gebhart/patrepeval huggingface dataset:
Diagnostic Microbiologic Methods in the GEMS-1 Case/Control Study (2012)

To understand the etiology of moderate-to-severe diarrhea among children in high mortality areas of sub-Saharan Africa and South Asia, we performed a comprehensive case/control study of children aged <5 years at 7 sites. Each site employed an identical case/control study design and each utilized a uniform comprehensive set of microbiological assays to identify the likely bacterial, viral and protozoal etiologies. The selected assays effected a balanced consideration of cost, robustness and performance, and all assays were performed at the study sites. Identification of bacterial pathogens employed streamlined conventional bacteriologic biochemical and serological algorithms. Diarrheagenic Escherichia coli were identified by application of a multiplex polymerase chain reaction assay for enterotoxigenic, enteroaggregative, and enteropathogenic E. coli. Rotavirus, adenovirus, Entamoeba histolytica, Giardia enterica, and Cryptosporidium species were detected by commercially available enzyme immunoassays on stool samples. Samples positive for adenovirus were further evaluated for adenovirus serotypes 40 and 41. We developed a novel multiplex assay to detect norovirus (types 1 and 2), astrovirus, and sapovirus. The portfolio of diagnostic assays used in the GEMS study can be broadly applied in developing countries seeking robust cost-effective methods for enteric pathogen detection.
Appearance of Metallic Reflectance due to Conversion from Precursor Polymer to Poly(2,5-thienylenevinylene) (1988)

The optical absorption and reflectance of poly(2,5-thienylenevinylene) and its precursor polymer thin films were measured. It was found that the optical properties drastically changed and metallic reflectance appeared during conversion from the precursor polymer to poly(2,5-thienylenevinylene).
Tables S1-S2 from Discovery of Selective Estrogen Receptor Covalent Antagonists for the Treatment of ERα<sup>WT</sup> and ERα<sup>MUT</sup> Breast Cancer (2023)

&lt;p&gt;Crystallography and amino acid coordinates&lt;/p&gt;
Singlet Oxygen Signaling: From Intimate to Global (2004)

Reactive oxidizing species (ROS), such as hydrogen peroxide, nitric oxide, superoxide anion, and singlet oxygen, can damage cells as well as initiate responses such as new gene expression. The cell response evoked is strongly dependent on several factors. The subcellular location for formation of an ROS may be especially important for a highly reactive ROS, because it diffuses only a very short distance before reacting with a cellular molecule. How does a short-lived, locally acting ROS trigger responses at distant subcellular sites? This issue is discussed in light of a study of gene expression initiated by singlet oxygen, a ROS that exists for less than 100 ns in cells. Singlet oxygen is generated after a photosensitizer absorbs light energy and transfers the energy to molecular oxygen. To assess the role of singlet oxygen in light-induced gene expression in Arabidopsis, a mutant was used that accumulates the photosensitizer protochlorphyllide in chloroplasts. Three mechanisms are discussed that may connect the site of singlet oxygen formation to the signal transduction components: (i) direct oxidation of a signaling component by singlet oxygen, (ii) formation of oxidation products near the sites of singlet oxygen formation that diffuse to and react with signaling components, and (iii) alteration of the redox balance of the cell to a more oxidized state such that a greater proportion of a signaling pathway component is oxidized.
Correction for Fleissner et al., Site-directed spin labeling of a genetically encoded unnatural amino acid (2010)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Topology Optimization of Sub-Wavelength Antennas (2010)

We propose a topology optimization strategy for the systematic design of a three-dimensional (3D), conductor-based sub-wavelength antenna. The post-processed finite-element (FE) models of the optimized structure are shown to be self-resonant, efficient and exhibit distorted omnidirectional, elliptically polarized far-field radiation patterns. The computed approximate <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> value for this antenna is Q <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Z</sub> (ω <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> )≈ 7.74 for ω <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> =2π × 350.8 MHz and it is 1.64 times larger than the theoretical lower bound value.
Evaluation of CdS Interfacial Layers in ZnO Nanowire/Poly(3‐Hexylthiophene) Solar Cells (2012)

