gebhart/patrepeval huggingface dataset:
The involvement of mRNA secondary structure in protein synthesis (1987)

Translation initiation in eukaryotes is a complex process involving many factors. A key step in this process is the binding of mRNA to the 43S preinitiation complex. This is generally the rate-limiting step in translation initiation and consequently a major determinant of mRNA translational efficiency. The primary and secondary structure of the mRNA 5' noncoding region have been implicated in modulating translational efficiency. Translational efficiency was shown to be inversely proportional to the degree of secondary structure at the mRNA 5' noncoding region. Furthermore, it was shown that cap-binding proteins that interact with the 5' cap structure (m7GpppN) of eukaryotic mRNAs are involved in the "unwinding" of the mRNA secondary structure, in an ATP hydrolysis mediated event, to facilitate ribosome binding. Thus, cap-binding proteins can potentially regulate mRNA translation. Here, we discuss the available data supporting the notion that eukaryotic 5' mRNA secondary structure plays an important role in translation initiation and the possible regulation of this process.
AQP5: A novel biomarker that predicts poor clinical outcome in colorectal cancer (2014)

The aquaporins (AQPs) are water channel proteins that exhibit several properties related to tumor development. However, the expression and clinical significance of AQP5 in colorectal cancer, particularly the correlation with circulating tumor cells (CTCs), has not been elucidated. The aim of the present study was to determine whether or not the expression of AQP5 is a strong prognostic biomarker for colorectal cancer. The results showed that of 45 tumor specimens, 14 (31.1%) had high levels of expression of AQP5, 29 (64.4%) exhibited a moderate (intermediate) level of staining, and 2 (4.4%) had an absence of AQP5 staining. AQP5 was only occasionally detected in para-neoplastic [3/45 (6.67%)] and normal tissues [3/45 (6.67%)]. AQP5 protein overexpression frequently accompanied gene amplification detection with fluorescence in situ hybridization (FISH). Moreover, AQP5 expression in colorectal cancer cells was upregulated compared to normal colon cells. AQP5 overexpression was also associated with TNM stage (P=0.002), lymph node metastasis (P=0.016), and distant metastasis (P=0.000). The relationships between age, gender, histologic grade and tumor size with expression of AQP5 were not significant (P>0.05). A positive correlation between the number of CTCs and AQP5 expression (P<0.05) was demonstrated. In addition, patients who did not express AQP5 had a superior cumulative survival rate compared to patients with AQP5 positivity. AQP5 may be used as a novel biomarker for colorectal cancer aggressiveness and metastasis, but it does not reflect drug resistance.
Architecture of MPEG-2 digital set-top-box for CATV VOD system (1996)

We describe an MPEG-2 compliant VOD (video on demand) terminal (e.g. set-top-box) developed for field trial purposes. The hardware architecture of the set-top-box is discussed with emphasis on the graphics system which integrates the MPEG-2 format video, computer graphics and NTSC analog format video. A key point in the implementation of this architecture is the development of a clock rate conversion circuit. The set-top-box contains a one-chip MPEG-2 decoder.
Selected strategies for improving sensitivity and reliability of immunoassays (1994)

Selected recent advances in immunoassay are reviewed. Development has continued on new labels (beta-lactamase, pyrophosphatase, luciferases, photoproteins, pyridopyridazines, europium cryptates, metal carbonyl complexes, porphines, phosphors) and label-detection methods (e.g., chemiluminescence assays, thermometric assays, NADP(+)- and FADP-based coupled assays). Various methods have been explored to increase assay sensitivity, including label amplification via catalyzed reporter deposition (peroxidase label) and immuno-polymerase chain reaction (DNA label). The focus of new immunoassay strategies has been on improved reliability (bispecific antibodies), assay simplification (piezoelectric and surface plasmon resonance immunosensors, phase-modulation fluorescence spectroscopy, polymerized bilayer assemblies), and simultaneous multianalyte testing (e.g., quadruple labeling with lanthanides, one-step test devices for drugs of abuse).
CONVERSION OF LIGNOCELLULOSIC MATERIAL TO CHEMICALS AND FUELS (2001)

