gebhart/patrepeval huggingface dataset:
Actin, Spectrin, and Associated Proteins Form a Periodic Cytoskeletal Structure in Axons (2012)

Actin and spectrin play important roles in neurons, but their organization in axons and dendrites remains unclear. We used stochastic optical reconstruction microscopy to study the organization of actin, spectrin, and associated proteins in neurons. Actin formed ringlike structures that wrapped around the circumference of axons and were evenly spaced along axonal shafts with a periodicity of ~180 to 190 nanometers. This periodic structure was not observed in dendrites, which instead contained long actin filaments running along dendritic shafts. Adducin, an actin-capping protein, colocalized with the actin rings. Spectrin exhibited periodic structures alternating with those of actin and adducin, and the distance between adjacent actin-adducin rings was comparable to the length of a spectrin tetramer. Sodium channels in axons were distributed in a periodic pattern coordinated with the underlying actin-spectrin-based cytoskeleton.
Impairment of PARK14-dependent Ca2+ signalling is a novel determinant of Parkinson’s disease (2016)

The etiology of idiopathic Parkinson's disease (idPD) remains enigmatic despite recent successes in identification of genes (PARKs) that underlie familial PD. To find new keys to this incurable neurodegenerative disorder we focused on the poorly understood PARK14 disease locus (Pla2g6 gene) and the store-operated Ca(2+) signalling pathway. Analysis of the cells from idPD patients reveals a significant deficiency in store-operated PLA2g6-dependent Ca(2+) signalling, which we can mimic in a novel B6.Cg-Pla2g6(ΔEx2-VB) (PLA2g6 ex2(KO)) mouse model. Here we demonstrate that genetic or molecular impairment of PLA2g6-dependent Ca(2+) signalling is a trigger for autophagic dysfunction, progressive loss of dopaminergic (DA) neurons in substantia nigra pars compacta and age-dependent L-DOPA-sensitive motor dysfunction. Discovery of this previously unknown sequence of pathological events, its association with idPD and our ability to mimic this pathology in a novel genetic mouse model opens new opportunities for finding a cure for this devastating neurodegenerative disease.
Chronic Frequent Headache in the General Population: Prevalence and Associated Factors (2006)

We studied the prevalence and short-term natural course of chronic frequent headache (CFH) in the general population and identified risk factors. In the Netherlands everyone is registered at a single general practice. We sent questionnaires to all persons (n = 21 440) aged 25-55 years, registered at 16 general practices. We compared the characteristics of 177 participants with CFH (>14 headache days/month for >3 months) with 141 participants with infrequent headache (1-4 days/month) and 526 without headache (<1 day/month). The prevalence of CFH was 3.7% [95% confidence interval (CI) 3.4, 4.0]. In 5 months, 12% showed a clinically relevant decrease to <7 days/month. In both headache groups 70% were women vs. 41% in the group without headache. Compared with the group with infrequent headache, the CFH group had more subjects with low educational level [35% vs. 11%; odds ratio (OR) 4.3, 95% CI 2.3, 7.8], medication overuse (62% vs. 3%; OR 38.4, 95% CI 13.8, 106.9), sleeping problems (44% vs. 8%; OR 8.1, 95% CI 3.6, 18.1), a history of head/neck trauma (36% vs. 14%; OR 4.0, 95% CI 2.2, 7.1), high scores on the General Health Questionnaire (62% vs. 34%; OR 2.7, 95% CI 1.3, 3.6) and more smokers (45% vs. 19%; OR 3.1, 95% CI 1.9, 5.3). We conclude that headache frequency fluctuates. CFH is common and associated with overuse of analgesics, psychopathology, smoking, sleeping problems, a history of head/neck trauma and low educational level. Female sex is a risk factor for headache, not for chronification of headache.
Amelioration of acute inflammation by systemic administration of a cell‐permeable peptide inhibitor of NF‐κB activation (2005)

