gebhart/patrepeval huggingface dataset:
Systematic Optimization of Long Gradient Chromatography Mass Spectrometry for Deep Analysis of Brain Proteome (2014)

The development of high-resolution liquid chromatography (LC) is essential for improving the sensitivity and throughput of mass spectrometry (MS)-based proteomics. Here we present systematic optimization of a long gradient LC-MS/MS platform to enhance protein identification from a complex mixture. The platform employed an in-house fabricated, reverse-phase long column (100 μm × 150 cm, 5 μm C18 beads) coupled to Q Exactive MS. The column was capable of achieving a peak capacity of ∼700 in a 720 min gradient of 10-45% acetonitrile. The optimal loading level was ∼6 μg of peptides, although the column allowed loading as many as 20 μg. Gas-phase fractionation of peptide ions further increased the number of peptide identification by ∼10%. Moreover, the combination of basic pH LC prefractionation with the long gradient LC-MS/MS platform enabled the identification of 96,127 peptides and 10,544 proteins at 1% protein false discovery rate in a post-mortem brain sample of Alzheimer's disease. Because deep RNA sequencing of the same specimen suggested that ∼16,000 genes were expressed, the current analysis covered more than 60% of the expressed proteome. Further improvement strategies of the LC/LC-MS/MS platform were also discussed.
INSECTICIDAL CONTROL OF PEPPER WEEVIL ON JALAPENO PEPPER, 2009 (2011)

Pepper weevil is a serious pest of pepper in the southern parts of the US which destroys fruit through larval feeding. Control is difficult because all life stages but the adult are contained within the fruit. On 15 Sep, greenhouse-raised pepper seedlings were transplanted 24 inches apart in six single rows, 240 ft in length and covered with whiteface polyethylene film mulch at the Southwest Florida Research and Education Center in Immokalee FL. A RCB design was used with 4 replicates and 12 treatments (Table Each plot contained 10 plants with two plants left between plots as a buffer zone. Granular 12-3-12 NPK fertilizer was preplant soil incorporated to provide 25% of the total requirement with the remainder applied as liquid 8-0-8 delivered through drip irrigation over the growing season. Maintenance sprays included Kocide (1.0 lbs/acre) and Manex (1.5 qt/acre) as a tank mix applied weekly to control foliar disease in particular bacterial spot. Oberon (8.5 oz/acre) was applied on 6 Nov and Agri-mek (8.0 oz /acre) plus JMS Stylet Oil were applied on 9, 17, 24 Nov, 1 Dec to control broadmite. All applications were made with a high clearance sprayer operating at 180 psi at 2.3 mph with the spray delivered through two vertical booms using yellow Albuz hollow cone nozzles. The gpa for each treatment application and date are reported in Table Fallen fruit was held on the bed adjacent to plants by a strip of wood lathing secured to the top edges of the bed with wire stakes. Fruit 2.0 inches or more in length was removed and all fallen fruit collected from 6 plants per plot on 17, 24 Nov. and 1, 8, 15, 22 Dec. Visibly damaged fruit was removed from the harvested fruit and counted. Twenty five of the remaining fruit in each plot were then cut open longitudinally and inspected for presence of pepper weevil larvae/pupae and rated for damage. The number of weevil-damaged fruit was calculated by using the percentage of damaged fruit in this sub-sample and applying it to the total number of fruit without visible damage. The total number of damaged fruit was then estimated to be the number visibly damaged fruit plus the number of fruit with internal damage plus the number of fallen fruit. The sum of all fruit obtained from the six harvests was assessed using ANOVA with mean separation by LSD upon a significant F (P>0.05 LSD).
Integrating virtual patients into courses: follow‐up seminars and perceived benefit (2012)

High case processing intensity was related to positive perceptions of the benefit of VPs. However, the low interest in more assessment and feedback on the use of VPs indicates the need to clearly communicate the added value of the follow-up seminar. The findings suggest that a more intense follow-up pays off in terms of the benefit perceived by students. This study illustrates the need to consider VPs from the perspective of a holistic course design and not as isolated add-ons.
Derivative-based image quality measure for autofocus in electron microscopy (2010)

