gebhart/patrepeval huggingface dataset:
Abstract IA11: Detecting and targeting cellular heterogeneity of the lymphoid blood malignancies (2020)

Abstract Multiple lines of evidence have convincingly demonstrated tumor neoantigens as an important class of immunogenic tumor antigens, and have motivated the development of personalized cancer neoantigen targeting approaches. Neoantigens arise from amino acid changes encoded by somatic mutations in the tumor cell and have the potential to bind to and be presented by personal HLA molecules. Because the immune response has the capacity of addressing multiple tumor neoantigens simultaneously, immune-based therapy has a potential for directly address tumor heterogeneity. As a field, we have now successfully moved beyond the first wave proof-of-concept studies that have demonstrated the safety, feasibility and high immunogenicity of these personalized neoantigen-targeting vaccines. An imperative now is to address the challenges of discovering and optimizing the selection of antigens to target, the delivery approach, and extending this promising approach to a broader array of cancer settings. Citation Format: Catherine J. Wu. Detecting and targeting cellular heterogeneity of the lymphoid blood malignancies [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr IA11.
Thalidomide treatment for refractory Crohn's disease: a review of the history, pharmacological mechanisms and clinical literature (2001)

Several recent case reports and clinical trials have demonstrated that thalidomide is emerging as an efficacious alternative in the treatment of selected patients with refractory Crohn's disease. The effects of thalidomide are at least partly mediated by down-regulation of tumour necrosis factor (TNF)-alpha, a potent proinflammatory cytokine. However, thalidomide is also known to inhibit angiogenesis, and it has several other well-described immunomodulatory properties. Clinical studies have confirmed that previously refractory Crohn's disease patients respond to thalidomide, and many enter clinical remission. Efficacy usually occurs within 4 weeks. Thalidomide also has steroid-sparing properties, and it is particularly useful in treating oral and fistulous complications of Crohn's disease. Although it is usually tolerable, careful monitoring is recommended to prevent toxicities, such as birth defects and peripheral neuropathy. This review provides a detailed summary of the literature to date on the use of thalidomide treatment for Crohn's disease. Special attention is directed towards its history, mechanisms, and proposed role. The recent development of thalidomide analogues is also discussed briefly.
Type III hypersensitivity reactions to a B cell epitope antigen are abrogated using a depot forming vaccine platform (2017)

Peptide antigens are combined with an adjuvant in order to increase immunogenicity in vivo. The immunogenicity and safety of a RSV vaccine formulated in a novel oil-based platform, DepoVax™ (DPX), was compared to an alum formulation. A peptide B cell epitope derived from RSV small hydrophobic ectodomain (SHe) served as the antigen. Both vaccines induced SHe-specific antibodies after immunization of mice. A single dose of the DPX-based formulation resulted in anti-SHe titres for up to 20 weeks. Boosting with Alum-SHe, but not with DPX-SHe, led to unexpected clinical signs such as decreased activity, cyanosis and drop in body temperature in mice but not in rabbits. The severity of adverse reactions correlated with magnitude of SHe-specific IgG immune responses and decreased complement component 3 plasma levels, indicating a type III hypersensitivity reaction. By RP-HPLC analysis, we found that only 8-20% of the antigen was found to be adsorbed to alum in vitro, indicating that this antigen is likely released systemically upon injection in vivo. Clinical signs were not observed in rabbits, indicating the response correlates with peptide dose relative to size of animal. These results suggest that peptide antigens targeted to produce B cell mediated response may result in increased incidence of type III hypersensitivity reactions when delivered in non-depot forming vaccines. The DPX formulation induced strong antibody titres to the antigen without causing adverse events, likely due to the strength of the depot in vivo, and demonstrates the potential safety and immunogenicity of this platform for B cell peptide antigens.
Control of the positional relationship between a sample collection instrument and a surface to be analyzed during a sampling procedure with image analysis (2023)

