gebhart/patrepeval huggingface dataset:
Exposure of differentiated airway smooth muscle cells to serum stimulates both induction of hypoxia-inducible factor-1α and airway responsiveness to ACh (2007)

Airway smooth muscle (ASM) cells are characterized by phenotypic plasticity and can switch between differentiated and proliferative phenotypes. In rabbit tracheal ASM cells that had been differentiated in vitro by serum starvation, readdition of FBS caused initiation of proliferation and induction of nuclear and transcriptionally active hypoxia-inducible factor (HIF)-1alpha. In addition, FBS stimulated the induction of HIF-1alpha by the hypoxia mimetic cobalt. Treatment with actinomycin D, cycloheximide, the phosphatidylinositol 3-kinase inhibitors LY-294002 and wortmannin or the reactive oxygen species scavenger diphenyleneiodonium inhibited the FBS-dependent induction of HIF-1alpha. These data indicate that, in differentiated ASM cells, FBS upregulates HIF-1alpha by a transcription-, translation-, phosphatidylinositol 3-kinase-, and reactive oxygen species-dependent mechanism. Interestingly, addition of FBS and cobalt also induced HIF-1alpha in organ cultures of rabbit trachea strips and synergistically increased their contractile response to ACh, suggesting that HIF-1alpha might be implicated in airway hypercontractility.
Biofilms in Dental Unit Waterlines: Ultrastructural and Cytochemical Analysis (1997)

Dental unit waterlines are heavily colonized by bacteria which contaminate the water used to perform intra-oral, and sometimes invasive, procedures. There is little information on the nature of the biofilm colonizing the flexible plastic tubing used to supply water to the different handpieces. We have therefore undertaken quantitative microbial analysis and ultrastructural studies of these biofilms by direct counting with the epifluorescent filter technique and by transmission and scanning electron microscopy after staining with ruthenium red and periodic acid-thiosemicarbazide-silver proteinate to visualize the composition and the distribution of exopolysaccharides and intracellular polysaccharides. The biofilm was revealed as a non-uniform structure characterized by an uneven cell distribution in an extracellular matrix. The microbial community of the biofilm was composed of metabolically active Gram-negative, short rod and coccoid bacteria that formed microcolonies embedded in a multilayer exopolysaccharides envelope. Our results indicate that even though the biomass of dental unit waterlines biofilms increases with time there is no direct correlation with the concentration of free floating bacteria in the water. It can be concluded that the biofilm structure described herein is responsible for the high level of bacteria in some medical devices. The consequences are of clinical significance as it is known that this extracellular material limits the action of biocides and host defense.
Relative Risk of Progressive Glaucomatous Visual Field Loss in Patients Enrolled and Not Enrolled in a Prospective Longitudinal Study (2006)

Selection bias may reduce the risk of progressive visual field loss in patients enrolled in longitudinal studies.
Why do anti-inflammatory signals of bone marrow-derived stromal cells improve neurodegenerative conditions where anti-inflammatory drugs fail? (2020)

