gebhart/patrepeval huggingface dataset:
O5‐04‐02: Altered Protein Expression in Amyloid Plaques in Rapidly Progressive Alzheimer's Disease (2016)

Rapidly progressive Alzheimer's disease (rpAD) is a particularly aggressive form of Alzheimer's disease (AD). Survival is limited to 2-3 years after diagnosis. It is not yet known why AD develops so rapidly in these patients and previous research into this type of AD is limited. Studying cases of rpAD provides a unique opportunity to look for mechanistic factors associated with the development of AD pathology as these factors may be enhanced or distinct in the accelerated disease process. In this study we used our recently developed method to perform quantitative proteomics on amyloid plaques microdissected from formalin-fixed paraffin embedded hippocampal sections from patients with rpAD (n=22) and typical, sporadic AD (n=19). Plaque proteins were extracted after formic acid treatment and individual protein levels were quantified using label free LC-MS. On average, 825 proteins were quantified in amyloid plaques, providing the most comprehensive dataset to date of proteins present in amyloid plaques. Our approach was validated by the abundant detection of known plaque associated proteins such as beta amyloid, apolipoprotein E, ubiquitin and tau. Importantly, we also discovered many novel plaque associated proteins. Quantitative LC-MS revealed that rpAD plaques had a significantly different protein composition than sporadic AD plaques. One striking observation that was generated using protein network analysis was that rpAD plaques contained significantly more neuronal proteins (p<0.00001), while sporadic AD plaques contained significantly more astrocytic proteins (p<0.0001). Examples of specific proteins with significantly altered levels in rpAD included many that are known to contribute to the development of amyloid plaques such as beta amyloid (p<0.001), alpha-synuclein (p<0.001), gelsolin (p<0.01) and GFAP (p<0.0001). We have identified a set of specific proteins that contribute to rapid plaque development in AD and have identified protein networks that are unique to rpAD. Data from this study also provides a new way to examine both the individual proteins as well as protein networks involved in the formation of amyloid plaques, which could provide novel drug targets in the future.
Open lung approach associated with high-frequency oscillatory or low tidal volume mechanical ventilation improves respiratory function and minimizes lung injury in healthy and injured rats (2010)

Open lung ventilatory strategies associated with HFOV or BP-CMV improved respiratory function and minimized lung injury compared to LP-CMV. Therefore, HFOV with PmeanHFOV set 2 cm H2O above the PmeanBP-CMV following a recruitment manoeuvre is as beneficial as BP-CMV.
Void formation in short‐fiber thermoplastic composites (1989)

Abstract Voids, or bubbles, are formed in short‐fiber thermoplastic composites because of entrapment of air in the compounding and melt flow processing steps and as a result of uneven shrinkage due to temperature gradients involved in the solidification step by cooling. The experimental results suggest that bubble nucleation takes place at fiber ends and their volume content depends on processing conditions. The shape and distribution of the voids were studied by optical examination of longitudinal sections of extrudates, using standard metallographic polishing technique and reflected light microscopy. The void volume fraction of extrudates was found to increase with increasing extrusion rate, temperature, fiber concentration, and fiber length, and with a decreasing draw ratio. The void content in fiber‐glass‐reinforced injection moldings is low, ≈︁1% by volume; however, by heating these moldings, the contained pressurized bubbles expand and significant void volume fractions are observed.
Replication of <i>Heliothis ze</i><i>a</i> Baculovirus in an Insect Cell Line (1981)

The baculovirus, Heliothis zea nuclear polyhedrosis virus (HzSNPV), was grown in the H. zea cell line, IPLB-1075. Light microscopy observations showed that 95% of inoculated cells had CPE by 6 days postinoculation (p.i.). Growth curves of intracellular and extracellular virus showed that maximum titers (TCID50 units) were reached 3-4 days p.i. Studies on HzSNPV morphogenesis revealed that ultrastructural events were typical of baculovirus replication in vitro. EcoRI restriction enzyme analyses of viral DNA produced in larvae and in cell culture were identical and indicated that this virus was HzSNPV.
Platinum germanides for long-wavelength infrared plasmonics (2014)

