gebhart/patrepeval huggingface dataset:
Faculty Opinions recommendation of A protein functionalization platform based on selective reactions at methionine residues. (2018)

Nature displays a remarkable ability to carry out site-selective post-translational modification of proteins, therefore enabling a dramatic increase in their functional diversity1. Inspired by this, chemical tools have evolved for the synthetic manipulation of protein structure and function, and have become essential to the continued advancement of chemical biology, molecular biology and medicine. However, the number of chemical transformations suitable for effective protein functionalization is limited because the stringent demands inherent to biological systems preclude the applicability of many potential processes2. Put simply, these chemical transformations often need to be selective at a single site on a protein, proceed with very fast reaction rates, operate under biologically ambient conditions and should provide homogeneous products with near perfect conversion2-7. While many elegant bioconjugation methods exist at cysteine, lysine and tyrosine, we reasoned that a method targeting a less explored amino acid would significantly expand the protein functionalization toolbox. Herein, we report the development of a multifacetedapproach to protein functionalization based on chemoselective labelling at methionine residues. By exploiting the unique electrophilic reactivity of a bespoke hypervalent iodine reagent, one can target the S-Me group in the side-chain of methionine. The bioconjugation reaction is fast, selective, operates at low M concentrations and is complementary to existing bioconjugation strategies. Moreover, the new reaction produces a protein conjugate that is, itself, a high energy intermediate with reactive properties that can serve as a platform for the development of secondary, visible-light mediated bioorthogonal protein functionalization processes. Taken together, the merger of these approaches provides a versatile platform for the development of distinct transformations that can deliver versatile, information-rich protein conjugates directly from the native biomacromolecules.
A linear Fick’s law calorimeter (1982)

A small animal calorimeter is described that is based on the direct application of Fick’s law. Heat flow is channeled through a circular disk of magnesium and the temperature difference between the inside and outside surface of the disk is detected by means of solid-state temperature transducers. The device is calibrated using a light-weight electrical resistive source and is shown to be linear in its response and to have an e-folding time of 4.8 min. A rat was introduced into the calorimeter and its heat energy expenditure rate was observed in both the sedated and unsedated states.
A Highly Linear Broadband CMOS LNA Employing Noise and Distortion Cancellation (2007)

This paper presents a broadband very low <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3<sup>rd</sup></i> ⁃order intermodulation inductor-less low-noise amplifier (LNA) implemented in 0.13 <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">μ</i> m CMOS technology. The LNA consists of a common-gate input stage for wideband impedance matching, followed by two parallel common source amplifiers which perform noise and distortion cancellation. Third-order distortion due to amplifier's second-order interaction is further minimized by employing a low second-order distortion PMOS/NMOS input pair. This LNA achieves +16 dBm <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">IIP<sub>3</sub></i> in both the 900 MHz and 2 GHz bands. The LNA maintains minimum internal gain 14.5 dB, noise figure below 2.6 dB from 800 MHz-2.1 GHz while drawing 11.6 mA from a supply of 1.5 V.
Analysis and design of fast settling voltage-controlled delay line with dual-input interpolating delay cells (2010)

An analysis of the delay characteristic of a voltage-controlled delay line (VCDL) exploiting a dual-input interpolating delay cell is presented and a design technique to incorporate the VCDL for a multiphase delay-locked loop is proposed. A recurrence relation of delay time of each delay cell in the VCDL and its closed-form expression show that the delay of each delay cell converges to a specific value with an error-decaying rate which depends on the weight of interpolation. A weight-adjusted delay cell is inserted to reduce the initial error and thereby the delay of the following delay cell converges fast. The validity of the analysis and the feasibility of the proposed scheme are verified by circuit simulation.
Effect of laparoscopic splenectomy on portal hypertensive gastropathy in cirrhotic patients with portal hypertension (2009)

PHG may be associated with splenomegaly, and laparoscopic splenectomy may have a beneficial effect on PHG, at least for a short time.
Mode density inside an omnidirectional mirror is heavily directional but not small (2000)

