gebhart/patrepeval huggingface dataset:
Chronic Invasive Fungal Sinusitis: A Report of Two Atypical Cases (2002)

The purpose of this article is to describe a chronic variant of invasive fungal sinusitis (IFS) and discuss its management. This is a retrospective review of two cases of IFS that were characterized by atypical clinical courses. Patient 1 was a 75-year-old man with noninsulin-dependent diabetes mellitus who came to us with a 5-month history of headache. Computed tomography detected an opacified left sphenoid sinus. After the man failed to respond to medical therapy, he underwent a left endoscopic sphenoidotomy. Pathologic examination revealed that septate, branching fungal hyphae had invaded the soft tissues. The patient was started on oral itraconazole, but later switched to intravenous amphotericin B in response to intracranial extension. The man's disease stabilized, but he died a little more than 1 year later of unrelated causes. Patient 2 was an otherwise healthy 41-year-old woman who came to us with nasal congestion and unilateral nasal polyps. She underwent endoscopic sinus surgery. Pathologic examination identified granulomatous sinusitis and septate, branching fungal hyphae that had invaded the soft tissue of the middle turbinate. The patient was not treated with systemic antifungal medications because of the localized nature of the fungal invasion and the lack of bone invasion or erosion. She has now been symptom-free for 5 years. These two cases demonstrate that IFS can appear in a chronic variant form that is characterized by an indolent course and histologic evidence of tissue invasion by fungal hyphae. The type of treatment is dependent on the extent of the disease on initial examination and the rapidity of its progression.
Discovery of Cyclic Acylguanidines as Highly Potent and Selective β-Site Amyloid Cleaving Enzyme (BACE) Inhibitors: Part I—Inhibitor Design and Validation (2009)

A number of novel amidine containing heterocycles were designed to reproduce the unique interaction pattern, revealed by X-ray crystallography, between the BACE-1 catalytic diad and a weak NMR screening hit (3), with special attention paid to maintaining the appropriate basicity and limiting the number of H-bonding donors of these scaffolds. The iminohydantoin cores (10 and 23) were examined first and found to interact with the catalytic diad in one of two binding modes (A and B), each with the iminohydantoin core flipped 180 degrees in relation to the other. The amidine structural motif within each core forms a bidentate interaction with a different aspartic acid of the catalytic diad. Both modes reproduced a highly conserved interaction pattern between the inhibitors and the catalytic aspartates, as revealed by 3. Potent iminohydantoin BACE-1 inhibitors have been obtained, validating the molecular design as aspartyl protease catalytic site inhibitors. Brain penetrant small molecule BACE inhibitors with high ligand efficiencies have been discovered, enabling multiple strategies for further development of these inhibitors into highly potent, selective and in vivo efficacious BACE inhibitors.
Vaccination against respiratoryPseudomonas aeruginosainfection (2014)

Respiratory infections caused by Pseudomonas aeruginosa are a major clinical problem globally, particularly for patients with chronic pulmonary disorders, such as those with cystic fibrosis (CF), non-CF bronchiectasis (nCFB) and severe chronic obstructive pulmonary disease (COPD). In addition, critically ill and immunocompromised patients are also at significant risk of P. aeruginosa infection. For almost half a century, research efforts have focused toward development of a vaccine against infections caused by P. aeruginosa, but a licensed vaccine is not yet available. Significant advances in identifying potential vaccine antigens have been made. Immunisations via both the mucosal and systemic routes have been trialled in animal models and their effectiveness in clearing acute infections demonstrated. The challenge for translation of this research to human applications remains, since P. aeruginosa infections in the human respiratory tract can present both as an acute or chronic infection. In addition, immunisation prior to infection may not be possible for many patients with CF, nCFB or COPD. Therefore, development of a therapeutic vaccine provides an alternative approach for treatment of chronic infection. Preliminary animal and human studies suggest that mucosal immunisation may be effective as a therapeutic vaccine against P. aeruginosa respiratory infections. Nevertheless, more research is needed to improve our understanding of the basic biology of P. aeruginosa and the mechanisms needed to upregulate the induction of host immune pathways to prevent infection. Recognition of variability in the host immune responses for a range of patient health conditions at risk from P. aeruginosa infection is also required to support development of a successful vaccine delivery strategy and vaccine. Activation of mucosal immune responses may provide improved efficacy of vaccination for P. aeruginosa during both acute exacerbations and chronic infection.
Lenses of diabetic patients "yellow" at an accelerated rate similar to older normals. (1991)

