gebhart/patrepeval huggingface dataset:
Nature's neutron probe: Land surface hydrology at an elusive scale with cosmic rays (2010)

Fast neutrons are generated naturally at the land surface by energetic cosmic rays. These “background” neutrons respond strongly to the presence of water at or near the land surface and represent a hitherto elusive intermediate spatial scale of observation that is ideal for land surface studies and modeling. Soil moisture, snow, and biomass each have a distinct influence on the spectrum, height profile, and directional intensity of neutron fluxes above the ground, suggesting that different sources of water at the land surface can be distinguished with neutron data alone. Measurements can be taken at fixed sites for long‐term monitoring or in a moving vehicle for mapping over large areas. We anticipate applications in many previously problematic contexts, including saline environments, wetlands and peat bogs, rocky soils, the active layer of permafrost, and water and snow intercepted by vegetation, as well as calibration and validation of data from spaceborne sensors.
Point sampling with uniformly distributed lines (2005)

In this paper we address the problem of extracting representative point samples from polygonal models. The goal of such a sampling algorithm is to find points that are evenly distributed. We propose star-discrepancy as a measure for sampling quality and propose new sampling methods based on global line distributions. We investigate several line generation algorithms including an efficient hardware-based sampling method. Our method contributes to the area of point-based graphics by extracting points that are more evenly distributed than by sampling with current algorithms.
Echoprint: An Open Music Identification Service (2011)

We discuss Echoprint, an open source and open data music identification service available to anyone. Echoprint is efficient and speedy and works by generating dozens of hashes a second from input audio (microphone or files) and then matching those hashes in a large scale inverted index for queries. We discuss the signal code generator and the server component.
Travelling wave-driven microfabricated electrohydrodynamic pumps for liquids (1994)

S.217-226
Semisynthesis of Proteins by Expressed Protein Ligation (2003)

Expressed protein ligation (EPL) is a protein engineering approach that allows recombinant and synthetic polypeptides to be chemoselectively and regioselectively joined together. The approach makes the primary structure of most proteins accessible to the tools of synthetic organic chemistry, enabling the covalent structure of proteins to be modified in an unprecedented fashion. The ability to incorporate noncoded amino acids, biophysical probes, and stable isotopes into specific locations within proteins provides research tools to peer into the inner workings of these molecules. In this review I discuss the development of this technology, its broad application to biological systems, and its possible role in the area of proteomics.
Neuromuscular electrical stimulation for skeletal muscle function. (2012)

Lack of neural innervation due to neurological damage renders muscle unable to produce force. Use of electrical stimulation is a medium in which investigators have tried to find a way to restore movement and the ability to perform activities of daily living. Different methods of applying electrical current to modify neuromuscular activity are electrical stimulation (ES), neuromuscular electrical stimulation (NMES), transcutaneous electrical nerve stimulation (TENS), and functional electrical stimulation (FES). This review covers the aspects of electrical stimulation used for rehabilitation and functional purposes. Discussed are the various parameters of electrical stimulation, including frequency, pulse width/duration, duty cycle, intensity/amplitude, ramp time, pulse pattern, program duration, program frequency, and muscle group activated, and how they affect fatigue in the stimulated muscle.
European Handbook of Plant Diseases (1988)

Viruses I: General: Major virus groups Viruses II: Minor virus groups and virus complexes Viruses III: Ungrouped viruses and virus complexes Viruses IV: Diseases assumed to be due to viruses Mollicutes and rickettsia-like organisms Bacteria I: Pseudomonas and Xanthomonas Bacteria II: Agrobacterium, Corynebacterium, Erwinia and other bacteria Oomycetes Chytridiomycetes, Plasmodiophoromycetes, Zygomycetes Ascomycetes I: General: Endomycetales, Taphrinales, Eurotiales, Erysiphales Ascomycetes II: Clavicipitales, Hypocreales Ascomycetes III: Ophiostomatales, Diaporthales, Polystigmatales, Sphaeriales, Diatrypales, Coryneliales Ascomycetes IV: Dothideales Ascomycetes V: Rhytismatales, Caliciales, Pezizales, Caliciales Helotiales Basidiomycetes I: Ustilaginales Basidiomycetes II: Uredinales Basidiomycetes III: Hymenomycetes Pathogen index Host index
Electrochemical Sensing in Microfluidic Systems Using Electrogenerated Chemiluminescence as a Photonic Reporter of Redox Reactions (2002)

