gebhart/patrepeval huggingface dataset:
Unveiling Current Controversies in Acute Kidney Injury (2011)

Acute kidney injury (AKI) is a deadly and incompletely understood disorder in which sudden impairment of kidney function occurs secondary to one or more of a variety of underlying conditions. Mortality associated with AKI is very high and treatment is unsatisfactory. The condition primarily affects acutely ill and injured patients and disproportionably affects the elderly. Many of those that survive have permanent kidney failure and other long-term morbidities, which may include cardiovascular disease and immune dysfunction. While the term 'acute kidney injury' dates back to the early 20th century, when it was used in reference to acute mercury poisoning, it has only recently been applied to describe impaired kidney function in the setting of critical illness. In 2002, during an Acute Dialysis Quality Initiative (ADQI) conference held in Vicenza, AKI was defined using the now widely accepted consensus criteria known as RIFLE (Risk, Injury, Failure, Loss, End-Stage Kidney Disease). AKI replaced the term acute renal failure in part because of the recognition that acute impairment in renal function, even when relatively mild and far less than frank failure, was associated with worse clinical outcomes. Criteria for AKI were therefore set at small changes in serum creatinine or urine output. Thanks to consensus criteria for AKI, we now know that this condition is very common, occurring in as many as two thirds of ICU patients and about 2,100 per million population, and is associated with dramatic reductions in survival -as much as a 3-to 8-fold decrement at hospital discharge compared to controls without AKI.
Regulation of immune receptor kinase plasma membrane nanoscale organization by a plant peptide hormone and its receptors (2022)

Spatial partitioning is a propensity of biological systems orchestrating cell activities in space and time. The dynamic regulation of plasma membrane nano-environments has recently emerged as a key fundamental aspect of plant signaling, but the molecular components governing it are still mostly unclear. The receptor kinase FERONIA (FER) controls ligand-induced complex formation of the immune receptor kinase FLAGELLIN SENSING 2 (FLS2) with its co-receptor BRASSINOSTEROID-INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1), and perception of the endogenous peptide hormone RAPID ALKALANIZATION FACTOR 23 (RALF23) by FER inhibits immunity. Here, we show that FER regulates the plasma membrane nanoscale organization of FLS2 and BAK1. Our study demonstrates that akin to FER, leucine-rich repeat (LRR) extensin proteins (LRXs) contribute to RALF23 responsiveness and regulate BAK1 nanoscale organization and immune signaling. Furthermore, RALF23 perception leads to rapid modification of FLS2 and BAK1 nanoscale organization, and its inhibitory activity on immune signaling relies on FER kinase activity. Our results suggest that perception of RALF peptides by FER and LRXs actively modulates plasma membrane nanoscale organization to regulate cell surface signaling by other ligand-binding receptor kinases.
2-Amino-2-oxazolines as Subtype Selective α2 Adrenoceptor Agonists (2000)

Cyclohexylamino oxazoline 1 (AGN 190837), an analogue of 2 (Bay a6781), is a potent alpha(2) adrenoceptor agonist. On the basis of a design generated by receptor-ligand modeling, a number of cyclohexyl and norbornyl analogues were synthesized wherein the propyl group of 1 was replaced by phenylalkyl subsituents. This resulted in compound 6 being an alpha(2c) selective agonist, as well as 7 and 9 being alpha(2a)/alpha(2c) selective.
Hard X-ray Phase-Contrast Tomographic Nanoimaging (2011)

Synchrotron‐based full‐field tomographic microscopy established itself as a tool for noninvasive investigations. Many beamlines worldwide routinely achieve micrometer spatial resolution while the isotropic 100‐nm barrier is reached and trespassed only by few instruments, mainly in the soft x‐ray regime. We present an x‐ray, full‐field microscope with tomographic capabilities operating at 10 keV and with a 3D isotropic resolution of 144 nm recently installed at the TOMCAT beamline of the Swiss Light Source. Custom optical components, including a beam‐shaping condenser and phase‐shifting dot arrays, were used to obtain an ideal, aperture‐matched sample illumination and very sensitive phase‐contrast imaging. The instrument has been successfully used for the nondestructive, volumetric investigation of single, unstained cells.
Design of Alphavirus Virus-Like Particles Presenting Circumsporozoite Junctional Epitopes That Elicit Protection against Malaria (2021)