PtxGe1-x compositions were formed by thermal-annealing. Plasmonic characteristics such as propagation length, loss, and mode confinement were determined from measured complex permittivities. Fabricated grating structures were characterized via LWIR reflection taken at multiple incident angles.
ChemInform Abstract: Studies Directed Toward the Synthesis of (+)‐Mycotrienin I. Asymmetric Synthesis of the C9‐N21 Aromatic Synthon. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Dynamic One‐Pot Three‐Component Catalytic Asymmetric Transformation by Combination of Hydrogen‐Bond‐Donating and Amine Catalysts (2011)

In control: The first dynamic one-pot three-component asymmetric transformation between aldehydes, protected α-cyanoglycine esters, and enals catalyzed by a combination of a simple hydrogen-bond-donating catalyst and a chiral amine catalyst is disclosed. Polysubstituted proline derivatives, which have a quaternary α stereocenter, were synthesized with high endo-, diastereo-, and enantioselectivities (93–99 % ee). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Disparity-guided demosaicking of light field images (2014)

Light-field imaging has been recently introduced to mass market by the hand held plenoptic camera Lytro. Thanks to a microlens array placed between the main lens and the sensor, the captured data contains different views of the scene from different view points. This offers several post-capture applications, e.g., computationally changing the main lens focus. The raw data conversion in such cameras is however barely studied in the literature. The goal of this paper is to study the particularly overlooked problem of demosaicking the views for plenoptic cameras such as Lytro. We exploit the redundant sampling of scene content in the views, and show that disparities estimated from the mosaicked data can guide the demosaicking, resulting in minimum artifacts compared to the state of art methods. Besides, by properly addressing the view demultiplexing step, we take the first step towards light field super-resolution with negligible computational overload.
New Fimbrial Gene Cluster of S-Fimbrial Adhesin Family (2000)

Fimbrial adhesins that mediate attachment to host cells are produced by most virulent Escherichia coli isolates. These virulence factors play an important role in the initial stages of bacterial colonization and also in determination of the host and tissue specificity. Isolates belonging to serotype O78 are known to cause a large variety of clinical syndromes in farm animals and humans and have been shown to produce several types of adherence fimbriae. We studied the fimbrial adhesin from an avian septicemic E. coli isolate of serotype O78. Analysis of the genetic organization of the fac (fimbria of avian E. coli) gene cluster indicates that it belongs to the S-fimbrial adhesin family. Seven open reading frames coding for major and minor structural subunits were identified, and most of them showed a high degree of homology to the corresponding Sfa and Foc determinants. The least-conserved open reading frame was facS, encoding a protein known to play an important role in determining adherence specificity in other S-fimbrial gene clusters.
Isolation and characterization of patient-derived CNS metastasis-associated stromal cell lines (2019)

The functional role of human derived stromal cells in the tumor microenviornment of CNS metastases (CM) remain understudied. The purpose of the current study was to isolate and characterize stromal cells of the tumor microenvironment in CM. Four different patient-derived cell lines (PDCs) of stromal and one PDC of tumorigenic origin were generated from breast or lung CM. PDCs were analyzed by DNA/RNA sequencing, DNA methylation profiling, and immunophenotypic assays. The stromal derived PDCs were termed CNS metastasis-associated stromal cells (cMASCs). Functional analysis of cMASCs was tested by co-implanting them with tumorigenic cells in mice. cMASCs displayed normal genotypes compared with tumorigenic cell lines. RNA-seq and DNA methylation analyses demonstrated that cMASCs highly resembled each other, suggesting a common cell of origin. Additionally, cMASCs revealed gene expression signatures associated with cancer associated fibroblasts (CAFs), epithelial to mesenchymal transition, mesenchymal stem cells and expressed high levels of collagen. Functionally, cMASCs restricted tumor growth, and induced desmoplasia in vivo, suggesting that cMASCs may promote a protective host response to impede tumor growth. In summary, we demonstrated the isolation, molecular characterization and functional role of human derived cMASCs, a subpopulation of cells in the microenvironment of CM that have tumor inhibitory functions.
Phase and fluorescence imaging with a surprisingly simple microscope based on chromatic aberration (2020)