Neurodegenerative disorders share the final degenerative pathway, the inflammation-induced apoptosis and/or necrosis, irrespective of their etiology, be it of acute and chronic traumatic, vascular and idiopathic origin. Although disease-modifying strategies are an unmet need in these disorders, lately, (pre)clinical studies suggested favorable effects after an intervention with bone marrow-derived stromal cells (bm-SC). Recent interventions with intrathecal transplantation of these cells in preclinical rodent models improved the functional outcome and reduced the inflammation, but not anti-inflammatory drugs. The benefit of bm-SCs was demonstrated in rats with an acute (traumatic spinal cord injury, tSCI) and in mice with a chronic [amyotrophic lateral sclerosis (ALS)-like FUS 1-358 or SOD1-G93-A mutation] neurodegenerative process. Bm-SCs, were found to modify underlying disease processes, to reduce final clinical SCI-related outcome, and to slow down ALS-like clinical progression. After double-blind interventions with bm-SC transplantations, Vehicle (placebo), and (non)steroidal anti-inflammatory drugs (Methylprednisolone, Riluzole, Celecoxib), clinical, histological and histochemical findings, serum/spinal cytokines, markers for spinal microglial activation inclusive, evidenced the cell-to-cell action of bm-SCs in both otherwise healthy and immune-deficient tSCI-rats, as well as wild-type and FUS/SOD1-transgenic ALS-like mice. The multi-pathway hypothesis of the cell-to-cell action of bmSCs, presumably using extracellular vesicles (EVs) as carriers of messages in the form of RNAs, DNA, proteins, and lipids rather than influencing a single inflammatory pathway, could be justified by the reported differences of cytokines and other chemokines in the serum and spinal tissue. The mode of action of bm-SCs is hypothesized to be associated with its dedicated adjustment of the pro-apoptotic glycogen synthase kinase-3β level towards an anti-apoptotic level whereas their multi-pathway hypothesis seems to be confirmed by the decreased levels of the pro-inflammatory interleukin (IL)-1β and tumor necrosis factor (TNF) as well as the level of the marker of activated microglia, ionized calcium binding adapter (Iba)-1 level.
Self‐Assembly: Alginate Encapsulation of Bioengineered Protein‐Coated Polyhydroxybutyrate Particles: A New Platform for Multifunctional Composite Materials (Adv. Funct. Mater. 37/2019) (2019)

In article number 1901893, Bernd H. A. Rehm and Kampachiro Ogura engineer bacterial cell factories to assemble nano-sized polyester particles coated with proteins of interest. These functionalized polyester particles are stable and show promising performance as bioseparation resins and enzyme carriers. The functionality of these non-porous protein-coated polyester beads is strongly enhanced by controlled encapsulation into porous alginate microspheres that enable flow-through bioseparation or catalytic conversion applications.
Wayside Charging and Hydrogen Hybrid Bus: Extending the Range of Electric Shuttle Buses (2015)

This report documents the results completed by the Center for Energy, Transportation and the Environment (CETE) at the University of Tennessee at Chattanooga (UTC) under Federal Transit Administration Cooperative Agreement TN-26-7034. This research has addressed the limited range of electric shuttle buses by two different methods: first, by wayside charging using inductive power transfer, and second, by adding a small (10 kW) on-board generator set powered by an internal combustion engine (ICE) fueled by hydrogen. Wayside charging reduced fuel costs to less than $0.10 per mile while eliminating tailpipe emissions that would have been produced by a similar diesel bus. The hydrogen hybrid bus eliminated emission of CO2, but the cost was found to be prohibitive because of the relatively poor thermodynamic efficiency of the ICE and the high cost of hydrogen. Better results were obtained when the ICE was fueled with compressed natural gas (CNG), which resulted in a range in excess of 170 miles at a lower fuel cost per mile than a comparable diesel-fueled hybrid bus.
Tumor production in vivo and cell transformation in vitro by two SV20 strains. (1967)

Two serologically distinguishable SV20 strains induced a high incidence (43 to 92%) of tumors in hamsters and were found to transform BHK-21 cells. Both virus strains produced a common tumor antigen, serologically distinct from SV40 tumor antigen. Its synthesis in infected tissue culture cells could be demonstrated by complement fixation and fluorescent antibody technics. Both strains induced a similar type of tumor in which the predominating pattern was the “fibrosarcoma” type, although areas suggesting a “lymphoma” or other types were also seen. Transformation of BHK-21 cells was obtained in cultures inoculated either as cell monolayers or as freshly trypsinized cell suspensions. The transformation was characterized by morphologic alteration of the cells and the development of SV20 tumor antigen without any detectable infectious virus. These cells did not react by fluorescent antibody tests with SV40 tumor antisera.
Sensitivity of SEM width measurements to model assumptions (2009)

