gebhart/patrepeval huggingface dataset:
Risk of Aluminum Accumulation in Patients With Burns and Ways to Reduce it (1994)

Severely burned patients experience a bone lesion consisting of markedly reduced bone formation and evidence of decreased resportion. The cause of the lesion may be multifactorial, but aluminum loading, which also occurs in patients with burns, has been documented to produce this type of injury in both humans and animals. To assess the risk of aluminum loading with patients with burns, we analyzed fluids, creams, and medication used in the management of acute burn injury for aluminum content. These substances were classified according to route of administration: cutaneous, enteral, or parenteral, to assess the risk of aluminum loading. Cutaneous exposure to aluminum is greatest from baths, which may provide up to 8 mg aluminum. However, the dynamics of aluminum entry into the blood via a damaged skin barrier are unclear. Enteral exposure to aluminum is no greater than daily dietary exposure. Parenteral sources of aluminum, especially 25% human serum albumin and calcium gluconate, provide the most significant risk of loading because of direct introduction of aluminum into the circulation. Substitution with a different brand of albumin and calcium chloride can reduce the parenteral aluminum load by as much as 95% and minimize any role aluminum may play in the pathogenesis of this bone lesion.
The Role of Egfl7 in Vascular Morphogenesis (2007)

EGFL7 was identified by a number of groups as a putative secreted factor produced by the vascular endothelial cells (ECs). In a recent publication, we showed that EGFL7 regulates midline angioblast migration in zebrafish embryos-a key step in vascular tubulogenesis. In this study, we further characterized the zebrafish vasculature in the Egfl7 knockdown embryos at the ultrastructural level, and found that malformation of axial vessels is indeed due to the accumulation of angioblasts and aberrant connection among themselves, but not abnormal interaction between ECs and other cell types. Using in vitro biochemical assays, we demonstrated that EGFL7 is tightly associated with the extracellular matrix (ECM), and it supports EC migration either as a single factor or in combination with other ECM molecules. In order to evaluate if the biological function of EGFL7 is evolutionarily conserved, we generated Egfl7 knockout mice and analysed vascular development in a number of tissues. We found that vascular coverage of a given tissue is reduced or delayed, and vascular morphogenesis is defective in the Egfl7 mutant mice. Taken together, we conclude that EGFL7 provides a proper microenvironment for endothelial cell migration, thereby enabling accurate patterning. Our study indicates that the molecular composition of the ECM influences vascular morphogenesis.
Structural Basis for Platelet Antiaggregation by Angiotensin II Type 1 Receptor Antagonist Losartan (DuP-753) via Glycoprotein VI (2010)

GPVI is a key receptor for collagen-induced platelet activation. Loss or inhibition of GPVI causes only mildly prolonged bleeding times but prevents arterial thrombus formation in animal models. Therefore, GPVI is considered to be a potent target molecule for therapy of thrombotic diseases. Recently, it was reported that the AT(1)-receptor antagonist losartan (DuP-753) and EXP3179 inhibit platelet adhesion and aggregation via GPVI. However, it is still not clear how losartan is associated with inhibition of binding between GPVI and collagen at the molecular level. Here, we show by NMR that losartan directly interacts with the hydrophobic region consisting of strands C' and E in the N-terminal Ig-like domain of GPVI. A reliable GPVI-losartan complex model is presented by using a combination of NMR data and in silico tools. These data indicated that the phenyl group with the tetrazole ring in losartan plays a crucial role in the interaction with GPVI.
Insights into Microalga and Bacteria Interactions of Selected Phycosphere Biofilms Using Metagenomic, Transcriptomic, and Proteomic Approaches (2017)