A system and method utilizes an image analysis approach for controlling the collection instrument-to-surface distance in a sampling system for use, for example, with mass spectrometric detection. Such an approach involves the capturing of an image of the collection instrument or the shadow thereof cast across the surface and the utilization of line average brightness (LAB) techniques to determine the actual distance between the collection instrument and the surface. The actual distance is subsequently compared to a target distance for re-optimization, as necessary, of the collection instrument-to-surface during an automated surface sampling operation.
Supplementary data for publication from Three-Dimensional Breast Cancer Models Mimic Hallmarks of Size-Induced Tumor Progression (2023)

&lt;p&gt;Supplementary Materials and Methods&lt;/p&gt;
Thermal Imaging of Block Copolymers with Sub-10 nm Resolution (2021)

Thermal silicon probes have demonstrated their potential to investigate the thermal properties of various materials at high resolution. However, a thorough assessment of the achievable resolution is missing. Here, we present a probe-based thermal-imaging technique capable of providing sub-10 nm lateral resolution at a sub-10 ms pixel rate. We demonstrate the resolution by resolving microphase-separated PS-<i>b</i>-PMMA block copolymers that self-assemble in 11 to 19 nm half-period lamellar structures. We resolve an asymmetry in the heat flux signal at submolecular dimensions and assess the ratio of heat flux into both polymers in various geometries. These observations are quantitatively compared with coarse-grained molecular simulations of energy transport that reveal an enhancement of transport along the macromolecular backbone and a Kapitza resistance at the internal interfaces of the self-assembled structure. This comparison discloses a tip-sample contact radius of <i>a</i> ≈ 4 nm and identifies combinations of enhanced intramolecular transport and Kapitza resistance.
Enable Blind Users’ Experience in 3D Virtual Environments: The Scene Weaver Prototype (2023)

Three-dimensional virtual environments are currently inaccessible to people who are blind, as current screen-reading solutions for 2D content are not fully extensible to achieve the needed embodied spatial presence. Forefronting perceptual agency as key to any access approach for users who are blind, we offer Scene Weaving as an interactional metaphor that allows users to choose how and when they perceive the environment and the people in it. We illustrate how this metaphor can be implemented in an example prototype system. In this interactivity, users can control how and when they perceive a virtual museum environment and people within it through a range of interaction mechanisms.
Periodic organosilica hollow nanospheres as anode materials for lithium ion rechargeable batteries (2011)

Polymeric micelles with core-shell-corona architecture have been found to be the efficient colloidal templates for synthesis of periodic organosilica hollow nanospheres over a broad pH range from acidic to alkaline media. In alkaline medium, poly (styrene-b-[3-(methacryloylamino)propyl] trimethylammonium chloride-b-ethylene oxide) (PS-PMAPTAC-PEO) micelles yield benzene-silica hollow nanospheres with molecular scale periodicity of benzene groups in the shell domain of hollow particles. Whereas, an acidic medium (pH 4) produces diverse hollow particles with benzene, ethylene, and a mixture of ethylene and dipropyldisulfide bridging functionalities using poly(styrene-b-2-vinyl pyridine-b-ethylene oxide) (PS-PVP-PEO) micelles. These hollow particles were thoroughly characterized by powder X-ray diffraction (XRD), dynamic light scattering (DLS), thermogravimetric analysis (TG/DTA), Fourier transformation infrared (FTIR) spectroscopy, transmission electron microscopy (TEM), magic angle spinning-nuclear magnetic resonance ((29)Si MAS NMR and (13)CP-MAS NMR), Raman spectroscopy, and nitrogen adsorption/desorption analyses. The benzene-silica hollow nanospheres with molecular scale periodicity in the shell domain exhibit higher cycling performance of up to 300 cycles in lithium ion rechargeable batteries compared with micron-sized dense benzene-silica particles.
Production of new anthracycline antibiotics by microbial 4-O-methylation using a specific daunorubicin-negative mutant. (1992)

Microbial 4-O-methylation using a specific daunorubicin-blocked, nonproducing mutant provided the new anthracycline antibiotics 4-O-methylbetaclamycin T, 4-O-methylyellamycin A and 4-O-methyl-13-hydroxyoxaunomycin, from which 4-O-methyloxaunomycin and 4-O-methyl-6-deoxyoxaunomycin were then prepared by further photochemical N-demethylation. Antitumor activities in vitro and in vivo against L1210 cells were compared with those of their 4-O-demethyl derivatives. It was found that all the 4-O-methyl derivatives had a markedly reduced cytotoxicity in vitro as compared with the 4-O-demethyl compounds. However, some of them were endowed with a significantly improved antitumor activity in vivo.
Search for events with a pair of displaced vertices from long-lived neutral particles decaying into hadronic jets in the ATLAS muon spectrometer in $ pp $ collisions at $\sqrt{s} = 13 TeV $ (2022)