A direct conversion of cellulosic wastes, including resin-bonded furniture and building waste, to levulinate esters is being investigated with the view to producing fuels, solvents, and chemical intermediates as well as other useful by-products in an inexpensive process. The acid-catalyzed reaction of cellulosic materials with ethanol or methanol at 200 C gives good yields of levulinate and formate esters, as well as useful by-products, such as a solid residue (charcoal) and a resinous lignin residue. An initial plant design showed reasonable rates of return for production of purified ethyl levulinate and by-products. In this project, investigations have been performed to identify and develop reactions that utilize esters of levulinic acid produced during the acid-catalyzed ethanolysis reaction. We wish to develop uses for levulinate esters that allow their marketing at prices comparable to inexpensive polymer intermediates. These prices will allow a sufficient rate of return to justify building plants for utilizing the waste lignocellulosics. If need is demonstrated for purified levulinate, the initial plant design work may be adequate, at least until further pilot-scale work on the process is performed.
Hepatocyte Growth Factor Induces Gefitinib Resistance of Lung Adenocarcinoma with Epidermal Growth Factor Receptor–Activating Mutations (2008)

Lung cancer with epidermal growth factor receptor (EGFR)-activating mutations responds favorably to the EGFR tyrosine kinase inhibitors gefitinib and erlotinib. However, 25% to 30% of patients with EGFR-activating mutations show intrinsic resistance, and the responders invariably acquire resistance to gefitinib. Here, we showed that hepatocyte growth factor (HGF), a ligand of MET oncoprotein, induces gefitinib resistance of lung adenocarcinoma cells with EGFR-activating mutations by restoring the phosphatidylinositol 3-kinase/Akt signaling pathway via phosphorylation of MET, but not EGFR or ErbB3. Strong immunoreactivity for HGF in cancer cells was detected in lung adenocarcinoma patients harboring EGFR-activating mutations, but no T790M mutation or MET amplification, who showed intrinsic or acquired resistance to gefitinib. The findings indicate that HGF-mediated MET activation is a novel mechanism of gefitinib resistance in lung adenocarcinoma with EGFR-activating mutations. Therefore, inhibition of HGF-MET signaling may be a considerable strategy for more successful treatment with gefitinib.
VLSI Implementation of a Wormhole Run-time Reconfigurable Processor (2001)

Until now, the performance improvement of computing machines was a mostly a result of shrinking transistor geometries and increasing clock speeds. With the advent of signal processing applications that have stringent performance requirements from processing hardware, the field of configurable computing has received a lot of attention. Efforts are being made to improve computation bandwidth by architectural innovations. Among these, the wormhole runtime reconfigurable architecture introduces the concept of stream processing. It enables dynamic reconfiguration of hardware with little overheads and is very much suited for data-path based computations with deep computational pipelines. Stallion, second in the generation of Wormhole runtime reconfigurable processors, demonstrates the efficacy of wormhole runtime reconfiguration. The work presented here deals with the VLSI implementation of Stallion and discusses the full-custom physical design flow adopted for Stallion. Also, the tools and techniques to customize this flow are detailed. The Stallion design methodology offers a possible solution that can be pursued for executing similar efforts in future. ii
Mice deficient for PDGF B show renal, cardiovascular, and hematological abnormalities. (1994)

Platelet-derived growth factor (PDGF) affects the growth, migration, and function in vitro of mesenchymal cells, but little is known about its normal physiological functions in vivo. We show here that mice deficient for PDGF B die perinatally and display several anatomical and histological abnormalities. Kidney glomerular tufts do not form, apparently because of absence of mesangial cells. Instead, a single or a few distended capillary loops fill the glomerular space. The heart and some large arteries dilate in late-stage embryos. Most PDGF B mutant embryos develop fatal hemorrhages just prior to birth. Their hematological status includes erythroblastosis, macrocytic anemia, and thrombocytopenia. On the basis of these findings, we conclude that PDGF B has crucial roles in vivo in establishing certain renal and circulatory functions.
Expression of the chemokine receptor CCR6 in human renal inflammation (2010)

CCR6 and the corresponding ligand CCL20 might therefore be involved in the recruitment of T and B cells to organized nodular infiltrates in chronic renal inflammation. The functional role of endothelial CCR6 needs to be evaluated in further studies.
Human Immunodeficiency Virus Type 1 Protease Inhibitors (1997)

