gebhart/patrepeval huggingface dataset:
Three patterns of cytokine expression potentially involved in epithelial‐fibroblast interactions of human ocular surface (1995)

Signals transmitted from mesenchyme to epithelia or vice versa constitute the basis of reciprocal epithelial-mesenchymal interactions. As a first step toward understanding epithelial-mesenchymal interactions on the ocular surface where the transit amplifying cell-containing corneal epithelium is anatomically separated from the stem cell-containing limbal epithelium, we sought to characterize the expression patterns of cytokines and their receptors by primary epithelial and early-passaged fibroblast cultures of human cornea and limbus. Northern hybridization with oligonucleotide and cDNA probes to a total of 25 cytokines and 12 of their receptors revealed that the positively expressed cytokines could be divided into the following four patterns. Type I: TGF-alpha, IL-1 beta, and PDGF-B were expressed exclusively by epithelial cells but their respective receptors EGFR and IL-1R were predominantly and PDGFR-beta was exclusively expressed by fibroblasts. Type II: IGF-I, TGF-beta 1, -beta 2, LIF, and bFGF, and their receptors were expressed by both epithelial cells and fibroblasts. FGFR-1 (flg) and FGFR-2 (bek) were expressed more by fibroblasts and bFGF was expressed more by corneal than limbal epithelial cells. Type III: keratinocyte growth factor (KGF) and hepatocyte growth factor (HGF) were expressed exclusively by fibroblasts and their respective receptors, KGFR and c-met, were predominantly expressed by epithelial cells. Combined with RT-PCR, the quantity of KGF and KGFR transcripts was highest in limbal fibroblasts and epithelial cells, respectively. In contrast, the quantity of HGF and HGFR (c-met) transcripts was highest in corneal fibroblasts and epithelial cells, respectively. Type IV: M-CSF and IL-8 were expressed by fibroblasts and/or epithelial cells but their receptors were not expressed by epithelial cells nor fibroblasts, but by immune or inflammatory cells. In addition to these potential paracrine actions, autocrine actions mediated by TGF-alpha/EGFR, IL-1 beta/IL1-R, and bFGF/FGFR-1 were more expressed by corneal than limbal epithelial cells. Immunofluorescence staining on human corneoscleral cryosections confirmed that EGFR and bFGF were not expressed by the limbal basal epithelium, but expressed strongly by the corneal epithelium, a pattern consistent with Northern hybridization. These results indicate that ocular surface epithelial cells and fibroblasts can express a myriad of cytokines, among which the first three patterns constitute the network of potential epithelial-mesenchymal cytokine dialogues. The difference of certain cytokine expression between corneal and limbal regions suggests that this network participates in normal epithelial growth and differentiation, and plays an important role in wound healing.
Modelling cooperation in mobile ad hoc networks: a formal description of selfishness (2003)

The advance in wireless technologies makes now viable to start to develop ad hoc networks. However, without a mechanism that prevents misbehaviors, these networks could result easily unreliable. We develop a model, based on game theory, capable of formally explaining characteristics of ad hoc networks (as the nodes&amp;apos; selfishness or the network mobility). It also allows to formally study and analyze strategies for cooperation. As example, we describe a simple strategy that enforces packet forwarding among nodes.
The Preparation and Intra- and Intermolecular Addition Reactions of Acyclic N-Acylimines:  Application to the Synthesis of (±)-Sertraline (2001)

Intramolecular endo-cyclization reactions of N-acyliminium ions have seen wide application for the synthesis of heterocyclic compounds. The corresponding exocyclic variant, which would provide 1-aminotetralin derivatives, for example, has little precedent. We have discovered that acyclic N-acylcarbamates can be readily reduced to the corresponding N-acylhemiaminal derivatives in high yield using DIBAL as the reducing agent. These intermediates are remarkably stable and, if desired, can be purified and stored. The acyclic N-acylhemiaminals undergo both intra- and intermolecular nucleophilic addition reactions mediated by strong Lewis acids, such as TiCl(4). Diastereoselectivity, induced either by a substituent on the newly formed ring, or by utilizing a chiral ester on the carbamic acid, was disappointingly low. This methodology was successfully applied to the synthesis of the racemic form of the marketed antidepressant sertraline.
CD1d-Mediated Antigen Presentation to Natural Killer T (NKT) Cells (2003)

CD1d molecules are lipid antigen-presenting molecules. They are involved in presenting these antigens to a unique subpopulation of T cells called natural killer T (NKT) cells, which have the capacity to produce both T helper (Th) 1 and Th2 cytokines. Thus, it is possible that the antigens presented by CD1d and/or the level at which they are presented could have profound effects on the immunoregulation of autoimmune and infectious diseases, as well as cancer. Because of the ability of CD1d-binding ligands to modulate NKT cell responses, targeting CD1d-mediated antigen presentation as a novel approach for new therapies in these and other diseases holds great promise.
Maize rbcS promoter activity depends on sequence elements not found in dicot rbcS promoters. (1991)