A search for events with two displaced vertices from long-lived particles (LLP) pairs using data collected by the ATLAS detector at the LHC is presented. This analysis uses 139~fb$^{-1}$ of proton-proton collision data at $\sqrt{s}=13$ TeV recorded in 2015-2018. The search employs techniques for reconstructing vertices of LLPs decaying to jets in the muon spectrometer displaced between 3 m and 14 m with respect to the primary interaction vertex. The observed numbers of events are consistent with the expected background and limits for several benchmark signals are determined. For the Higgs boson with a mass of 125 GeV, the paper reports the first exclusion limits for branching fractions into neutral long-lived particles below 0.1%, while branching fractions above 10% are excluded at 95% confidence level for LLP proper lifetimes ranging from 4 cm to 72.4 m. In addition, the paper present the first results for the decay of LLPs into into $t\overline{t}$ in the ATLAS muon spectrometer.
Enhanced LVRT Control Strategy for DFIG-Based WECS in Weak Grid (2013)

An enhanced coordinated low voltage ride-through, LVRT, control strategy for a Doubly-fed Induction generator (DFIG)-based wind energy conversion system, WECS, connected to a weak grid is presented in this paper. The compliance with the grid code commitments is also considered. A proposed decoupled double synchronous reference frame (DDSRF) current controller is adopted for the design of grid side converter, GSC, controller to counteract current oscillations during asymmetrical faults and tackle the DC link voltage run-away. For a precise detection of the grid voltage position even under severe voltage dips/unbalanced conditions, A DDSRF-PLL is proposed and analyzed to extract clean synchronization signal in order to improve the overall system performance. Moreover, a fast decomposition based positive and negative sequence algorithm is utilized for rapid fault detection and to engage the LVRT protection scheme. Furthermore, additional compensation terms are incorporated with the traditional GSC and rotor side converter, RSC, controllers to effectively suppress rotor as well as stator currents and meanwhile regulate the rotor speed. A diverse set of voltage excursions are conducted to evaluate the effectiveness of the proposed control strategy using MATLAB/SIMULINK platform.
Impact of Short-Circuit Ratio and Phase-Locked-Loop Parameters on the Small-Signal Behavior of a VSC-HVDC Converter (2014)

The impact of phase-locked loop (PLL) parameters on the dynamic and steady-state behavior of a voltage-source converter (VSC) in an HVDC transmission system is determined as a function of the system strength [parameterized by the short-circuit ratio (SCR)]. This is achieved by using a linearized small-signal model of the converter system and its controls. The model is validated via electromagnetic transients simulation of the fully detailed large signal model. An interesting result from this study is that the maximum power transfer capability of the VSC-HVDC converter is affected by the PLL gains, and that the theoretical limit (obtained from static voltage stability analysis) is approachable as the PLL gains become very small. This paper shows that gains of the PLL, particularly at low SCRs, greatly affect the operation of the VSC-HVDC converter and that operation at low SCRs approaching 1.3 is very difficult.
Photonic chip-based optical nanoscopy (2021)

A photonic chip-based approach is shown as alternative to conventional super-resolution fluorescence microscopy. By making use of photonic circuits, more compact, cost-effective and higher resolving setups can allow for a wider implementation of these techniques.
A Small Molecule Inhibitor of PDK1/PLCγ1 Interaction Blocks Breast and Melanoma Cancer Cell Invasion (2016)