Automatic focusing methods are based on an image quality measure, which is a realvalued\nestimation of an image’s sharpness. In this paper we study L_1- or L_2-norm derivative-based image quality measures. For a bench mark case these measures turn out to be quadratic, which implies that after obtaining of at least three images one can find the position of the optimal defocus. The resulting autofocus method is demonstrated for a reference scanning transmission electron microscopy application.\nKeywords: Electron microscopy · Autofocus · Linear image formation · Image quality\nmeasure.
The WHO World Mental Health (WMH) Surveys (2009)

The paper presents an overview of the WHO World Mental Health (WMH) Survey Initiative and summarizes recent WMH results regarding the prevalence and societal costs of mental disorders. The WMH surveys are representative community surveys that were carried out in 28 countries throughout the world aimed at providing information to mental health policy makers about the prevalence, burden, and unmet need for treatment of common mental disorders. Results show that mental disorders are commonly occurring in all participating countries. The inter-quartile range (IQR: 25(th)-75(th) percentiles) of lifetime DSM-IV disorder prevalence estimates (combining anxiety, mood, disruptive behavior, and substance disorders) is 18.1-36.1%. The IQR of 12-month prevalence estimates is 9.8-19.1%. Analysis of age-of-onset reports shows that many mental disorders begin in childhood-adolescence and have significant adverse effects on subsequent role transitions. Adult mental disorders are found in the WMH data to be associated with high levels of role impairment. Despite this burden, the majority of mental disorders go untreated. Although these results suggest that expansion of treatment could be cost-effective from both the employer perspective and the societal perspective, treatment effectiveness trials are needed to confirm this suspicion. The WMH results regarding impairments are being used to target several such interventions.
A silent Mw 4.7 slip event of October 2006 on the Superstition Hills fault, southern California (2009)

During October 2006, the 20‐km‐long Superstition Hills fault (SHF) in the Salton Trough, southern California, slipped aseismically, producing a maximum offset of 27 mm, as recorded by a creepmeter. We investigate this creep event as well as the spatial and temporal variations in slip history since 1992 using ERS‐1/2 and Envisat satellite data. During a 15‐year period, steady creep is punctuated by at least three events. The first two events were dynamically triggered by the 1992 Landers and 1999 Hector Mine earthquakes. In contrast, there is no obvious triggering mechanism for the October 2006 event. Field measurements of fault offset after the 1999 and 2006 events are in good agreement with the interferometric synthetic aperture radar data indicating that creep occurred along the 20‐km‐long fault above 4 km depth, with most of the slip occurring at the surface. The moment released during this event is equivalent to a M w 4.7 earthquake. This event produced no detectable aftershocks and was not recorded by the continuous GPS stations that were 9 km away. Modeling of the long‐term creep from 1992 to 2007 creep using stacked ERS‐1/2 interferograms also shows a maximum creep depth of 2–4 km, with slip tapering with depth. Considering that the sediment thickness varies between 3 km and 5 km along the SHF, our results are consistent with previous studies suggesting that shallow creep is controlled by sediment depth, perhaps due to high pore pressures in the unconsolidated sediments.
Distinguishing Judgments About What From Judgments About Why : Effects of Behavior Extremity on Correspondent Inferences and Causal Attributions (1999)

Several researchers have reported findings indicating that dispositional inferences and causal attributions differ. This suggests that such findings may reflect a more general difference between correspondent inferences (both dispositional and situational) and causal attributions. Current theory suggests that correspondent inferences are more closely linked to perceived behavior than are causal attributions. If so, then the extremity of behavior should have a greater impact on correspondent inferences than on causal attributions. In support of this hypothesis, our 1st investigation found that perceivers' interpretations of behavior predicted correspondent inferences better than causal attributions. Our 2nd investigation found that a manipulation of the behavior interpretation influenced correspondent inferences but not causal attributions. We discuss implications for current models of attribution.
Recent advances in cystic fibrosis (1991)