The most advanced malaria vaccine, RTS,S, includes the central repeat and C-terminal domains of the <i>Plasmodium falciparum</i> circumsporozoite protein (PfCSP). We have recently isolated human antibodies that target the junctional region between the N-terminal and repeat domains that are not included in RTS,S. Due to the fact that these antibodies protect against malaria challenge in mice, their epitopes could be effective vaccine targets. Here, we developed immunogens displaying PfCSP junctional epitopes by genetic fusion to either the N-terminus or B domain loop of the E2 protein from chikungunya (CHIK) alphavirus and produced CHIK virus-like particles (CHIK-VLPs). The structural integrity of these junctional-epitope-CHIK-VLP immunogens was confirmed by negative-stain electron microscopy. Immunization of these CHIK-VLP immunogens reduced parasite liver load by up to 95% in a mouse model of malaria infection and elicited better protection than when displayed on keyhole limpet hemocyanin, a commonly used immunogenic carrier. Protection correlated with PfCSP serum titer. Of note, different junctional sequences elicited qualitatively different reactivities to overlapping PfCSP peptides. Overall, these results show that the junctional epitopes of PfCSP can induce protective responses when displayed on CHIK-VLP immunogens and provide a basis for the development of a next generation malaria vaccine to expand the breadth of anti-PfCSP immunity.
Three-dimensional range geometry compression via phase encoding (2017)

One of the state-of-the-art methods for three-dimensional (3D) range geometry compression is to encode 3D data within a regular 24-bit 2D color image. However, most existing methods use all three color channels to solely encode 3D data, leaving no room to store other information (e.g., texture) within the same image. This paper presents a novel method which utilizes geometric constraints, inherent to the structured light 3D scanning device, to reduce the amount of data that need be stored within the output image. The proposed method thus only requires two color channels to represent 3D data, leaving one channel free to store additional information (such as a texture image). Experimental results verify the overall robustness of the proposed method. For example, a compression ratio of 3038:1 can be achieved, versus the STL format, with a root-mean-square error of 0.47% if the output image is compressed with JPEG 80%.
Production of muon-meson atoms in ultrarelativistic heavy-ion collisions (1993)

Ultrarelativistic heavy-ion collisions should produce hydrogen-atom-like Coulomb bound states of muons and mesons. Such atoms could provide a convenient way to measure the muon momentum distribution. We estimate the production rate of pion-muon atoms expected from heavy-ion colliders.
Application of triple quadrupole mass spectrometry for the characterization of antibody–drug conjugates (2019)

Antibody-drug conjugates (ADCs) are an inherently heterogeneous class of biotherapeutics, the development of which requires extensive characterization throughout. During the earliest phases of preclinical development, when synthetic routes towards the desired conjugate are being assessed, the main interest lies in the determination of the average drug-to-antibody ratio (DAR) of a given batch as well as information about different conjugation species. There has been a trend in mass spectrometry (MS)-based characterization of ADCs towards the use of high-resolving mass spectrometry for many of these analyses. Considering the high cost for such an instrument, the evaluation of cheaper and more accessible alternatives is highly motivated. We have therefore tested the applicability of a quadrupole mass analyzer for the aforementioned characterizations. Eight ADCs consisting of trastuzumab and varying stoichiometries of Mc-Val-Cit-PABC-monomethyl auristatin E conjugated to native cysteines were synthesized and served as test analytes. The average DAR value and molecular weights (Mw) of all detected chains from the quadrupole mass analyzer showed surprisingly high agreement with results obtained from a time-of-flight (TOF) mass analyzer and hydrophobic interaction chromatography (HIC)-derived values for all investigated ADC batches. Acquired Mw were within 80 ppm of TOF-derived values, and DAR was on average within 0.32 DAR units of HIC-derived values. Quadrupole mass spectrometers therefore represent a viable alternative for the characterization of ADC in early-stage development. Graphical abstract.
Recovering Fine Details for Neural Implicit Surface Reconstruction (2023)