Strong evidence suggests that phospholipase Cγ1 (PLCγ1) is a suitable target to counteract tumourigenesis and metastasis dissemination. We recently identified a novel signalling pathway required for PLCγ1 activation which involves formation of a protein complex with 3-phosphoinositide-dependent protein kinase 1 (PDK1). In an effort to define novel strategies to inhibit PLCγ1-dependent signals we tested here whether a newly identified and highly specific PDK1 inhibitor, 2-O-benzyl-myo-inositol 1,3,4,5,6-pentakisphosphate (2-O-Bn-InsP5), could affect PDK1/PLCγ1 interaction and impair PLCγ1-dependent cellular functions in cancer cells. Here, we demonstrate that 2-O-Bn-InsP5 interacts specifically with the pleckstrin homology domain of PDK1 and impairs formation of a PDK1/PLCγ1 complex. 2-O-Bn-InsP5 is able to inhibit the epidermal growth factor-induced PLCγ1 phosphorylation and activity, ultimately resulting in impaired cancer cell migration and invasion. Importantly, we report that 2-O-Bn-InsP5 inhibits cancer cell dissemination in zebrafish xenotransplants. This work demonstrates that the PDK1/PLCγ1 complex is a potential therapeutic target to prevent metastasis and it identifies 2-O-Bn-InsP5 as a leading compound for development of anti-metastatic drugs.
Topologically-imposed vacancies and mobile solid 3He on carbon nanotube (2022)

Low dimensional fermionic quantum systems are exceptionally interesting because they reveal distinctive physical phenomena, including among others, topologically protected excitations, edge states, frustration, and fractionalization. Our aim was to confine <sup>3</sup>He on a suspended carbon nanotube to form 2-dimensional Fermi-system. Here we report our measurements of the mechanical resonance of the nanotube with adsorbed sub-monolayer down to 10 mK. At intermediate coverages we have observed the famous 1/3 commensurate solid. However, at larger monolayer densities we have observed a quantum phase transition from 1/3 solid to an unknown, soft, and mobile solid phase. We interpret this mobile solid phase as a bosonic commensurate crystal consisting of helium dimers with topologically-induced zero-point vacancies which are delocalized at low temperatures. We thus demonstrate that <sup>3</sup>He on a nanotube merges both fermionic and bosonic phenomena, with a quantum phase transition between fermionic solid 1/3 phase and the observed bosonic dimer solid.
Functional Recombinants Designed from a Fetuin/Asialofetuin-Specific Marine Algal Lectin, Rhodobindin (2015)

Plant lectins have attracted much attention for biomedical applications including targeted drug delivery system and therapy against tumors and microbial infections. The main problem of using lectins as a biomedical tool is a batch-to-batch variation in isoforms content. The production of lectins using recombination tools has the advantage of obtaining high amounts of proteins with more precise properties, but there are only a handful of functional recombinant lectins presently available. A fetuin/asialo-fetuin specific lectin, Rhodobindin, has unique tandem repeats structure which makes it useful in exploiting for recombinant lectin. We developed three functional recombinant lectins using E. coli expression system: one from full cDNA sequence and two from fragmentary sequences of Rhodobindin. Hemagglutinating activity and solubility of the recombinant lectins were highest at OD 0.7 cell concentration at 20 °C. The optimized process developed in this study was suitable for the quality-controlled production of high amounts of soluble recombinant lectins.
Fatty acid dependent regulation of renin transcription by nuclear hormone receptor HNF‐4 (2008)

Production and release of renin are pivotal in controlling the Renin‐angiotensin‐system (RAAS), a main long‐term regulator of blood pressure and electrolyte homeostasis. In this context, the regulation of renin transcription by hormonal and nutritional agents is of fundamental interest. Fatty acid dependent transcription factors LXRalpha and PPARgamma have already been shown to affect renin gene transcription. We focussed our attention on another member of the nuclear hormone receptor family, HNF‐4, which is bound by fatty acyl CoA modulating its transcriptional activity. In co‐transfection experiments, HNF‐4 activated a luciferase reporter construct containing 5797bp upstream the transcriptional start site of the renin gene more than five‐fold. This effect could be completely abolished by the addition of omega3 fatty acids at a concentration of 500μM. Using computational methods, we identified five potential binding sites for HNF‐4 in this sequence. There is first evidence that HNF‐4 binds to these sites depending on the presence of fatty acyl CoAs. As HNF‐4 is expressed abundantly in proximal tubular cells our results could shed light on the regulation of local proximal tubular RAAS by fatty acids, indicating a new potential role of HNF‐4 in the kidney. Down‐regulation of renin gene expression may contribute to the antihypertensive effect of fish oil omega3 fatty acids.
Supplementary Tables S18-20 from Functional Kinomics Identifies Candidate Therapeutic Targets in Head and Neck Cancer (2023)