Although the molecular mechanisms of dicot photosynthetic gene regulation have been pursued actively, comparable studies of monocot regulation have been slow to come forth. We show here that monocot (maize and wheat) but not dicot (pea, tobacco, and Arabidopsis) ribulose-1,5-bisphosphate carboxylase small subunit (rbcS) gene promoters are active in maize mesophyll protoplasts. The evolutionarily conserved GT and G boxes of dicot rbcS promoters are not essential for light-responsive expression in monocot leaf cells. Instead, at least six constitutive and light-sensitive regulatory elements are likely important for maize rbcS expression. Synergism between upstream and downstream promoter elements is required. Whereas in dicots, light triggers coupled leaf development and photosynthetic gene expression, in monocots, light regulation of rbcS is uncoupled from leaf development. Light regulation of maize rbcS may be divided into direct and indirect contributions mediated by different regulatory elements. Because wheat and maize rbcS promoters show sequence homologies and similar expression patterns in monocot and dicot leaf cells, it appears likely that monocots share conserved regulatory elements irrespective of whether they utilize the C3 or C4 pathway for carbon fixation.
Janus Particle Synthesis, Assembly, and Application (2017)

Janus particles are colloidal particles with more than a single type of surface chemistry or composition, ranging in size from hundreds of nanometers to a few micrometers. Like traditional colloids, they are large enough to be observed under optical microscopy in real time and small enough to diffuse by Brownian motion, but their interesting and useful new properties of directional interaction bring new research opportunities to the fields of soft matter and fundamental materials research as well as to applications in other disciplines and in technologies such as electronic paper and other multiphase engineering. In this review, a variety of methods that have been used to synthesize Janus particles are introduced. Following this, we summarize the use of Janus particles as basic units that assemble into novel structures and tune important material properties. The concluding sections highlight some of the technological applications, including recent progress in using Janus particles as microprobes, micromotors, electronic paper, and solid surfactants.
Role of the b subunit of the Escherichia coli proton-translocating ATPase. A mutagenic analysis. (1985)

A plasmid that carries the uncF gene of Escherichia coli, which codes for the b subunit of the proton-translocating ATPase (F1F0), was mutagenized with hydroxylamine and ethyl methanesulfonate. Mutated plasmids were characterized by complementation analysis and by in vitro transcription/translation. Eleven of the plasmids mutated specifically in uncF were studied in detail: the nucleotide sequences of their uncF genes were determined and their effects on the F1F0 were measured. The results suggest that a C-terminal portion of the b subunit that involves the glycine residue at position 131, is required for the formation of a functional proton pore as well as for the binding of F1 to F0. A mutation in the N-terminal portion of the b subunit, in the glycine residue at position 9, also prevented the formation of a functional proton pore, but had only a small effect on the binding of F1 to F0.
THE NEW FOREST (2007)

The New Forest: William the Conqueror planted it to hunt stags in; his son, William II (Rufus), was shot dead hunting one in it. Recently it has become a National Park. Woods of oak and chestnut (many ancient and magnificent still) and other trees still sweep magnificently over the sandy soil with moorland between, streams, and pretty and interesting villages hidden in clearings. Deer live in it and much other wildlife and ponies, but fewer people than in most English places. Lovely for wandering, riding and picnicking in woodland glades. Lyndhurst is its main centre; Cadnam and Minstead are pretty villages. It extends to the Beaulieu River estuary and the coast at Lymington, from where ferries to the Isle of Wight. The New Forest
Molecular cloning, functional expression and characterisation of RCC reductase involved in chlorophyll catabolism (2000)

Red chlorophyll catabolite (RCC) reductase (RCCR) and pheophorbide (Pheide) a oxygenase (PaO) catalyse the key reaction of chlorophyll catabolism, porphyrin macrocycle cleavage of Pheide a to a primary fluorescent catabolite (pFCC). RCCR was purified from barley and a partial gene sequence was cloned (pHvRCCR). The gene was expressed at all stages of leaf development and in roots. By comparison with different databases, genomic sequences and expressed sequence tags similar to RCCR were found in phylogenetically diverse species, and activity of RCCR was demonstrated in two of them, Arabidopsis thaliana and Marchantia polymorpha. The gene of A. thaliana (AtRCCR) was employed for molecular cloning, heterologous expression and the production of polyclonal antibodies. With recombinant RCCR, the major product of RCC reduction was pFCC-1, but small quantities of its C1 epimer, pFCC-2, also accumulated. The reaction required reduced ferredoxin and was sensitive to oxygen. AtRCCR encoded a 35 kDa protein which was used for chloroplast import experiments. Upon transport, it was processed to a mature form of 31 kDa. The significance of cloning of RCCR is discussed in respect to the evolution of chlorophyll catabolism and to the cloning of PaO.
A convenient preparation of carbonates from alcohols and carbon dioxide (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA convenient preparation of carbonates from alcohols and carbon dioxideWilliam A. Hoffman IIICite this: J. Org. Chem. 1982, 47, 26, 5209–5210Publication Date (Print):December 1, 1982Publication History Published online1 May 2002Published inissue 1 December 1982https://pubs.acs.org/doi/10.1021/jo00147a037https://doi.org/10.1021/jo00147a037research-articleACS PublicationsRequest reuse permissionsArticle Views429Altmetric-Citations43LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Corneal Cross-Linking and Safety Issues (2011)

