation for total hip and total knee arthroplasties was 8.6 and 2.3 months, respectively. Eight patients did not have relapse of candidal PJI following delayed reimplantation arthroplasty after a median duration of follow-up of 50.7 months (range, 2--73 months). Candidal PJI can be successfully treated with delayed reimplantation arthroplasty after receipt appropriate antifungal therapy.
Synthesis, Optical Properties, and Aggregation Behavior of a Triad System Based on Perylene and Oligo(p-phenylene vinylene) Units (2002)

A donor-acceptor-donor triad molecule with a perylene bisimide derivative as electron acceptor, and an oligo(p-phenylene vinylene) (OPV) derivative as electron donor was synthesized (OPV-PERY-OPV). The structure of the triad was characterized by (1)H and (13)C NMR spectroscopy, size-exclusion chromatography (SEC), and MALDI-TOF spectrometry. Absorbance spectra and CD spectroscopic measurements of the triad molecule indicated the formation of aggregates in solvents such as toluene, chloroform, and tetrachloroethane, whereas it was present in the molecularly dissolved state in THF. The (1)H NMR spectra of the molecule in chloroform had, unexpectedly, four doublet peaks for the perylene protons, instead of the two doublets that is generally seen in N,N'-substituted perylene molecules. To understand the aggregation behavior and the splitting of the signals in the (1)H NMR spectra, a simple model compound was synthesized, in which the OPV units were replaced by phenyl groups (Ph-PERY-Ph). (1)H NMR spectra in CDCl(3) and tetrachloroethane again had four doublet peaks for the perylene protons, whereas in THF the perylene protons gave only a single peak. NOE and COSY spectroscopy were used to assign the peaks to their corresponding perylene protons. UV/Vis and CD spectroscopic measurements indicated that, similar to the OPV-PERY-OPV triad molecule, the model compound Ph-PERY-Ph was also present in the aggregated form in solvents such as toluene, chloroform, and tetrachloroethane, and in the molecularly dissolved state in THF. IR measurements of the model molecule in the first set of solvents indicated carbamate bond (bond;OCObond;NHbond;)-induced intermolecular hydrogen bonding, whereas in THF, the molecule was mostly present in the free form. CPK models with a dimeric structure, in which two perylene molecules are held together by intermolecular hydrogen bonding with the perylene core shifted slightly with respect to one another, could account for the optical properties and the observation of the four different peaks in the (1)H NMR spectra in polar solvent. Temperature-dependent (1)H NMR spectroscopic, UV/Vis, and CD measurements indicated that the transition from the aggregated to the molecularly dissolved state took place at higher temperatures. The electrochemical studies indicated that OPV-PERY-OPV was both p- and n-dopable, whereas Ph-PERY-Ph was only n-dopable. Cyclic voltammetry measurements of Ph-PERY-Ph in THF had two reduction peaks corresponding to the reduction of the perylene core to the monoanion and dianion, respectively. In dichloromethane, however, an additional reduction peak at lower potential was observed. This new reduction peak might arise from the hydrogen-bonded species.
STAP-2 protein promotes prostate cancer growth by enhancing epidermal growth factor receptor stabilization (2017)

Signal-transducing adaptor family member-2 (STAP-2) is an adaptor protein that regulates various intracellular signaling pathways and promotes tumorigenesis in melanoma and breast cancer cells. However, the contribution of STAP-2 to the behavior of other types of cancer cells is unclear. Here, we show that STAP-2 promotes tumorigenesis of prostate cancer cells through up-regulation of EGF receptor (EGFR) signaling. Tumor growth of a prostate cancer cell line, DU145, was strongly decreased by STAP-2 knockdown. EGF-induced gene expression and phosphorylation of AKT, ERK, and STAT3 were significantly decreased in STAP-2-knockdown DU145 cells. Mechanistically, we found that STAP-2 interacted with EGFR and enhanced its stability by inhibiting c-CBL-mediated EGFR ubiquitination. Our results indicate that STAP-2 promotes prostate cancer progression via facilitating EGFR activation.
Electron Enhanced Growth of Crystalline Gallium Nitride Thin Films at Room Temperature and 100 °C Using Sequential Surface Reactions (2016)

