gebhart/patrepeval huggingface dataset:
Minor Hemoglobins, Diabetic "Control," and Diseases of Postsynthetic Protein Modification (1977)

International challenges have become the standard for validation of biomedical image analysis methods. Given their scientific impact, it is surprising that a critical analysis of common practices related to the organization of challenges has not yet been performed. In this paper, we present a comprehensive analysis of biomedical image analysis challenges conducted up to now. We demonstrate the importance of challenges and show that the lack of quality control has critical consequences. First, reproducibility and interpretation of the results is often hampered as only a fraction of relevant information is typically provided. Second, the rank of an algorithm is generally not robust to a number of variables such as the test data used for validation, the ranking scheme applied and the observers that make the reference annotations. To overcome these problems, we recommend best practice guidelines and define open research questions to be addressed in the future.
Single-Shot Picosecond Optical Pulse Waveform Measurements Based on a Spatial Sampling System (1990)

Single-shot picosecond optical pulse waveform measurement has been investigated by an electrooptic sampling technique. A spatial optical gate driven by an ultrafast photoconductive switch is employed as an optoelectronic sampler. Discrete sampled signals are coupled into an optical fiber array consisting of fibers of different lengths to control the time delay. The output of the optical fiber array is detected by a photodetector and their envelope is displayed on an oscilloscope with an expanded time scale. For measurement of an optical pulse of 100 ps duration, the temporal resolution of the system is estimated to be about 13 ps.
Epigenetic Regulation of Gene Expression as an Anticancer Drug Target (2011)

Epigenetic processes play a key regulatory role in cancer. Hypermethylation in the CpG islands of the promoter regions of many tumour suppressor genes leads to the recruitment of co-repressors, altered chromatin structure, and ultimately transcriptional silencing. Key components in the regulation of DNA methylation are DNA methyltransferases (DNMT1, 2, 3A and 3B) and methyl CpG-binding proteins, which recognize methyl cytosine residues and recruit transcriptional repressor complexes, including histone deacetylases (HDAC). DNMT1 is responsible for the maintenance of DNA methylation patterns during replication. Inhibitors of this enzyme may potentially lead to DNA hypomethylation, and re-expression of tumour suppressor genes. Several DNMT inhibitors are currently being evaluated in preclinical and clinical studies, include various analogues of adenosine, cytidine or deoxycytidine. However, such drugs have had limited clinical success, perhaps because of cytotoxicity associated with their incorporation into DNA. Non-nucleoside small molecule inhibitors of DNMTs can directly block DNMT activity, and may be able to circumvent this cytotoxicity. Post-translational modifications of histones play a key role, not only in regulating chromatin structure and gene expression, but also in genomic stability. Histone acetylation (HAT) and histone deacetylation (HDAC) affect chromatin condensation, with concomitant effects on gene transcription. A further range of compounds is being evaluated for clinical use as HDAC inhibitors, including hydroxamic acids such as Trichostatin A (TSA) and Suberoyl anilide bishydroxamide (SAHA). MicroRNAs are also found to play a key role in cancer development, and novel approaches to their regulation may provide a susceptible anticancer drug target. Because of the interdependence of epigenetic processes, combinations of these approaches may have maximum clinical efficacy.
The Effect of Physical and Chemical Cues on Hepatocellular Function and Morphology (2014)

Physical topographical features and/or chemical stimuli to the extracellular matrix (ECM) provide essential cues that manipulate cell functions. From the physical point of view, contoured nanostructures are very important for cell behavior in general, and for cellular functions. From the chemical point of view, ECM proteins containing an RGD sequence are known to alter cell functions. In this study, the influence of integrated physical and chemical cues on a liver cell line (HepG2) was investigated. To mimic the physical cues provided by the ECM, amorphous TiO2 nanogratings with specific dimensional and geometrical characteristics (nanogratings 90 nm wide and 150 nm apart) were fabricated. To mimic the chemical cues provided by the ECM, the TiO2 inorganic film was modified by immobilization of the RGD motif. The hepatic cell line morphological and functional changes induced by simultaneously combining these diversified cues were investigated, including cellular alignment and the expression of different functional proteins. The combination of nanopatterns and surface modification with RGD induced cellular alignment and expression of functional proteins, indicating that physical and chemical cues are important factors for optimizing hepatocyte function.
Demonstration of a Surface Stress Sensitive Films for Skin Friction Measurements in a Variety of Flows (2010)