During the last year, there have been significant advances in our understanding of the genetics and pathophysiology of cystic fibrosis. Over 60 individual rare mutations have been identified, and there is evidence that pancreatic sufficiency and milder disease occur with increased frequency in patients with less common mutations. The cystic fibrosis transmembrane conductance regulator (CFTR) protein has been shown to be a membrane-associated glycoprotein that can be phosphorylated in vitro by cyclic AMP-dependent protein kinase. It has been speculated that CFTR is involved in the transport of small molecules or in the modulation of CI- channel function and that mutant CFTR is incompletely processed in the endoplasmic reticulum. However, the exact function of CFTR remains unknown. Retrovirus-mediated gene transfer has been used to insert the full-length CFTR-complementary DNA into a cystic fibrosis pancreatic adenocarcinoma cell line and has been shown to normalize ion transport. Based on better understanding of the pathophysiology of cystic fibrosis lung injury, a number of new therapies are being evaluated, including mucolytics such as the sodium channel blocker amiloride and recombinant human DNase, as well as systemic and aerosol anti-inflammatory agents. There have also been advances in heart-lung and bilateral lung transplantation and in the treatment of cystic fibrosis liver disease.
Realizing Zones Using UPnP (2009)

This paper describes the concept of "zone" and also the method of realizing a zone using UPnP. We present the details of how a mobile device can detect that it is in a zone using RFID based mechanism. In this paper we propose a framework for creating a zone, discovering zone and service delivery by leveraging the existing technologies like UPnP and short range wireless radio as a bearer.
ECSim++: An INET-Based Simulation Tool for Modeling and Control in Edge Cloud Computing (2018)

As the overwhelming growth of smart devices and massive arrival of new application, network traffic volume has been growing rapidly. The traditional centralized network architecture, such as locating services at core cloud, causes a heavy burden on the backhaul link and long latency. Edge Cloud Computing has been introduced to reduce traffic bottlenecks in the core, backhaul network and service delay by pushing data intensive tasks towards the edge and locally processing data in proximity to the users. This paper introduces a new simulation framework, so-called ECSim++, based on the OMNeT++ simulator [15] and INET framework [2] to enable exploration of computing, caching, communication or energy efficiency related issues in Edge Cloud Computing. ECSim++ is designed not only to allow researchers to customize caching protocols, edge services, but also to analyze, debug and evaluate easily for Edge Cloud Computing environment. In addition, ECSim++ also provides an energy consumption model so that researchers could deploy and evaluate their energy strategies.
Optical Probing of Local pH and Temperature in Complex Fluids with Covalently Functionalized, Semiconducting Carbon Nanotubes (2015)

We show that local pH can be optically probed through defect photoluminescence from semiconducting carbon nanotubes covalently functionalized with aminoaryl groups. Switching between protonated and deprotonated forms of the amino moiety produces an energy shift in the defect state of the functionalized nanotube by as much as 33 meV in the near-infrared region. This unexpected observation enables a new optical pH sensor that features ultrabright near-infrared II (1.1–1.4 μm) photoluminescence, a sensitivity for pH changes as small as 0.2 pH units over a wide working window that covers the entire physiologic pH range, and potentially molecular resolution. Independent of pH, this nanoprobe can simultaneously act as a nanothermometer by monitoring temperature-modulated changes in photoluminescence intensity, which follows the van’t Hoff equation. This work opens new opportunities for quantitative probing of local pH and temperature changes in complex biological systems.
Long-Range Hopping Conductivity in Proteins (2022)

Abstract Single molecule measurements show that many proteins, lacking any redox cofactors, nonetheless exhibit electrical conductance on the order of a nanosiemen, implying that electrons can transit an entire protein in less than a nanosecond when subject to a potential difference of less than 1V. In the conventional fast transport scenario where the free energy barrier is zero, the hopping rate is determined by the reorganization energy of approximately 0.8 eV, which sets the time scale of a single hopping event to at least 1μs. Furthermore, the Fermi energies of metal electrodes used in experiments are far-removed from the equilibrium redox states of the aromatic residues of the protein, which should additionally slow down the electron transfer. Here, we combine all-atom molecular dynamics (MD) simulations of non-redox active proteins (consensus tetratricopeptide repeats) with an electron transfer theory to demonstrate a molecular mechanism that can account for the unexpectedly fast electron transfer. According to our MD simulations, the reorganization energy produced by the energy shift on charging (the Stokes shift) is close to the conventional value of 0.8 eV. However, the nonergodic sampling of molecular configurations by the protein results in reorganization energies, extracted directly from the distribution of the electrostatic energy fluctuations, that are only ~ 0.2 eV, which is small enough to enable long-range hopping. Using the MD values of the reorganization energies we calculate a current decay with distance that is in agreement with experiment. Significance Electron transfer is fundamental to biology, facilitating a range of metabolic processes and efficient energy conversion. Conventionally, electron transfer through proteins is thought to occur via a chain of metal or organic co-factors connecting one side of the protein to another. Recent experiments, however, show that proteins lacking any co-factors can nonetheless transport electrons with high efficiency if properly connected to metal electrodes. This study provides a theoretical model of such cofactor-less transfer, showing that transient occupation of non-equilibrium states of the protein’s aromatic residues reduces the barrier to electron hopping, facilitating long range and rapid transport. Our results widen the pool of proteins potentially involved in biological electron transport and provide theoretical underpinning to design of protein molecular electronics.
Supplementary Figure 2 from Inhibition of <i>S</i>-adenosylmethionine decarboxylase by inhibitor SAM486A connects polyamine metabolism with p53-Mdm2-Akt/protein kinase B regulation and apoptosis in neuroblastoma (2023)