Low energy electrons may provide mechanisms to enhance thin film growth at low temperatures. As a proof of concept, this work demonstrated the deposition of gallium nitride (GaN) films over areas of ∼5 cm<sup>2</sup> at room temperature and 100 °C using electrons with a low energy of 50 eV from an electron flood gun. The GaN films were deposited on Si(111) wafers using a cycle of reactions similar to the sequence employed for GaN atomic layer deposition (ALD). Trimethylgallium (Ga(CH<sub>3</sub>)<sub>3</sub>, TMG), hydrogen (H) radicals and ammonia (NH<sub>3</sub>) were employed as the reactants with electron exposures included in the reaction cycle after the TMG/H and NH<sub>3</sub> exposures. A number of <i>ex situ</i> techniques were then employed to analyze the GaN films. Spectroscopic ellipsometry measurements revealed that the GaN films grew linearly with the number of reaction cycles. Linear growth rates of up to 1.3 Å/ cycle were obtained from the surface areas receiving the highest electron fluxes. Grazing incidence X-ray diffraction analysis revealed polycrystalline GaN films with the wurtzite crystal structure. Transmission electron microscopy (TEM) images showed crystalline grains with diameters between 2 and 10 nm depending on the growth temperature. X-ray photoelectron spectroscopy depth-profiling displayed no oxygen contamination when the GaN films were capped with Al prior to atmospheric exposure. However, the carbon concentrations in the GaN films were 10-35 at. %. The mechanism for the low temperature GaN growth is believed to result from the electron stimulated desorption (ESD) of hydrogen. Hydrogen ESD yields dangling bonds that facilitate Ga-N bond formation. Mass spectrometry measurements performed concurrently with the reaction cycles revealed increases in the pressure of H<sub>2</sub> and various GaN etch products during the electron beam exposures. The amount of H<sub>2</sub> and GaN etch products increased with electron beam energy from 25 to 200 eV. These results indicate that the GaN growth occurs with competing GaN etching during the reaction cycles.
The genome of the green anole lizard and a comparative analysis with birds and mammals (2011)

The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.
Chemical Processing in High-Pressure Aqueous Environments. 4. Continuous-Flow Reactor Process Development Experiments for Organics Destruction (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical Processing in High-Pressure Aqueous Environments. 4. Continuous-Flow Reactor Process Development Experiments for Organics DestructionDouglas C. Elliott, M. R. Phelps, L. John Sealock Jr., and Eddie G. BakerCite this: Ind. Eng. Chem. Res. 1994, 33, 3, 566–574Publication Date (Print):March 1, 1994Publication History Published online1 May 2002Published inissue 1 March 1994https://pubs.acs.org/doi/10.1021/ie00027a013https://doi.org/10.1021/ie00027a013research-articleACS PublicationsRequest reuse permissionsArticle Views667Altmetric-Citations100LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A note on Helly’s theorem (1955)

The aim of this note is to give a new elementary proof of Helly's theorem [l] on the intersection of convex sets in n dimensional Euclidean space E n . Like other elementary proofs, our proof avoids the use of limit concepts and is thus valid for any n dimensional affine space with coordinates in a real number field. In 3 we remark that Carathe'odory's theorem on convex hulls may be derived from Helly's theorem. This is a reverse procedure of the one adopted iby Rademacher and Schoenberg We shall prove the following version of Helly's theorem.
Ultra-Low-Loss Silicon Waveguides for Heterogeneously Integrated Silicon/III-V Photonics (2018)

Integrated ultra-low-loss waveguides are highly desired for integrated photonics to enable applications that require long delay lines, high-Q resonators, narrow filters, etc. Here we present an ultra-low-loss silicon waveguide on 500 nm thick SOI platform. Meter-scale delay lines, million-Q resonators and tens of picometer bandwidth grating filters are experimentally demonstrated. We design a low-loss low-reflection taper to seamlessly integrate the ultra-low-loss waveguide with standard heterogeneous Si/III-V integrated photonics platform to allow realization of high-performance photonic devices such as ultra-low-noise lasers and optical gyroscopes.
Experimental evaluation of digitally-verifiable photonic computing for blockchain and cryptocurrency (2022)