&lt;p&gt;Tables S18-20: Table S18. Secondary validation assay statistical analysis (absolute viability) Table S19. Differential viability and caspase 3/7 dependent apoptosis AUC of secondary validation assay Table S20. Statistical analysis summary differential viability and caspase 3/7 dependent apoptosis&lt;/p&gt;
Antiglomerular basement membrane disease (2010)

Antiglomerular basement membrane disease (anti-GBM disease, also known as Goodpasture’s disease) is a rare autoimmune disease caused by pathogenic autoantibodies directed against the noncollagenous, C-terminal domain of the α‎-3 chain of type IV collagen (α‎3(IV)NC1). Immunohistology is characteristic, with linear deposition of IgG (sometimes with IgA or IgM) and complement C3 along the GBMs....
TOTAL HIP ARTHROPLASTY POLYETHYLENE WEAR AT TEN YEARS: INFLUENCE OF FEMORAL OFFSET (2005)

Purpose: Polyethylene wear in total hip arthroplasty remains the most limiting factor for implant survival. Several predictive factors are well identified, but the position of the articulating pieces remains to be studied in detail. We searched for a correlation between polyethylene wear and the position of the femoral and acetabular pieces, particularly the femoral offset. Material and methods: Sixty-six patients underwent total hip arthroplasty for osteoarthritis or osteonecrosis. The patients were reviewed at 10.8 years (four bilateral prostheses). The preoperative, immediate postoperative (1 month) and last follow-up (10 years) AP pelvis views were digitalized. A dedicated software traced the different axes for measurement. Wear at ten years, femoral offset, cup eccentration or medialisation, ascent or descent, and cup inclination were measured. Results: Mean polyethylene wear was 1.23 mm at ten years with linear curve of 0.11 mm/yr. Preoperative femoral offset was restored in 71.4% of the cases. Univariate regression analysis revealed that only femoral offset was correlated with less wear at ten years. Polyethylene wear at ten years fell from 1.26 mm for preoperative offset restitution less than 98% to 1.13 mm for restitution greater than 102%. Discussion: Image processing allowed greater accuracy in the measurement of polyethylene wear. The rate of wear reported in the literature ranges from 0.1 to .015 mm/yr. Restitution of femoral offset guarantees less wear due to the reduction in the resultant force applied on the articulation as well as stress on the implants. Furthermore hip stability is improved. Several factors are involved in production of wear debris and correct restitution of the centre of rotation is only one of the elements which reduce wear. Conclusion: Wear was not excessive in this series. Among the position parameters, only femoral offset had an influence, having a beneficial effect on polyethylene wear. This emphasises the importance of having a wide variety of implants available in order to respond to the different anatomic presentations of the femur.
Rationalization of Intercalation Potential and Redox Mechanism for A2Ti3O7 (A = Li, Na) (2013)

Na2Ti3O7 was recently reported to be highly promising as a negative electrode material for Na-ion batteries, thanks to its very low intercalation voltage (0.3 V vs Na+/Na0) and high capacity (200 mAh/g). The investigation of the redox mechanism in A2Ti3O7 (A = Li, Na) upon additional alkali ion intercalation concomitant to reduction of titanium is reported in this paper. Even if the low stability of the reduced phases (A2+xTi3O7) precluded a direct study, density functional theory (DFT) calculations allowed us to propose structural models for the reduced phases (A2+xTi3O7), which were further successfully confronted to the available experimental data. The alkali atoms are octahedrally coordinated in the reduced A2+xTi3O7 phase, so that the whole resulting structure can be considered rocksalt type. The very different potentials at which ion insertion is observed for A = Li or A = Na clearly prove that analogies between lithium and sodium systems cannot be taken for granted. In this case, such findings can be fully rationalized through DFT and arise from the differences in polarizing character between lithium and sodium ions that cause, respectively, contraction and expansion of the cell volume and the destabilization of the inserted materials derived from the larger size of sodium ions.