gebhart/patrepeval huggingface dataset:
LAIR-1 Limits Neutrophilic Airway Inflammation (2019)

Neutrophils are crucial to antimicrobial defense, but excessive neutrophilic inflammation induces immune pathology. The mechanisms by which neutrophils are regulated to prevent injury and preserve tissue homeostasis are not completely understood. We recently identified the collagen receptor leukocyte-associated immunoglobulin-like receptor (LAIR)-1 as a functional inhibitory receptor on airway-infiltrated neutrophils in viral bronchiolitis patients. In the current study, we sought to examine the role of LAIR-1 in regulating airway neutrophil responses <i>in vivo</i>. LAIR-1-deficient (<i>Lair1</i><sup>-/-</sup>) and wild-type mice were infected with respiratory syncytial virus (RSV) or exposed to cigarette smoke as commonly accepted models of neutrophil-driven lung inflammation. Mice were monitored for cellular airway influx, weight loss, cytokine production, and viral loads. After RSV infection, <i>Lair1</i><sup>-/-</sup> mice show enhanced airway inflammation accompanied by increased neutrophil and lymphocyte recruitment to the airways, without effects on viral loads or cytokine production. LAIR-1-Fc administration in wild type mice, which blocks ligand induced LAIR-1 activation, augmented airway inflammation recapitulating the observations in <i>Lair1</i><sup>-/-</sup> mice. Likewise, in the smoke-exposure model, LAIR-1 deficiency enhanced neutrophil recruitment to the airways and worsened disease severity. Intranasal CXCL1-mediated neutrophil recruitment to the airways was enhanced in mice lacking LAIR-1, supporting an intrinsic function of LAIR-1 on neutrophils. In conclusion, the immune inhibitory receptor LAIR-1 suppresses neutrophil tissue migration and acts as a negative regulator of neutrophil-driven airway inflammation during lung diseases. Following our recent observations in humans, this study provides crucial <i>in-vivo</i> evidence that LAIR-1 is a promising target for pharmacological intervention in such pathologies.
Controlled Movement of Complex Double Emulsions via Interfacially Confined Magnetic Nanoparticles (2020)

Controlled, dynamic movement of materials through noncontacting forces provides interesting opportunities in systems design. Confinement of magnetic nanoparticles to the interfaces of double emulsions introduces exceptional control of double emulsion movement. We report the selective magnetic functionalization of emulsions by the <i>in situ</i> selective reactions of amine-functionalized magnetic nanoparticles and oil-soluble aldehydes at only one of the double emulsion's interfaces. We demonstrate morphology-dependent macroscopic ferromagnetic behavior of emulsions induced by the interfacial confinement of the magnetic nanoparticles. The attraction and repulsion of the emulsions to applied magnetic fields results in controlled orientation changes and rotational movement. Furthermore, incorporation of liquid crystals into the double emulsions adds additional templating capabilities for precision assembly of magnetic nanoparticles, both along the interface and at point defects. Applying a magnetic field to liquid crystal complex emulsions can produce movement as well as reorganization of the director field in the droplets. The combination of interfacial chemistry and precise assembly of magnetic particles creates new systems with potentially useful field-responsive properties.
Outcomes of Burkitt lymphoma with central nervous system involvement: evidence from a large multicenter cohort study (2021)