As blockchain technology and cryptocurrency become increasingly mainstream, ever-increasing energy costs required to maintain the computational power running these decentralized platforms create a market for more energy-efficient hardware. Photonic cryptographic hash functions, which use photonic integrated circuits to accelerate computation, promise energy efficiency for verifying transactions and mining in a cryptonetwork. Like many analog computing approaches, however, current proposals for photonic cryptographic hash functions that promise similar security guarantees as Bitcoin are susceptible to systematic error, so multiple devices may not reach a consensus on computation despite high numerical precision (associated with low photodetector noise). In this paper, we theoretically and experimentally demonstrate that a more general family of robust discrete analog cryptographic hash functions, which we introduce as LightHash, leverages integer matrix-vector operations on photonic mesh networks of interferometers. The difficulty of LightHash can be adjusted to be sufficiently tolerant to systematic error (calibration error, loss error, coupling error, and phase error) and preserve inherent security guarantees present in the Bitcoin protocol. Finally, going beyond our proof-of-concept, we define a ``photonic advantage'' criterion and justify how recent developments in CMOS optoelectronics (including analog-digital conversion) provably achieve such advantage for robust and digitally-verifiable photonic computing and ultimately generate a new market for decentralized photonic technology.
Prophylactic transfer of CD8-depleted donor lymphocytes after T-cell–depleted reduced-intensity transplantation (2006)

Allogeneic hematopoietic stem cell transplantation (SCT) regimens incorporating the lymphocytotoxic CD52 antibody alemtuzumab demonstrate efficient engraftment and reduced graft-versus-host disease (GVHD). However, these protocols substantially impair posttransplantation antiviral and antitumor immunity. To accelerate immune reconstitution after alemtuzumab-based reduced-intensity SCT, we administered prophylactic CD8-depleted donor lymphocyte infusions (DLIs) starting on days 60 and 120 after transplantation. DLIs were processed in an immunomagnetic good manufacturing practice depletion procedure resulting in a 2.5- to 6-log reduction in CD8 T cells. Of 23 high-risk patients with hematologic malignancies, 11 received a total of 21 CD8-depleted DLIs. Five patients developed transient grade I acute GVHD following transfer. Only 2 patients with HLA-C-mismatched donors showed grade II and III acute GVHD and subsequently progressed to limited chronic GVHD. Following DLIs, 4 patients with declining hematopoietic donor chimerism converted to full chimeras. A 2.1-fold median increase of circulating CD4 T cells was observed within 2 weeks after infusion. Non-DLI patients did not show a comparable rise in CD4 counts. Four patients demonstrated enhanced frequencies of cytomegalovirus-specific CD4 and CD8 T cells following transfer. Our results suggest that prophylactic CD8-depleted DLIs accelerate immune reconstitution after lymphodepleted HLA-matched SCT and carry a low risk of inducing severe GVHD.
Microfabricated therapeutic actuators and release mechanisms therefor (2023)

Microfabricated therapeutic actuators are fabricated using a shape memory polymer (SMP), a polyurethane-based material that undergoes a phase transformation at a specified temperature (Tg). At a temperature above temperature Tg material is soft and can be easily reshaped into another configuration. As the temperature is lowered below temperature Tg the new shape is fixed and locked in as long as the material stays below temperature Tg. Upon reheating the material to a temperature above Tg, the material will return to its original shape. By the use of such SMP material, SMP microtubing can be used as a retaining/release actuator for the delivery of material, such as embolic coils, for example, through catheters into aneurysms, for example. The microtubing can be manufactured in various sizes and the phase change temperature Tg is determinate for an intended temperature target and intended use. The SMP microtubing can be positioned around or within an end of a deposit material. Various heating arrangements can be utilized with the SMP release mechanism, and the SMP microtubing can include a metallic coating for enhanced light absorption.
Error recognition for rehabilitation and microsurgery (1998)

Manual positioning error is a significant problem in rehabilitation and surgical applications of human-machine interaction. Effective means for error recognition and suppression can enhance lifestyle independence for persons with movement disorders and improve task performance in microsurgery. This paper describes algorithms for real-time estimation of both tremor and non-tremor components of undesired motion. Applications in command filtering for rehabilitative humanmachine interfaces, and in an intelligent handheld microsurgical instrument for active compensation of error, are also presented.