These studies further establish NF-kappaB as a target for antiinflammatory therapy and provide support for the use of the NBD peptide as a possible therapeutic agent for inflammatory diseases.
B compensation in 3T cardiac imaging using short 2DRF pulses (2008)

The purpose of this study was to determine if tailored 2DRF pulses could be used to compensate for in-plane variations of the transmitted RF field at 3T. Excitation pulse profiles were designed to approximate the reciprocal of the measured RF transmit variation where the variation over the left ventricle was approximated as unidirectional. A simple 2DRF pulse design utilizing three subpulses was used, such that profiles could be quickly and easily adapted to different regions of interest. Results are presented from phantom and in vivo cardiac imaging. Compared with conventional slice-selective excitation, the average flip angle variation over the left ventricle (measured as the standard deviation divided by the mean flip angle) was reduced with P < 0.001 and the average reduction was 41% in cardiac studies at 3T.
The first steps towards hearing: mechanisms of otic placode induction (2007)

The entire inner ear, together with the neurons that innervate it, derive from a simple piece of ectoderm on the side of the embryonic head the otic placode. In this review, we describe the current state of the field of otic placode induction. Several lines of evidence suggest that all craniofacial sensory organs, including the inner ear, derive from a common "pre-placodal region" early in development. We review data showing that assumption of a pre-placodal cell state correlates with the competence of embryonic ectoderm to respond to otic placode inducing signals, such as members of the fibroblast growth factor (FGF) family. We also review evidence for FGF-independent signals that contribute to the induction of the otic placode. Finally, we review recent evidence suggesting that Wnt signals may act after FGF signaling to mediate a cell fate decision between otic placode and epidermis.
Low-threat security patches and tools (1997)

We consider the problem of distributing potentially dangerous information to a number of competing parties. As a prime example, we focus on the issue of distributing security patches to software. These patches implicitly contain vulnerability information that may be abused to jeopardize the security of other systems. When a vendor supplies a binary program patch, different users may receive it at different times. The differential application times of the patch create a window of vulnerability until all users have installed the patch. An abuser might analyze the binary patch before others install it. Armed with this information, he might be able to abuse another user's machine. A related situation occurs in the deployment of security tools. However, many tools will necessarily encode vulnerability information or explicit information about security “localisms”. This information may be reverse-engineered and used against systems. We discuss several ways in which security patches and tools may be made safer. Among these are: customizing patches to apply to only one machine; disguising patches to hinder their interpretation; synchronizing patch distribution to shrink the window of vulnerability; applying patches automatically; and using cryptoprocessors with enciphered operating systems. We conclude with some observations on the utility and effectiveness of these methods
Potent δ-Opioid Receptor Agonists Containing the Dmt−Tic Pharmacophore (2002)

Conversion of delta-opioid receptor antagonists containing the 2',6'-dimethyl-L-tyrosine (Dmt)-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic) pharmacophore into potent delta-agonists required a third heteroaromatic nucleus, such as 1H-benzimidazole-2-yl (Bid) and a linker of specified length both located C-terminally to Tic in the general formula H-Dmt-Tic-NH-CH(R)-R'. The distance between Tic and Bid is a determining factor responsible for the acquisition of delta agonism (2, 2', 3, 4, 6) or delta antagonism (8). Compounds containing a C-terminal Ala (1, 1'), Asp (5), or Asn (7) with an amide (1, 1', 5) or free acid group (7) served as delta-antagonist controls lacking the third heteroaromatic ring. A change in chirality of the spacer (2, 2') or inclusion of a negative charge via derivatives of Asp (4, 6) resulted in potent delta agonism and moderate mu agonism, although delta-receptor affinity decreased about 10-fold for 4 while mu affinity fell by over 2 orders of magnitude. Repositioning of the negative charge in the linker altered activity: H-Dmt-Tic-NH-CH(CH(2)-Bid)COOH (6) maintained high delta affinity (K(i) = 0.042 nM) and delta agonism (IC(50) = 0.015 nM), but attachment of the free acid group to Bid [H-Dmt-Tic-NH-CH(2)-Bid(CH(2)-COOH) (9)] reconstituted delta antagonism (K(e) = 0.27 nM). The data demonstrate that a linker separating the Dmt-Tic pharmacophore and Bid, regardless of the presence of a negative charge, is important in the acquisition of opioids exhibiting potent delta agonism and weak mu agonism from a parent delta antagonist.
Biosynthesis of the Fungal Wall-Mechanisms and Implications The First Fleming Lecture (1977)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Chiral capillary electrophoresis: Facts and fiction on the reproducibility of resolution with randomly substituted cyclodextrins (2004)

