gebhart/patrepeval huggingface dataset:
Antitumor activity of ALK1 in pancreatic carcinoma cells (2007)

In this study, the authors investigated the expression of activin receptor-like kinase 1 (ALK1) in pancreatic carcinoma and evaluated its potential role as a tumor suppressor in vitro and in vivo. Endogenous ALK1 expression was demonstrated by immunohistochemistry in both pancreatic tumor tissue and peritumoral normal tissue from 6 patients and by RT-PCR in 8/12 established pancreatic cancer cell lines. Ectopic expression of a constitutively active (ca) ALK1 mutant in TGF-beta sensitive PANC-1 and COLO-357 cells augmented transcriptional activation of a Smad2/3 responsive reporter, and slowed down basal growth in vitro. Both effects were further enhanced by TGF-beta/ALK5 stimulation, suggesting largely independent nuclear Smad signaling by both type I receptors. Upon orthotopic transplantation of PANC-1-caALK1 into immunodeficient mice, tumor size was strongly reduced and was associated with a lower microvessel density in the PANC-1-caALK1-derived tumors. In vitro, this mutant efficiently blocked TGF-beta-induced epithelial-to-mesenchymal transdifferentiation and suppressed TGF-beta/ALK5-mediated activation of the p38 MAPK pathway. Mechanistically, caALK1 silenced MyD118, an immediate TGF-beta target gene whose protein product, GADD45beta, couples Smad signaling to p38 activation. These results show that ALK1 activation in pancreatic tumor cells is antioncogenic by inducing ALK5-independent growth inhibition and by blocking TGF-beta/ALK5-mediated epithelial-to-mesenchymal transdifferentiation and, possibly, invasion and metastatic progression.
Transcriptional expression profiles of oral squamous cell carcinomas (2002)

No statistically significant differences in gene expression were found between early-stage disease and late-stage disease or between metastatic tumors and nonmetastatic tumors. The implications of these findings for the prediction of clinical outcome and for the discovery of new OSCC tumor markers are discussed.
Guided Differentiation of Embryonic Stem Cells into Pdx1-Expressing Regional-Specific Definitive Endoderm (2008)

The generation of specific lineages of the definitive endoderm from embryonic stem (ES) cells is an important issue in developmental biology, as well as in regenerative medicine. This study demonstrates that ES cells are induced sequentially into regional-specific gut endoderm lineages, such as pancreatic, hepatic, and other cell lineages, when they are cultured directly on a monolayer of mesoderm-derived supporting cells. A detailed chronological analysis revealed that Activin, fibroblast growth factor, or bone morphogenetic protein signals are critical at various steps and that additional short-range signals are required for differentiation into Pdx1-expressing cells. Under selective culture conditions, definitive endoderm (47%) or Pdx1-positive pancreatic progenitors (30%) are yielded at a high efficiency. When transplanted under the kidney capsule, the Pdx1-positive cells further differentiated into all three pancreatic lineages, namely endocrine, exocrine, and duct cells.
Tyrosylprotein Sulfotransferase-2 Expression Is Required for Sulfation of RNase 9 and Mfge8 in Vivo (2008)

Protein-tyrosine sulfation is mediated by two Golgi tyrosyl-protein sulfotransferases (TPST-1 and TPST-2) that are widely expressed in vivo. However, the full substrate repertoire of this enzyme system is unknown and thus, our understanding of the biological role(s) of tyrosine sulfation is limited. We reported that whereas Tpst1(-/-) male mice have normal fertility, Tpst2(-/-) males are infertile despite normal spermatogenesis. However, Tpst2(-/-) sperm are severely defective in their motility in viscous media and in their ability to fertilize eggs. These findings suggest that sulfation of unidentified substrate(s) is crucial for normal sperm function. We therefore sought to identify tyrosine-sulfated proteins in the male genital tract using affinity chromatography on PSG2, an anti-sulfotyrosine monoclonal antibody, followed by mass spectrometry. Among the several candidate tyrosine-sulfated proteins identified, RNase 9 and Mfge8 were examined in detail. RNase 9, a catalytically inactive RNase A family member of unknown function, is expressed only in the epididymis after onset of sexual maturity. Mfge8 is expressed on mouse sperm and Mfge8(-/-) male mice are subfertile. Metabolic labeling coupled with sulfoamino acid analysis confirmed that both proteins are tyrosine-sulfated and both proteins are expressed at comparable levels in wild type, Tpst1(-/-), and Tpst2(-/-) epididymides. However, we demonstrate that RNase 9 and Mfge8 are tyrosine-sulfated in wild type and Tpst1(-/-), but not in Tpst2(-/-) mice. These findings suggest that lack of sulfation of one or both of these proteins may contribute mechanistically to the infertility of Tpst2(-/-) males.
The Gesture Watch: A Wireless Contact-free Gesture based Wrist Interface (2007)