The authors used a psychophysical method to measure lens transmission of young, type I diabetic patients and normal controls. The results from normal controls agreed with previously published reports of decreasing lens transmission with age, and those from diabetic subjects suggested that lenses of young, type I diabetic patients age or "yellow" at an accelerated rate that was similar to that of normal controls over the age of 60 yr. The rate of accelerated lens density that occurs per year with the duration of diabetes is similar to the rate of accelerated lens density that occurs per year with patient age over 60 yr. A possible molecular explanation for the accelerated lens yellowing in both populations is discussed. Both diabetic individuals and the older normal populations have elevated plasma glucose levels and therefore may have accelerated glycosylation of lens proteins which causes increased lens yellowing.
Nanosphere lithography: A materials general fabrication process for periodic particle array surfaces (1995)

In this article nanosphere lithography (NSL) is demonstrated to be a materials general fabrication process for the production of periodic particle array (PPA) surfaces having nanometer scale features. A variety of PPA surfaces have been prepared using identical single-layer (SL) and double-layer (DL) NSL masks made by self-assembly of polymer nanospheres with diameter, D=264 nm, and varying both the substrate material S and the particle material M. In the examples shown here, S was an insulator, semiconductor, or metal and M was a metal, inorganic ionic insulator, or an organic π-electron semiconductor. PPA structural characterization and determination of nanoparticle metrics was accomplished with atomic force microscopy. This is the first demonstration of nanometer scale PPA surfaces formed from molecular materials.
LAP (NF-IL6) transactivates the collagen alpha 1(I) gene from a 5' regulatory region. (1994)

Although collagen is known to enhance hepatocyte differentiation and hepatocytes produce collagen in vivo, the transcriptional factors responsible for collagen type I gene expression in hepatic cells are not known. LAP (Liver Activator Protein) is a member of the C/EBP family, which in differentiated hepatocytes contributes to the high levels of liver-specific gene expression. In this study we show that LAP binds to the collagen alpha 1(I) promoter at both reverse CCAAT motifs and activates transcription. Furthermore, an upstream element, collagen element I (-370/-344), which shares homology with the LAP binding cis-element of the albumin promoter (9 of 13 bp) is described. This collagen element I stimulates transcription in both orientations and when placed in front of either a homologous or a heterologous chimeric report construct. These experiments suggest that LAP may be important in the expression of collagen in differentiated hepatocytes through both the promoter and a newly described upstream element.
Potent and Broad Neutralization of HIV-1 Subtype C by Plasma Antibodies Targeting a Quaternary Epitope Including Residues in the V2 Loop (2011)

The targets of broadly cross-neutralizing (BCN) antibodies are of great interest in the HIV vaccine field. We have identified a subtype C HIV-1-superinfected individual, CAP256, with high-level BCN activity, and characterized the antibody specificity mediating breadth. CAP256 developed potent BCN activity peaking at 3 years postinfection, neutralizing 32 (76%) of 42 heterologous viruses, with titers of antibodies against some viruses exceeding 1:10,000. CAP256 showed a subtype bias, preferentially neutralizing subtype C and A viruses over subtype B viruses. CAP256 BCN serum targeted a quaternary epitope which included the V1V2 region. Further mapping identified residues F159, N160, L165, R166, D167, K169, and K171 (forming the FN/LRD-K-K motif) in the V2 region as crucial to the CAP256 epitope. However, the fine specificity of the BCN response varied over time and, while consistently dependent on R166 and K169, became gradually less dependent on D167 and K171, possibly contributing to the incremental increase in breadth over 4 years. The presence of an intact FN/LRD-K-K motif in heterologous viruses was associated with sensitivity, although the length of the adjacent V1 loop modulated the degree of sensitivity, with a shorter V1 region significantly associated with higher titers. Repair of the FN/LRD-K-K motif in resistant heterologous viruses conferred sensitivity, with titers sometimes exceeding 1:10,000. Comparison of the CAP256 epitope with that of the PG9/PG16 monoclonal antibodies suggested that these epitopes overlapped, adding to the mounting evidence that this may represent a common neutralization target that should be further investigated as a potential vaccine candidate.
Hepatic differentiation from embryonic stem cells in vitro. (2003)