A new technology for distributed measurements of skin friction and pressure has been developed. The active element for this sensor is a thin film made of an elastomer with known thickness and shear modulus. The film deforms under load but does not compress or yield. The measurement is accomplished by monitoring the normal and tangential deformations of the film surface and then converting these deformations into pressure and skin friction using a finite element analysis model. The key advantages offered by this technique include excellent common mode rejection between pressure and skin friction response and the ability to tune the sensitivity of the system over a very wide range of forces. This second advantage is demonstrated as this technology is currently under development for measurements of skin friction and pressure in wind tunnels, water tunnels, and for contact forces. In this paper, we report the results from several experiments that demonstrate the operation of the sensor. Measurements are conducted in a fully developed channel to validate the quantitative accuracy of the sensor and the dynamic response of the film is demonstrated by investigating the flow behind a backward facing step. The flow at a strutendwall junction was investigated at Penn State in the ARL 12-inch water tunnel to demonstrate distributed pressure and skin friction measurements in water. Finally, contact force measurements were demonstrated by investigating the pressure and shear distribution under an automotive tire.
High Remaining Factors in the Photovoltaic Performance of Perovskite Solar Cells after High-Fluence Electron Beam Irradiations (2019)

Metal halide perovskite solar cells have progressed rapidly over the past decade, providing an exceptional opportunity for space photovoltaic (PV) power applications. However, the solar cells to be used for space power have to demonstrate a stable operation under extreme conditions, particularly concerning harsh radiations. In contrast to previously reported superior stability of low PV performance perovskite solar cells against high-energy radiation, we investigate the effects of high-energy electron beam irradiation on the degradation of perovskite solar cells with a high-power conversion efficiency exceeding 20%. We find very high remaining factors of >87.7% in the open-circuit voltage (VOC) and >93.5% in the fill factor (FF) and a significantly decreased short-circuit current density (JSC) after the exposure to high-fluence electron irradiations of 1015 e/cm2. The pronounced loss of JSC is due to the decreasing transmittance of the soda-lime glass substrate and the partial decomposition of the perovskite absorber layers. The irradiated cells retained superior remaining factors in both VOC and FF, demonstrating a superior tolerance of perovskite solar cells after the exposure to the electron irradiation. These results show that perovskite solar cells hold great potential for space PV power applications if stable perovskite compositions and space-suitable substrates are employed.
A high blood endocan profile during COVID-19 distinguishes moderate from severe acute respiratory distress syndrome (2021)

International audience
Evaluation of the Annealing Temperature Effect on the Mechanical Properties of a IF Steel by Means of Physical Simulation (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Doping Properties of Amphoteric C, Si, and Ge Impurities in GaN and AlN (1996)

Electronic structure of substitutional group-IV impurities C, Si, and Ge in hexagonal GaN and AlN were studied by quantum molecular dynamics. Cis is a very shallow acceptor, and thus a promising p-type dopant. Both Si and Ge are excellent donors in GaN. However, in AlGaN alJoys the DX configurations are stable for a sufficiently high Al content, which quenches the doping efficiency. Electronic structure of nearest-neighbor catin- pairs is also discussed.
Evidence That Very Small Embryonic-Like Stem Cells Are Mobilized into Peripheral Blood (2008)

Recently, we identified in murine adult tissues, including bone marrow, a population of very small embryonic-like (VSEL) stem cells. Here, we provide further evidence that under steady-state conditions these cells circulate at very low levels in peripheral blood (PB) ( approximately 100-200 cells/ml) and could be additionally mobilized during pharmacological granulocyte-colony-stimulating factor-induced or stress-related mobilization, as demonstrated in a model of toxic liver or skeletal muscle damage induced by injection of carbon tetrachloride or cardiotoxin, respectively. The number of circulating VSEL stem cells under steady-state conditions in PB of 2-month-old animals was five times higher than that in 1-year-old mice. In conclusion, this study supports a hypothesis that VSEL stem cells are a mobile pool of primitive stem cells that could be released from the stem cell niches into PB. Further studies are needed, however, to see whether the level of these cells circulating in PB could become a prognostic indicator to assess the regenerative potential of an adult organism and/or clinical outcome from an injury. Disclosure of potential conflicts of interest is found at the end of this article.
SLiMAn: an integrative web server for exploring short linear motif-mediated interactions in interactomes (2022)