We show that ominidirectional reflection is not a sufficient signature of a photonic bandgap. Although dramatic angular redistribution takes place, the mode density of the electromagnetic field is hardly altered within the ominidirectional reflection range but rather has characteristics typical of a waveguide. The strikingly large polarization anisotropy is due to the huge dielectric contrast but not to a photonic bandgap.
User-Centered Design in New Product Development: A Case Study in Developing New Sports Earphone (2011)

A user-centered new product development process is discussed in this paper. The design of a new sports earphone is illustrated as a case study. User study methods such as questionnaires, survey, interviews and observations are used. Quantitative and qualitative methods are used to create Persona, scenario and discover user requirements. Quality Function Deployment (QFD) method is used to translate the users' requirements into technical requirements. The Analytic Hierarchy Process (AHP) is applied in QFD to quantify the user requirements, relate those elements to overall customer satisfaction goal and evaluate different design alternatives.
MilkyWay@home: Harnessing volunteer computers to constrain dark matter in the Milky Way (2013)

Abstract MilkyWay@home is a volunteer computing project that allows people from every country in the world to volunteer their otherwise idle processors to Milky Way research. Currently, more than 25,000 people (150,000 since November 9, 2007) contribute about half a PetaFLOPS of computing power to our project. We currently run two types of applications: one application fits the spatial density profile of tidal streams using statistical photometric parallax, and the other application finds the N -body simulation parameters that produce tidal streams that best match the measured density profile of known tidal streams. The stream fitting application is well developed and is producing published results. The Sagittarius dwarf leading tidal tail has been fit, and the algorithm is currently running on the trailing tidal tail and bifurcated pieces. We will soon have a self-consistent model for the density of the smooth component of the stellar halo and the largest tidal streams. The N -body application has been implemented for fitting dwarf galaxy progenitor properties only, and is in the testing stages. We use an Earth-Mover Distance method to measure goodness-of-fit for density of stars along the tidal stream. We will add additional spatial dimensions as well as kinematic measures in a piecemeal fashion, with the eventual goal of fitting the orbit and parameters of the Milky Way potential (and thus the density distribution of dark matter) using multiple tidal streams.
SCARA's race to the finish (1989)

The German Institute IPA has carried out the first comparative study of SCARA robots. After a year of tests the first results have been released.
Quasispin Glass in a Geometrically Frustrated Magnet (2013)

The spin glass state in the spinel ZnCr(2(1-x))Ga(2x)O(4) is studied with magnetization and specific heat for x < 0.05. The freezing temperature is independent of disorder, despite a two-level-like density of states that varies linearly with x. This relationship implies the energy scale for freezing is independent of disorder, in contrast to mean field theories of spin glass. We suggest that the degrees of freedom are shielded spin vacancies, quasispins, which interact via an emergent long-range force mediated by the frustrated spin background.
Synthesis of Substituted Benzene Derivatives by Homo‐ and Hetero‐Coupling of 2‐Bromobenzaldehyde and Bromovinylaldehydes Followed by McMurry Coupling. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Dynamical Mechanism May Avoid High-Oxidation State Ir(V)–H Intermediate and Coordination Complex in Alkane and Arene C–H Activation by Cationic Ir(III) Phosphine (2018)

Organometallic reaction mechanisms are assumed to be appropriately described by minimum energy pathways mapped out by density functional theory calculations. For the two-step oxidative addition/reductive elimination mechanism for C-H activation of methane and benzene by cationic Cp*(PMe<sub>3</sub>)Ir<sup>III</sup>(CH<sub>3</sub>), we report quasiclassical direct dynamics simulations that demonstrate the Ir<sup>V</sup>-H intermediate is bypassed in a significant amount of productive trajectories initiated from vibrationally averaged velocity distributions of oxidative addition transition states. This organometallic dynamical mechanism is akin to the σ-bond metathesis pathway but occurs on the oxidative addition/reductive elimination energy surface and blurs the line between two- and one-step mechanisms. Quasiclassical trajectories also reveal that the momentum of crossing the reductive elimination structure always induces complete alkane and arene dissociation from the Ir metal center, skipping weak C-H σ and π coordination complexes. This suggests that these weak coordination complexes after reductive elimination are not necessarily on the reaction pathway and likely result from a solvent cage.
Face recognition using binary image metrics (2002)