Recent works on implicit neural representations have made significant strides. Learning implicit neural surfaces using volume rendering has gained popularity in multi-view reconstruction without 3D supervision. However, accurately recovering fine details is still challenging, due to the underlying ambiguity of geometry and appearance representation. In this paper, we present D-NeuS, a volume rendering-base neural implicit surface reconstruction method capable to recover fine geometry details, which extends NeuS by two additional loss functions targeting enhanced reconstruction quality. First, we encourage the rendered surface points from alpha compositing to have zero signed distance values, alleviating the geometry bias arising from transforming SDF to density for volume rendering. Second, we impose multi-view feature consistency on the surface points, derived by interpolating SDF zerocrossings from sampled points along rays. Extensive quantitative and qualitative results demonstrate that our method reconstructs high-accuracy surfaces with details, and outperforms the state of the art. <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup>
Wear mechanism of cBN tools in turning of hardened steel (2016)

The parameters that the effecting wear mechanism of cBN tools on the hardened steel (SCr420) turning was investigated. In the previous report, it was suggested that cutting speed had an effect on volume of crater wear and the cutting fluid had an influenced on rake face of low cBN content sintered compact. In this paper, we investigated effect of binder around cBN particles of sintered compact using coated cBN particles on the wear damage pattern. As the result, it was found that aluminum compound around cBN particle had an effect on wear damage pattern on flank face and rake face of cBN content sintered compact.
Human Umbilical Cord Blood for Transplantation Therapy in Myocardial Infarction (2012)

Cell-based therapy is a promising therapy for myocardial infarction. Endogenous repair of the heart muscle after myocardial infarction is a challenge because adult cardiomyocytes have a limited capacity to proliferate and replace damaged cells. Pre-clinical and clinical evidence has shown that cell based therapy may promote revascularization and replacement of damaged myocytes after myocardial infarction. Adult stem cells can be harvested from different sources including bone marrow, skeletal myoblast, and human umbilical cord blood cells. The use of these cells for the repair of myocardial infarction presents various advantages over other sources of stem cells. Among these are easy harvesting, unlimited differentiation capability, and robust angiogenic potential. In this review, we discuss the milestone findings and the most recent evidence demonstrating the therapeutic efficacy and safety of the transplantation of human umbilical cord blood cells as a stand-alone therapy or in combination with gene therapy, highlighting the importance of optimizing the timing, dose and delivery methods, and a better understanding of the mechanisms of action that will guide the clinical entry of this innovative treatment for ischemic disorders, specifically myocardial infarction.
Gross quaternary changes in aspartate carbamoyltransferase are induced by the binding of N-(phosphonacetyl)-L-aspartate: A 3.5-A resolution study. (1982)

The three-dimensional structure of the complex of N-(phosphonacetyl)-L-aspartate with aspartate carbamoyltransferase (carbamoylphosphate:L-aspartate carbamoyltransferase, EC 2.1.3.2) has been determined to a nominal resolution of 3.5 A by single-crystal x-ray diffraction methods. Initial phases were obtained by the method of "molecular tectonics": beginning with the structure of the CTP-protein complex, the domains of the catalytic and regulatory chains were manipulated as separate rigid bodies. The resulting coordinates were used to calculate an electron density map, which was then back transformed to give a set of calculated amplitudes and phases. Using all observed data, we obtained a crystallographic R factor between observed and calculated amplitudes Fo and Fc of 0.46. An envelope was then applied to a 2Fo - Fc map and the density was averaged across the molecular twofold axis. Two cycles of averaging yielded an R factor of 0.25. In this complex, we find that the two catalytic trimers have separated from each other along the threefold axis by 11-12 A and have rotated in opposing directions around the threefold axis such that the total relative reorientation is 8-9 degrees. This rotation places the trimers in a more nearly eclipsed configuration. In addition, two domains in a single catalytic chain have changed slightly their spatial relationship to each other. Finally, the two chains of one regulatory dimer have rotated 14-15 degrees around the twofold axis, and the Zn domains have separated from each other by 4 A along the threefold axis. These movements enlarge the central cavity of the molecule and allow increased accessibility to this cavity through the six channels from the exterior surface of the enzyme.
Quantifying adipose and fibroglandular breast tissue properties using MRI-guided NIR tomography (2005)