Abstract Cells express thousands of macromolecules, and their functioning relies on multiple networks of intermolecular interactions. These interactions can be experimentally determine at different spatial and temporal resolutions. But, physical interfaces are not often delineated directly especially in high-throughput experiments. However, numerous three-dimensional structures of complexes have been already solved and sequence conservation allows comparative modeling of additional complexes. A large fraction of protein-protein interactions involves domain and so-called SLiMs (for Short Linear Motifs). Often, SLiMs lie in disordered regions or loops. Their small size and loosely folded nature prevent straightforward detection. SLiMAn (Short Linear Motif Analysis), a new web server is provided to help thorough analysis of interactomics data. Starting from a list of putative interactants such as the output of an interactomics study, SLiMs (from ELM) and SLiM-recognition domains (from Pfam) are extracted and potential pairing are displayed. Additionally, filters are available to dig into the predicted results such as the motif E-value, IUpred2 scoring functions for disorder or BioGRID interaction matches. When structural templates are available, a given SLiM and its recognition domain can be modeled using SCWRL. We illustrate, here, the use of SLiMAn on three distinct examples including one real-case study. We oversee wide-range applications for SLiMAn in the context of massive analysis of protein-protein interactions at proteome-wide scale. This new web server is made freely available at http://sliman.cbs.cnrs.fr .
Henry's Law Constants and Micellar Partitioning of Volatile Organic Compounds in Surfactant Solutions (1999)

Partitioning of volatile organic compounds (VOCs) into surfactant micelles affects the apparent vapor−liquid equilibrium of VOCs in surfactant solutions. This partitioning will complicate removal of VOCs from surfactant solutions by standard separation processes. Headspace experiments were performed to quantify the effect of four anionic surfactants and one nonionic surfactant on the Henry's law constants of 1,1,1-trichloroethane, trichloroethylene, toluene, and tetrachloroethylene at temperatures ranging from 30 to 60 °C. Although the Henry's law constant increased markedly with temperature for all solutions, the amount of VOC in micelles relative to that in the extramicellar region was comparatively insensitive to temperature. The effect of adding sodium chloride and isopropyl alcohol as cosolutes also was evaluated. Significant partitioning of VOCs into micelles was observed, with the micellar partitioning coefficient (tendency to partition from water into micelle) increasing according to the following series: trichloroethane < trichloroethylene < toluene < tetrachloroethylene. The addition of surfactant was capable of reversing the normal sequence observed in Henry's law constants for these four VOCs.
Experimental evaluation of BBR congestion control (2017)

BBR is a recently proposed congestion control. Instead of using packet loss as congestion signal, like many currently used congestion controls, it uses an estimate of the available bottleneck link bandwidth to determine its sending rate. BBR tries to provide high link utilization while avoiding to create queues in bottleneck buffers. The original publication of BBR shows that it can deliver superior performance compared to Cubic TCP in some environments. This paper provides an independent and extensive experimental evaluation of BBR at higher speeds. The experimental setup uses BBR's Linux kernel 4.9 implementation and typical data rates of 10Gbit/s and 1 Gbit/s at the bottleneck link. The experiments vary the flows' round-trip times, the number of flows, and buffer sizes at the bottleneck. The evaluation considers throughput, queuing delay, packet loss, and fairness. On the one hand, the intended behavior of BBR could be observed with our experiments. On the other hand, some severe inherent issues such as increased queuing delays, unfairness, and massive packet loss were also detected. The paper provides an in-depth discussion of BBR's behavior in different experiment setups.
Radioembolization-induced liver disease: a systematic review (2016)

Radioembolization (RE) is a relatively novel treatment modality for primary and secondary hepatic malignancies. Microspheres embedded with a β-emitting radioisotope are injected into the hepatic artery, resulting in microsphere deposition in the tumor arterioles and normal portal triads. Microsphere deposition in nontumorous parenchyma can result in radiation-induced liver injury, with lethal RE-induced liver disease (REILD) at the outer end of the spectrum. The primary aim of this study was to evaluate RE-related hepatotoxicity and present an overview of the currently applied definitions and clinically relevant characteristics of REILD. A systematic literature search on REILD was performed. Studies after the introduction of the term REILD (2008) were screened for definitions of REILD. Hepatotoxicity and applied definitions of REILD were compared. Liver biochemistry test abnormalities occur in up to 100% of patients after RE, mostly self-limiting. The incidence of symptomatic REILD varied between 0 and 31%, although in most reports, the incidence was 0-8%, with a lethal outcome in 0-5%. With the exception of bilirubin, the presentation of hepatotoxicity and REILD was similar for cirrhotic and noncirrhotic patients. No uniform definition of REILD was established in the current literature. Here, we propose a unifying definition and grading system for REILD. RE-related hepatotoxicity is a common phenomenon; symptomatic REILD, however, is rare. Currently, reporting of REILD is highly variable, precluding reliable comparison between studies, identification of risk factors, and treatment developments.
Monoallelic loss-of-function THPO variants cause heritable thrombocytopenia (2020)