Central nervous system (CNS) involvement in Burkitt lymphoma (BL) poses a major therapeutic challenge, and the relative ability of contemporary regimens to treat CNS involvement remains uncertain. We described prognostic significance of CNS involvement and incidence of CNS recurrence/progression after contemporary immunochemotherapy using real-world clinicopathologic data on adults with BL diagnosed between 2009 and 2018 across 30 US institutions. We examined associations between baseline CNS involvement, patient characteristics, complete response (CR) rates, and survival. We also examined risk factors for CNS recurrence. Nineteen percent (120/641) of patients (age 18-88 years) had CNS involvement. It was independently associated with HIV infection, poor performance status, involvement of ≥2 extranodal sites, or bone marrow involvement. First-line regimen selection was unaffected by CNS involvement (P=0.93). Patients with CNS disease had significantly lower rates of CR (59% versus 77% without; P<0.001), worse 3-year progression-free survival (adjusted hazard ratio [aHR], 1.53, 95% confidence interval [CI], 1.14-2.06, P=0.004) and overall survival (aHR, 1.62, 95%CI, 1.18-2.22, P=0.003). The 3-year cumulative incidence of CNS recurrence was 6% (95%CI, 4-8%). It was significantly lower among patients receiving other regimens (CODOX-M/IVAC, 4%, or hyperCVAD/MA, 3%) compared with DA-EPOCH-R (13%; adjusted sub-HR, 4.38, 95%CI, 2.16-8.87, P<0.001). Baseline CNS involvement in BL is relatively common and portends inferior prognosis independent of first-line regimen selection. In real-world practice, regimens with highly CNS-penetrant intravenous systemic agents were associated with a lower risk of CNS recurrence. This finding may be influenced by observed suboptimal adherence to the strict CNS staging and intrathecal therapy procedures incorporated in DA-EPOCH-R.
Canine Models of Ocular Disease: Outcross Breedings Define a Dominant Disorder Present in the English Mastiff and Bull Mastiff Dog Breeds (2003)

Progressive retinal atrophies (PRA) are a heterogeneous group of inherited eye diseases common to both dogs and man. Over 100 individual canine breeds display some sort of retinal degeneration, making the dog an extremely valuable resource both for finding the genetic determinants of inherited blindness and for developing naturally occurring animal models that mimic human disease. Progressive retinal atrophies within the English mastiff displayed an ambiguous mode of inheritance. By conducting outcross matings between affected English mastiffs and normal animals from other breeds, the mode of inheritance was confirmed as dominant. This directed candidate gene analysis and led to identification of two synonymous mutations and one nonsynonymous mutation within the canine rhodopsin gene. The nonsynonymous mutation (T4R) is the cause of PRA in the English mastiff, and a test was developed to investigate its presence in 17 additional breeds. Testing of PRA-affected animals from 16 breeds revealed that none carry the T4R mutation, indicating a different cause of PRA. Analysis of two affected bull mastiffs revealed one heterozygote (+/T4R) and one homozygous normal individual (+/+). These findings suggest that the genetic origin of PRA is often breed specific and underline the value of outcross mating to circumvent problems that act to mask the mode of inheritance.
Biomechanical properties of endothelial glycocalyx: An imperfect pendulum (2021)

Endothelial glycocalyx plays a crucial role in hemodynamics in health and disease, yet studying it is met by multiple technical hindrances. We attempted to outline our views on some biomechanical properties of endothelial glycocalyx, which are potentially amenable to mathematical modeling. We start with the null-hypothesis ascribing to glycocalyx the properties of a pendulum and reject this hypothesis on the grounds of multiple obstacles for pendulum behavior, such as rich decoration with flexible negatively charged side-chains, variable length and density, fluid fixation to the plasma membrane. We next analyze the current views on membrane attachments to the cortical actin web, its pulsatile contraction-relaxation cycles which rebound to the changes in tension of the plasma membrane. Based on this, we consider the outside-in signaling, the basis for mechanotransduction, and the dampening action of the inside-out signaling. The aperiodic oscillatory motions of glycocalyx and cortical actin web underlie our prediction of two functional pacemakers. We next advance an idea that the glycocalyx, plasma membrane, and cortical actin web represent a structure-functional unit and propose the concept of tensegrity model. Finally, we present our recent data suggesting that erythrocytes are gliding or hovering and rotating over the surface of intact glycocalyx, whereas the rotational and hovering components of their passage along the capillaries are lost when glycocalyx of either is degraded. These insights into the mechanics of endothelial glycocalyx motions may be of value in crosspollination between biomechanics, physiology, and pathophysiology for deeper appreciation of its rich untapped resources in health and pharmacotherapy in disease.
Ets homologous factor (EHF) has critical roles in epithelial dysfunction in airway disease (2020)

