gebhart/patrepeval huggingface dataset:
Nanopore Detection of Single Molecule RNAP–DNA Transcription Complex (2012)

In the past decade, a number of single-molecule methods have been developed with the aim of investigating single protein and nucleic acid interactions. For the first time we use solid-state nanopore sensing to detect a single E. coli RNAP-DNA transcription complex and single E. coli RNAP enzyme. On the basis of their specific conductance translocation signature, we can discriminate and identify between those two types of molecular translocations and translocations of bare DNA. This opens up a new perspectives for investigating transcription processes at the single-molecule level.
Skeletal effects of selective oestrogen receptor modulators (SERMs) (2000)

Women suffer a higher incidence of osteoporosis than men, in part due to oestrogen deficiency after menopause. In fact, the administration of oestrogen to post-menopausal women is associated with a decrease of bone resorption. Tamoxifen is a widely used selective oestrogen receptor modulator in women with breast cancer, which has been shown an agonistic profile in bone. However, tamoxifen seems less effective than oestradiol as an anti-resorptive agent and has no effect when the endogenous production of oestrogen is normal. Additionally, tamoxifen exhibits agonistic activity on the endometrium and has been suggested an oncogenic potential on that tissue. Raloxifene, a selective oestrogen receptor modulator from the benzothiophene family, behaves also as an agonist on the bone in both laboratory and clinical studies. Ongoing clinical trials confirm a protective effect of raloxifene similar to oestrogens. The Multiple Outcome of Raloxifene Evaluation (MORE) study is a prospective, randomized trial which, in a recent 2 year interim analysis, has shown that women suffering from osteoporosis receiving raloxifene had 42% fewer vertebral fractures than women receiving a placebo.
PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome (2006)

PrimerStation (http://ps.cb.k.u-tokyo.ac.jp) is a web service that calculates primer sets guaranteeing high specificity against the entire human genome. To achieve high accuracy, we used the hybridization ratio of primers in liquid solution. Calculating the status of sequence hybridization in terms of the stringent hybridization ratio is computationally costly, and no web service checks the entire human genome and returns a highly specific primer set calculated using a precise physicochemical model. To shorten the response time, we precomputed candidates for specific primers using a massively parallel computer with 100 CPUs (SunFire 15 K) about 3 months in advance. This enables PrimerStation to search and output qualified primers interactively. PrimerStation can select highly specific primers suitable for multiplex PCR by seeking a wider temperature range that minimizes the possibility of cross-reaction. It also allows users to add heuristic rules to the primer design, e.g. the exclusion of single nucleotide polymorphisms (SNPs) in primers, the avoidance of poly(A) and CA-repeats in the PCR products, and the elimination of defective primers using the secondary structure prediction. We performed several tests to verify the PCR amplification of randomly selected primers for ChrX, and we confirmed that the primers amplify specific PCR products perfectly.
An Equilibrium Queuing Model of Bribery (1985)

It is sometimes argued that bribery is inefficient because bureaucrats may cause delays for attracting more bribes. This hypothesis is examined in the context of a queue where customers having different values of time are ranked by their bribe payments to the queue's server. The Nash equilibrium strategies of the customers are de- rived. It is shown that the server is unlikely to slow down the allocation process when bribery is allowed. The model does not have strin- gent informational requirements, and the equilibrium outcome minimizes the average value of time costs of the queue. It also suggests a useful auctioning procedure.
Topoisomerase IIα gene (TOP2A) amplification and deletion in cancer – more common than anticipated (2003)