This paper describes a microfluidics-based sensing system that relies on electrochemical detection and electrogenerated chemiluminescent (ECL) reporting. The important result is that the ECL reporting reaction is chemically decoupled from the electrochemical sensing reaction. That is, the electrochemical sensing reaction does not participate directly in the ECL process, but because electrochemical cells require charge balance, the sensing and ECL reactions are electrically coupled. This provides a convenient and sensitive means for direct photonic readout of electrochemical reactions that do not directly participate in an ECL reaction and thus broadens the spectrum of redox compounds that can be detected by ECL. The approach can be implemented in either a two-electrode or bipolar (single-electrode) configuration. By manipulating the placement and dimensions of the conductors, the photonic response can be enhanced. The system is used to electrochemically detect benzyl viologen present in solution and report its presence via Ru(bpy)(3)(2+) (bpy = 2,2'-bipyridine) luminescence.
The Putative Vitamin K-dependent γ-Glutamyl Carboxylase Internal Propeptide Appears to Be the Propeptide Binding Site (2002)

The vitamin K-dependent gamma-glutamyl carboxylase binds an 18-amino acid sequence usually attached as a propeptide to its substrates. Price and Williamson (Protein Sci. (1993) 2, 1997-1998) noticed that residues 495-513 of the carboxylase shares similarity with the propeptide. They suggested that this internal propeptide could bind intramolecularly to the propeptide binding site of carboxylase, thereby preventing carboxylation of substrates lacking a propeptide recognition sequence. To test Price's hypothesis, we created nine mutant enzyme species that have single or double mutations within this putative internal propeptide. The apparent K(d) values of these mutant enzymes for human factor IX propeptide varied from 0.5- to 287-fold when compared with that of wild type enzyme. These results are consistent with the internal propeptide hypothesis but could also be explained by these residues participating in propeptide binding site per se. To distinguish between the two alternative hypotheses, we measured the dissociation rates of propeptides from each of the mutant enzymes. Changes in an internal propeptide should not affect the dissociation rates, but changes to a propeptide binding site may affect the dissociation rate. We found that dissociation rates varied in a manner consistent with the apparent K(d) values measured above. Furthermore, kinetic studies using propeptide-containing substrates demonstrated a correlation between the affinity for propeptide and V(max). Taken together, our results indicated that these mutations affected the propeptide binding site rather than a competitive inhibitory internal propeptide sequence. These results agree with our previous observations, indicating that residues in this region are involved in propeptide binding.
Retinal Prosthesis (2005)

▪ Abstract Retinal prostheses represent the best near-term hope for individuals with incurable, blinding diseases of the outer retina. On the basis of the electrical activation of nerves, prototype retinal prostheses have been tested in blind humans and have demonstrated the capability to elicit the sensation of light and to give test subjects the ability to detect motion. To improve the visual function in implant recipients, a more sophisticated device is required. Simulations suggest that 600–1000 pixels will be required to provide visual function such as face recognition and reading. State-of-the-art implantable stimulator technology cannot produce such a device, which mandates the advancement of the state of the art in areas such as analog microelectronics, wireless power and data transfer, packaging, and stimulating electrodes.
Cell-Type-Dependent Targeting of Human Immunodeficiency Virus Type 1 Assembly to the Plasma Membrane and the Multivesicular Body (2004)