We propose a simple and compact microscope combining phase imaging with multi-color fluorescence using a standard bright-field objective. The phase image of the sample is reconstructed from a single, approximately 100 μm out-of-focus image taken under semi-coherent illumination, while fluorescence is recorded in-focus in epi-fluorescence geometry. The reproducible changes of the focus are achieved with specifically introduced chromatic aberration in the imaging system. This allows us to move the focal plane simply by changing the imaging wavelength. No mechanical movement of neither sample nor objective or any other part of the setup is therefore required to alternate between the imaging modality. Due to its small size and the absence of motorized components the microscope can easily be used inside a standard biological incubator and allows long-term imaging of cell culture in physiological conditions. A field-of-view of 1.2 mm<sup>2</sup> allows simultaneous observation of thousands of cells with micro-meter spatial resolution in phase and multi-channel fluorescence mode. In this manuscript we characterize the system and show a time-lapse of cell culture in phase and multi-channel fluorescence recorded inside an incubator. We believe that the small dimensions, easy usage and low cost of the system make it a useful tool for biological research.
Peroxisome Proliferator-Activated Receptor-γ-Deficient Heterozygous Mice Develop an Exacerbated Neural Antigen-Induced Th1 Response and Experimental Allergic Encephalomyelitis (2003)

Peroxisome proliferator-activated receptor-gamma (PPARgamma) is a nuclear receptor transcription factor that regulates cell growth, differentiation, and homeostasis. PPARgamma agonists are potent therapeutic agents for type 2 diabetes, obesity, and inflammation. Experimental allergic encephalomyelitis (EAE) is a Th1 cell-mediated inflammatory demyelinating autoimmune disease model of multiple sclerosis. We have shown recently that PPARgamma agonists inhibit EAE by blocking IL-12 production, IL-12 signaling, and neural Ag-induced Th1 differentiation. In this study, we show that the PPARgamma-deficient heterozygous mice develop an exacerbated EAE with prolonged clinical symptoms than the wild-type littermates, following immunization with myelin oligodendrocyte glycoprotein (MOG) p35-55 peptide. The exacerbation of EAE in PPARgamma(+/-) mice associates with an increased expansion of CD4(+) and CD8(+) T cells and expression of CD40 and MHC class II molecules in response to MOGp35-55 Ag. The PPARgamma(+/-) mice also showed an increase in T cell proliferation and Th1 response to MOGp35-55 Ag than the wild-type littermates. These findings suggest that PPARgamma be a critical physiological regulator of CNS inflammation and demyelination in EAE and perhaps multiple sclerosis and other Th1 cell-mediated autoimmune diseases.
59.1: A Backlight System with a Phosphor Sheet Providing both Wider Color Gamut and Higher Efficiency (2013)

Abstract A phosphor sheet in which green‐emitting thiogallate phosphor and red‐emitting sulfide phosphor are contained was developed. The LCD using it and blue LEDs can realize wider color gamut. Employing blue LEDs with spherical encapsulates in it increases light extraction of them and can provide the backlight with higher efficiency as well as wider color gamut.
Catalytic Enantioselective Alkylations of Tetrasubstituted Olefins. Synthesis of All‐Carbon Quaternary Stereogenic Centers Through Cu‐Catalyzed Asymmetric Conjugate Additions of Alkylzinc Reagents to Enones. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Bigger DNA: New Double Helix with Expanded Size (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Abstract 1446: GRP78 targeting peptides deliver liposomal doxorubicin specifically to cancer and enhance the efficacy of radiation therapy (2021)