In solid tumours the predominant genetic mechanism for oncogene activation is through amplification of genes. The HER-2 (also known as ErbB2/c-erbB2/HER-2/neu) oncogene is the most frequently amplified oncogene in breast cancer and is also commonly amplified in other forms of cancer. The HER-2 amplicon also contains other biologically relevant genes with altered copy numbers, among these genes is the topoisomerase IIalpha (TOP2A). TOP2A gene is located adjacent to the HER-2 oncogene at the chromosome location 17q12-q21 and is either amplified or deleted, with equal frequency, in almost 90% of HER-2 amplified primary breast tumours. Recent data suggest that amplification and deletion of TOP2A may account for both sensitivity and resistance to topoII-inhibitor-chemotherapy, depending on the specific genetic defect at the TOP2A locus. In this issue of the Cytopathology, Bofin et al. present preliminary evidence for high prevalance of TOP2A amplification and deletion not only in the HER-2 amplified breast tumours, but also in the primary breast tumours without the HER-2 amplification. This finding together with the concept that TOP2A gene amplification and deletion seem to account for both relative chemosensitivity and resistance to topoII-inhibitor therapy further highlights the importance of screening for TOP2A gene copy number aberrations when topoII-inhibitors are considered either alone or in combination of other chemotherapeutic drugs for the treatment of cancer patients.
The metabolism of L‐3–0‐methyldopa, aprecursor of dopa in man (1971)

L‐2‐ 14 C‐3‐methoxy, 4‐hydroxyphenylalanine (L‐ 14 C‐O‐methyldopa) has a biological half‐life of approximately 15 hours in human blood. 3‐Methoxy, 4‐hydroxyphenyllactic acid, homovanillic acid, and 3,4‐dihydroxyphenylacetic acid are metabolites found in the blood. The urinary excretion of radioactivity is slow and only a small proportion of excreted radioactivity represents unchanged O‐methyldopa. The same metabolites are found as in the blood as weU as small amounts of dopa, dopamine, and 3‐methoxytyramine. It is concluded that in man part of the L‐O‐methyldopa undergoes demethylation to dopa, which is further metabolized to dopamine and phenolcarboxylic acids.
Studies on the transferring gene to tobacoo by the low energy ion beam (2000)

The etching function of ion beam on the tobacoo seeds(NC-89) was investigated by means scanning electron microscope(SEM) and elecron spin resonance(SER), which provides the morphological structure basis of using ion beam in transgenic technique. The seeds of tobacoo were treated by 20Kev N + ion beam, then immediately immerged in SSC solution by containing PB II21 DNA (50mg/ml) which encodes NPT II R and GUS gene. Three NPT II R plants were obtained by selecting in two months tissue culture on MS media supplemented with 100mg/L kanamycin. Leaves from NPT II R plants were differentiated and regenerated into NPT II R plants. PCR and Southern blot results showed that the NPT II R and GUS gene on the plasmid PB II21 had been integrated into the genome of the tobacco.
Fluorescence-activated cell analysis and sorting of viable mammalian cells based on beta-D-galactosidase activity after transduction of Escherichia coli lacZ. (1988)

We demonstrate that individual cells infected with and expressing a recombinant retrovirus carrying the Escherichia coli beta-galactosidase gene (lacZ) can be viably stained, analyzed, sorted, and cloned by fluorescence-activated cell sorting based on the levels of lacZ expressed. To accomplish this we have devised a method to enzymatically generate and maintain fluorescence in live mammalian cells. Accumulation of fluorescent products in cells is linear with time, with a direct correlation of fluorescence to enzymatic activity. This technology for beta-galactosidase detection is more sensitive than other available cytochemical or biochemical methods. We have used this procedure to show that the expression of psi-2-MMuLVSVnlsLacZ in the T-cell lymphoma BW5147 and the B-cell hybridoma SP2/0 is not completely stable and that subclones selected by the fluorescence-activated cell sorter for low lacZ activity demonstrate distinctly lower average expression of LacZ. These findings indicate the utility of beta-galactosidase as a reporter molecule at the single-cell level for studies of gene regulation, including studies of promoter efficacy, enhancer activity, trans-acting factors, and other regulatory elements.
High Al-Content Visible (AlGa)As Multiple Quantum Well Heterostructure Lasers Grown by Metalorganic Chemical Vapor Deposition (1983)