We introduce the Gesture Watch, a mobile wireless device worn on a user's wrist that allows hand gesture control of other devices. The Gesture Watch utilizes an array of infrared proximity sensors to sense hand gestures made over the device and interprets the gestures using hidden Markov models. The Gesture Watch maps intuitive gross hand gestures to control signals such as the play and pause commands commonly found on mobile media players. We present our evaluation of the Gesture Watch designed to determine its the accuracy and usability. In our study, 10 participants used the Gesture Watch in both mobile and stationary conditions as well as indoors and outdoors. Overall, we attained a recognition accuracy of 95.5% and found that the Gesture Watch worked well in both indoor and outdoor environments and while mobile.
Mechanisms of spinal cord stimulation in neuropathic pain (2000)

The understanding of the mode of action of spinal cord stimulation (SCS) as treatment of neuropathic pain is still fragmentary. SCS evolved from the gate-control theory postulating a spinal modulation of noxious inflow, but there is little evidence that SCS influences nociceptive pain; pain relief in peripheral vascular disease and angina pectoris is presumably secondary to other SCS effects. In man, SCS may effectively abolish both continuous and evoked pain (tactile/thermal allodynia) whereas induced, acute nociceptive pain is unaffected. Recent SCS studies performed on rat models of mononeuropathy have demonstrated a preferential effect on A beta fiber mediated functions, and the hyperexcitability of wide-dynamic-range dorsal horn neurons was attenuated. These effects were coupled to increased release of GABA and reduced glutamate and aspartate release in the dorsal horn. Intrathecal administration of GABA, baclofen and adenosine enhanced the SCS effect on tactile allodynia even in previously non-responsive rats. Preliminary results indicate that gabapentin may have a similar effect. GABAergic and adenosine-related mechanisms conceivably represent only examples of a number of putative receptor systems involved in SCS. Clinical trials have been initiated exploring the possibility to improve the efficacy of SCS by concomitant pharmacotherapy.
Infrared to visible up-conversion using GaP light-emitting diodes (1983)

Electroluminescence excited by infrared radiation has been observed in GaP light-emitting diodes (LED’s) at low temperatures providing a new efficient method to convert infrared radiation within a broad spectral range into visible light. Using 10.6-μm radiation of a CO2 laser an up-conversion quantum efficiency of 3.4×10−6 was found. If a low dark current photomultiplier is employed to detect the LED emission the dominant noise source is due to conversion of thermal background radiation yielding a noise equivalent power of NEP=1.6×10−9 W/Hz1/2.
Innovative Indoor Geolocation Using RF Multipath Diversity (2006)

A new concept is presented for indoor geolocation in multipath environments where direct paths are sometimes undetectable. In contrast to previous statistically-based approaches, the multipath delays are modeled using a geometry-based argument. Assuming a series of specular reflections off of planar surfaces, the model contains a maximum of three unknown multipath parameters per path which may be estimated when geolocation accuracy is sufficiently high. If some of the direct paths subsequently become undetectable, it is possible under certain conditions to maintain geolocation accuracy using only the indirect path length measurements. The new concept is illustrated via simulation using a relatively simple representative scenario. Performance is compared to a traditional method which uses only direct path measurements, indicating the potential for significantly improved indoor geolocation accuracy in environments dominated by multipath. Since the estimated multipath parameters are geometry-dependent, this approach allows the possibility of building up indoor map information as the geolocation process commences.
An Essential Phosphorylation-site Domain of Human cdc25C Interacts with Both 14-3-3 and Cyclins (2000)