We introduce a novel methodology applicable to face matching and fast screening of large facial databases. The proposed shape comparison method operates on edge maps and derives holistic similarity measures without the explicit need for point-to-point correspondence. While the use of edge images is important to introduce robustness to changes in illumination, the lack of point-to-point matching delivers speed and tolerance to local non-rigid distortions. In particular, we propose a face similarity measure derived as a variant of the Hausdorff distance by introducing the notion of a neighborhood function and associated penalties. Experimental results on a large set of face images demonstrate that our approach produces excellent recognition results even when less than 1% of the original grey scale face image information is stored in the face database (gallery). These results implicate that the process of face recognition may start at a much earlier stage of visual processing than it was earlier suggested.
Effects of Par1a Deletion on Tubulointerstitial Fibrosis in Folic Acid Mouse Models of Renal Injury (2018)

Chronic Kidney Disease (CKD) affects 1 out of 7 adults in the United States and causes significant morbidity and mortality. Development of tubulointerstitial fibrosis, and the accompanying loss of functional tubular cells, leads to CKD progression. The Notch signaling pathway is required for renal development, however, sustained Notch activation in adult mice induces tubulointerstitial fibrosis. Dual deletion of Par1a and Par1b, serine threonine kinases, in developing mouse kidneys impaired Notch activation and resulted in the formation of abnormal glomeruli and proximal tubules. Deletion of either Par1a or 1b does not affect kidney development.We hypothesize that Par1a or 1b deletion in mice would protect against folic acid (FA) induced tubulointerstitial fibrosis.\nFA models of renal fibrosis were induced in Par1a WT and Par1a KO mice with intraperitoneal injections of 250 mg/kg FA dissolved in 300 nM NaHCO3. Mice were examined 7 days after injection—the time of earliest fibrosis and peak Notch expression. Sirius red collagen staining was used to quantify the severity of fibrosis. Immunohistochemical staining for Notch signaling components and Par1a were performed. It was observed that Par1a expression was increased after FA injection. Par1a colocalized in tubules with increased Jag1 expression. Sirius red staining demonstrated less fibrosis in Par1a KO vs. WT mice.\nTogether, our results suggest Par1a deletion may be protective against renal fibrosis. Par1-Notch interactions may be mediated by effects on Jag1. Par1-Notch signaling could be a novel target for therapeutic intervention and potentially attenuate CKD progression.
[Psychiatric and psychological consequences of abortion]. (2007)

Over the last decades a debate on the psychological and psychiatric consequences of the right to abortion took place. Abortion is a word-wide phenomenon linked to different aspects of public health. Although negative consequences are assumed to occur after abortion, most of the women who decide to terminate their pregnancy show several signs of relief. For instance, a decrease of signs of anxiety and depression may occur during the first month after abortion. Actually, the critical moment is the pre-abortion period. In this phase, most of the psychiatric and psychologic manifestations take place. Moreover, recent studies reinforce the importance to address the consequences of abortion with a multidisciplinary approach integrating somatic and psychologic components.
Decreased Ratios of Interleukin-1&lt;i&gt;β&lt;/i&gt; and Intercellular Adhesion Molecule 1 in Gingival Crevicular Fluid after Scaling and Root Planing Associated with Periodontal Pocket Healing (2017)