The airway epithelium forms a barrier between the internal and external environments. Epithelial dysfunction is critical in the pathology of many respiratory diseases, including cystic fibrosis. Ets homologous factor (EHF) is a key member of the transcription factor network that regulates gene expression in the airway epithelium in response to endogenous and exogenous stimuli. EHF , which has altered expression in inflammatory states, maps to the 5' end of an intergenic region on Chr11p13 that is implicated as a modifier of cystic fibrosis airway disease. Here we determine the functions of EHF in primary human bronchial epithelial (HBE) cells and relevant airway cell lines. Using EHF ChIP followed by deep sequencing (ChIP-seq) and RNA sequencing after EHF depletion, we show that EHF targets in HBE cells are enriched for genes involved in inflammation and wound repair. Furthermore, changes in gene expression impact cell phenotype because EHF depletion alters epithelial secretion of a neutrophil chemokine and slows wound closure in HBE cells. EHF activates expression of the SAM pointed domain-containing ETS transcription factor, which contributes to goblet cell hyperplasia. Our data reveal a critical role for EHF in regulating epithelial function in lung disease.
A Complete Mitochondrial Genome Sequence from a Mesolithic Wild Aurochs (Bos primigenius) (2010)

For all nucleotide positions where both Sanger and Illumina Genome Analyzer sequencing methods gave high-confidence calls, no discrepancies were observed. Sequence analysis reveals evidence of heteroplasmy in this sample and places this mitochondrial genome sequence securely within a previously identified aurochsen haplogroup (haplogroup P), thus providing novel insights into pre-domestic patterns of variation. The high proportion of authentic, endogenous aurochs DNA preserved in this sample bodes well for future efforts to determine the complete genome sequence of a wild ancestor of domestic cattle.
Extreme obesity due to impaired leptin signaling in mice does not cause knee osteoarthritis (2009)

Extreme obesity due to impaired leptin signaling induced alterations in subchondral bone morphology without increasing the incidence of knee OA. Systemic inflammatory cytokine levels remained largely unchanged in ob/ob and db/db mice. These findings suggest that body fat, in and of itself, may not be a risk factor for joint degeneration, because adiposity in the absence of leptin signaling is insufficient to induce systemic inflammation and knee OA in female C57BL/6J mice. These results imply a pleiotropic role of leptin in the development of OA by regulating both the skeletal and immune systems.
PRIMME_SVDS: A High-Performance Preconditioned SVD Solver for Accurate Large-Scale Computations (2017)

The increasing number of applications requiring the solution of large-scale singular value problems has rekindled an interest in iterative methods for the SVD. Some promising recent advances in large-scale iterative methods are still plagued by slow convergence and accuracy limitations for computing smallest singular triplets. Furthermore, their current implementations in MATLAB cannot address the required large problems. Recently, we presented a preconditioned, two-stage method to effectively and accurately compute a small number of extreme singular triplets. In this research, we present a high-performance library, PRIMME_SVDS, that implements our hybrid method based on the state-of-the-art eigensolver package PRIMME for both largest and smallest singular values. PRIMME_SVDS fills a gap in production level software for computing the partial SVD, especially with preconditioning. The numerical experiments demonstrate its superior performance compared to other state-of-the-art software and its good parallel performance under strong and weak scaling.
Tunable surface nanofibrous structures and nanoporosity for superhydrophobic and superoleophobic properties (2014)

International audience
Abstracting meaning from complex information (gist reasoning) in adult traumatic brain injury (2015)

Gist reasoning (abstracting meaning from complex information) was compared between adults with moderate-to-severe traumatic brain injury (TBI, n = 30) at least one year post injury and healthy adults (n = 40). The study also examined the contribution of executive functions (working memory, inhibition, and switching) and memory (immediate recall and memory for facts) to gist reasoning. The correspondence between gist reasoning and daily function was also examined in the TBI group. Results indicated that the TBI group performed significantly lower than the control group on gist reasoning, even after adjusting for executive functions and memory. Executive function composite was positively associated with gist reasoning (p < .001). Additionally, performance on gist reasoning significantly predicted daily function in the TBI group beyond the predictive ability of executive function alone (p = .011). Synthesizing and abstracting meaning(s) from information (i.e., gist reasoning) could provide an informative index into higher order cognition and daily functionality.
Frequency planning strategies for frequency hopping GSM (2002)