Abstract Traditional radiation therapy is often associated with significant toxicity to normal cells that could limit cancer therapy's success. The greater understanding of the molecular differences between cancer cells and normal cells has led to targeted therapies in cancer treatment. We discovered the radiation-inducible expression of Glucose regulated protein 78kDa (GRP78) in cancer using phage-display peptide libraries. In this study, we screened a peptide library and discovered novel peptides targeting GRP78. The top ten peptides were further evaluated for their affinity of binding to recombinant GRP78 using surface plasmon resonance technology. Since GRP78 is induced on cancer cells' surface, we irradiated the lung cancer cell lines A549 and H460 to evaluate peptide binding. Flow cytometry analysis of Dylight 488 conjugated peptides led to identifying peptides A and K with the highest binding level to irradiated A549 and H460. Peptides A and K were compared for their efficacy to deliver liposomal doxorubicin specifically to tumors. Copper-free click-chemistry was used to conjugate peptides to the liposome surface. Whole-body near-infrared imaging was performed to evaluate the biodistribution of the peptide conjugated liposomes in nude mice bearing A549 and H460 tumors. Both peptides A and K specifically delivered liposomes to the tumors compared to the non-targeted liposomes. In pilot tumor growth experiments, we found that GRP78 targeting peptide conjugated liposomes delayed the growth of tumors in nude mice compared to non-targeted liposomes. The inhibition of tumor growth was further enhanced in combination with radiation, indicating efficient delivery of the radiation-sensitizer doxorubicin specifically to tumors. Currently, studies are underway to evaluate the microscopic biodistribution of doxorubicin in tumor sections. Mass spectrometry analysis of various organs will be performed to determine the pharmacokinetics of liposomal doxorubicin delivered by GRP78 targeting peptides. In conclusion, our novel GRP78 targeting peptides specifically deliver liposomal doxorubicin to tumors. Doxorubicin encapsulated in GRP78 targeting peptide conjugated liposomes enhances the tumor growth inhibitory activity of radiation therapy. Specific delivery of radiation-sensitizing drugs encapsulated in a liposome by peptides that target radiation-inducible GRP78 is a promising therapeutic strategy for various cancers. Citation Format: Abhay K. Singh, Chandresh Shyam, Calvin Lewis, Wendy Zhang, Sapna Deore, Vaishali Kapoor, Dennis E. Hallahan. GRP78 targeting peptides deliver liposomal doxorubicin specifically to cancer and enhance the efficacy of radiation therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1446.
Impact of obesity with or without hypertension on systemic haemodynamic and renal responses to lower body negative pressure (2020)

NCT01734096.
Close-Field Electroporation Gene Delivery Using the Cochlear Implant Electrode Array Enhances the Bionic Ear (2014)

The cochlear implant is the most successful bionic prosthesis and has transformed the lives of people with profound hearing loss. However, the performance of the "bionic ear" is still largely constrained by the neural interface itself. Current spread inherent to broad monopolar stimulation of the spiral ganglion neuron somata obviates the intrinsic tonotopic mapping of the cochlear nerve. We show in the guinea pig that neurotrophin gene therapy integrated into the cochlear implant improves its performance by stimulating spiral ganglion neurite regeneration. We used the cochlear implant electrode array for novel "close-field" electroporation to transduce mesenchymal cells lining the cochlear perilymphatic canals with a naked complementary DNA gene construct driving expression of brain-derived neurotrophic factor (BDNF) and a green fluorescent protein (GFP) reporter. The focusing of electric fields by particular cochlear implant electrode configurations led to surprisingly efficient gene delivery to adjacent mesenchymal cells. The resulting BDNF expression stimulated regeneration of spiral ganglion neurites, which had atrophied 2 weeks after ototoxic treatment, in a bilateral sensorineural deafness model. In this model, delivery of a control GFP-only vector failed to restore neuron structure, with atrophied neurons indistinguishable from unimplanted cochleae. With BDNF therapy, the regenerated spiral ganglion neurites extended close to the cochlear implant electrodes, with localized ectopic branching. This neural remodeling enabled bipolar stimulation via the cochlear implant array, with low stimulus thresholds and expanded dynamic range of the cochlear nerve, determined via electrically evoked auditory brainstem responses. This development may broadly improve neural interfaces and extend molecular medicine applications.
HIDDEN MARKOV MODELS FOR MODELING AND RECOGNIZING GESTURE UNDER VARIATION (2001)

Conventional application of hidden Markov models to the task of recognizing human gesture may suffer from multiple sources of systematic variation in the sensor outputs. We present two frameworks based on hidden Markov models which are designed to model and recognize gestures that vary in systematic ways. In the first, the systematic variation is assumed to be communicative in nature, and the input gesture is assumed to belong to gesture family. The variation across the family is modeled explicitly by the parametric hidden Markov model (PHMM). In the second framework, variation in the signal is overcome by relying on online learning rather than conventional offline, batch learning.
O-Alkoxyamidine Prodrugs of Furamidine:  In Vitro Transport and Microsomal Metabolism as Indicators of in Vivo Efficacy in a Mouse Model of Trypanosoma brucei rhodesiense Infection (2004)