Objectives: Several researchers have investigated inflammatory cytokines in gingival crevicular fluid (GCF) from chronic periodontitis with clinical parameters after periodontal treatment. The aim of the present study was to identify the inflammatory cytokines present in GCF associated with periodontal pocket healing after scaling and root planing (SRP). Methods: Twenty patients were enrolled, and clinical examinations including probing pocket depth (PPD) and bleeding on probing (BOP) were performed at the first visit, and before and after SRP. The periodontal epithelial surface area (PESA) and periodontal inflamed surface area (PISA) were also calculated. GCF samples were collected before and after SRP to measure the levels of 40 inflammatory cytokines using antibody array. Correlations between changes in cytokine levels and clinical improvements were assessed by single and multiple regression analyses. Results: PPD, PESA and PISA significantly decreased after SRP, while there were no significant differences in the levels of cytokines before (PreSRP) and one week after SRP (PostSRP). Clinical improvements (ΔPPD, ΔPESA and ΔPISA) were calculated using the formula PreSRP-PostSRP, while changes in the levels of inflammatory cytokines were calculated using three formulas: PreSRP-PostSRP, PostSRP/PreSRP and Log(PostSRP/PreSRP). Log (PostSRP/PreSRP) for interleukin-1β (IL-1β) significantly correlated with ΔPESA (R = -0.512). PostSRP/PreSRP and Log(PostSRP/PreSRP) for intercellular adhesion molecule 1 (ICAM-1) significantly correlated with ΔPISA (R = -0.669, -0.573). Two good fit models were generated by multiple linear regression. Log(PostSRP/PreSRP) for IL-1β significantly affected ΔPESA (R2 = 0.566). PostSRP/PreSRP for ICAM-1 significantly affected ΔPISA (R2 = 0.615). Conclusion: Changes (PreSRP-PostSRP) in any cytokines in GCF after SRP were not associated with clinical improvements. However, the present study indicates that lower PostSRP/PreSRP ratios for IL-1β and ICAM-1 in GCF lead to a greater decrease in PESA and PISA, respectively. Periodontal pocket healing might be affected by a decreased ratio of inflammatory cytokines such as IL-1β and ICAM-1 at an early stage after SRP.
Erythropoietic protoporphyria, heterozygous cystinuria, and reduced peptidase A activity in a patient with 46,XX/46,XX,18q--mosaicism. (1978)

An interesting patient with a deletion of the long arm of chromosome 18 is presented. Her symptoms are severe in comparison with some other 18q--patients, yet she was found to have a mosaicism with a normal 46,XX karyotype in about 20% of her cultured lymphocytes. In addition, she had erythropoietic protoporphyria, was heterozygous for type II or III cystinuria, and had reduced levels of peptidase A activity. Detailed studied on the patient, her family, and two additional 18q--patients suggest that the association with erythropoietic protoporphyria is coincidental and that the cystinuria gene was inherited from the patient's father. The reduced peptidase A activity, however, supports earlier observations that the peptidase A locus maps in the q22 to terminus region of chromosome 18.
Prejunctional Neuropeptide Y Receptors in Human Kidney and Atrium (1997)

The aim of our study was to characterize functionally prejunctional neuropeptide Y (NPY) receptors in human and rabbit renal cortex, as well as in human right atrium. Segments of human atrial appendages and of human and rabbit renal cortex were preincubated with [3H]noradrenaline, superfused with Krebs-Henseleit solution and stimulated electrically in superfusion chambers. The stimulation-induced outflow of radioactivity was taken as an index of endogenous noradrenaline release. The effects of subtype-selective NPY analogs on the stimulation-induced noradrenaline release were studied. NPY, its endogenous analog, peptide YY, and its C-terminal fragment, NPY13-36, but not its analog, [Leu31,Pro34]NPY, concentration dependently (1-100 nM) inhibited [3H]noradrenaline release in all tissues studied. NPY-induced inhibition of [3H]noradrenaline release in human and rabbit kidney was abolished by pretreatment with pertussis toxin. We conclude that prejunctional inhibition of noradrenaline release in human heart and human and rabbit kidney occurs through NPY receptors of the Y2 subtype, which appear to couple to a pertussis toxin-sensitive G protein.
Tumor Expression ofmiR-10b, miR-21, miR-143andmiR-145Is Related to Clinicopathological Features of Gastric Cancer in a Central European Population (2018)

Our results indicate that selected tissue microRNAs have the potential to serve as relevant diagnostic and prognostic biomarkers of GC in a central European population.
Integrity control for high temperature structural applications (1993)

High temperature composite materials in combination with advanced design and manufacturing concepts are becoming more and more important for space transportation systems like hypersonic flight and reusable reentry vehicles. In order to meet the challenging demands for thermostructural applications Carbon/-Carbon and Ceramic Matrix Composites are the most promising materials with respect to weight, stiffness, strength and heat resistance. An ESA supported study has been undertaken to define an Integrity Control Methodology for thermostructural elements made from these high temperature composite materials.
Automatic exposure control (AEC) for dual energy computed tomography (DECT) (2007)