Until recently, treatment for human immunodeficiency virus type 1 (HIV-1) infection was limited to the use of nucleoside inhibitors of the viral enzyme reverse transcriptase. While these agents initially offered promise, they have only modest antiviral activity and the benefits of treatment are limited by the emergence of drug resistance and dose-limiting toxic effects. Development of more potent drugs that target different stages of the virus life cycle has thus been aggressively pursued. Efforts to develop inhibitors of HIV-1 protease have yielded a potent new class of compounds that suppress HIV-1 replication to an extent far greater than was previously attainable. Four protease inhibitors, saquinavir mesylate, ritonavir, nelfinavir, and indinavir sulfate, have been approved by the Food and Drug Administration. Other agents are undergoing active investigation. The purpose of this article is to review the currently available data on those agents that have been approved for clinical use.
Cross-Layer Multi-Rate Routing Strategies in Wireless Multi-Hop Random Access Networks (2007)

In this paper, we develop and study combined multi- rate and packet forwarding and routing operations in the context of multi-hop ad hoc wireless networks. Nodes are assumed to employ a software controlled radio that is programmed to use several modulation/coding schemes (MCSs) that operate at different data rates. The underlying MAC scheme is assumed to be based on a random access (pure ALOHA type) protocol. We propose a distributed QoS-aware cross-layer joint routing and rate control algorithm. It is used by nodal stations to jointly select, for each packet that traverses multi-hop routes across the network, the transmit data rate and the neighboring node to which the packet should be routed towards its destination. Each station monitors certain station and network activity states, and uses these data to adapt the selection of its parameter vectors. The mechanism strives to ensure that flow throughput and end- to-end packet delay target levels are met. Once satisfied, the algorithm selects parameters that serve to enhance the transport throughput level, thus occupying limited overall network wide resources. Simulation results demonstrate the significant performance enhancements that are achieved under the use of the proposed scheme. Our analytical models and mechanisms provide important guidelines for the design of such joint channel rate, MAC and routing based operations algorithms.
Origin matters: Differences in embryonic tissue origin and Wnt signaling determine the osteogenic potential and healing capacity of frontal and parietal calvarial bones (2009)

Calvarial bones arise from two embryonic tissues, namely, the neural crest and the mesoderm. In this study we have addressed the important question of whether disparate embryonic tissue origins impart variable osteogenic potential and regenerative capacity to calvarial bones, as well as what the underlying molecular mechanism(s). Thus, by performing in vitro and in vivo studies, we have investigated whether differences exist between neural crest-derived frontal and paraxial mesodermal-derived parietal bone. Of interest, our data indicate that calvarial bone osteoblasts of neural crest origin have superior potential for osteogenic differentiation. Furthermore, neural crest-derived frontal bone displays a superior capacity to undergo osseous healing compared with calvarial bone of paraxial mesoderm origin. Our study identified both in vitro and in vivo enhanced endogenous canonical Wnt signaling in frontal bone compared with parietal bone. In addition, we demonstrate that constitutive activation of canonical Wnt signaling in paraxial mesodermal-derived parietal osteoblasts mimics the osteogenic potential of frontal osteoblasts, whereas knockdown of canonical Wnt signaling dramatically impairs the greater osteogenic potential of neural crest-derived frontal osteoblasts. Moreover, fibroblast growth factor 2 (FGF-2) treatment induces phosphorylation of GSK-3beta and increases the nuclear levels of beta-catenin in osteoblasts, suggesting that enhanced activation of Wnt signaling might be mediated by FGF. Taken together, our data provide compelling evidence that indeed embryonic tissue origin makes a difference and that active canonical Wnt signaling plays a major role in contributing to the superior intrinsic osteogenic potential and tissue regeneration observed in neural crest-derived frontal bone.
Elevated Levels of Activin A in Heart Failure (2004)

Together with our demonstration of activin A-induced gene expression in neonatal cardiomyocytes of mediators related to myocardial remodeling, the expression pattern of activin A during clinical and experimental HF suggests an involvement of this cytokine in the pathogenesis of HF.
Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays (2000)