The human immunodeficiency virus type 1 (HIV-1) assembly-and-release pathway begins with the targeting of the Gag precursor to the site of virus assembly. The molecular mechanism by which Gag is targeted to the appropriate subcellular location remains poorly understood. Based on the analysis of mutant Gag proteins, we and others have previously demonstrated that a highly basic patch in the matrix (MA) domain of Gag is a major determinant of Gag transport to the plasma membrane. In this study, we determined that in HeLa and T cells, the MA mutant Gag proteins that are defective in plasma membrane targeting form virus particles in a CD63-positive compartment, defined as the late endosome or multivesicular body (MVB). Interestingly, we find that in primary human macrophages, both wild-type (WT) and MA mutant Gag proteins are targeted specifically to the MVB. Despite the fact that particle assembly in macrophages occurs at an intracellular site rather than at the plasma membrane, we observe that WT Gag expressed in this cell type is released as extracellular virions with high efficiency. These results demonstrate that Gag targeting to and assembly in the MVB are physiologically important steps in HIV-1 virus particle production in macrophages and that particle release in this cell type may follow an exosomal pathway. To determine whether Gag targeting to the MVB is the result of an interaction between the late domain in p6(Gag) and the MVB sorting machinery (e.g., TSG101), we examined the targeting and assembly of Gag mutants lacking p6. Significantly, the MVB localization of Gag was still observed in the absence of p6, suggesting that an interaction between Gag and TSG101 is not required for Gag targeting to the MVB. These data are consistent with a model for Gag targeting that postulates two different cellular binding partners for Gag, one on the plasma membrane and the other in the MVB.
Fc Receptor-Mediated Phagocytosis Makes a Significant Contribution to Clearance of Influenza Virus Infections (2001)

Fc receptors for IgG expressed on macrophages and NK cells are important mediators of opsonophagocytosis and Ab-dependent cell-mediated cytotoxicity. Phagocyte-mediated opsonophagocytosis is pivotal for protection against bacteria, but its importance in recovery from infection with intracellular pathogens is unclear. We have now investigated the role of opsonophagocytosis in protection against lethal influenza virus infection by using FcR gamma(-/-) mice. Absence of the FcR gamma-chain did not affect the expression of IFN-gamma and IL-10 in the lungs and spleens after intranasal immunization with an influenza subunit vaccine. Titers of serum and respiratory Abs of the IgM, IgG1, IgG2a, and IgA isotypes in FcR gamma(-/-) mice were similar to levels seen in FcR gamma(+/+) mice. Nevertheless, FcR gamma(-/-) mice were highly susceptible to influenza infection, even in the presence of anti-influenza Abs from immune FcR gamma(+/+) mice. NK cells were not necessary for the observed Ab-mediated viral clearance, but macrophages were found to be capable of actively ingesting opsonized virus particles. We conclude that Fc receptor-mediated phagocytosis plays a pivotal role in clearance of respiratory virus infections.
Inhibition of Vascular Endothelial Growth Factor in the Primate Ovary Up-Regulates Hypoxia-Inducible Factor-1α in the Follicle and Corpus Luteum (2008)

Vascular endothelial growth factor (VEGF)-dependent angiogenesis is crucial for follicular growth, and corpus luteum formation and function, in the primate ovary. In the ovary VEGF can be hormonally regulated, but in other systems, the main regulator of VEGF expression is hypoxia. We hypothesized that hypoxia was involved in the regulation of angiogenesis in the cycling ovary. We therefore used immunohistochemistry to localize hypoxia-inducible factor (HIF)-1alpha in the marmoset ovary across the ovarian cycle. We also investigated the effect of VEGF inhibition, using VEGF Trap (aflibercept), on HIF-1alpha localization during the follicular and luteal phases of the cycle. Finally, we studied the effect of chorionic gonadotropin stimulation of the corpus luteum during early pregnancy. Nuclear HIF-1alpha staining was largely absent from normally growing preantral and antral follicles. However, there was marked up-regulation of nuclear HIF-1alpha in the granulosa cells at ovulation that persisted into the early corpus luteum. Mature corpora lutea and those collected during early pregnancy had minimal nuclear HIF-1alpha staining. The inhibition of VEGF in the mid-luteal stage resulted in a time-dependent up-regulation of luteal nuclear HIF-1alpha staining (P < 0.05). There was never any nuclear HIF-1alpha in the theca cells of the follicle, but VEGF Trap treatment during the follicular (P < 0.001) or luteal (P < 0.001) phase increased the proportion of antral follicles with nuclear HIF-1alpha staining in the granulosa cells. These results indicate that HIF-1alpha is up-regulated after vascular inhibition, using VEGF Trap, in the follicle and corpus luteum. However, it is also acutely up-regulated during ovulation. This suggests a role for HIF-1alpha in both hypoxic and hormonal regulation of ovarian VEGF expression in vivo.
Coplanar Integration of Lattice-Mismatched Semiconductors with Silicon by Wafer Bonding Ge/Si[sub 1−x]Ge[sub x]/Si Virtual Substrates (2004)