Comparative enantioseparation of the enantiomers of 1,1'-binaphthyl-2,2'-diyl hydrogen phosphate was performed with cyclodextrin (CD)-modified capillary electrophoresis (CE). Two single isomers, beta-CD, heptakis(2,3,6-tri-O-methyl)-beta-CD (TM-beta-CD), and heptakis(2,6-di-O-methyl)-beta-CD (DM-beta-CD) of 98% purity as well as heptakis(2,3-di-O-acetyl)-beta-CD were used and compared in terms of resolution power to randomly methylated and corresponding acetylated beta-CDs, which were synthesized in our laboratory. The methylated ones were characterized by means of matrix-assisted laser desorption/ionization-time of flight-(MALDI-TOF) mass spectrometry. By testing defined mixtures of single isomers and comparing their resolution power to randomly substituted CDs of similar degree of substitution we could show, that a simple characterization by the average molecular degree of substitution (DS) is not sufficient. In order to get reproducible results, a clearly defined substitution pattern is necessary, which is not given using randomly substituted CDs. Taken together, a validation of a chiral separation with "undefined" CD derivatives is almost impossible.
ALS spinal neurons show varied and reduced mtDNA gene copy numbers and increased mtDNA gene deletions (2010)

At the time of ALS subjects' deaths, many but not all surviving anterior neurons in their cervical spinal cords have reduced mtDNA gene levels and increased mtDNA deletion abundances that arise for unclear reasons. If these anterior spinal neuron mtDNA gene deficiencies contribute to bioenergetic impairments, reduced synaptic function and increased risk of degeneration, then introduction into mitochondria and expression of intact mtDNA, now available through use of recently developed recombinant human TFAM, may reverse the course of ALS.
The Synthesis and Coating of Long, Thin Copper Nanowires to Make Flexible, Transparent Conducting Films on Plastic Substrates (2011)

Solution-processable transparent electrodes will facilitate the high-throughput production of low-cost photovoltaics. Copper nanowires are coated from solution onto plastic substrates to create high-performance, transparent conducting films that are highly flexible, stable in air, and can carry large currents. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Bacterial penetration in vitro through GTAM membrane with and without topical chlorhexidine application (1995)

Premature exposure of membrane in the oral cavity is considered the most common complication as well as a reason for failure or incomplete success of guided tissue regeneration, as the exposed membrane undergoes plaque accumulation. A method to control, or at least to reduce the bacterial invasion of the membrane allowing a delay in the membrane removal, could be of clinical interest. The purpose of the present study was to evaluate the possibility of treating, with topical chlorhexidine application, the bacterial colonization of exposed membranes. A special device was developed in order to evaluate, under an experimental environment, the bacterial colonization. This device was made from a removable acrylic denture base to which 5 gold cups were attached. The cups consisted of an internal compartment, isolated from the oral cavity by a GTAM membrane, and an external compartment exposed to the oral environment. 3 healthy subjects had this device fitted, bilaterally, in the molar-premolar region of the upper jaw. The cups of one side of each subject had 0.2% chlorhexidine gluconate gel applied 2x a day for 1 min, whereas those of the other side served as controls. 12 cups were removed after 2 weeks and the remainder removed after 1 month. The non-treated control specimens were characterized by greater amounts of plaque accumulation. In all the test sites, plaque deposits increased in thickness and quantity during the 4 weeks of the experiment. Complete invasion of the membrane and initial colonization of its internal surface were observed only in 4-week specimens. A relatively simple flora consisting mainly of cocci and short rods, was found in bacterial deposits forming under the influence of chlorhexidine, whereas in non-treated specimens, it was possible to observe a more mature and complex plaque, composed mostly of filamentous bacteria. In conclusion, topical application of chlorhexidine gel is an effective method of reducing plaque and calculus formation on the surface of GTAM membranes exposed to the oral cavity for up to 4 weeks. This study has, however, failed to demonstrate the capacity of chlorhexidine to prevent or to retard bacterial penetration through the thickness of the inner portion of the membranes.
DVFLEX: a flexible MPEG real time video codec (2002)