Human cdc25C is a dual-specificity phosphatase involved in the regulation of cell cycle progression in both unperturbed cells and in cells subject to DNA damage or replication checkpoints. In this study, we describe the structure-function relationship of an essential domain of human cdc25C that interacts with 14-3-3 proteins. We show that this domain is a bi-functional interactive motif that interacts with cyclins primarily through their P-box motif in addition to 14-3-3 proteins. Characterization of the structural features of this domain by NMR and circular dichroism reveals two distinct alpha helical moieties interconnected by a loop carrying the 14-3-3 binding site. Moreover, the helical folding is induced upon binding to 14-3-3, suggestive of a conformational regulation of this domain of cdc25C through interactions with partner proteins in vivo. Combining our structural and biochemical data, we propose a detailed model of the molecular mechanism of cdc25C regulation by differential association with 14-3-3 and cdc2-cyclin B.
Signal Transducer and Activator of Transcription 1 Regulates Both Cytotoxic and Prosurvival Functions in Tumor Cells (2007)

Elsewhere, we reported that multiple serial in vivo passage of a squamous cell carcinoma cells (SCC61) concurrent with ionizing radiation (IR) treatment resulted in the selection of radioresistant tumor (nu61) that overexpresses the signal transducer and activator of transcription 1 (Stat1)/IFN-dependent pathway. Here, we report that (a) the Stat1 pathway is induced by IR, (b) constitutive overexpression of Stat1 is linked with failure to transmit a cytotoxic signal by radiation or IFNs, (c) selection of parental cell line SCC61 against IFN-alpha and IFN-gamma leads to the same IR- and IFN-resistant phenotype as was obtained by IR selection, and (d) suppression of Stat1 by short hairpin RNA renders the IR-resistant nu61 cells radiosensitive to IR. We propose a model that transient induction of Stat1 by IFN, IR, or other stress signals activates cytotoxic genes and cytotoxic response. Constitutive overexpression of Stat1 on the other hand leads to the suppression of the cytotoxic response and induces prosurvival genes that, at high levels of Stat1, render the cells resistant to IR or other inducers of cell death.
Modulation of Juxtamembrane Cleavage (“Shedding”) of Angiotensin-Converting Enzyme by Stalk Glycosylation:  Evidence for an Alternative Shedding Protease (1999)

The role of juxtamembrane stalk glycosylation in modulating stalk cleavage and shedding of membrane proteins remains unresolved, despite reports that proteins expressed in glycosylation-deficient cells undergo accelerated proteolysis. We have constructed stalk glycosylation mutants of angiotensin-converting enzyme (ACE), a type I ectoprotein that is vigorously shed when expressed in Chinese hamster ovary cells. Surprisingly, stalk glycosylation did not significantly inhibit release. Introduction of an N-linked glycan directly adjacent to the native stalk cleavage site resulted in a 13-residue, proximal displacement of the cleavage site, from the Arg-626/Ser-627 to the Phe-640/Leu-641 bond. Substitution of the wild-type stalk with a Ser-/Thr-rich sequence known to be heavily O-glycosylated produced a mutant (ACE-JGL) in which this chimeric stalk was partially O-glycosylated; incomplete glycosylation may have been due to membrane proximity. Relative to levels of cell-associated ACE-JGL, rates of basal, unstimulated release of ACE-JGL were enhanced compared with wild-type ACE. ACE-JGL was cleaved at an Ala/Thr bond, 14 residues from the membrane. Notably, phorbol ester stimulation and TAPI (a peptide hydroxamate) inhibition of release-universal characteristics of regulated ectodomain shedding-were significantly blunted for ACE-JGL, as was a formerly undescribed transient stimulation of ACE release by 3, 4-dichloroisocoumarin. These data indicate that (1) stalk glycosylation modulates but does not inhibit ectodomain shedding; and (2) a Ser-/Thr-rich, O-glycosylated stalk directs cleavage, at least in part, by an alternative shedding protease, which may resemble an activity recently described in TNF-alpha convertase null cells [Buxbaum, J. D., et al. (1998) J. Biol. Chem. 273, 27765-27767].
Natural language text classification and filtering with trigrams and evolutionary nearest neighbour classifiers (2000)