The GSM system has two type of frequency carriers, namely the frequencies that carry the broadcast control channels (BCCH) and the frequencies carrying only traffic channel (TCH). Two basic frequency planning alternatives can be distinguished: one can either divide the available spectrum into two dedicated parts for BCCH and TCH frequencies respectively or use the entire band for both BCCH and TCH frequencies. The goal with this study has been to investigate which one to prefer, from an interference point of view, in a tightly planned frequency hopping system. Simulations of an interference limited system have been performed. The focus is on the downlink performance, i.e. it is assumed that the downlink is the limiting link in the system. The results show that using dedicated frequency bands for the BCCH and TCH is superior in the downlink. The second strategy, using the entire band for both BCCH and TCH frequencies, will suffer from heavy disturbance in the downlink mainly from BCCH transmitters and the gain from power control and discontinuous transmission cannot be fully utilized. Multiple reuse patterns, a frequency planning concept based on the dedicated bands method has also been analysed.
Die polykondensation von tripeptiden nach der „Eintopfmethode” (1973)

Abstract Es wird die Polykondensation von L ‐Prolyl‐ L ‐alanyl‐glycin und 2 analogen Tripeptiden mit Hilfe aktivierter Ester nach Art einer “Eintopfmethode” beschrieben. Besonders vorteilhaft ist der Ester von 3‐Hydroxy‐4‐oxo‐3,4‐dihydro‐1,2,3‐benzotriazin. Aus kurzzeitigen Kondensationen läßt sich das Hexapeptid isolieren.
Prion diseases (1998)

Although the nature of the infectious agent causing prion diseases is still debated, several of its molecular characteristics have been clarified in remarkable detail. The transmissibility of bovine spongiform encephalopathy to humans dramatically highlights the need for research focused at interference with prion replication and spread, and at prevention of brain damage. Precondition to achieving these goals is a thorough understanding of prion biology, and in particular of its protein chemistry.
Pulmonary microbiome patterns correlate with the course of the disease in patients with sepsis-induced ARDS (2019)

<title>Abstract</title> Background Patients with sepsis-induced Acute Respiratory Distress Syndrome (ARDS) are hallmarked by high mortality rates. An early and goal directed antibiotic therapy is crucial for patients’ survival. The clinical use of a Next Generation Sequencing (NGS)-based approach for pathogen identification might lead to an improved diagnostic performance. Therefore, the objective of this study was to examine changes in the pulmonary microbiome and resulting influences on patients’ outcome in septic ARDS, but also to compare NGS- and culture-based diagnostic methods for pathogen identification.Results In total, 30 patients in two groups were enrolled in the study: (1) 15 septic ARDS patients and (2) 15 patients undergoing oesophageal resection serving as controls. In the ARDS group, blood samples were collected at ARDS onset as well as 5 days and 10 days afterwards. At the same timepoints, bronchoalveolar lavages (BAL) were performed to collect epithelial lining fluid for culture-, as well as NGS-based analyses and to evaluate longitudinal changes in the pulmonary microbiome. In the control group, only one BAL and one blood sample were collected immediately prior to the surgical procedure. ARDS patients showed a significantly decreased α-diversity (p=0.003**) and an increased dominance (p=0.005**) in their pulmonary microbiome. The α-diversity index revealed a good correlation with the length of stay in the intensive care unit (ICU) (p-value=0.027) and the need for mechanical ventilation (p-value=0.027). In 42.9% of all ARDS patients, culture-based results were not concordant with NGS-based findings. Moreover, culture-based results remained negative in 5 cases where NGS-based diagnostics revealed signs of bacterial colonisation.Conclusion Sepsis-induced ARDS is associated with a significant dysbiosis of patients’ pulmonary microbiome, which is closely correlated with the clinical course of the disease. Furthermore, an NGS-based diagnostic approach was shown to be promising for pathogen identification in septic ARDS.
Modeling and Optimization of Woody Biomass Harvest and Logistics in the Northeastern United States (2014)