ES cells can differentiate into mature hepatocytes. Growth factors, such as aFGF and HGF, can enhance this differentiation and produce sufficient numbers of functional hepatocytes. This method may be a reliable new way of differentiating ES cells into hepatocytes for use in replacement therapy in the treatment of liver failure.
Stereoselective Preparation of (E)-(1,2-Difluoro-1,2-ethenediyl) Bis[tributylstannane] and Stereospecific Synthesis of (E)-1,2-Difluorostilbenes (2002)

[reaction: see text]. The novel bisstannane (E)-(1,2-difluoro-1,2-ethenediyl) bis[tributylstannane] 2 was stereoselectively prepared in a high overall yield through a sequential synthetic route from chlorotrifluoroethylene 1. The synthetic application of this novel bisstannane 2 was exemplified in the Pd(PPh3)4/CuI-catalyzed cross-coupling reactions with aryl iodides, yielding (E)-1,2-difluorostilbenes 3 in moderate to high yields.
Glaucoma filtration surgery in nonhuman primates using taxol and etoposide in polyanhydride carriers. (1993)

Use of polyanhydride disks containing taxol, but not etoposide, had a marked beneficial effect on intraocular pressure and bleb appearance after experimental filtration surgery in monkeys. The difference between the two agents may result from the greater antiproliferative potency of taxol and its greater duration of release from the polymer.
Transfer of Inter-α-inhibitor Heavy Chains to Hyaluronan by Surface-linked Hyaluronan-TSG-6 Complexes (2008)

Inter-alpha-inhibitor, TSG-6, and hyaluronan have important functions in fertility and inflammation. Two subunits of inter-alpha-inhibitor, the heavy chains, form covalent bonds with TSG-6 or hyaluronan in vitro. TSG-6-heavy chain complexes serve as intermediates in the transfer of heavy chains from inter-alpha-inhibitor to hyaluronan. In vivo, in addition to these complexes, stable ternary complexes of hyaluronan with both TSG-6 and heavy chains have been demonstrated in the ovulatory cumulus oophorus. In our ongoing efforts to characterize the multiple interactions between hyaluronan, TSG-6 and inter-alpha-inhibitor, we recently characterized the formation of highly stable complexes of TSG-6 with hyaluronan that had been tethered to a solid surface. Here we show that these hyaluronan-TSG-6 complexes are functionally active and transfer heavy chain subunits from inter-alpha-inhibitor to either free or surface-bound hyaluronan. Transitional hyaluronan-TSG-6-heavy chain complexes do not accumulate in vitro. Our data show the capability for heavy chain transfer by both free TSG-6 and preformed hyaluronan-TSG-6 complexes, suggesting that both might contribute to hyaluronan modification in vivo. Transfer of heavy chains to surface-tethered hyaluronan by either free TSG-6 or surface-tethered hyaluronan-TSG-6 complexes did not affect the CD 44-mediated binding of BW 5147 cells in vitro. We show how TSG-6 and hyaluronan together can deplete inter-alpha-inhibitor and generate bikunin, as has been observed in sepsis, and discuss the role of TSG-6 in the generation of hyaluronan-heavy chain complexes associated with ovulation, arthritis, and sepsis.
Radiosensitization of Hypoxic Mammalian Cells in Vitro by Some 5-substituted-4-nitroimidazoles (1981)