ABSTRACT The most accurate width measurements in a scanning electron microscope (SEM) re quire raw images to be corrected forinstrumental artifacts. Corrections are based upon a physical model that describes the sample-instrument interaction.Models differ in their approaches or ap proximations in the treatment of scatte ring cross sections, secondary electron (SE)generation, material properties, scattering at the surface potential barrier, etc. Corrections that use different modelsproduce different width estimates. We have implemented eight models in the JMONSEL SEM simulator. Two arephenomenological models based upon fitting measured yield vs. energy curves. Two are based upon a binary scatteringmodel. Four are variants of a dielectric function approach. These models are compared to each other in pairwisesimulations in which the output of one model is fit to the other by using adjustable parameters similar to those used to fitmeasured data. The differences in their edge position parameters is then a measure of how much these models differ withrespect to a width measurement. With electron landing energy, beam width, and other parameters typical of those used inindustrial critical dimension measurements, the models agreed to within ± 2.0 nm on silicon and ± 2.6 nm on copper in95% of comparisons.Keywords: critical dimension (CD), model-based metrology, Scanning Electron Microscopy (SEM), secondary electrongeneration, uncertainty
Review—Development of Diagnostic Process for Commercially Available Batteries, Especially Lithium Ion Battery, by Electrochemical Impedance Spectroscopy (2015)

Electrochemical impedance spectroscopy (EIS) can be utilized to characterize battery features, because it allows the dynamics of each elemental process of the battery reaction to be sensitively and separately determined without destruction of the cell. In addition, EIS is expected to be utilized for premonitory diagnosis of onboard batteries in electric vehicles. Here, an overview of the recent diagnosis technologies for determining the health of commercial lithium-ion batteries (LIB) using EIS is provided. We describe equivalent circuit design techniques while explaining and investigating physical and chemical phenomena for a wide range of measured impedance spectra, which are obtained using commercial LIBs. Attention is then focused on separation of the frequency responses of each electrode with or without a reference electrode, symmetric cell, and temperature control. Additionally, a square-current EIS (SC-EIS) technique, which we have proposed, is introduced for monitoring of large-scale LIB systems as a promising future technique.
ChemInform Abstract: Pt(IV)‐Catalyzed Generation and [4 + 2]‐Cycloaddition Reactions of o‐Quinone Methides. (2011)

Abstract A variety of dihydrobenzopyran derivatives is prepared by Pt(IV)‐catalyzed generation of o‐quinone methides and their subsequent inter‐ and intramolecular cycloaddition towards various dienophiles.
Selected Aspects of Navigation and Path Planning in Unmanned Aircraft Systems (2011)

Unmanned aircraft systems (UASs) are an important future technology with early generations already being used in many areas of application encompassing both military and civilian domains. This thesis proposes a number of integration techniques for combining control-based navigation with more abstract path planning functionality for UASs. These techniques are empirically tested and validated using an RMAX helicopter platform used in the UASTechLab at Linköping University. Although the thesis focuses on helicopter platforms, the techniques are generic in nature and can be used in other robotic systems. At the control level a navigation task is executed by a set of control modes. A framework based on the abstraction of hierarchical concurrent state machines for the design and development of hybrid control systems is presented. The framework is used to specify reactive behaviors and for sequentialisation of control modes. Selected examples of control systems deployed on UASs are presented. Collision-free paths executed at the control level are generated by path planning algorithms.We propose a path replanning framework extending the existing path planners to allow dynamic repair of flight paths when new obstacles or no-fly zones obstructing the current flight path are detected. Additionally, a novel approach to selecting the best path repair strategy based on machine learning technique is presented. A prerequisite for a safe navigation in a real-world environment is an accurate geometrical model. As a step towards building accurate 3D models onboard UASs initial work on the integration of a laser range finder with a helicopter platform is also presented. Combination of the techniques presented provides another step towards building comprehensive and robust navigation systems for future UASs.
Short Pc)per Overcoming class II-linked non-responsiveness to hepatitis B vaccine (1994)