Microalga are of high relevance for the global carbon cycling and it is well-known that they are associated with a microbiota. However, it remains unclear, if the associated microbiota, often found in phycosphere biofilms, is specific for the microalga strains and which role individual bacterial taxa play. Here we provide experimental evidence that <i>Chlorella saccharophila, Scenedesmus quadricauda</i>, and <i>Micrasterias crux-melitensis</i>, maintained in strain collections, are associated with unique and specific microbial populations. Deep metagenome sequencing, binning approaches, secretome analyses in combination with RNA-Seq data implied fundamental differences in the gene expression profiles of the microbiota associated with the different microalga. Our metatranscriptome analyses indicates that the transcriptionally most active bacteria with respect to key genes commonly involved in plant-microbe interactions in the Chlorella (Trebouxiophyceae) and Scenedesmus (Chlorophyceae) strains belong to the phylum of the α-Proteobacteria. In contrast, in the Micrasterias (Zygnematophyceae) phycosphere biofilm bacteria affiliated with the phylum of the Bacteroidetes showed the highest gene expression rates. We furthermore show that effector molecules known from plant-microbe interactions as inducers for the innate immunity are already of relevance at this evolutionary early plant-microbiome level.
The evolution of methane vents that pierce the hydrate stability zone in the world's oceans (2014)

Abstract We present a one‐dimensional model that couples the thermodynamics of hydrate solidification with multiphase flow to illuminate how gas vents pierce the hydrate stability zone in the world's oceans. During the propagation phase, a free‐gas/hydrate reaction front propagates toward the seafloor, elevating salinity and temperature to three‐phase (gas, liquid, and hydrate) equilibrium. After the reaction front breaches the seafloor, the temperature gradient in the gas chimney dissipates to background values, and salinity increases to maintain three‐phase equilibrium. Ultimately, a steady state is reached in which hydrate formation occurs just below the seabed at a rate necessary to replace salt loss. We show that at the Ursa vent in the Gulf of Mexico, the observed salinity and temperature gradients can be simulated as a steady state system with an upward flow of water equal to 9.5 mm yr −1 and a gas flux no less than 1.3 kg m −2 yr −1 . Many of the world's gas vents may record this steady state behavior, which is characterized by elevated temperatures and high salinities near the seafloor.
Construction, stable transformation, and function of an amber suppressor tRNA gene in Drosophila melanogaster. (1989)

Drosophila melanogaster strains with a stably incorporated amber suppressor tRNA gene have been generated. A tRNATyr gene was site specifically mutated to produce an anticodon sequence that recognizes the amber codon and then introduced into Drosophila by using P-element-mediated transformation. Transformants from four integration events were recovered. Two integrations resulted in both male and female sterility, whereas the other two resulted in male sterility but female fertility. Strains derived from the two female-fertile integration events were shown to have a low level of amber-suppressing activity by their ability to suppress an amber mutation in a chloramphenicol acetyltransferase gene.
Membrane physical properties influence transmembrane helix formation (2012)

The pHLIP peptide has three states: (I) soluble in aqueous buffer, (II) bound to the bilayer surface at neutral pH, and (III) inserted as a transmembrane (TM) helix at acidic pH. The membrane insertion of pHLIP at low pH can be used to target the acidic tissues characteristic of different diseases, such as cancer. We find that the α-helix content of state II depends on lipid acyl chain length but not cholesterol, suggesting the helicity of the bound state may be controlled by the bilayer elastic bending modulus. Experiments with the P20G variant show the proline residue in pHLIP reduces the α-helix content of both states II and III. We also observe that the membrane insertion pKa is influenced by membrane physical properties, following a biphasic pattern similar to the membrane thickness optima observed for the function of eukaryotic membrane proteins. Because tumor cells exhibit altered membrane fluidity, we suggest this might influence pHLIP tumor targeting. We used a cell insertion assay to determine the pKa in live cells, observing that the properties in liposomes held in the more complex plasma membrane. Our results show that the formation of a TM helix is modulated by both the conformational propensities of the peptide and the physical properties of the bilayer. These results suggest a physical role for helix-membrane interactions in optimizing the function of more complex TM proteins.
CT Demonstration of Gas in Dilated Pancreatic Duct (1986)

A case of "innocent" pancreatic gas is reported. The patient had cystic dilatation of the main pancreatic duct limited to the head. Air entered through the patulous ampulla of Vater. Pancreatic gas can be present without abscess or fistula.
Derivation of formulae and optimal design for Owen's resistive power divider (2020)