Hybrid NIR-MRI imaging has been used in a clinical breast imaging system to characterize breast tissue properties. The multi-spectral, frequency-domain tomography system operates inside a clinical scanner via long silica-glass optical fiber bundles and using a non-magnetic fiber-patient interface attached to a high resolution MR breast coil. Sixteen fiber bundles are positioned around the circumference of the female breast yielding 240 measurements of light transmission (amplitude and phase) at six optical wavelengths from 660-850nm through up to 12 cm of tissue. From optical measurements, we use a Newton-type algorithm to reconstruct images of tissue optical properties (absorption and scattering), and physiological tissue features such as oxy-hemoglobin [Hb-O<sub>2</sub>], deoxy-hemoglobin concentrations [Hb-R], water concentration [water], scattering amplitude, and scattering power. We are exploring the synergistic benefits of a combined NIR-MRI data set, specifically the ways in which MRI (i.e. high spatial resolution) can be used to enhance NIR (i.e. high contrast resolution) image reconstruction. A <i>priori</i> knowledge can be applied to image reconstruction in the form of spatial and spectral constraints to improve spatial resolution, contrast, and quantitative accuracy of NIR images. <i>In vivo</i> results suggest that this combined system can accurately quantify contrast between the properties of tissues present in the breast (i.e. adipose and fibroglandular) regardless of their varied and complex spatial organization. For a group of healthy female volunteers, we observe greater contrast between the properties of adipose and glandular tissues when we use MR-guidance than when we do not, and values of total hemoglobin and water content are more consistent with what is physiologically expected.
Electron impact mass spectrometry of permethylated disaccharides (1979)

The electron impact mass spectra of permethylated aldohexopyranosyl-(1 – x)-aldohexoses, where x = 1–6, are given. A scheme is presented to discriminate between the various types of glycosidic linkages. Moreover, their fragmentation mechanisms and mutual differences are examined with the aid of labelled compounds, high resolution measurements and information derived from metastable ions.
Air-silica microstructure fiber based variable optical attenuator device (2003)

We demonstrated an all-fiber variable attenuator using a tapered ASME Efficient modal field interaction between the propagating mode and tunable materials infused into the air-holes of the fiber results in a dynamic range of 30 dB, insertion loss 0.8 dB, and polarisation dispersion loss (PDL) of 0.5 dB. Further analysis of the device design, including optimization of polymer index, device length and taper diameter should result in reduced insertion loss and increased dynamic range.
Reduced current collapse in multi-fingered AlGaN/GaN MOS-HEMTs with dual field plate (2017)

This paper describes suppression of current collapse by field-plate (FP) in AlGaN/GaN MOS-HEMTs. Current collapse reduction was confirmed for a multi-gate fingered MOS-HEMT with a total gate width of 10 mm. Moreover, we have fabricated a 5-A class MOS-HEMT with both gate-FP and source-FP (dual-FP), showing more complete suppression in current collapse as compared to that with only gate-FP.
Perioperative Nerve Injury After Total Knee Arthroplasty (2011)

Jacob, Adam K.; Mantilla, Carlos B.; Sviggum, Hans P.; Schroeder, Darrell R.; Pagnano, Mark W.; Hebl, James R. Author Information
Reaction of the desulfoferrodoxin from Desulfoarculus baarsii with superoxide anion. Evidence for a superoxide reductase activity (2014)

International audience
Rotationally Constrained 2,4-Diamino-5,6-disubstituted Pyrimidines: A New Class of Histamine H4Receptor Antagonists with Improved Druglikeness and in Vivo Efficacy in Pain and Inflammation Models (2008)

A new structural class of histamine H 4 receptor antagonists (6-14) was designed based on rotationally restricted 2,4-diaminopyrimidines. Series compounds showed potent and selective in vitro H 4 antagonism across multiple species, good CNS penetration, improved PK properties compared to reference H 4 antagonists, functional H 4 antagonism in cellular and in vivo pharmacological assays, and in vivo anti-inflammatory and antinociceptive efficacy. One compound, 10 (A-943931), combined the best features of the series in a single molecule and is an excellent tool compound to probe H 4 pharmacology. It is a potent H 4 antagonist in functional assays across species (FLIPR Ca (2+) flux, K b < 5.7 nM), has high (>190x) selectivity for H 4, and combines good PK in rats and mice (t 1/2 of 2.6 and 1.6 h, oral bioavailability of 37% and 90%) with anti-inflammatory activity (ED 50 = 37 micromol/kg, mouse) and efficacy in pain models (thermal hyperalgesia, ED 50 = 72 micromol/kg, rat).
Graded index photonic hole: Analytical and rigorous full wave solution (2010)