The MPEG-2 video coding standard offers great latitude in implementation and covers a wide variety of applications. The DVFLEX video encoder allows one to take advantage of this flexibility by making the whole coding loop including the bitstream generation, software programmable. The DVFLEX architecture is basically an array of linearly-connected processing modules. These modules are based on the MVP (TMS320C80) and include dedicated I/O ports for video, bitstream and inter-processor communications. All these I/O ports allow the processing to be performed in parallel with I/Os. The processing workload is distributed among these modules on an image region per processor basis. As for the on-chip MVP processors, tasks assignment is much more constrained because of the bitstream handling problems. Although suboptimal, the solution we describe is simple and gives satisfactory results. However, the on-chip to off-chip memory I/Os have to be carefully handled so as to keep the processors busy.
Relationship of Plaque Size and Virulence for Chickens of 14 Representative Newcastle Disease Virus Strains (1968)

Ability of 14 Newcastle disease virus strains to produce large plaques was related to virulence for chickens. Plaque-size comparisons were made under standard conditions in chick embryo cell monolayers. All plaque-producing strains showed a range of plaque sizes modified to a degree by the overlay medium used. An increase in size was found for most strains under methyl-cellulose overlay medium. Markedly larger plaques were found under this medium for both Calif-RO and Calif-CG strains. Heterogeneity in plaque size was most pronounced in velogenic (high virulence) strains. Only populations of small plaques were found in mesogenic (intermediate virulence) strains, and plaques were rarely found in lentogenic (low virulence) strains. Statistical analysis showed that the plaque size of velogenic strains differed significantly from mesogenic strains. None of the 11 plaque-producing strains had a normal distribution of plaque sizes, owing primarily to the presence of different genotypes within the plaquing population of a strain. This was demonstrated by derivation of clones from two of the strains. The populations of the large (Herts L) and small (Herts S) clear plaque clones derived from Eng-Herts were homogenous and distinct from one another on the basis of plaque size. Herts L was more virulent than Herts S. Although Herts L became more heterogenous in respect to plaque size upon repeated passage in embryonated eggs, no decrease in virulence of the strain was observed.
Comprehensive gene expression profile of LPS-stimulated human monocytes by SAGE (2000)