High Al-content multiple quantum well heterostructure lasers, consisting of five (Al 0.14 Ga 0.86 )As wells 150 Å thick separated by four (Al 0.35 Ga 0.65 )As barriers 40 Å thick have been grown by metalorganic chemical vapor deposition (MOCVD) in an atmospheric pressure. The laser with a self aligned narrow stripe geometry is formed by the two step epitaxial technique. The room temperature CW threshold current for a device 250 µm long is typically 50 mA, which is 30% less than that of a conventional DH laser of the same geometry. Emission wavelength is 782 nm and the characteristic temperature T 0 is 232 K.
Rivera Ocean Seismic Experiment (ROSE) overview (1982)

The Rivera Ocean Seismic Experiment (ROSE) was designed as a combined sea and land seismic program to utilize both explosive sources and earthquakes to study a number of features of the structure and evolution of a mid‐ocean ridge, a major oceanic fracture zone, and the transition region between ocean and continent. The primary region selected for the experiment included the Rivera Fracture Zone, the crest and eastern flank of the East Pacific Rise north of the Rivera, and adjacent areas of Baja California and mainland Mexico. These areas were to be instrumented with land and ocean bottom seismographs in order to determine good source parameter and location data for natural events and to record these events along a large number of paths crossing various parts of the region. Explosive charges were to be detonated at sea to supplement the natural events. However, the necessary permission to conduct the experiment was not received from Mexican authorities; therefore an alternate plan was implemented whereby the marine program had to be moved southward outside of territorial waters. This had the effect of transforming this experiment into three, almost independent components: (1) an experiment to study the East Pacific Rise south of the Orozco Fracture Zone primarily using ocean bottom recording and explosive sources, (2) a seismicity program at the Orozco, and (3) a land‐based program of recording natural events along the coastal region of Mexico. A considerable amount of useful data was obtained in each of the three subprograms. In the marine parts of the experiment we were able to address a variety of problems including structure and evolution of young oceanic crust and mantle, structure and dynamics of the East Pacific Rise, seismicity of the Orozco Fracture Zone, and partitioning of energy transmission between the ocean volume and the crust/lithosphere. On land, the fortuitous occurrence of the Petatlan M 7.6 earthquake of March 14, 1979, permitted the acquisition of an excellent data set of foreshocks and aftershocks of this large event, which provide new insight into the filling of a major seismic gap in the region. This overview describes the scientific rationale and the design of the experiments, along with some general results. Other articles in this volume give preliminary scientific results from certain components of the overall experiment or, in some cases, report on other data pertinent to the scientific goals of ROSE.
Photoreactivity of 1-Pyrenylmethyl Esters. Dependence on the Structure of the Carboxylic Acid Moieties and the Nature of the Excited States (1987)

Abstract While the photolysis of 1-pyrenylmethyl phenylacetates in methanol gave the original phenylacetic acids, irradiation of the 1-naphthoate and 9-anthracenecarboxylate leads to the formation of the intramolecular exciplexes that are inert to the photolysis. The Φf and τf values of these esters have been determined.
Mechanical Tissue Resuscitation Protects Against Myocardial Ischemia-Reperfusion Injury (2013)

Treatment with mechanical tissue resuscitation during reperfusion reduces both early cell death and the delayed, programmed cell death after ischemia-reperfusion. This cardioprotection is also associated with a significant reduction in interstitial water. Additional cardioprotection may be derived from mechanical tissue resuscitation-induced increased blood flow. Mechanical tissue resuscitation, particularly with a resorbable device, is a straightforward and efficacious mechanical strategy for decreasing cardiomyocyte death following myocardial infarction as an adjunctive therapy to surgical revascularization.
Opposing Effects of Sirtuins on Neuronal Survival: SIRT1-Mediated Neuroprotection Is Independent of Its Deacetylase Activity (2008)