Supplementary Figure 2 from Inhibition of &lt;i&gt;S&lt;/i&gt;-adenosylmethionine decarboxylase by inhibitor SAM486A connects polyamine metabolism with p53-Mdm2-Akt/protein kinase B regulation and apoptosis in neuroblastoma
Myelin‐associated glycoprotein is phosphorylated by protein kinase C (1993)

The myelin-associated glycoprotein (MAG) is a neural recognition molecule involved in heterophilic interactions between myelin-forming cells and neurons. To characterize the molecular mechanisms underlying post-translational modifications which may be instrumental in signal transduction following the recognition event, we have studied the stimuli leading to modification of 32P-orthophosphate incorporation into MAG in cultures of oligodendrocytes or transformed differentiated Schwann cells. Here we show that in oligodendrocytes both the 67 and 72 kD isoforms of MAG were phosphorylated exclusively on serine, while in the transformed Schwann cells only the 67 kD isoform was found to be present and phosphorylated. The phorbol ester phorbol-12-myristoyl-13-acetate (PMA) did not affect biosynthesis of the protein backbone, but enhanced incorporation of phosphate by a factor of 2-3, indicating the involvement of protein kinase C. Exclusive phosphorylation of serine residues was also observed, when purified MAG was incubated with protein kinase C in the presence of [gamma-32P]ATP. In searching for the physiological stimuli which may trigger phosphorylation of MAG, cultures of oligodendrocytes were exposed to extracellular signals, such as coculture with dorsal root ganglion and spinal cord neurons carrying the MAG receptor, to membrane fractions of these neurons, monoclonal MAG antibody 513 binding to the recognition site of MAG, or platelet-derived growth factor. None of these additives modified the phosphorylation of MAG. These observations point to the possibility that phosphorylation of MAG is controlled by yet unknown intracellular cues rather than by extracellular signals interacting with cell surface receptors of oligodendrocytes.
The effect of geriatric intervention in frail elderly patients receiving chemotherapy for colorectal cancer: a randomized trial (GERICO) (2017)

ClinicalTrials.gov ID: NCT02748811 . The trial was registered retrospectively; registration date 04/28/2016.
Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development (2011)

Cancer is driven by somatically acquired point mutations and chromosomal rearrangements, conventionally thought to accumulate gradually over time. Using next-generation sequencing, we characterize a phenomenon, which we term chromothripsis, whereby tens to hundreds of genomic rearrangements occur in a one-off cellular crisis. Rearrangements involving one or a few chromosomes crisscross back and forth across involved regions, generating frequent oscillations between two copy number states. These genomic hallmarks are highly improbable if rearrangements accumulate over time and instead imply that nearly all occur during a single cellular catastrophe. The stamp of chromothripsis can be seen in at least 2%-3% of all cancers, across many subtypes, and is present in ∼25% of bone cancers. We find that one, or indeed more than one, cancer-causing lesion can emerge out of the genomic crisis. This phenomenon has important implications for the origins of genomic remodeling and temporal emergence of cancer.
The Pros and Cons of Carbon Dioxide Dumping (1998)

Global warming concerns have stimulated a search for carbon sequestration technologies.
Etre ou ne pas être… un corps de rêve – pratiques (2020)