The efficiencies of various 5-substituted-4-nitroimidazoles as radiation sensitizers have been determined in hypoxic Chinese hamster cells irradiated in vitro. Compared with published data on the sensitizing properties of substituted 2-nitro- and 5-nitroimidazoles, some of the 4-nitro derivatives show unusually high sensitizing efficiencies defined as the concentrations required to give an enhancement ratio of 1.6. The equilibrium one-electron reduction potentials of the compounds (E17) were measured by a pulse radiolysis technique and the results show that although sensitizing efficiencies are unexpectedly high, based on considerations of electron affinity, they still increase with increasing values of E17. Enhancement ratios were determined in two V79 cell lines for combinations of one of these compounds (a 4-nitroimidazole containing the group SO2.O.phenyl in the 5-position, NSC 38087) with various concentrations of misonidazole. The sensitization observed suggests that the two compounds may be operating by different mechanisms.
The detection of DNA-binding proteins by protein blotting (1980)

A method, called "protein blotting," for the detection of DNA-binding proteins is described. Proteins are separated on an SDA-polyacrylamide gel. The gel is sandwiched between 2 nitrocellulose filters and the proteins allowed to diffuse out of the gel and onto the filters. The proteins are tightly bound to each filter, producing a replica of the original gel pattern. The replica is used to detect DNA-binding proteins, RNA-binding proteins or histone-binding proteins by incubation of the filter with [32P]DNA, [125I]RNA, or [125I] histone. Evidence is also presented that specific protein-DNA interactions may be detected by this technique; under appropriate conditions, the lac repressor binds only to DNA containing the lac operator. Strategies for the detection of specific protein-DNA interactions are discussed.
Mechanisms of Hybrid Oligomer Formation in the Pathogenesis of Combined Alzheimer's and Parkinson's Diseases (2008)

These results support the contention that Abeta directly interacts with alpha-syn and stabilized the formation of hybrid nanopores that alter neuronal activity and might contribute to the mechanisms of neurodegeneration in AD and PD. The broader implications of such hybrid interactions might be important to the pathogenesis of other disorders of protein misfolding.
Three dimensional tracking for volumetric spectral-domain optical coherence tomography (2007)

We present a three-dimensional (3D) tracker for a clinical ophthalmic spectral domain optical coherence tomography (SD-OCT) system that combines depth-tracking with lateral tracking, providing a stabilized reference frame for 3D data recording and post acquisition analysis. The depth-tracking system is implemented through a real-time dynamic feedback mechanism to compensate for motion artifact in the axial direction. Active monitoring of the retina and adapting the reference arm of the interferometer allowed the whole thickness of the retina to be stabilized to within +/-100 mum. We achieve a relatively constant SNR from image to image by stabilizing the image of the retina with respect to the depth dependent sensitivity of SD-OCT. The depth tracking range of our system is 5.2 mm in air and the depth is adjusted every frame.nhancement in the stability of the images with the depth-tracking algorithm is demonstrated on a healthy volunteer.
A novel CT acquisition and analysis technique for breathing motion modeling (2013)

To report on a novel technique for providing artifact-free quantitative four-dimensional computed tomography (4DCT) image datasets for breathing motion modeling. Commercial clinical 4DCT methods have difficulty managing irregular breathing. The resulting images contain motion-induced artifacts that can distort structures and inaccurately characterize breathing motion. We have developed a novel scanning and analysis method for motion-correlated CT that utilizes standard repeated fast helical acquisitions, a simultaneous breathing surrogate measurement, deformable image registration, and a published breathing motion model. The motion model differs from the CT-measured motion by an average of 0.65 mm, indicating the precision of the motion model. The integral of the divergence of one of the motion model parameters is predicted to be a constant 1.11 and is found in this case to be 1.09, indicating the accuracy of the motion model. The proposed technique shows promise for providing motion-artifact free images at user-selected breathing phases, accurate Hounsfield units, and noise characteristics similar to non-4D CT techniques, at a patient dose similar to or less than current 4DCT techniques.
Characterization of the gene for human plasminogen, a key proenzyme in the fibrinolytic system. (1990)