Abstract A modified resistive power divider (RPD) was proposed by Owen and this structure has been shown to have higher isolation than a conventional RPD. However, it has a large insertion loss, which is a disadvantage. No theoretical studies have been published since Owen proposed this unique structure with specific resistor values. Thus far, the improvement of insertion loss has been achieved by trial and error to optimize performance by varying the resistor values. In this study, we perform a circuit analysis of the Owen's RPD and derive formulae to calculate performance. From the measured results, we demonstrate the validity of the derived formulae and show that the insertion loss could be improved by trade‐offs between performance.
There's an app for that: Teaching entomology in the online age (2022)

Abstract Effective educational tools are needed to facilitate learning of organismal and ecological sciences in the virtual setting. For entomology laboratory classes, physically collecting insects and curating them in formal collections encompass the traditional learning and assessment tools to introduce students to the natural world and increase their curiosity and interest in insects. Virtual learning, however, creates issues with this modality. Using pre‐ and post‐surveys across five universities based on a new lab activity, we sought to determine whether using a digital platform named iNaturalist stimulated observation, curiosity, and interest in insects. iNaturalist positively affected each measure, most strikingly among biology and zoology majors who increased observation by 15%, curiosity in identification by 39%, and interest by 16%. Increases in observation and curiosity in insects were positively correlated with increases in interest in entomology as a whole. Our findings suggest that virtual tools such as iNaturalist may promote positive course outcomes.
Cinobufagin Modulates Human Innate Immune Responses and Triggers Antibacterial Activity (2016)

The traditional Chinese medicine Chan-Su is widely used for treatment of cancer and cardiovascular diseases, but also as a remedy for infections such as furunculosis, tonsillitis and acute pharyngitis. The clinical use of Chan-Su suggests that it has anti-infective effects, however, the mechanism of action is incompletely understood. In particular, the effect on the human immune system is poorly defined. Here, we describe previously unrecognized immunomodulatory activities of cinobufagin (CBG), a major bioactive component of Chan-Su. Using human monocyte-derived dendritic cells (DCs), we show that LPS-induced maturation and production of a number of cytokines was potently inhibited by CBG, which also had a pro-apoptotic effect, associated with activation of caspase-3. Interestingly, CBG triggered caspase-1 activation and significantly enhanced IL-1β production in LPS-stimulated cells. Finally, we demonstrate that CBG upregulates gene expression of the antimicrobial peptides (AMPs) hBD-2 and hBD-3 in DCs, and induces secretion of HNP1-3 and hCAP-18/LL-37 from neutrophils, potentiating neutrophil antibacterial activity. Taken together, our data indicate that CBG modulates the inflammatory phenotype of DCs in response to LPS, and triggers an antibacterial innate immune response, thus proposing possible mechanisms for the clinical effects of Chan-Su in anti-infective therapy.
The Role of Total Abdominal Hysterectomy and Vaginectomy in Female Patients with Invasive Transitional Cell Carcinoma of the Bladder (1987)

No AccessJournal of Urology1 Jun 1987The Role of Total Abdominal Hysterectomy and Vaginectomy in Female Patients with Invasive Transitional Cell Carcinoma of the Bladder Melvin J. Duckett, John D. Young, Isabell A. Sesterhenn, and F. Kash Mostofi Melvin J. DuckettMelvin J. Duckett , John D. YoungJohn D. Young , Isabell A. SesterhennIsabell A. Sesterhenn , and F. Kash MostofiF. Kash Mostofi View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)75809-0AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "The Role of Total Abdominal Hysterectomy and Vaginectomy in Female Patients with Invasive Transitional Cell Carcinoma of the Bladder." The Journal of Urology, 137(6), p. 268A © 1987 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 137Issue 6June 1987Page: 268A Advertisement Copyright & Permissions© 1987 by The American Urological Association Education and Research, Inc.Metrics Author Information Melvin J. Duckett More articles by this author John D. Young More articles by this author Isabell A. Sesterhenn More articles by this author F. Kash Mostofi More articles by this author Expand All Advertisement PDF downloadLoading ...
Acousto-optic imaging using a powerful long pulse laser and digital holography. (2011)