We prepare ZnO:poly(3‐hexylthiophene) (P3HT) thin‐film solar cells and ZnO nanowire:P3HT nanostructured solar cells and evaluate the effect of adding an interfacial layer between the ZnO and P3HT as a function of the nanowire height. We evaluate several different interlayers of CdS deposited, using two different chemical bath deposition (CBD) recipes. The height of the nanowire array is varied from a bilayer device with no nanowires up to arrays with a height of 2 μ m. We find that achieving a conformal coating of the ZnO with the interfacial layer is critical to improve device performance and that CBD can be used to grow conformal films on nonuniform surfaces.
Uropathogenic Escherichia coli P and Type 1 Fimbriae Act in Synergy in a Living Host to Facilitate Renal Colonization Leading to Nephron Obstruction (2011)

The progression of a natural bacterial infection is a dynamic process influenced by the physiological characteristics of the target organ. Recent developments in live animal imaging allow for the study of the dynamic microbe-host interplay in real-time as the infection progresses within an organ of a live host. Here we used multiphoton microscopy-based live animal imaging, combined with advanced surgical procedures, to investigate the role of uropathogenic Escherichia coli (UPEC) attachment organelles P and Type 1 fimbriae in renal bacterial infection. A GFP+ expressing variant of UPEC strain CFT073 and genetically well-defined isogenic mutants were microinfused into rat glomerulus or proximal tubules. Within 2 h bacteria colonized along the flat squamous epithelium of the Bowman's capsule despite being exposed to the primary filtrate. When facing the challenge of the filtrate flow in the proximal tubule, the P and Type 1 fimbriae appeared to act in synergy to promote colonization. P fimbriae enhanced early colonization of the tubular epithelium, while Type 1 fimbriae mediated colonization of the center of the tubule via a mechanism believed to involve inter-bacterial binding and biofilm formation. The heterogeneous bacterial community within the tubule subsequently affected renal filtration leading to total obstruction of the nephron within 8 h. Our results reveal the importance of physiological factors such as filtration in determining bacterial colonization patterns, and demonstrate that the spatial resolution of an infectious niche can be as small as the center, or periphery, of a tubule lumen. Furthermore, our data show how secondary physiological injuries such as obstruction contribute to the full pathophysiology of pyelonephritis.
Supplementary Figure and Table Legends 1-2 from Progressive Chromatin Repression and Promoter Methylation of <i>CTNNA1</i> Associated with Advanced Myeloid Malignancies (2023)

Supplementary Figure and Table Legends 1-2 from Progressive Chromatin Repression and Promoter Methylation of &lt;i&gt;CTNNA1&lt;/i&gt; Associated with Advanced Myeloid Malignancies
Synaptic vesicle trafficking and Parkinson's disease (2011)

Presynaptic terminals maintain neurotransmitter release during repeated rounds of stimulation using local recycling of synaptic vesicles (SV). During each SV cycle, protein complex assembly and disassembly results in accumulation of inactive (unfolded) protein intermediates that may render synaptic terminals vulnerable to activity-dependent degeneration. SV trafficking is affected in many neurodegenerative conditions including Alzheimer' and Parkinson's disease (PD) suggesting that alteration of this process might be an important aspect of disease pathogenesis. This article reviews our current understanding for a role of causative PD genes in the SV cycle and speculates on the potential role of aberrant SV trafficking in the neurodegenerative cascade of PD.
Persistent Dopamine Functions of Neurons Derived from Embryonic Stem Cells in a Rodent Model of Parkinson Disease (2006)

The derivation of dopamine neurons is one of the best examples of the clinical potential of embryonic stem (ES) cells, but the long-term function of the grafted neurons has not been established. Here, we show that, after transplantation into an animal model, neurons derived from mouse ES cells survived for over 32 weeks, maintained midbrain markers, and had sustained behavioral effects. Microdialysis in grafted animals showed that dopamine (DA) release was induced by depolarization and pharmacological stimulants. Positron emission tomography measured the expression of presynaptic dopamine transporters in the graft and also showed that the number of postsynaptic DA D(2) receptors was normalized in the host striatum. These data suggest that ES cell-derived neurons show DA release and reuptake and stimulate appropriate postsynaptic responses for long periods after implantation. This work supports continued interest in ES cells as a source of functional DA neurons.
Characterizing Low-Data-Rate Power Line Communication Channels (2022)