N grams offer fast language independent multi-class text categorization. Text is reduced in a single pass to ngram vectors. These are assigned to one of several classes by a) nearest neighbor (KNN) and b) genetic algorithm operating on weights in a nearest neighbour classifier. 91% accuracy is found on binary classification on short multi-author technical English documents. This falls if more categories are used but 69% is obtained with 8 classes. Zipf law is found not to apply to trigrams. 1 1 INTRODUCTION It is increasingly important that organisation are able to direct electronic documents rapidly to the right person. Therefore automatic and particularly adaptive mechanisms which match documents to the interest profile of individuals are particularly interesting. Ngrams offer a means of storing and updating user interest profiles and rapid language independent means of comparing profiles and documents. We show trigrams (3-grams) in conjunction with a nearest neighbour...
HIV-1 Integrase Forms Stable Tetramers and Associates with LEDGF/p75 Protein in Human Cells (2002)

We studied human immunodeficiency virus, type 1 (HIV-1) integrase (IN) complexes derived from nuclei of human cells stably expressing the viral protein from a synthetic gene. We show that in the nuclear extracts IN exists as part of a large distinct complex with an apparent Stokes radius of 61 A, which dissociates upon dilution yielding a core molecule of 41 A. We isolated the IN complexes from cells expressing FLAG-tagged IN and demonstrated that the 41 A core is a tetramer of IN, whereas 61 A molecules are composed of IN tetramers associated with a cellular protein with an apparent molecular mass of 76 kDa. This novel integrase interacting protein was found to be identical to lens epithelium-derived growth factor (LEDGF/p75), a protein implicated in regulation of gene expression and cellular stress response. HIV-1 IN and LEDGF co-localized in the nuclei of human cells stably expressing IN. Furthermore, recombinant LEDGF robustly enhanced strand transfer activity of HIV-1 IN in vitro. Our findings indicate that the minimal IN molecule in human cells is a homotetramer, suggesting that at least an octamer of IN is required to accomplish coordinated integration of both retroviral long terminal repeats and that LEDGF is a cellular factor involved in this process.
Performance of Two-Way Channel Estimation Technique for Multi-User Distributed Antenna Systems with Spatial Precoding (2009)

This paper investigates the performance of a multiuser distributed antenna system (DAS) with spatial precoding in which mobile stations (MSs) just send back the received signals along with their training sequences. In this method, base stations (BSs) can obtain the channel state information of both the uplink and downlink without estimating the channels in MSs. This two-way multiple-input multiple-output (MIMO) channel estimation technique have been proposed and mathematically analyzed in the literature. However, implementation aspects of this method, such as forward gain and dynamic range, are not studied yet. In this paper, these aspects are investigated in order to confirm its feasibility in a multi-user DAS where a precoder is employed in BSs. Computer simulation results are presented to demonstrate the required hardware specs for an amplify and forward (AF) operation in MSs by examining the bit error rate (BER) performance. It is shown that an 8-bit A/D converter together with a fixed gain amplifier brings almost no degradation to the BER performance. Furthermore, a performance comparison with a vector feedback method is given.
A Subset of Epithelial Cells with CCSP Promoter Activity Participates in Alveolar Development (2010)

Alveolar formation is hallmarked by the transition of distal lung saccules into gas exchange units through the emergence of secondary crests and an exponential increase in surface area. Several cell types are involved in this complex process, including families of epithelial cells that differentiate into alveolar type I and II cells. Subsets of cells expressing Clara cell secretory protein (CCSP) have been identified in both lung and bone marrow compartments, and are described as a progenitor/stem cell pool involved in airway regeneration and alveolar homeostasis. Whether these cells also participate in alveolar formation during postnatal development remains unknown. Based on their regenerative capacity, we asked whether these cells participate in alveogenesis. We used a previously described transgenic mouse model (CCSP-tk) in which Ganciclovir exposure selectively depletes all cells with CCSP promoter activity through intracellular generation of a toxic metabolite of thymidine kinase. Our results showed that Ganciclovir treatment in newborn CCtk mice depleted this cell population in lung airways and bone marrow, and was associated with alveolar hypoplasia and respiratory failure. Hypoplastic lungs had fewer alveolar type I and II cells, with impaired secondary crest formation and decreased vascular endothelial growth factor expression in distal airways. These findings are consistent with a model in which a unique population of cells with CCSP promoter activity that expresses vascular endothelial growth factor participates in alveolar development.
Purification and Properties of Thermostable Xylanase fromTalaromyces byssochlamydoidesYH-50 (1981)