Key Points We report rare monoallelic variants of THPO that alter intracellular trafficking and diminish thrombopoietin secretion. Affected cases have autosomal-dominant thrombocytopenia but no other hematological features.
Fundamental physics of vacuum electron sources (2005)

The history of electron emission is reviewed from a standpoint of the work function that determines the electron emission capability and of applications in the fields of scientific instruments and displays. For years, in thermionic emission, a great deal of effort has been devoted to the search for low work function materials with high melting temperature, while reduction of the local change in time of the work function rather than the work function itself has been the main issue of field emission investigations. High brightness and long life are the central targets of emission material investigations for scientific instrument applications, while high current density and low power consumption are the guiding principles for display applications.
Clinical significance of hepatitis C virus genotypes and quasispecies. (2000)

Hepatitis C virus (HCV) is a major cause of morbidity and mortality worldwide. The infection becomes chronic in about 85% of infected individuals, in the face of a strong humoral and cellular immune response. One of the most important features of HCV is its high degree of genetic variability, which is due to the inherent low fidelity of the viral replication machinery. As a consequence, HCV circulates in vivo as a population of divergent, albeit closely related, genomes exhibiting a distribution that follows the model referred to as a quasispecies. The genetic variability of HCV is complex and has been classified into four hierarchical strata: genotypes, subgenotypes, isolates, and quasispecies. Over the past few years, an extraordinary interest has been focused on the biologic and clinical implications of the genetic variability of HCV. Although there is consensus that the genotypes may influence the out come of antiviral therapy, their clinical significance in the natural history of the disease, as well as in transmission, infectivity, and pathogenesis of HCV infection, remains elusive. Conversely, evidence has accumulated that the quasispecies nature of HCV provides a large reservoir of biologically different viral variants that may have important clinical implications for viral persistence by immune escape mechanisms, for the generation of antiviral drug resistance, and for the development of an effective vaccine. This article reviews the state of the art on the biologic and clinical implications of the genetic variability of HCV.
Trans fats increase proliferation and membrane complexity in A549 human lung carcinoma cells (2006)

The varied health benefits of polyunsaturated fatty acids (PUFA) are well‐documented and include prevention of cardiovascular disease and cancer. These beneficial lipids are typically long chain PUFA in the cis conformation, especially those of the omega‐3 class. Conversely those with a trans configuration, “trans fats,” have been implicated as a significant factor in heart disease. However, little is known about their relation to cancer. This study seeks to ascertain the effects of trans fats in comparison to cis‐PUFA on lung carcinoma in vitro. It was shown that incubation of A549 human lung carcinoma cells with trans fats such as elaidic acid (EA, 18:1, n‐9) increased proliferation and membrane complexity as compared to incubation with cis‐lipids, several of which including docosohexaenoic acid (DHA, 22:6, n‐3) and linolenic acid (LLA, 18:3, n‐6) decreased proliferation. Caspase‐3 activation, a late step in the apoptosis pathway, was accordingly higher in cells treated with cis‐PUFA as compared to the untreated control. Those treated with trans fats showed a reduction in caspase‐3. Chemotaxis was reduced by nearly all the tested cis‐ and trans‐PUFA, while each lipid increased adhesion. Marked increases in adhesion were irrelevant of conformation, with petroselenic acid (PSA, 18:1, n‐6), (cis), transvassenic acid (TVA, 18:1, n‐11) and linoelaidic acid (LEA, 18:2, n‐9, 11) (both trans) showing the greatest increase. This work suggests that trans fats may have a complex role in some aspects of cancer proliferation, while any role in cell migration and adhesion remain questionable. The in vitro work outlined here provides a basis for further in vivo investigation. Supported by NIH
Spin and charge signatures of topological superconductivity in Rashba nanowires (2017)

We consider a Rashba nanowire with a proximity gap which can be brought into the topological phase by tuning external magnetic field or chemical potential. We study spin and charge of the bulk quasiparticle states when passing through the topological transition for open and closed systems. We show, analytically and numerically, that the spin of bulk states around the topological gap reverses its sign when crossing the transition due to band inversion, independent of the presence of Majorana fermions in the system. This spin reversal can be considered as a bulk signature of topological superconductivity that can be accessed experimentally. We find a similar behavior for the charge of the bulk quasiparticle states, also exhibiting a sign reversal at the transition. We show that these signatures are robust against random static disorder.
Introduction to a How I Treat series on major complications after allogeneic stem cell transplantation (2020)

In this commissioned series introduced by Associate Editor Robert Zeiser, experts contribute seminal discussions of the 3 major pitfalls following allogeneic stem cell transplantation. Through exploration of instructive real-world cases, they provide up-to-date personal recommendations for solving these common problems.