We have demonstrated a general process which could be used for the integration of lattice-mismatched semiconductors onto large, Si-sized wafers by wafer bonding virtual substrates. The challenges for implementing this procedure for large diameter Ge-on-insulator (GOI) have been identified and solved, resulting in the transfer of epitaxial to a Si wafer. We found that planarization of Ge virtual substrates was a key limiting factor in the transfer process. To circumvent this problem, an oxide layer was first deposited on the Ge film before planarization using a standard oxide chemical mechanical planarization process. The GOI structure was created using -induced layer exfoliation (Smartcut™) and a buried etch-stop layer, which was used to subsequently remove the surface damage with a hydrogen peroxide selective etch. After selective etching, the crosshatched surface morphology of the original virtual substrate was preserved with roughness of <15 nm rms as measured on a scale and a scale roughness of Using an etch-stop layer, the transferred device layer thickness is defined epitaxially allowing for future fabrication of ultrathin GOI as well as III-V films directly on large-diameter Si wafers. © 2004 The Electrochemical Society. All rights reserved.
SURGICAL RELIEF OF PAIN IN PARAPLEGIC PATIENTS (1947)

FROM the recent worldwide conflict approximately 2,000 persons returned to this country with severe injuries to the spinal cord and spinal nerves. Of these, some 600 have been under our care for varying periods. Recent years have brought the wholesale discard of older concepts of paraplegic care, and the life expectancy of the average patient with severe injury of the spinal cord has been lengthened from about eighteen months to perhaps a normal one. In consequence of the renewed hope for this type of patient, the administration of drugs which produce addiction for the relief of pain can no longer be countenanced. It is our firm belief that pain can kill, if not outright as in a case recorded by Tinsley,<sup>1</sup>then at least insidiously through its continued action in bringing about starvation. For the purpose of simplification, pain in the paraplegic patient can be classified into three types.
Cardiovascular Effects of Ozone Exposure in Human Volunteers (1998)

We hypothesized that ozone (O3) exposure acutely affects cardiovascular hemodynamics in humans and, in particular, in subjects with essential hypertension. We studied 10 nonmedicated hypertensive and six healthy male adults. Each subject, after catheterization of the right heart and a radial artery, was exposed in an environmentally controlled chamber to filtered air (FA) on one day and to 0.3 ppm O3 on the following day for 3 h with intermittent exercise. Relative to FA exposure, O3 exposure induced no statistically significant changes in cardiac index, ventricular performance, pulmonary artery pressure, pulmonary and systemic vascular resistances, ECG, serum cardiac enzymes, plasma catecholamines and atrial natriuretic factor, and SaO2. The overall results did not indicate major acute cardiovascular effects of O3 in either the hypertensive or the control subjects. However, mean preexposure to postexposure changes were significantly (p < 0.02) larger with O3 than with FA for rate-pressure product (1,353 beats/min/mm Hg) and for heart rate (8 beats/min); these responses were not significantly different between the hypertensive and the control subjects. Significant O3 effects were also observed for mean FEV1 (-6%), and AaPO2 (> 10 mm Hg increase), which were not significantly different between the two groups. These results suggest that O3 exposure can increase myocardial work and impair pulmonary gas exchange to a degree that might be clinically important in persons with significant preexisting cardiovascular impairment, with or without concomitant lung disease.
Glucose Deprivation Contributes to the Development of KRAS Pathway Mutations in Tumor Cells (2009)