As long as the corneal stroma treated has a minimal thickness of 400 microns (as recommended), neither corneal endothelium nor deeper structures such as lens and retina will suffer any damages. The light source should provide a homogenous irradiance avoiding hot spots.
Testing malware detectors (2004)

In today's interconnected world, malware, such as worms and viruses, can cause havoc. A malware detector (commonly known as virus scanner) attempts to identify malware. In spite of the importance of malware detectors, there is a dearth of testing techniques for evaluating them. We present a technique based on program obfuscation for generating tests for malware detectors. Our technique is geared towards evaluating the resilience of malware detectors to various obfuscation transformations commonly used by hackers to disguise malware. We also demonstrate that a hacker can leverage a malware detector's weakness in handling obfuscation transformations and can extract the signature used by a detector for a specific malware. We evaluate three widely-used commercial virus scanners using our techniques and discover that the resilience of these scanners to various obfuscations is very poor.
Lnk controls mouse hematopoietic stem cell self-renewal and quiescence through direct interactions with JAK2 (2008)

In addition to its role in megakaryocyte production, signaling initiated by thrombopoietin (TPO) activation of its receptor, myeloproliferative leukemia virus protooncogene (c-Mpl, or Mpl), controls HSC homeostasis and self-renewal. Under steady-state conditions, mice lacking the inhibitory adaptor protein Lnk harbor an expanded HSC pool with enhanced self-renewal. We found that HSCs from Lnk-/- mice have an increased quiescent fraction, decelerated cell cycle kinetics, and enhanced resistance to repeat treatments with cytoablative 5-fluorouracil in vivo compared with WT HSCs. We further provide genetic evidence demonstrating that Lnk controls HSC quiescence and self-renewal, predominantly through Mpl. Consistent with this observation, Lnk-/- HSCs displayed potentiated activation of JAK2 specifically in response to TPO. Biochemical experiments revealed that Lnk directly binds to phosphorylated tyrosine residues in JAK2 following TPO stimulation. Of note, the JAK2 V617F mutant, found at high frequencies in myeloproliferative diseases, retains the ability to bind Lnk. Therefore, we identified Lnk as a physiological negative regulator of JAK2 in stem cells and TPO/Mpl/JAK2/Lnk as a major regulatory pathway in controlling stem cell self-renewal and quiescence.
A microfluidic device for dry sample preservation in remote settings (2013)

This paper describes a microfluidic device for dry preservation of biological specimens at room temperature that incorporates chemical stabilization matrices. Long-term stabilization of samples is crucial for remote medical analysis, biosurveillance, and archiving, but the current paradigm for transporting remotely obtained samples relies on the costly "cold chain" to preserve analytes within biospecimens. We propose an alternative approach that involves the use of microfluidics to preserve samples in the dry state with stabilization matrices, developed by others, that are based on self-preservation chemistries found in nature. We describe a SlipChip-based device that allows minimally trained users to preserve samples with the three simple steps of placing a sample at an inlet, closing a lid, and slipping one layer of the device. The device fills automatically, and a pre-loaded desiccant dries the samples. Later, specimens can be rehydrated and recovered for analysis in a laboratory. This device is portable, compact, and self-contained, so it can be transported and operated by untrained users even in limited-resource settings. Features such as dead-end and sequential filling, combined with a "pumping lid" mechanism, enable precise quantification of the original sample's volume while avoiding overfilling. In addition, we demonstrated that the device can be integrated with a plasma filtration module, and we validated device operations and capabilities by testing the stability of purified RNA solutions. These features and the modularity of this platform (which facilitates integration and simplifies operation) would be applicable to other microfluidic devices beyond this application. We envision that as the field of stabilization matrices develops, microfluidic devices will be useful for cost-effectively facilitating remote analysis and biosurveillance while also opening new opportunities for diagnostics, drug development, and other medical fields.
A 1.8 kb alternative transcript from the human epidermal growth factor receptor gene encodes a truncated form of the receptor (1996)