It is well established that T-cell help can be provided to a hapten by linking this to an amino acid sequence well recognized by MHC class II molecules ~ 6. This sequence, referred to as TD h, can also provide help even when not covalently linked to the hapten v. These findings suggested to us that an individual who fails to respond to a protein because of lack of recognition of a TDh within its sequence, might be rendered a responder by immunization with this 'haptenic' protein and a TD h peptide chosen to satisfy the class II restriction of this individual. To test this hypothesis we immunized SJL/J (H-2 s) and BI0M (H-2 f) mice, two strains of non-responders to the S region of hepatitis B surface antigen 8'9, with a recombinant surface antigen, only composed of the S region, in conjunction with a short synthetic peptide well recognized by class II molecules of SJL/J but not by those of B 10M. We provide below experimental evidence that this simple immunization strategy allows not only the manipulation of the humoral response against an 'haptenic' protein, but is also a convenient way of studying which TDh sequences are useful to potentiate the inducton of antibodies in the context of a given restriction. The results are also discussed in terms of the lack of humoral response of a small percentage of humans following immunization with the hepatitis B vaccine.
Whole-body compliance for multi-arm space robotic capturing of large tumbling target in connection compliant phase (2018)

Based on the characteristics of large tumbling space debris, this article proposes an effective method for whole-body compliant controller to eliminate the effects of the relative velocity between chaser and target which is not zero after the capture hands hold their corresponding handles tightly that is named as connection compliant phase. First, the kinematics and dynamics models are established, including tumbling target, free-floating chaser and chaser–target, respectively. Second, to analyse the characteristics of capturing of a large tumbling target, a simplified kinematics model about the centre of mass of the chaser is established, and a Cartesian-space compliant controller is designed in order to achieve the desired gross force as the input of multi-arm compliant distribution. Subsequently, we propose a method based on centre of forces to distribute the desired gross force to each arm optimized first and also a closed-loop regulator based on the dissipation vectors online as the second step. Then, a passivity-based control strategy is used in order to enhance the robustness of the system. Finally, the effectiveness of the control strategy mentioned above is verified by the simulation and air-bearing experiment in the horizontal plane partially.
The structure of receptor‐associated protein (RAP) (2007)

The receptor-associated protein (RAP) is a molecular chaperone that binds tightly to certain newly synthesized LDL receptor family members in the endoplasmic reticulum (ER) and facilitates their delivery to the Golgi. We have adopted a divide-and-conquer strategy to solve the structures of the individual domains of RAP using NMR spectroscopy. We present here the newly determined structure of domain 2. Based on this structure and the structures of domains 1 and 3, which were solved previously, we utilized experimental small-angle neutron scattering (SANS) data and a novel simulated annealing protocol to characterize the overall structure of RAP. The results reveal that RAP adopts a unique structural architecture consisting of three independent three-helix bundles that are connected by long and flexible linkers. The flexible linkers and the quasi-repetitive structural architecture may allow RAP to adopt various possible conformations when interacting with the LDL receptors, which are also made of repetitive substructure units.
A Late-onset and Relatively Rapidly Progressive Case of Pure Spinal Form Cerebrotendinous Xanthomatosis with a Novel Mutation in the <i>CYP27A1</i> Gene (2020)

A 61-year-old Japanese man with the pure spinal form of cerebrotendinous xanthomatosis developed dysesthesia of the lower limbs and gait disturbance at 57 years of age. At 61 years old, he was unable to walk without support. A neurological examination showed spasticity and sensory disturbance in the lower limbs. Spinal MRI showed long hyperintense lesions involving the lateral and posterior funiculus in the cervical and thoracic cord on T2-weighted images. His serum cholestanol level was markedly elevated. A CYP27A1 gene analysis identified two missense variants, p.R474W, and a novel p.R262C variant. Combination therapy with chenodeoxycholic acid and 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase decreased his serum cholestanol level.
Invasive Methicillin-Resistant Staphylococcus aureus USA500 Strains from the U.S. Emerging Infections Program Constitute Three Geographically Distinct Lineages (2018)