Electric power lines could, in principle, provide a ubiquitous wired communication network linking electrical loads, power meters, and other devices. This communication infrastructure could unlock new sensing and control capabilities, improving the efficiency and reliability of power system operations. In practice, however, power line communication (PLC) is complicated by both known and variable difficulties related to background noise, signal attenuation, and unknown line impedances. This article develops instrumentation that characterizes and verifies line characteristics for PLC applications, especially for demand response and control applications. This instrumentation provides a window to key variables that affect communication on a local power distribution network. With these measurements, limits on PLC communication can be verified before an installation, and a PLC system may also be adaptively tuned to measurements of the current local environment. Field experiments in a challenging microgrid and a 24-floor apartment building demonstrate an appropriately tailored PLC system communicating reliably in locations where conventional PLC fails.
Growth and development of GaInAsP for use in high-efficiency solar cells. Annual subcontract report, 1 July 1991--30 June 1992 (1993)

This report describes work done during Phase II of the subcontract. Goals for Phase II include the following: (1) Optimize the GaInAsP cell on GaAs and demonstrate a 500-sun at air mass (AM) 1.5 efficiency of >23%. (2) Develop a window layer, including the evaluation of AlGaAs, GaInP, AlGaAsP, AlGaInP, and GaP. (3) Develop a front-surface contact, with a grid designed for 500-sun concentration, and a goal of a contact resistivity of {approximately}10{sup 5} ohm-cm{sup 2}. (4) Grow GaInAsP cells on Ge, with a goal of a 1-sun (AM 1.5) efficiency of >15%. Accomplishments reported herein include (1) the fabrication of p-on-n and n-on-p GaInAsP cells on GaAs, with the n-on-p cell demonstrating a 10-sun (AM 1.5) active-area efficiency of 23.4% as measured at NREL (2) the evaluation of Al{sub x}Ga({sub 1-x})As, GaInP{sub 2}, and AlInP{sub 2} window layers; and (3) the fabrication of GaInAsP cells on Ge, with the demonstration of a p-on-n GaInAsP cell grown on Ge with a 1-sun (AM 1.5) active-area efficiency of 14.4%.
Theoretical analysis on pruning nearest neighbor candidates by locality sensitive hashing (2010)

Locality Sensitive Hashing (LSH) is one of the most popular methods of the approximate near neighbor search. In applications that require the nearest neighbors of queries in a short time, LSH is sometimes used in pruning of the candidates of nearest neighbors. While the pruning reduces the processing time greatly, it also reduces the chances of retrieving the exact nearest neighbors. However, the pruning of nearest neighbor candidates using LSH has not been considered theoretically. Thus in this paper, we investigate the pruning effect by deriving the formulae of retrieval accuracy and computational cost of distance calculation for uniformly distributed data. Furthermore, we make evaluations on the formulae by comparison between simulation results and the theoretical values.
Waveform Design for Wireless Power Transfer With Limited Feedback (2017)

Waveform design is a key technique to jointly exploit a beamforming gain, the channel frequency selectivity, and the rectifier nonlinearity, so as to enhance the end-to-end power transfer efficiency of wireless power transfer (WPT). Those waveforms have been designed, assuming perfect channel state information at the transmitter. This paper proposes two waveform strategies relying on limited feedback for multi-antenna multi-sine WPT over frequency-selective channels. In the waveform selection strategy, the energy transmitter (ET) transmits over multiple timeslots with every time a different waveform precoder within a codebook, and the energy receiver (ER) reports the index of the precoder in the codebook that leads to the largest harvested energy. In the waveform refinement strategy, the ET sequentially transmits two waveforms in each stage, and the ER reports one feedback bit indicating an increase/decrease in the harvested energy during this stage. Based on multiple one-bit feedback, the ET successively refines waveform precoders in a tree-structured codebook over multiple stages. By employing the framework of the generalized Lloyd’s algorithm, novel algorithms are proposed for both strategies to optimize the codebooks in both space and frequency domains. The proposed limited feedback-based waveform strategies are shown to outperform a set of baselines, achieving higher harvested energy.
3D Characterization of the Columnar-to-Equiaxed Transition in Additively Manufactured Inconel 718. (2021)

Abstract not provided.
Cover Picture: Hepatocyte‐Specific Delivery of siRNAs Conjugated to Novel Non‐nucleosidic Trivalent N‐Acetylgalactosamine Elicits Robust Gene Silencing in Vivo (ChemBioChem 6/2015) (2015)