Acousto-optic tomography is a technique that couples ultrasounds and light in order to measure local optical properties through thick and highly scattering media, e.g. human breast tissues. Thanks to the acousto-optic effect, we can get the optical contrast information given by light and get the spatial localization from the ultrasound longitudinal waves. The use of a powerful long pulse laser (1 ms, 200 mJ) helps to improve the sensitivity of the technique by raising the optical peak power and collect more ultrasound tagged photons. Moreover, its tunable wavelength around 780 nm is appropriate for biological imaging since it is where light has its maximum penetrating depth in tissues. Detection of acousto-optic signals is done by off-axis heterodyne digital holography on a high speed CMOS camera. This enables us to make a tunable spatio-temporal filter with a high signal to noise ratio. Experimentally, this technique enables to image optical absorbers embedded within a thick scattering media (a few centimetres). It is also theoretically possible to use a conventional pulsed ultrasound scanner to generate acousto-optic signals that can at the same time record ultrasound images, which will be a step toward multimodal imaging for breast cancer detection.
Clearance of rat C-reactive protein in vivo and by perfused liver (1992)

The clearance in vivo of rat C-reactive protein (CRP) was studied: (i) in the whole animal and (ii) by using a rat liver perfusion system. Rat CRP is a glycosylated serum protein containing a complex-type biantennary carbohydrate structure on each of its five subunits. The half-life of rat asialo CRP was approximately 5 min. More than 75% of the radioactivity associated with rat asialo CRP and asialo alpha 1-acid glycoprotein (AGP) was recovered in the liver. A small amount of radioactivity (0.8%) associated with rat CRP and rat asialo CRP was found in the lungs. Competitive inhibition of the clearance of 125I-labelled rat asialo CRP from the circulation by asialo AGP was dose dependent, and resulted in a corresponding decrease in the recovery of radioactivity associated with rat asialo CRP in the liver. This indicated that asialo AGP and rat asialo CRP were cleared by the hepatic asialoglycoprotein receptor. This observation was confirmed when the clearance of rat asialo CRP was studied using a rat liver perfusion system. Using this system, the clearance of rat asialo CRP and asialo AGP from the perfusate was inhibited by N-acetylgalactosamine, but not by phosphorylcholine, a ligand through which most of the CRP reactions are mediated. This study provides an example of a circulating serum glycoprotein containing a biantennary carbohydrate structure that is cleared by the asialoglycoprotein receptor.
Biocompatibility of Synthetic and Bio-Material Fusion (2017)

This communication proposes methods to improve the biocompatibility performance of synthetic materials for biological and biological material for synthetic applications. π-cloud extension by suitable ligand- ligand/metal-ligand interactions can make the synthetic-biological fusion suitable for such applications. The judicious use of ligands for π-cloud extension can be applied to carbon transformations and target-oriented drug delivery systems. Embedded metal-centre catalysts for synthetic-biological fusion include: (i) axial coordination via bridging ligands; (ii) ligands with weak to intermediate field strength and multidenticities; (iii) design of inert complexes, and (iv) development of multi-nuclear complexes.
A geno-clinical decision model for the diagnosis of myelodysplastic syndromes (2021)

The differential diagnosis of myeloid malignancies is challenging and subject to interobserver variability. We used clinical and next-generation sequencing (NGS) data to develop a machine learning model for the diagnosis of myeloid malignancies independent of bone marrow biopsy data based on a 3-institution, international cohort of patients. The model achieves high performance, with model interpretations indicating that it relies on factors similar to those used by clinicians. In addition, we describe associations between NGS findings and clinically important phenotypes and introduce the use of machine learning algorithms to elucidate clinicogenomic relationships.
Spatiotemporal characterization of the field-induced insulator-to-metal transition (2021)

Many correlated systems feature an insulator-to-metal transition that can be triggered by an electric field. Although it is known that metallization takes place through filament formation, the details of how this process initiates and evolves remain elusive. We use in-operando optical reflectivity to capture the growth dynamics of the metallic phase with space and time resolution. We demonstrate that filament formation is triggered by nucleation at hotspots, with a subsequent expansion over several decades in time. By comparing three case studies (VO<sub>2</sub>, V<sub>3</sub>O<sub>5</sub>, and V<sub>2</sub>O<sub>3</sub>), we identify the resistivity change across the transition as the crucial parameter governing this process. Our results provide a spatiotemporal characterization of volatile resistive switching in Mott insulators, which is important for emerging technologies, such as optoelectronics and neuromorphic computing.
TrustyAI Explainability Toolkit (2021)