Thermostable xylanase from Talaromyces byssochlamydoides YH-50 was fractionated into three components, tentatively named X-a, X-b-I and X-b-II during the purification steps. X-a, X-b-I and X-b-II were further purified by consecutive column chromatographies until found to be in homogeneous states on disc electrophoresis. X-a, X-b-I and X-b-II contained 36.6%, 31.5% and 14.2% carbohydrate residues, respectively. The carbohydrate residues were glucose, mannose and fucose. X-a, X-b-I and X-b-II were optimally active at 70 ~ 75°C and pH 4.5 ~ 5.5. X-a, X-b-I and X-b-II retained 65, 54 and 30%, respectively, of the original activity after heating at 95°C for 5 min. The activities of X-a, X-b-I and X-b-II were considerably inhibited by HgCl2 and KMnO4. The hydrolysis products from xylan with X-a were xylose, arabinose, glucose, xylobiose and other xylooligosaccharides, whereas the hydrolysis products from xylan with X-b-I and X-b-II were xylose and xylobiose.
Moisture-driven crack growth in blanket low dielectric constant and ultralow dielectric constant films (2004)

Moisture-driven crack growth was measured as a function of film thickness for a variety of low dielectric constant and ultralow dielectric constant films and a comparison of the crack driving force was made. By plotting the crack velocity versus the crack driving force, a series of universal curves was produced which showed that fracture resistance scales with the dielectric constant.
Internucleosomal DNA fragmentation during phorbol ester-induced monocytic differentiation and G0/G1 arrest. (1992)

The treatment of human myeloid leukemia cell lines with phorbol esters, such as 12-O-tetradecanoylphorbol-13-acetate (TPA), is associated with loss of proliferative capacity and induction of monocytic differentiation. The present results demonstrate that treatment of asynchronous human U-937 leukemia cells with 10 nM TPA is also associated with oligonucleosomal DNA cleavage. This pattern of DNA fragmentation, which is observed in programmed cell death, was detectable in populations of TPA-treated cells that had entered a nonproliferative G0/G1 phase. Similar findings were obtained after TPA treatment of a synchronous population of G1 cells. These cells progressed through S and G2/M phases before undergoing internucleosomal DNA cleavage during G0/G1 arrest. These G0/G1 cells displayed characteristics of monocytic differentiation, including down-regulation of c-myc expression and induction of c-fms transcripts. DNA fragmentation was also studied in cells treated with 5 nM TPA for 48 h and then monitored in drug-free long-term culture. Endonucleolytic cleavage was similarly observed in the differentiated G0/G1 population. However, longer periods of culture were associated with a decrease in DNA fragmentation to undetectable levels. This effect was followed by retrodifferentiation and reentry of cells into cycle. Taken together, these findings demonstrate that internucleosomal DNA fragmentation occurs during induction of monocytic differentiation, and that both of these events are detectable in G0/G1 cells.
Efficacy of a Pneumococcal Conjugate Vaccine against Acute Otitis Media (2001)

The heptavalent pneumococcal polysaccharide-CRM197 conjugate vaccine is safe and efficacious in the prevention of acute otitis media caused by the serotypes included in the vaccine.
RECTIFICATION AND INDUCTANCE IN THE SQUID GIANT AXON (1941)

Previous measurements have shown that the electrical properties of the squid axon membrane are approximately equivalent to those of a circuit containing a capacity shunted by an inductance and a rectifier in series. Selective ion permeability of a membrane separating two electrolytes may be expected to give rise to the rectification. A quasi-crystalline piezoelectric structure of the membrane is a plausible explanation of the inductance. Some approximate calculations of behavior of an axon with these membrane characteristics have been made. Fair agreement is obtained with the observed constant current subthreshold potential and impedance during the foot of the action potential. In a simple case a formal analogy is found between the calculated membrane potential and the excitability defined by the two factor formulations of excitation. Several excitation phenomena may then be explained semi-quantitatively by further assuming the excitability proportional to the membrane potential. Some previous measurements and subthreshold potential and excitability observations are not consistent with the circuit considered and indicate that this circuit is only approximately equivalent to the membrane.