The cover picture shows recognition of siRNA conjugated to trivalent N-acetylgalactosamine by the asialoglycoprotein receptor (ASGPR) expressed on the surface of a hepatocyte, and intracellular events that result in gene silencing. In nature, ASGPR mediates clearance of “dead” glycoproteins from circulation. This natural molecular machinery, which recognizes exposed galactoses, has been exploited to deliver nucleic acid-based drugs into hepatocytes. Engineered GalNAc moieties in favorable proximity and optimal spatial orientation serve as ligand mimics and are recognized by ASGPR leading to cargo internalization. GalNAc monomers were synthesized by using non-nucleosidic tethers and incorporated via phosphodiester linkages into oligonucleotides. The optimal siRNA-GalNAc conjugate was prepared by sequential covalent incorporation of three single GalNAc moieties at the 3′-end of the sense strand of siRNA. The siRNA–GalNAc conjugate elicited robust gene silencing in liver. Clinical experience with siRNA–GalNAc indicates that this strategy is a breakthrough in the tissue-specific delivery of therapeutic nucleic acids. For more details see the communication by K. G. Rajeev, M. Manoharan et al. on p. 903 ff.
Demonstration of a low-voltage three-transistor-per-pixel CMOS imager based on a pulse-width-modulation readout scheme employed with a one-transistor in-pixel comparator (2007)

To realize a low-voltage CMOS imager with a small pixel size, we have proposed a new pixel structure composed of only three transistors without any circuit sharing technique. The pixel has a gate-common transistor that compares a photodiode voltage on the gate node with a ramp signal on the source node to perform a single-slope A/D conversion based on a pulse-width-modulation pixel-reading scheme. The large gain of the in-pixel comparator contribute to the small input-referred noise and surpress column-to-column fixed-pattern-noise (FPN). Pixel-to-pixel FPN is suppressed by a feedback reset. Our CMOS imager can lower the operating voltage with less degradation of the dynamic range than that of ordinary active pixel sensors. We have fabricated a 128×96-pixel prototype sensor with an on-chip ramp generator and bootstrap circuits in a 0.35-&mgr;m CMOS technology, and successfully demonstrated its operations with a 1.5-V single power-supply voltage.
ChemInform Abstract: Fluorine‐Substituted Ferracyclopentadiene Complexes with an Unprecedented Fluorine Bridge Between Boron and Carbon. (1990)

Abstract The title complexes (III) are the first examples of any type of compound with a fluorine atom bridging between C and B atoms.
Cbx3 maintains lineage specificity during neural differentiation (2017)

Chromobox homolog 3 (Cbx3/heterochromatin protein 1γ [HP1γ]) stimulates cell differentiation, but its mechanism is unknown. We found that Cbx3 binds to gene promoters upon differentiation of murine embryonic stem cells (ESCs) to neural progenitor cells (NPCs) and recruits the Mediator subunit Med26. RNAi knockdown of either Cbx3 or Med26 inhibits neural differentiation while up-regulating genes involved in mesodermal lineage decisions. Thus, Cbx3 and Med26 together ensure the fidelity of lineage specification by enhancing the expression of neural genes and down-regulating genes specific to alternative fates.
Additional file 1: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus (2017)

Genome statistics and information. (XLSX 97 kb)
CuH-Catalyzed Enantioselective Ketone Allylation with 1,3-Dienes: Scope, Mechanism, and Applications (2018)

Chiral tertiary alcohols are important building blocks for the synthesis of pharmaceutical agents and biologically active natural products. The addition of carbon nucleophiles to ketones is the most common approach to tertiary alcohol synthesis, but traditionally relies on stoichiometric organometallic reagents that are difficult to prepare, sensitive, and uneconomical. We describe a mild and efficient method for the copper-catalyzed allylation of ketones, using widely available 1,3-dienes as allylmetal surrogates. Homoallylic alcohols bearing a wide range of functional groups are obtained in high yield and with good regio-, diastereo-, and enantioselectivity. Mechanistic investigations using density functional theory (DFT) implicate the in situ formation of a rapidly equilibrating mixture of isomeric copper(I) allyl complexes, from which Curtin-Hammett kinetics determine the major isomer of product. A stereochemical model is provided to explain the high diastereo- and enantioselectivity of this process. Finally, this method was applied toward the preparation of an important drug, (R)-Procyclidine, and a key intermediate in the synthesis of several pharmaceuticals.
Monochromatic synchrotron radiation μCT reveals disuse-mediated canal network rarefaction in cortical bone of growing rat tibiae (2005)