DECT means acquiring the same object at two different energies, respectively two different tube voltages U1 and U2. The rawdata q1 and q2 undergo a decomposition process of type p = p(q1, q2). The rawdata p are reconstructed to obtain monochromatic images of the attenuation mu, of the object density p or of a specific material distribution. Given p and a rawdata-based projection-wise patient dose estimation D (alpha) we determine the optimal tube current curves I1(alpha) and I2 (alpha), with alpha being the view angle, that minimizes image noise for a given patient dose level. AEC for DECT can perform online, I1(alpha) and I2 (alpha) can be determined during the scan. Simulation studies using semianthropomorphic phantom data were carried out. In particular functions p that generate mu-images and density images were evaluated. Image quality was compared to standard scans at Uo = 120 kV (clinical CT) and Uo = 45 kV (micro-CT) that were taken at the same dose level (Do = D1 + D2) and identical spatial resolution. Appropriate choice of p(q1,q2) allows to obtain mu images that are both artifact-free and show image noise levels comparable to the noise of the standard scan. Here, mu images at 25 keV (micro-CT) and 70 keV (clinical CT) turned out to be optimal. Non-optimal choice of the decomposition function will, however, significantly increase image noise. In particular mu images at 511 keV, as needed for PET/CT attenuation correction, exhibit more than twice as much image noise as the standard scan. With DECT-AEC, that guarantees best dose usage possible, monochromatic images are generated with only slightly increased noise levels at the same dose compared to a standard scan. The benefit of significantly decreased artifacts appears to allow using DECT-AEC-generated monochromatic images in daily routine.
Characterization of Cerebrospinal Fluid via Data-Independent Acquisition Mass Spectrometry (2018)

Cerebrospinal fluid (CSF) is in direct contact with the brain and serves as a valuable specimen to examine diseases of the central nervous system through analyzing its components. These include the analysis of metabolites, cells as well as proteins. For identifying new suitable diagnostic protein biomarkers bottom-up data-dependent acquisition (DDA) mass spectrometry-based approaches are most popular. Drawbacks of this method are stochastic and irreproducible precursor ion selection. Recently, data-independent acquisition (DIA) emerged as an alternative method. It overcomes several limitations of DDA, since it combines the benefits of DDA and targeted methods like selected reaction monitoring (SRM). We established a DIA method for in-depth proteome analysis of CSF. For this, four spectral libraries were generated with samples from native CSF ( n = 5), CSF fractionation (15 in total) and substantia nigra fractionation (54 in total) and applied to three CSF DIA replicates. The DDA and DIA methods for CSF were conducted with the same nanoLC parameters using a 180 min gradient. Compared to a conventional DDA method, our DIA approach increased the number of identified protein groups from 648 identifications in DDA to 1574 in DIA using a comprehensive spectral library generated with DDA measurements from five native CSF and 54 substantia nigra fractions. We also could show that a sample specific spectral library generated from native CSF only increased the identification reproducibility from three DIA replicates to 90% (77% with a DDA method). Moreover, by utilizing a substantia nigra specific spectral library for CSF DIA, over 60 brain-originated proteins could be identified compared to only 11 with DDA. In conclusion, the here presented optimized DIA method substantially outperforms DDA and could develop into a powerful tool for biomarker discovery in CSF. Data are available via ProteomeXchange with the identifiers PXD010698, PXD010708, PXD010690, PXD010705, and PXD009624.
77 GHz Automotive Radar Simulation (2018)

This paper shows the analysis of radar scan angle errors of sensors working at 77 GHz inside bumper and vehicle surroundings by using full wave 3D EM simulations.
Identification of urinary biomarkers of colorectal cancer: Towards the development of a colorectal screening test in limited resource settings (2022)

Effective urinary biomarkers for CRC screening do exist. These results could be transferred into a simple, POC urinary test for screening CRC patients in Africa.