We present a rigorous full wave approach to the omnidirectional photonic hole (PH), an optical system inspired by celestial phenomena and characterized by a radially graded refractive index $n(r)\ensuremath{\sim}1/{r}^{\ensuremath{\alpha}/2}$. It is analytically demonstrated that light capture is effective for $\ensuremath{\alpha}\ensuremath{\ge}{\ensuremath{\alpha}}_{c}=2$. Our analyses are corroborated by precise numerical simulations of steady-state and time-evolution behaviors. The simulations indicate that the optical energy entering the PH system can be kept in captivity for a time duration ${t}_{d}$ scaling as ${t}_{d}\ensuremath{\sim}1/({\ensuremath{\alpha}}_{c}\ensuremath{-}\ensuremath{\alpha})$ when $\ensuremath{\alpha}$ approaches ${\ensuremath{\alpha}}_{c}$. A crucial difference in the time evolution of fields is shown between the cases with $\ensuremath{\alpha}$ close to and equal to ${\ensuremath{\alpha}}_{c}$.
CoCrFeNi High-Entropy Alloy Thin Films Synthesised by Magnetron Sputter Deposition from Spark Plasma Sintered Targets (2021)

Two magnetron sputter targets of CoCrFeNi High-Entropy Alloy (HEA), both in equal atomic ratio, were prepared by spark plasma sintering. One of the targets was fabricated from a homogeneous HEA powder produced via gas atomisation; for the second target, a mixture of pure element powders was used. Economic benefits can be achieved by mixing pure powders in the intended ratio in comparison to the gas atomisation of the specific alloy composition. In this work, thin films deposited via magnetron sputtering from both targets are analysed. The surface elemental composition is investigated by X-ray photoelectron spectroscopy, whereas the bulk stoichiometry is measured by X-ray fluorescence spectroscopy. Phase information and surface microstructure are investigated using X-ray diffraction and scanning electron microscopy, respectively. It is demonstrated that the stoichiometry, phase composition and microscopic structure of the as-deposited HEA thin films are almost identical if the same deposition parameters are used.
Inside Cover: Oxygen‐binding Protein Fiber and Microgel: Supramolecular Myoglobin–Poly(acrylate) Conjugates (Chem. Asian J. 7/2016) (2016)

Neckless-like myoglobin assemblies along a poly(acrylate) chain were constructed using a supramolecular heme–heme pocket interaction. The neckless-like nanostructures of connected myoglobins were obtained using the heme-modified poly(acrylate) as a scaffold. The combination of heme-modified poly(acrylate) and an apo-form of myoglobin dimer generates a microgel encapsulating myoglobins capable of binding gas molecules. More information can be found in the Full Paper by Akira Onoda, Takashi Hayashi et al. on page 1036 in Issue 7, 2016 (DOI: 10.1002/asia.201501415).
Alternative medicine: therapeutic effects on gastric original signet ring carcinoma via ascorbate and combination with sodium alpha lipoate (2022)

This study highlights the potential of AA and LA + AA in treating gastric origin SRCC, and demonstrates the influence of order in which the drugs are administered.
The Bcl-2/Bax ratio of lymphocytes from human systemic lupus erythematosus patients (1997)

Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease. It has recently been suggested that a failure of apoptosis wherein autoreactive lymphocytes continue to survive is a major factor in the pathogenesis of SLE. Fas antigen is increased on peripheral blood lymphocytes from human SLE patients while Bcl-2 protein, which inhibits apoptosis, is highly expressed in peripheral T lymphocytes of SLE patients. The Bcl-2 family includes homologs that are believed to be related to regulation of apoptosis. Of these, Bax is capable of forming heterodimers with Bcl-2, thereby counteracting the action of Bcl-2. The present study examines the ratio of Bcl-2 to Bax in relation to the activity of SLE, with implications relating to the survival or death of lymphocytes. The ratio of Bcl-2 to Bax in active SLE was significantly higher than in inactive SLE and in normal controls. Although the exact role of apoptosis in SLE is still unclear, a high ratio of Bcl-2 to Bax in active SLE patients might support the survival of autoreactive cells.