The purpose of this study was to demonstrate the ability of computed microtomography based on monochromatic synchrotron radiation (SRmuCT) in microstructural analysis of cortical bone. Tibial diaphyses of growing rats (14 wk, n = 8) undergoing unilateral sciatic neurectomy 8 wk before study were imaged with spatial volume resolution of 5.83 x 5.83 x 5.83 microm3 by SRmuCT (20 keV) at the synchrotron radiation facility (SPring-8). Reconstructed image data were translated into local mineral densities by using a calibrated linear relationship between linear absorption coefficients and concentrations of homogeneous K2HPO4 solution. Pure bone three-dimensional images, produced by simple thresholding at a bone mineral density of 0.82 g/cm3, were analyzed for macro- and microscopic structural properties. In neurectomized hindlimbs, cortical canal network rarefaction as well as bone atrophy were found. The former was characterized by 30% smaller porosity, 11% smaller canal density in transverse section, and 38% smaller canal connectivity density than those in contralateral bone. On the other hand, no difference was found in bone mineral density between neurectomized and intact hindlimbs (1.37 vs. 1.36 g/cm3). In conclusion, SRmuCT is a promising method for the three-dimensional analysis of cortical microstructure and the degree of mineralization in small animals.
Different Regulation of Connexin26 and ZO-1 in Cochleas of Developing Rats and of Guinea Pigs with Endolymphatic Hydrops (2001)

Using confocal microscopy and morphometry, we analyzed the expression of connexin26 (Cx26) and ZO-1 in rat cochlea during the postnatal period to elucidate spatiotemporal changes in gap junctions and tight junctions during auditory development. We also studied changes in these junctions in experimental endolymphatic hydrops in the guinea pig. In the adult rat cochlear lateral wall, Cx26 was detected in fibrocytes in the spiral ligament and in the basal cell layer of the stria vascularis, whereas ZO-1 was detected in the apical surfaces of marginal cells and in the basal cell layer. During postnatal development, Cx26 expression increased mainly in the spiral ligament, whereas ZO-1 expression increased in the basal cell layer. The morphometry of Cx26 showed a sigmoid time course with a rapid increase on postnatal day (PND) 14, whereas that of ZO-1 showed a marked increase on PND 7. In experimental endolymphatic hydrops, the expression of Cx26 significantly decreased, whereas there were no obvious changes in the expression of ZO-1. These results indicate that gap junctions and tight junctions in the cochlea increase in a different spatiotemporal manner during the development of auditory function and that gap junctions and tight junctions in the cochlea are differentially regulated in experimental endolymphatic hydrops. (J Histochem Cytochem 49:573-586, 2001)
An Alu variable polyA repeat polymorphism upstream of L-myc at 1p32 (1992)

Journal Article An Alu variable polyA repeat polymorphism upstream of L-myc at 1p32 Get access Tomi P. Mäkelä, Tomi P. Mäkelä Cancer Biology Laboratory, Departments of Virology and Pathology, University of Helsinki00290 Helsinki Search for other works by this author on: Oxford Academic PubMed Google Scholar Elina Hellsten, Elina Hellsten 1Laboratory of Molecular Genetics, National Public Health Institute, 00300 HelsinkiFinland Search for other works by this author on: Oxford Academic PubMed Google Scholar Jouni Vesa, Jouni Vesa 1Laboratory of Molecular Genetics, National Public Health Institute, 00300 HelsinkiFinland Search for other works by this author on: Oxford Academic PubMed Google Scholar Kari Alitalo, Kari Alitalo Cancer Biology Laboratory, Departments of Virology and Pathology, University of Helsinki00290 Helsinki Search for other works by this author on: Oxford Academic PubMed Google Scholar Leena Peltonen Leena Peltonen 1Laboratory of Molecular Genetics, National Public Health Institute, 00300 HelsinkiFinland Search for other works by this author on: Oxford Academic PubMed Google Scholar Human Molecular Genetics, Volume 1, Issue 3, June 1992, Page 217, https://doi.org/10.1093/hmg/1.3.217-a Published: 01 June 1992