The organization and structure of the gene coding for plasminogen has been determined by a combination of in vitro amplification of leukocyte DNA from normal individuals and isolation of unique clones from three different human genomic libraries. These clones were characterized by restriction mapping, Southern blotting, and DNA sequencing. The gene for human plasminogen spanned about 52.5 kilobases of DNA and consisted of 19 exons separated by 18 introns. DNA sequence analysis revealed that the five kringle structures in plasminogen were coded by two exons. The nucleotides in the introns at the intron-exon boundaries were GT-AG analogous to those found in other eukaryotic genes. Three polyadenylation sites for plasminogen mRNA were also identified. When the amino acid sequences deduced from the genomic DNA and cDNAs of plasminogen were compared with that of the plasma protein determined by amino acid sequence analysis, an apparent amino acid polymorphism was observed in several positions of the polypeptide chain. Nucleotide sequence analysis of the amplified genomic DNAs and genomic clones also revealed that the plasminogen gene was very closely related to several other proteins, including apolipoprotein(a). This protein may have evolved via duplication and exon shuffling of the plasminogen gene. The presence of another plasminogen-related gene(s) in the human genomic library was also observed.
The importance of velocity, or why speed may matter more than distance (2012)

Theory and research on self-regulation emphasizes the importance of goals for guiding human behavior. Critical phenomena within the self-regulation literature are discrepancies between actual states and goal states. When such discrepancies are detected, they capture attention and effort is mobilized to move actual states closer to goal states (or in some cases align the latter with the former). While discrepancy feedback, or the distance between actual and goal states, is important, so too is velocity feedback, or the rate at which actual–goal discrepancies are decreasing. Unfortunately, research has mostly ignored the role played by velocity in the self-regulation process. To redress this limitation, we review the concept of velocity, the empirical studies that have examined this concept, and how velocity is commonly measured. We then discuss the role of velocity as it pertains to three self-regulatory functions at work: achieving performance goals, satisfying belonging needs, and satisfying esteem needs.
Hop as an Interesting Source of Resveratrol for Brewers:  Optimization of the Extraction and Quantitative Study by Liquid Chromatography/Atmospheric Pressure Chemical Ionization Tandem Mass Spectrometry (2004)

Nowadays, hop is used almost exclusively by brewers for bitterness and flavor. Although hop polyphenols have been widely studied in the past decade for their antioxidant activity in the boiling kettle, very little is known about their real impact on health. The discovery of resveratrol in hop pellets highlights the potential health-promoting effect of moderate beer consumption. Here, we have optimized a quantitative extraction procedure for resveratrol in hop pellets. Preliminary removal of hydrophobic bitter compounds with toluene and cyclohexane at room temperature allows 99% trans-resveratrol recovery by ethanol:water (75:25, v/v) solid/liquid extraction at 60 degrees C. Reverse phase liquid chromatography proves an excellent means of separating isomers. In addition, we have compared two mass spectrometry ionization methods-atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI)-in both the positive and the negative modes. On the basis of standard additions applied with the optimized extraction procedure and reverse phase high-performance liquid chromatography-APCI(+)-tandem mass spectrometry, it appears that Tomahawk hop pellets (T90, harvest 2002) contain 0.5 ppm trans-resveratrol, 2 ppm trans-piceid, no cis-resveratrol, and 0.9 ppm cis-piceid.
MRI measurements of carotid plaque in the atherosclerosis risk in communities (ARIC) study: Methods, reliability and descriptive statistics (2010)

The most important limiting factor for MRI measurements of plaque components is reader variability. Measurement error depends largely on the analyzed structure's size.
SBNet: Sparse Blocks Network for Fast Inference (2018)

Conventional deep convolutional neural networks (CNNs) apply convolution operators uniformly in space across all feature maps for hundreds of layers - this incurs a high computational cost for real-time applications. For many problems such as object detection and semantic segmentation, we are able to obtain a low-cost computation mask, either from a priori problem knowledge, or from a low-resolution segmentation network. We show that such computation masks can be used to reduce computation in the high-resolution main network. Variants of sparse activation CNNs have previously been explored on small-scale tasks and showed no degradation in terms of object classification accuracy, but often measured gains in terms of theoretical FLOPs without realizing a practical speed-up when compared to highly optimized dense convolution implementations. In this work, we leverage the sparsity structure of computation masks and propose a novel tiling-based sparse convolution algorithm. We verified the effectiveness of our sparse CNN on LiDAR-based 3D object detection, and we report significant wall-clock speed-ups compared to dense convolution without noticeable loss of accuracy.