Overall, our study makes three contributions - (a) it represents the first analysis of SIRT3-7 in the regulation of neuronal survival, (b) it shows that neuroprotection by SIRT1 can be mediated by a novel, non-catalytic mechanism, and (c) that subcellular localization may be an important determinant in the effect of SIRT5 on neuronal viability.
Neuronal Ca2+/Calmodulin-Dependent Protein Kinases (1992)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
An error control scheme for large-scale multicast applications (2002)

Retransmission based error control for large scale multicast applications is difficult because of implosion and exposure. Existing schemes (SRM, RMTP, TMTP LBRRM) have good solutions to implosion, but only approximate solutions to exposure. We present a scheme that achieves finer grain fault recovery by exploiting new forwarding services that allow us to create a dynamic hierarchy of receivers. We extend the IP multicast service model so that routers provide a more refined form of multicasting (which may be useful to other applications), that enables local recovery. The new services are simple to implement and do not require routers to examine or store application packets; hence, they do not violate layering. Besides providing better implosion control and less exposure than other schemes, our scheme integrates well with the current IP model, has small recovery latencies (it requires no back-off delays), and completely isolates group members from topology. Our scheme can be used with a variety of multicast routing protocols, including DVMRP and PIM. We have implemented our scheme in NetBSD Unix, using about 250 lines of new C-code. The implementation requires two new IP options, 4 additional bytes in each routing entry and a slight modification to IGMP reports. The forwarding overhead incurred by the new services is actually lower than forwarding normal multicast traffic.
Determination of Optimal Sample Size for Quantification of β-Cell Area, Amyloid Area and β-Cell Apoptosis in Isolated Islets (2015)

Culture of isolated rodent islets is widely used in diabetes research to assess different endpoints, including outcomes requiring histochemical staining. As islet yields during isolation are limited, we determined the number of islets required to obtain reliable data by histology. We found that mean values for insulin-positive β-cell area/islet area, thioflavin S-positive amyloid area/islet area and β-cell apoptosis do not vary markedly when more than 30 islets are examined. Measurement variability declines as more islets are quantified, so that the variability of the coefficient of variation (CV) in human islet amyloid polypeptide (hIAPP) transgenic islets for β-cell area/islet area, amyloid area/islet area and β-cell apoptosis are 13.20% ± 1.52%, 10.03% ± 1.76% and 6.78% ± 1.53%, respectively (non-transgenic: 7.65% ± 1.17% β-cell area/islet area and 8.93% ± 1.56% β-cell apoptosis). Increasing the number of islets beyond 30 had marginal effects on the CV. Using 30 islets, 6 hIAPP-transgenic preparations are required to detect treatment effects of 14% for β-cell area/islet area, 30% for amyloid area/islet area and 23% for β-cell apoptosis (non-transgenic: 9% for β-cell area/islet area and 45% for β-cell apoptosis). This information will be of value in the design of studies using isolated islets to examine β cells and islet amyloid.
IFN-α and CD46 stimulation are associated with active lupus and skew natural T regulatory cell differentiation to type 1 regulatory T (Tr1) cells (2011)

Immune suppressive activities exerted by regulatory T-cell subsets have several specific functions, including self-tolerance and regulation of adaptive immune reactions, and their dysfunction can lead to autoimmune diseases and contribute to AIDS and cancer. Two functionally distinct regulatory T-cell subsets are currently identified in peripheral tissues: thymus-developed natural T regulatory cells (nTregs) controlling self-tolerance and antiinflammatory IL-10-secreting type 1 regulatory T cells (Tr1) derived from Ag-stimulated T cells, which regulate inflammation-dependent adaptive immunity and minimize immunopathology. We establish herein that cell contact-mediated nTreg regulatory function is inhibited by inflammation, especially in the presence of the complement C3b receptor (CD46). Instead, as with other T-cell subsets, the latter inflammatory conditions of stimulation skew nTreg differentiation to Tr1 cells secreting IL-10, an effect potentiated by IFN-α. The clinical relevance of these findings was verified in a study of 152 lupus patients, in which we showed that lupus nTreg dysfunction is not due to intrinsic defects but is rather induced by C3b stimulation of CD46 and IFN-α and that these immune components of inflammation are directly associated with active lupus. These results provide a rationale for using anti-IFN-α Ab immunotherapy in lupus patients.
A luminescence probe for metallothionein in liver tissue: emission intensity measured directly from copper metallothionein induced in rat liver (1989)