To examine the utility and performance of 50mer oligonucleotide (oligonucleotide probe) microarrays, gene-specific oligonucleotide probes were spotted along with PCR probes onto glass microarrays and the performance of each probe type was evaluated. The specificity of oligonucleotide probes was studied using target RNAs that shared various degrees of sequence similarity. Sensitivity was defined as the ability to detect a 3-fold change in mRNA. No significant difference in sensitivity between oligonucleotide probes and PCR probes was observed and both had a minimum reproducible detection limit of approximately 10 mRNA copies/cell. Specificity studies showed that for a given oligonucleotide probe any 'non-target' transcripts (cDNAs) >75% similar over the 50 base target may show cross-hybridization. Thus non-target sequences which have >75-80% sequence similarity with target sequences (within the oligonucleotide probe 50 base target region) will contribute to the overall signal intensity. In addition, if the 50 base target region is marginally similar, it must not include a stretch of complementary sequence >15 contiguous bases. Therefore, knowledge about the target sequence, as well as its similarity to other mRNAs in the target tissue or RNA sample, is required to design successful oligonucleotide probes for quality microarray results. Together these results validate the utility of oligonucleotide probe (50mer) glass microarrays.
Dynamic Glycosylation of Nuclear and Cytosolic Proteins (1997)

O-Linked N-acetylglucosamine (O-GlcNAc) glycosylation is a dynamic modification of eukaryotic nuclear and cytosolic proteins analogous to protein phosphorylation. We have cloned and characterized a novel gene for an O-GlcNAc transferase (OGT) that shares no sequence homology or structural similarities with other glycosyltransferases. The OGT gene is highly conserved (up to 80% identity) in all eukaryotes examined. Unlike previously described glycosyltransferases, OGT is localized to the cytosol and nucleus. The OGT protein contains multiple tandem repeats of the tetratricopeptide repeat motif. The presence of tetratricopeptide repeats, which can mediate protein-protein interactions, suggests that OGT may be regulated by protein interactions that are independent of the enzyme's catalytic site. The OGT is also modified by tyrosine phosphorylation, indicating that tyrosine kinase signal transduction cascades may play a role in modulating OGT activity.
A generalized correlation for the viscosity of dextrans in aqueous solutions as a function of temperature, concentration, and molecular weight at low shear rates (1989)

Abstract An expression relating the viscosity of dextran solutions to polymer concentration ( c ), molecular weight ( M ), and temperature ( T ) has been derived from experimental data in the following ranges: 5 &lt; c &lt; 25% (wt/wt), 298.2 &lt; T &lt; 363.2 K, and 71,500 &lt; M &lt; 531,000 g/mol. The experimental work was based on capillary viscosimeters. Thermodynamic data (entropy and energy of activation for the viscous flow of a Newtonian fluid) are also presented as a function of polymer concentration for the three molecular weights studied. This thermodynamic analysis suggests that dextrans in aqueous solutions behave as flexible polymers. Application of our expression to existing viscosity data for ethylene/vinylacetate copolymers in paraffin has resulted in improved goodness of fit with respect to established correlations.
SPHK1 (sphingosine kinase 1) induces epithelial-mesenchymal transition by promoting the autophagy-linked lysosomal degradation of CDH1/E-cadherin in hepatoma cells (2017)

SPHK1 (sphingosine kinase 1), a regulator of sphingolipid metabolites, plays a causal role in the development of hepatocellular carcinoma (HCC) through augmenting HCC invasion and metastasis. However, the mechanism by which SPHK1 signaling promotes invasion and metastasis in HCC remains to be clarified. Here, we reported that SPHK1 induced the epithelial-mesenchymal transition (EMT) by accelerating CDH1/E-cadherin lysosomal degradation and facilitating the invasion and metastasis of HepG2 cells. Initially, we found that SPHK1 promoted cell migration and invasion and induced the EMT process through decreasing the expression of CDH1, which is an epithelial marker. Furthermore, SPHK1 accelerated the lysosomal degradation of CDH1 to induce EMT, which depended on TRAF2 (TNF receptor associated factor 2)-mediated macroautophagy/autophagy activation. In addition, the inhibition of autophagy recovered CDH1 expression and reduced cell migration and invasion through delaying the degradation of CDH1 in SPHK1-overexpressing cells. Moreover, the overexpression of SPHK1 produced intracellular sphingosine-1-phosphate (S1P). In response to S1P stimulation, TRAF2 bound to BECN1/Beclin 1 and catalyzed the lysine 63-linked ubiquitination of BECN1 for triggering autophagy. The deletion of the RING domain of TRAF2 inhibited autophagy and the interaction of BECN1 and TRAF2. Our findings define a novel mechanism responsible for the regulation of the EMT via SPHK1-TRAF2-BECN1-CDH1 signal cascades in HCC cells. Our work indicates that the blockage of SPHK1 activity to attenuate autophagy may be a promising strategy for the prevention and treatment of HCC.
The presence of cytomegalovirus nucleic acids in arterial walls of atherosclerotic and nonatherosclerotic patients. (1989)