USA500 isolates are clonal complex 8 (CC8) <i>Staphylococcus aureus</i> strains closely related to the prominent community- and hospital-associated USA300 group. Despite being relatively understudied, USA500 strains cause a significant burden of disease and are the third most common methicillin-resistant <i>S. aureus</i> (MRSA) strains identified in the U.S. Emerging Infections Program (EIP) invasive <i>S. aureus</i> surveillance. To better understand the genetic relationships of the strains, we sequenced the genomes of 539 USA500 MRSA isolates from sterile site infections collected through the EIP between 2005 and 2013 in the United States. USA500 isolates fell into three major clades principally separated by their distribution across different U.S. regions. Clade C1 strains, found principally in the Northeast, were associated with multiple IS<i>256</i> insertion elements in their genomes and higher levels of antibiotic resistance. C2 was associated with Southern states, and E1 was associated with Western states. C1 and C2 strains all shared a frameshift in the gene encoding AdsA surface-attached surface protein. We propose that the term "USA500" should be used for CC8 strains sharing a recent common ancestor with the C1, C2, and E1 strains but not in the USA300 group.<b>IMPORTANCE</b> In this work, we have removed some of the confusion surrounding the use of the name "USA500," placed USA500 strains in the context of the CC8 group, and developed a strategy for assignment to subclades based on genome sequence. Our new phylogeny of USA300/USA500 will be a reference point for understanding the genetic adaptations that have allowed multiple highly virulent clonal strains to emerge from within CC8 over the past 50 years.
Oxidative stress and nerve damage: Role in chemotherapy induced peripheral neuropathy (2014)

Peripheral neuropathy is a severe dose limiting toxicity associated with cancer chemotherapy. Ever since it was identified, the clear pathological mechanisms underlying chemotherapy induced peripheral neuropathy (CIPN) remain sparse and considerable involvement of oxidative stress and neuroinflammation has been realized recently. Despite the empirical use of antioxidants in the therapy of CIPN, the oxidative stress mediated neuronal damage in peripheral neuropathy is still debatable. The current review focuses on nerve damage due to oxidative stress and mitochondrial dysfunction as key pathogenic mechanisms involved in CIPN. Oxidative stress as a central mediator of apoptosis, neuroinflammation, metabolic disturbances and bioenergetic failure in neurons has been highlighted in this review along with a summary of research on dietary antioxidants and other nutraceuticals which have undergone prospective controlled clinical trials in patients undergoing chemotherapy.
A Novel Three-Dimensional Approach Towards Evaluating Endomyocardial Biopsies for Follow-Up After Heart Transplantation: X-Ray Phase Contrast Imaging and Its Agreement With Classical Histopathology (2023)

Endomyocardial biopsies are the gold standard for surveillance of graft rejection following heart transplantation, and are assessed by classical histopathology using a limited number of previously stained slices from several biopsies. Synchrotron propagation-based X-ray phase contrast imaging is a non-destructive method to image biological samples without tissue preparation, enabling virtual 2D and 3D histopathology. We aimed to show the feasibility of this method to assess acute cellular rejection and its agreement to classical histopathology. Right ventricular biopsies were sampled from 23 heart transplantation recipients (20 males, mean age 54±14 years) as part of standard follow-up. The clinical diagnosis of potential rejection was made using classical histopathology. One additional study sample was harvested and imaged by X-ray phase contrast imaging, producing 3D datasets with 0.65 μm pixel size, and up to 4,320 images per sample. An experienced pathologist graded both histopathological and X-ray phase contrast images in a blinded fashion. The agreement between methods was assessed by weighted kappa, showing substantial agreement (kappa up to 0.80, <i>p</i> < 0.01) between X-ray phase contrast imaging and classical histopathology. X-ray phase contrast imaging does not require tissue processing, allows thorough analysis of a full myocardial sample and allows identification of acute cellular rejection.