We report the first use of an emission probe based on the Cu(I)-thiolate chromophore, for the direct observation of copper metallothionein located in samples of rat liver. Elevated synthesis of Cu-MT in the rat liver was induced by subcutaneous injections of a series of aqueous CuCl2 solutions containing increasing amounts of Cu(II). Luminescence intensity in the 600 nm region, detected from frozen solutions of Cu-MT and from slices of the liver frozen at 77 K, following excitation in the 300 nm region, was dependent on the concentration of the Cu(II) used in the inducing solution. No such luminescence intensity was found for control samples obtained from the livers of rats not exposed to copper salts. It is suggested that this new method will allow direct visualization of Cu-MT in tissue where genetic disorders impare copper metabolism.
Differential localization within human kidney of five membrane proteins expressed on acute lymphoblastic leukemia cells. (1986)

The reactivity of a panel of monoclonal antibodies (MAb) produced against non-T, non-B acute lymphoblastic leukemia cells was investigated by immunoperoxidase staining of sections of normal human kidney. The antigens of kidney reactive with the MAb were isolated by immunoaffinity chromatography and were purified further by immunoprecipitation. Two MAb, 44D7 and 44H9, reacted with determinants found exclusively on the basolateral membranes of proximal convoluted tubules. The 44D7 antigen isolated from kidney was biochemically similar to that isolated from leukemic cells. It was resolved as a multimeric complex with an apparent m.w. of 120,000 when analyzed by SDS-PAGE under nonreducing conditions. The 44H9 antigen has not yet been purified from kidney. MAb 50B4 reacted with components of the interstitium and with the mesangium of glomeruli. It immunoprecipitated a polypeptide chain of apparent m.w. 85,000, similar to that of the 50B4 antigen isolated from leukemic cells. MAb 44G4 also reacted with the mesangium of glomeruli and with the interstitium of the kidney. However, the endothelium of glomerular capillaries and of interstitial blood vessels has also reacted with MAb 44G4. The kidney antigen recognized by MAb 44G4 was characterized as a major polypeptide band, 95,000 m.w. (reduced) and 125,000 m.w. (nonreduced), a subunit structure analogous to the 44G4 antigen isolated from leukemic cells. MAb 44E3 reacted with all cellular elements of glomeruli, tubules, blood vessels, and interstitium. Two polypeptide chains of apparent m.w. 94,000 and 90,000 were immunoprecipitated from kidney by MAb 44E3, while a single polypeptide chain of 94,000 m.w. was precipitated from leukemic cells. Our results describe five new antigens with distinctive cellular distributions within kidney.
Study of ADI (After Develop Inspection) using electron beam (2006)

In this paper, we established a method to detect defects with a size of 40nm, which is required in the machine to inspect defects on the photo resist of hp65nm generation. First of all, we clarified the mechanism of nuisance generation by electron beam and established a method to control nuisances. Next, we examined the inspection conditions required for detection of minute defects. As a result, the relation between the landing energy, brightness, or contrast and the defect detection ratio were clarified. We successfully detected minute defects of 40nm in the inspection based on a strategies obtained from these examination results to confirm that we established a method to detect minute defects. In addition, we compared defects on photo resist in electron beam inspection and electric defects in the wiring resistance measurement. As a result, the defect distribution on photo resist was found identical to the electric defect distribution. Thus, we proved that the defect inspection on photo resist using electron beam was detecting the killer defects. Therefore, we showed that the resist defect inspection using electron beam is effective for the 65nm generation.