Monocytes play a pivotal role in various human infectious and inflammatory diseases. To reveal a whole picture of pathophysiologic function of activated human monocytes, this study used the serial analysis of gene expression (SAGE) procedure in lipopolysaccharide (LPS)-stimulated human monocytes. A total of 35 874 tags corresponding to more than 12 000 different transcripts were sequenced. Comparison of gene expression profile with that of resting monocytes revealed the LPS-inducible gene expression profile. Many cytokines and chemokines, including interleukin (IL)-6, IL-1alpha, IL-1beta, tumor necrosis factor (TNF)-alpha, macrophage inflammatory protein (MIP)-1beta, MIP-2beta, MIP-2alpha, liver and activation-regulated chemokine (LARC), MIP-1alpha, thymus and activation-regulated chemokine (TARC), macrophage-derived chemokine (MDC), regulated on activation, normal T cell expressed and secreted (RANTES), growth-regulated oncogene (GRO) alpha, and IL-8, were observed in the highest inducible transcripts. Other genes encoding plasminogen activator inhibitor type 2 (PAI-2), Hc-gp39, apolipoproteins, malate dehydrogenase, matrix metalloproteinase-9 (MMP-9), and cyclooxygenase (COX2) were also highly elevated in LPS-stimulated monocytes. Moreover, up-regulation of Naf1beta, IL-7 receptor, adenosine receptor A2a, and many novel genes was newly identified. These results suggest that the LPS-inducible gene products may be involved in cell activation and migration, angiogenesis, tissue remodeling, and metabolism, and thus may orchestrate the inflammatory reactions. On the other hand, the expression of numerous sets of novel genes was discovered to be down-regulated on LPS stimulation. This study represents the first comprehensive analysis of LPS-inducible gene expression in human monocytes and provides tremendous novel information for the function of LPS-activated monocytes and targets for diagnosing, monitoring, and treating sepsis and various human infectious and inflammatory diseases.
Low-Dose, Long-Wave UV Light Does Not Affect Gene Expression of Human Mesenchymal Stem Cells (2015)

Light is a non-invasive tool that is widely used in a range of biomedical applications. Techniques such as photopolymerization, photodegradation, and photouncaging can be used to alter the chemical and physical properties of biomaterials in the presence of live cells. Long-wave UV light (315 nm-400 nm) is an easily accessible and commonly used energy source for triggering biomaterial changes. Although exposure to low doses of long-wave UV light is generally accepted as biocompatible, most studies employing this wavelength only establish cell viability, ignoring other possible (non-toxic) effects. Since light exposure of wavelengths longer than 315 nm may potentially induce changes in cell behavior, we examined changes in gene expression of human mesenchymal stem cells exposed to light under both 2D and 3D culture conditions, including two different hydrogel fabrication techniques, decoupling UV exposure and radical generation. While exposure to long-wave UV light did not induce significant changes in gene expression regardless of culture conditions, significant changes were observed due to scaffold fabrication chemistry and between cells plated in 2D versus encapsulated in 3D scaffolds. In order to facilitate others in searching for more specific changes between the many conditions, the full data set is available on Gene Expression Omnibus for querying.
Software pixel interpolation for digital still cameras suitable for a 32-bit MCU (1998)

This paper discusses the interpolation technique applied to the Bayer primary color method, used frequently as the pixel structure of CCD image sensors for digital still cameras. Eight typical types of interpolation methods are discussed from three viewpoints: the characteristics of the interpolated images, the processing time required to realize their methods based on a 32-bit MCU for embedded applications, and the quality of the resultant images. In terms of reducing the occurrences of pseudocolor and achieving good color restoration, the linear interpolation method taking G's correlation determined by using R/B pixels into consideration was found to be excellent. The measured machine cycle of the interpolation methods was approximately 46 cycles per pixel. Therefore, every method was able to interpolate a VGA-size image in approximately 0.2 seconds with the MCU operating at 60 MHz. In terms of the S/N ratio, a good image quality was obtained through the linear interpolation methods, even with shorter processing time. Based on these results it is concluded that the linear interpolation method, which takes correlation into consideration, is the most suitable for consumer product applications such as digital still cameras.
Biodegradable Nanoparticles Composed Entirely of Safe Materials that Rapidly Penetrate Human Mucus (2011)

Slipping through: Pluronic molecules adsorb onto nanoparticle surfaces through their polypropylene oxide (PPO) segments with the flanking polyethylene glycol (PEG) segments forming a dense muco-inert brush (see picture; top). While uncoated particles are immobilized in mucus through adhesive interactions with mucus mesh elements, coated particles diffuse rapidly through spaces in the mucus mesh (bottom). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.