The presence of cytomegalovirus (CMV) nucleic acids was demonstrated in abdominal aortas and femoral arteries of patients with and without atherosclerosis by dot blot and in situ DNA hybridization using a DNA probe derived from immediate early genomic regions. Viral antigens could not be detected by immunohistochemistry and infectious virus could not be recovered from the arterial wall by virus isolation techniques. The high percentage (55%) of vascular wall specimens containing CMV nucleic acids, in atherosclerotic as well as in control material and the location of CMV-containing cells in arteries without gross changes indicative of atherosclerosis suggest that the human arterial wall may be a site of latency for this virus.
Uniform-phase uniform-amplitude resonant-load global clock distributions (2005)

This work presents a new approach to global clock distribution in which tree-driven grids are augmented with on-chip spiral inductors to resonate the clock capacitance. In this scheme, the energy of the fundamental frequency resonates between electric and magnetic forms, with the reduced admittance of the clock network allowing for significantly lower gain requirements in the buffering network. The substantial improvements in jitter and power resulting from this approach are presented using measurement results from two test chips, one fabricated in a 90-nm and the other in a 0.18-/spl mu/m CMOS technology.
Chip-based Brillouin lasers as spectral purifiers for photonic systems (2012)

High coherence lasers are essential in a wide range of applications, however, such performance is normally associated with large laser cavities, because increasing energy storage reduces quantum phase noise and also renders the laser frequency less sensitive to cavity vibration. This basic scaling rule is at odds with an emerging set of optical systems that place focus on compact (optimally integrable) sources of high coherence light. These include phase-coherent optical communication using quadrature-amplitude-modulation, and also record-low phase noise microwave sources based upon optical comb techniques. In this work, the first, chip-based Brillouin laser is demonstrated. It features high-efficiency and single-line operation with the smallest recorded Schawlow-Townes frequency noise for any chip-based laser. Because the frequency offset between the laser's emission and the input pump is relatively small, the device provides a new function: spectral purification of compact, low coherence sources such as semiconductor lasers.
Progression of tubulointerstitial injury by osteopontin-induced macrophage recruitment in advanced diabetic nephropathy of transgenic (mRen-2)27 rats (2002)

These findings suggest that osteopontin expression and macrophage accumulation may play a role in the tubulointerstitial injury in diabetic nephropathy, and that inhibition of osteopontin expression may be one of the mechanisms by which blockade of the renin-angiotensin system confers a renoprotective effect.
Universal bispecific antibody for targeting tumor cells for destruction by cytotoxic T cells. (1988)

Previous studies have demonstrated that bispecific hybrid antibodies produced by cell-cell fusion or chemically conjugated heteroaggregates can direct cytotoxic T lymphocytes to kill target cells for which they have no intrinsic specificity, a phenomenon we call effector cell retargeting (ECR). These studies used bispecific reagents with one specificity directed to CD3 or Ti on the effector cell and the other directed to a target cell antigen. To avoid the need to create different hybrid hybridomas for each target antigen we have developed a universal means to elicit ECR through the use of an antiglobulin step. We have constructed a bispecific hybrid antibody with dual specificity for CD3 and a rat immunoglobulin light chain allotype. This bispecific antibody could mediate ECR to a range of target cells, each coated with distinct surface-binding rat monoclonal antibodies. A particular advantage of targeting to surface-bound monoclonal antibodies is that all other available effector systems may also attack the same antibody-coated target cell.