Femmes fatales, Lolitas de 9 ans, corps livres a leurs cœurs defendant, poids plume contre poids lourd...
Silent mutations in secondary Shine–Dalgarno sequences in the cDNA of human serum amyloid A4 promotes expression of recombinant protein in Escherichia coli (2001)

The serum amyloid A (SAA) superfamily comprises a number of differentially expressed genes with a high degree of homology in mammalian species. SAA4, an apolipoprotein constitutively expressed only in humans and mice, is associated almost entirely with lipoproteins of the high-density range. The presence of SAA4 mRNA and protein in macrophage-derived foam cells of coronary and carotid arteries suggested a specific role of human SAA4 during inflammation including atherosclerosis. Here we underline the importance of ribosome binding site (rbs)-like sequences (also known as Shine-Dalgarno sequences) in the SAA4 cDNA for expression of recombinant SAA4 protein in Escherichia coli. In contrast to rbs sequences coded by the expression vectors, rbs-like sequences in the cDNA of target protein(s) are known to interfere with protein translation via binding to the small 16S ribosome subunit, yielding low or even no expression. Here we show that PCR mutations of two rbs-like sequences in the human SAA4 cDNA promote expression of considerable amounts of recombinant SAA4 in E.coli.
CHAPTER 3: Gelatinization, Pasting, and Retrogradation (1999)

Cereals & Grains Association is a nonprofit organization dedicated to advancing the knowledge and understanding of cereal grain science through research leadership, education, superior technical service, and advocacy.
Starvation Induces Vacuolar Targeting and Degradation of the Tryptophan Permease in Yeast (1999)

In Saccharomyces cerevisiae, amino acid permeases are divided into two classes. One class, represented by the general amino acid permease GAP1, contains permeases regulated in response to the nitrogen source. The other class, including the high affinity tryptophan permease, TAT2, consists of the so-called constitutive permeases. We show that TAT2 is regulated at the level of protein stability. In exponentially growing cells, TAT2 is in the plasma membrane and also accumulates in internal compartments of the secretory pathway. Upon nutrient deprivation or rapamycin treatment, TAT2 is transported to and degraded in the vacuole. The ubiquitination machinery and lysine residues within the NH(2)-terminal 31 amino acids of TAT2 mediate ubiquitination and degradation of the permease. Starvation-induced degradation of internal TAT2 is blocked in sec18, sec23, pep12, and vps27 mutants, but not in sec4, end4, and apg1 mutants, suggesting that, upon nutrient limitation, internal TAT2 is diverted from the late secretory pathway to the vacuolar pathway. Furthermore, our results suggest that TAT2 stability and sorting are controlled by the TOR signaling pathway, and regulated inversely to that of GAP1.
Chromatographic Behaviour Predicts the Ability of Potential Nootropics to Permeate the Blood-Brain Barrier (2013)

The log BB parameter is the logarithm of the ratio of a compound's equilibrium concentrations in the brain tissue versus the blood plasma. This parameter is a useful descriptor in assessing the ability of a compound to permeate the blood-brain barrier. The aim of this study was to develop a Hansch-type linear regression QSAR model that correlates the parameter log BB and the retention time of drugs and other organic compounds on a reversed-phase HPLC containing an embedded amide moiety. The retention time was expressed by the capacity factor log k'. The second aim was to estimate the brain's absorption of 2-(azacycloalkyl)acetamidophenoxyacetic acids, which are analogues of piracetam, nefiracetam, and meclofenoxate. Notably, these acids may be novel nootropics. Two simple regression models that relate log BB and log k' were developed from an assay performed using a reversed-phase HPLC that contained an embedded amide moiety. Both the quadratic and linear models yielded statistical parameters comparable to previously published models of log BB dependence on various structural characteristics. The models predict that four members of the substituted phenoxyacetic acid series have a strong chance of permeating the barrier and being absorbed in the brain. The results of this study show that a reversed-phase HPLC system containing an embedded amide moiety is a functional in vitro surrogate of the blood-brain barrier. These results suggest that racetam-type nootropic drugs containing a carboxylic moiety could be more poorly absorbed than analogues devoid of the carboxyl group, especially if the compounds penetrate the barrier by a simple diffusion mechanism.