The epidermal growth factor receptor (EGFR) is encoded by the c-erbB1 proto-oncogene and plays an important role in the control of cell growth and differentiation. To study the potential growth regulatory role of soluble EGF receptors, we have isolated cDNA clones encoding a truncated, secreted form of the human EGFR. The 5' sequence of this cDNA is identical to the EGFR transcript encoding the full-length receptor through exon 10. The unique 3' sequence encodes two additional amino acid residues before encountering an in-frame stop codon, a poly(A) addition site and a poly(A)+ tail. Sequence comparison with genomic DNA sequences demonstrates that this alternative transcript arises by read-through of a splice donor site. As a result, this transcript encodes a portion of the extracellular ligand-binding domain, but lacks the transmembrane domain and the intracellular tyrosine kinase catalytic domain present in the EGFR. Conditioned medium from transfected fibroblast cells contains a 60 kDa protein that is specifically immunoprecipitated by an EGFR monoclonal antibody. These findings demonstrate that alternative processing of the human EGFR transcript produces a secreted product composed of only the extracellular ligand-binding domain.
Microwave breast tumor detection and size estimation using contrast-agent-loaded magnetotactic bacteria (2013)

We propose a new approach to microwave breast tumor detection based on the use of bio-compatible flagellated magnetotactic bacteria (MTB). Previous work has shown that the directions and speeds of these bacterial microrobots adapted to operate in human microvasculature can be guided along preplanned paths deep inside the human body through external magnetic fields. Furthermore, a microwave contrast agent can be loaded onto MTB to alter the dielectric properties of tissues near the agent. Based on these two phenomena, we illustrate how multiple agglomerations of MTB released into human breast could be tracked simultaneously and monitored using differential microwave imaging (DMI) techniques. We also present novel strategies to detect and localize a breast cancerous mass as well as estimate its size through this new DMI-trackable bacterial propulsion and steering approach, and use an anatomically realistic breast model as a testbed to verify the feasibility of this breast cancer diagnostic technique.
Induction of class I MHC-restricted, peptide-specific cytolytic T lymphocytes by peptide priming in vivo. (1989)

The present study investigated the possibility that protein Ag fragments in the form of peptides could serve as the priming Ag in the generation of a MHC class I-restricted immune response. Trypsin-digested chicken ovalbumin (OVA-TD) fragments were used as the model Ag. The results demonstrate the peptides within OVA-TD, when injected into C57BL/6 mice, could prime T cells which lysed H-2b Ia-EL4 target cells in an OVA-TD-specific manner. In contrast to priming with OVA-TD, immunization of mice with intact OVA did not lead to generation of CTL against OVA-TD or OVA. Furthermore, target cells sensitized with intact OVA failed to be recognized by OVA-peptide-specific CTL indicating that the target cells serving as APC were unable to generate the relevant peptide determinants recognized by the T cells. These results support the idea that the processing pathway within APC for class I-restricted T cells may differ from that used for class II-restricted T cells. Using OVA-TD-specific CTL clones (phenotypically Thy 1+, CD8+, CD4-, Pgp-1+) isolated from primed animals to screen OVA-TD fractions separated by HPLC, two T cell peptide determinants were identified corresponding to OVA sequences 111-122 and 370-381. Both determinants were recognized by CTL clones in the context of the H-2Db molecule.
An electronic system for extracellular neural stimulation and recording (2007)

A system for extracellular neural interfacing that had the capability for stimulation and recording at multiple electrodes was presented. As the core of this system was a custom integrated circuit (IC) that contained low-noise amplifiers, stimulation buffers, and artifact-elimination circuitry. The artifact-elimination circuitry was necessary to prevent the activity of the stimulation buffers from interfering with the normal functioning of the low-noise amplifiers.\n The integrated circuits were fabricated in in a 0.35 micron CMOS process. We measured input-referred noise levels for the amplifiers as low as 3.50 microvolts (rms) in the in the bandwidth 30 Hz-3 kHz, corresponding to the frequency range of neural action potentials. The power consumption was 120 microwatts, corresponding to a noise-efficiency factor of 14.5. It was possible to resume recording signals within 2 ms of a stimulation, using the same electrode for both stimulation and recording.\n\tA filtering algorithm to remove the post-discharge artifact was also presented. The filtering was implemented using a field-programmable gate array (FPGA). The filtering algorithm itself consisted of blanking for the duration of the stimulation and artifact-elimination, followed by a wavelet de-noising. The wavelet de-noising split the signal into frequency ranges, discarded those ranges that did not correspond to neural signals, applied a threshold to the retained signals, and recombined the different frequency ranges into a single signal. The combination of the filtering with the artifact-elimination IC resulted in the capability for artifact-free recordings.