Tumor progression is driven by genetic mutations, but little is known about the environmental conditions that select for these mutations. Studying the transcriptomes of paired colorectal cancer cell lines that differed only in the mutational status of their KRAS or BRAF genes, we found that GLUT1, encoding glucose transporter-1, was one of three genes consistently up-regulated in cells with KRAS or BRAF mutations. The mutant cells exhibited enhanced glucose uptake and glycolysis and survived in low-glucose conditions, phenotypes that all required GLUT1 expression. In contrast, when cells with wild-type KRAS alleles were subjected to a low-glucose environment, very few cells survived. Most surviving cells expressed high levels of GLUT1, and 4% of these survivors had acquired KRAS mutations not present in their parents. The glycolysis inhibitor 3-bromopyruvate preferentially suppressed the growth of cells with KRAS or BRAF mutations. Together, these data suggest that glucose deprivation can drive the acquisition of KRAS pathway mutations in human tumors.
Inhibition of Neurofibrillary Degeneration: A Promising Approach to Alzheimers Disease and Other Tauopathies (2004)

Neurofibrillary degeneration (ND) is both a pivotal and a primary lesion of Alzheimer disease (AD) and related tauopathies. To date in all known tauopathics including AD, the neurofibrillary changes, whether of paired helical filaments (PHF), twisted ribbons or straight filaments (SF) are made up of abnormally hyperphosphorylated tau, and the number of these lesions directly correlates to the degree of dementia in the affected individuals. Unlike normal tau which promotes assembly and maintains structure of microtubules, the abnormal tau not only lacks these functions but also sequesters normal tau, MAPI and MAP2, and causes disassembly of microtubules. This toxic behavior of the abnormal tau is solely due to its hyperphosphorylation because dephosphorylation restores it into a normal-like protein. The abnormal hyperphosphorylation also promotes the self-assembly of tau into PHF/SF. Missense mutations in tau that cosegregate with the disease in inherited cases of frontotemporal dementia make it a more favorable substrate for hyperphosphorylation. A cause of the abnormal hyperphosphorylation in AD brain is a decrease in the activity of protein phosphatase (PP)-2A, a major regulator of the phosphorylation of tau. The abnormal hyperphosphorylation of tau and neurofibrillary degeneration may be inhibited by increasing the activity of PP-2A, inhibiting the activity of one or more tau kinases or by the sequestration of normal tau by the abnormally hyperphosphorylated tau. A great advantage of developing therapeutic drugs to inhibit neurofibrillary degeneration is that the efficacy of these drugs can be monitored by assaying the CSF levels of phosphotau and total tau, both of which are elevated in AD. Thus, the development of drugs that inhibit neurofibrillary degeneration is a very promising and feasible therapeutic approach to AD and related tauopathies.
Strongly emissive individual DNA-encapsulated Ag nanoclusters as single-molecule fluorophores (2007)

The water-soluble, near-IR-emitting DNA-encapsulated silver nanocluster presented herein exhibits extremely bright and photostable emission on the single-molecule and bulk levels. The photophysics have been elucidated by intensity-dependent correlation analysis and suggest a heavy atom effect of silver that rapidly depopulates an excited dark level before quenching by oxygen, thereby conferring great photostability, very high single-molecule emission rates, and essentially no blinking on experimentally relevant time scales (0.1 to >1,000 ms). Strong antibunching is observed from these biocompatible species, which emit >10(9) photons before photobleaching. The significant dark-state quantum yield even enables bunching from the emissive state to be observed as a dip in the autocorrelation curve with only a single detector as the dark state precludes emission from the emissive level. These species represent significant improvements over existing dyes, and the nonpower law blinking kinetics suggest that these very small species may be alternatives to much larger and strongly intermittent semiconductor quantum dots.