Artificial intelligence (AI) is becoming increasingly more popular and can be found in workplaces and homes around the world. The decisions made by such "black box" systems are often opaque; that is, so complex as to be functionally impossible to understand. How do we ensure that these systems are behaving as desired? TrustyAI is an initiative which looks into explainable artificial intelligence (XAI) solutions to address this issue of explainability in the context of both AI models and decision services. This paper presents the TrustyAI Explainability Toolkit, a Java and Python library that provides XAI explanations of decision services and predictive models for both enterprise and data science use-cases. We describe the TrustyAI implementations and extensions to techniques such as LIME, SHAP and counterfactuals, which are benchmarked against existing implementations in a variety of experiments.
ChemInform Abstract: Planar Chiral Phosphoramidites with a Paracyclophane Scaffold: Synthesis, Gold(I) Complexes, and Enantioselective Cycloisomerization of Dienynes. (2016)

Abstract Key structural feature of the new phosphoramidites is a paracyclophane scaffold in which two aryl rings are tethered by both a 1,8‐biphenylene unit and a O—P—O bridge.
Partitioning of Web graphs by community topology (2005)

We introduce a stricter Web community definition to overcome boundary ambiguity of a Web community defined by Flake, Lawrence and Giles [2], and consider the problem of finding communities that satisfy our definition. We discuss how to find such communities and hardness of this problem.We also propose Web page partitioning by equivalence relation defined using the class of communities of our definition. Though the problem of efficiently finding all communities of our definition is NP-complete, we propose an efficient method of finding a subclass of communities among the sets partitioned by each of n-1 cuts represented by a Gomory-Hu tree [10], and partitioning a Web graph by equivalence relation defined using the subclass.According to our preliminary experiments, partitioning by our method divided the pages retrieved by keyword search into several different categories to some extent.
Role of adhesive proteins in platelet tumor interaction in vitro and metastasis formation in vivo. (1988)

Platelet-adhesive protein-tumor cell interaction was studied in vitro and in vivo. Monoclonal antibody 10E5, which inhibits binding of fibronectin and von Willebrand factor to the platelet membrane glycoprotein GPIIb-GPIIIa complex, inhibited the binding of mouse CT26 and human HCT8 colon carcinoma cells to platelets by 63-65%, whereas an irrelevant monoclonal antibody, 3B2, had no effect. Monoclonal antibody 6D1, which inhibits binding of von Willebrand factor to GPIb, also had no effect. RGDS, a tetrapeptide that represents the adhesive domain of fibronectin and von Willebrand factor inhibited binding of the tumors to platelets by 64-69%. Monospecific polyclonal antifibronectin antibody inhibited binding by 60-82%; anti-von Willebrand factor antibody inhibited binding by 75-81%. In vivo, polyclonal monospecific anti-mouse von Willebrand factor antibody inhibited pulmonary metastases induced by CT26 tumor cells by 53-64%, B16a amelanotic melanoma cells by 45% and T241 Lewis bladder cells by 46% without induction of thrombocytopenia. Pulmonary metastases with CT26 cells could be inhibited by induction of thrombocytopenia, and reconstituted by infusion of either murine or human platelets. Reconstitution of pulmonary metastases with human platelets could be inhibited 77% by preincubation of human platelets with monoclonal antibody 10E5 before infusion of platelets into mice. Thus, platelets appear to contribute to metastases by their adhesive interaction with tumor cells via the adhesive proteins fibronectin and von Willebrand factor.
Switching to Preservative-Free Tafluprost/Timolol Fixed-Dose Combination in the Treatment of Open-Angle Glaucoma or Ocular Hypertension: Subanalysis of Data from the VISIONARY Study According to Baseline Monotherapy Treatment (2022)

European Union electronic Register of Post-Authorization Studies (EU PAS) register number: EUPAS22204.