Five O-alkoxyamidine analogues of the prodrug 2,5-bis[4-methoxyamidinophenyl]furan were synthesized and evaluated against Trypanosoma brucei rhodesiense in the STIB900 mouse model by oral administration. The observed in vivo activity of these prodrugs demonstrates that compounds with an O-methoxyamidine or O-ethoxyamidine group effectively cured all trypanosome-infected mice, whereas prodrugs with larger side-chains did not completely cure the mice. Permeability across Caco-2 cell monolayers and microsomal metabolism were used to identify the underlying mechanisms of prodrug efficacy.
Using the Argumentative Structure of Scientific Literature to Improve Information Access (2013)

MEDLINE/PubMed contains structured abstracts that can provide argumentative labels. Selection of abstract sentences based on the argumentative label has shown to improve the performance of in- formation retrieval tasks. These abstracts make up less than one quarter of all the abstracts in MEDLINE/PubMed, so it is worthwhile to learn how to automatically label the non-structured ones. We have compared several machine learn- ing algorithms trained on structured ab- stracts to identify argumentative labels. We have performed an intrinsic evalua- tion on predicting argumentative labels for non-structured abstracts and an extrinsic evaluation to predict argumentative labels on abstracts relevant to Gene Reference Into Function (GeneRIF) indexing. Intrinsic evaluation shows that argumen- tative labels can be assigned effectively to structured abstracts. Algorithms that model the argumentative structure seem to perform better than other algorithms. Extrinsic results show that assigning ar- gumentative labels to non-structured ab- stracts improves the performance on GeneRIF indexing. On the other hand, the algorithms that model the argumentative structure of the abstracts obtain lower per- formance in the extrinsic evaluation.
Voltage-offset resistive control for DC-DC converters in photovoltaic applications (2012)

Photovoltaic (PV) systems must be able to maintain stable operation near the maximum power point (MPP) regardless of environmental conditions. Voltage-offset resistive control (VRC) exhibits inherently low sensitivity to irradiance changes and supports effective inner-loop control to maintain MPP operation. Small- and large-signal analysis show that VRC employed with a boost converter is stable for PV applications. VRC is tested on an experimental setup using a digital controller, PV boost converter, and dc-link load. Irradiance and control parameter step responses are observed through simulated and experimental results. VRC exhibits stable and fast transient response. Traditional and VRC maximum power point tracking (MPPT) methods that utilize sample-and-hold operation are compared through simulation. The fractional open-circuit voltage VRC and MPP-current-based VRC methods are identified as effective, simple control solutions for PV systems that seek to maintain high efficiency under irradiance transients.
Cathepsin B‐Specific Metabolic Precursor for In Vivo Tumor‐Specific Fluorescence Imaging (2016)

Abstract Recently, metabolic glycoengineering with bioorthogonal click reactions has focused on improving the tumor targeting efficiency of nanoparticles as delivery vehicles for anticancer drugs or imaging agents. It is the key technique for developing tumor‐specific metabolic precursors that can generate unnatural glycans on the tumor‐cell surface. A cathepsin B‐specific cleavable substrate (KGRR) conjugated with triacetylated N ‐azidoacetyl‐ d ‐mannosamine (RR‐S‐Ac 3 ManNAz) was developed to enable tumor cells to generate unnatural glycans that contain azide groups. The generation of azide groups on the tumor cell surface was exogenously and specifically controlled by the amount of RR‐S‐Ac 3 ManNAz that was fed to target tumor cells. Moreover, unnatural glycans on the tumor cell surface were conjugated with near infrared fluorescence (NIRF) dye‐labeled molecules by a bioorthogonal click reaction in cell cultures and in tumor‐bearing mice. Therefore, our RR‐S‐Ac 3 ManNAz is promising for research in tumor‐specific imaging or drug delivery.