World energy consumption is at an all-time high and is projected to continue growing for the foreseeable future. Currently, much of the energy that is produced comes from non-renewable fossil energy sources, which includes the burden of increased greenhouse gas emissions and the fear of energy insecurity. Woody biomass is being considered as a material that can be utilized to reduce the burden caused by fossil energy. While the technical capability to convert woody biomass to energy has been known for a long period of time, the cost of the feedstock has been considered too costly to be implemented in a large commercial scale. Increasing the use of woody biomass as an energy source requires that the supply chains are setup in a way that minimizes cost, the locational factors that lead to development are understood, the facilities are located in the most favorable locations and local resource assessments can be made.;A mixed integer linear programming model to efficiently configure woody biomass supply chain configurations and optimize the harvest, extraction, transport, storage and preprocessing of the woody biomass resources to provide the lowest possible delivered price. The characteristics of woody biomass, such as spatial distribution and low bulk density, tend to make collection and transport difficult as compared to traditional energy sources. These factors, as well as others, have an adverse effect on the cost of the feedstock. The average delivered cost was found to be between {dollar}64.69-98.31 dry Mg for an annual demand of 180,000 dry Mg. The effect of resource availability and required demand was examined to determine the impact that each would have on the total cost.;The use of woody biomass for energy has been suggested as a way to improve rural economies through job creation, reduction of energy costs and regional development. This study examined existing wood using bio-energy facilities in the northeastern United States to define the drivers of establishment of bio-energy projects. Using a spatial econometric framework, a spatial autoregressive probit model was estimated based on the Bayesian methods to define the factors that impact the location of wood using bio-energy facilities in the United States. Through the analysis it was found that the energy policy of the state is the biggest driver of the choice of location for bioenergy facilities.;The choice of site is of great importance when trying to meet the goal of producing cost-effective biofuels, due to the spatial dispersion of
Optically Responsive Gold Nanorod−Polypeptide Assemblies (2008)

Environmentally responsive nanoassemblies based on polypeptides and nanoparticles can have a number of promising biological/biomedical applications. We report the generation of gold nanorod (GNR)-elastin-like polypeptide (ELP) nanoassemblies whose optical response can be manipulated based on exposure to near-infrared (NIR) light. Cysteine-containing ELPs were self-assembled on GNRs mediated by gold-thiol bonds, leading to the generation of GNR-ELP nanoassemblies. Exposure of GNR-ELP assemblies to NIR light resulted in the heating of GNRs due to surface plasmon resonance. Heat transfer from the GNRs resulted in an increase in temperature of the self-assembled ELP above its transition temperature (Tt), which led to a phase transition and aggregation of the GNR-ELP assemblies. This phase transition was detected using an optical readout (increase in optical density); no change in optical behavior was observed in the case of either ELP alone or GNR alone. The optical response was reproducibele and reversible across a number of cycles following exposure to or removal of the laser excitation. Our results indicate that polypeptides may be interfaced with GNRs resulting in optically responsive nanoasssemblies for sensing and drug delivery applications.
Analysis of slanted air-gap structure of interior permanent magnet synchronous motor with brushless field excitation (2009)

This paper introduces a new air-gap structure, the slanted air-gap, for increasing the speed limit of an interior permanent magnet synchronous motor (IPMSM) for application in a hybrid electric vehicle. This unique slanted air-gap is intended to maximize the ratio of the back-emf of a machine that is controllable by brushless field excitation (BFE). The BFE structure offers high torque per ampere per core length at low speed and weakened flux at high speed. Although the irregularly shaped air-gap reduces the air-gap flux, it also makes a flux barrier along the d-axis flux path and decreases the d-axis inductance. Therefore, the reluctance torque of the machine increases to compensate for the decreased permanent magnet torque; as a result, the machine achieves a higher ratio of the magnitude of controllable back-emf without losing the high torque capability resulting from the BFE.
Editorial The continuing search for cancer-causing somatic mutations (2007)

It is known that cancer is caused by an accumulation of mutations in DNA. Many genes have been associated with tumour progression either through germline or somatic mutations, but mutations in these genes by no means account for all instances of the disease. The availability of the completed human genome sequence and reduced costs of sequencing have allowed largescale screens to uncover genes that are somatically mutated in cancer. In this issue, Chanock and colleagues present a screen of 91 breast cancers for somatic variants in a set of 21 genes. Over recent years, kinase genes have received much attention in this field because of their central role in many cellular processes, especially cell growth and proliferation [1-8]. Mutations in kinases have also been linked with cancer progression and have proved to be a successful target for