gebhart/patrepeval huggingface dataset:
Cloning of rabbit LCAT cDNA: increase in LCAT mRNA abundance in the liver of cholesterol-fed rabbits. (1996)

Structure of rabbit lecithin:cholesterol acyltransferase (LCAT) and molecular basis for the effects of cholesterol feeding on LCAT expression were investigated by cloning and sequencing LCAT cDNA from rabbit. The rabbit and human sequences are 91% identical at the nucleotide level and 93% identical at the amino acid level. The interfacial substrate active site, asparagine-linked glycosylation sites, and sites at which rare mutations cause human familial LCAT deficiency are all highly conserved in the rabbit protein. The apparent molecular mass of rabbit LCAT, as determined by immunoblot analysis, was approximately equal to that of human LCAT. Rabbits showed 2.6- and 5.5-fold increases in serum LCAT activity 3 and 6 weeks, respectively, after switching to a cholesterol-enriched diet. Northern blot analysis revealed that the abundance of LCAT mRNA in liver increased 1.6- and 2.8-fold after 3 and 6 weeks, respectively, of cholesterol feeding. The marked temporal relation between the increase in serum LCAT activity and the liver LCAT mRNA abundance suggest that the regulation of LCAT activity in vivo may be primarily determined by changes in the amount of LCAT mRNA.
Optimizing TCP and RLC interaction in the UMTS radio access network (2006)

TCP, the dominant transport protocol for Internet applications, suffers severe performance degradation due to packet losses when a wireless link is present in the end-to-end path. For this reason, the 3G specification entity, 3GPP, has defined a reliable link layer protocol, RLC, to support packet switched services over UMTS. RLC provides error recovery in the radio access network by means of an ARQ algorithm. Early studies supported the benefit of using a reliable link protocol, while more recent studies outline new problems arising from RLC and TCP interaction and how to overcome them. This article describes the most relevant issues concerning TCP-RLC interaction and evaluates the most practical enhancement approaches, based on optimum parameter configuration at the transport and link layers. We devote special attention to RLC, whose specific configuration decisions are left to operators, and provide specific guidelines for setting its parameters. In addition, we propose two operational changes for enhancing the buffer management strategy, one of the main drawbacks of RLC
Entity-based Classification of Twitter Messages (2012)

Twitter is a popular micro-blogging service on theWeb, where people can enter short messages, which then become visible to some other users of the service. While the topics of these messages varies, there are a lot of messages where the users express their opinions about some companies or their products. These messages are a rich source of information for companies for sentiment analysis or opinion mining. There is however a great obstacle for analyzing the messages directly: as the company names are often ambiguous (e.g. apple, the fruit vs. Apple Inc.), one needs first to identify, which messages are related to the company. In this paper we address this question. We present various techniques for classifying tweet messages containing a given keyword, whether they are related to a particular company with that name or not. We first present simple techniques, which make use of company profiles, which we created semi-automatically from external Web sources. Our advanced techniques take ambiguity estimations into account and also automatically extend the company profiles from the twitter stream itself. We demonstrate the effectiveness of our methods through an extensive set of experiments. Moreover, we extensively analyze the sources of errors in the classification. The analysis not only brings further improvement, but also enables to use the human input more efficiently.
Modulation of apelin and APJ receptor in normal and preeclampsia-complicated placentas. (2007)

Apelin is an endogenous ligand of the human orphan receptor APJ. This peptide is produced through processing from the C-terminal portion in the pre-pro-protein consisting of 77 amino acid residues and exists in multiple molecular forms. Although the main physiological functions of apelin have not yet been clarified, it is known that apelin is involved in the regulation of blood pressure, blood flow and central control of body fluid homeostasis in different organs. Since human placenta is a tissue where vasculogenesis, blood pressure and flow are dramatically important to allow a normal embryonic and fetal growth and development, the aim of the present study was to investigate the immunohistochemical distribution of apelin and APJ in normal placentas throughout pregnancy and in preeclampsia-complicated placentas. Specifically, we observed that in normal placentas the expression levels of apelin decreased from the first to the third trimester of gestation in both cytotrophoblast and syncytiotrophoblast cells and in the stroma of placental villi, in contrast with increased expression levels of APJ in the cytoplasm of cytotrophoblast cells and in the cytoplasm of endothelial cells of normal placenta samples. In contrast, in preeclampsia-complicated pregnancies, we observed a very strong increase of expression levels of both apelin and APJ receptor in all the placental compartments, cytotrophoblast, syncytiotrophoblast and stroma with a particular increase in endothelial cells inside preeclamptic placental villi. Our data seem to indicate an important role of apelin and APJ in the regulation of fetal development through a correct regulation of human placenta formation during pregnancy. Moreover, the strong expression levels of apelin and APJ in preeclamptic placentas, suggest their possible involvement in the onset of this pathology.
Computer-assisted interpretation of visual fields in glaucoma. (1992)

Visual field abnormality is an important diagnostic sign in glaucoma. Therefore, the presence or absence of visual field loss most often strongly influences diagnostic and therapeutic decisions in glaucoma management. Interpretation of visual field results is often difficult, however. Physiological variability of perimetric sensitivity values contributes to these difficulties. It has been our aim to develop improved computer-assisted methods for the recognition of early glaucomatous field loss. Our approach has therefore been to design techniques that are highly sensitive to small but significant departures from normality. We have investigated normal physiological variability in perimetric results and combined the obtained knowledge with pathophysiological models which are sensitive to the spatial patterns of field loss commonly seen in glaucoma. Thus, we have devised probability scores in order to take the complex physiological variability into account, and developed a hemifield analysis and an arcuate cluster analysis based on the normal anatomy of the retinal nerve fibre layer. A fundamental approach in the collection of normative data and the selection of glaucoma cases used in this project has been to select subjects using non-perimetric criteria (except for the removal of large field defects). Our objective here was to reduce bias from pre-conceived ideas of visual fields. This approach was used for (1) empirical studies on physiological variability, (2) development of analysis methods, and (3) evaluation of such methods. Glaucoma patients were selected based on evaluations of optic disc appearance. Normal subjects were never eliminated on the basis of perimetric results alone. The new methods developed in these studies have significantly improved discrimination between normal and glaucomatous field results, as compared with previously available techniques. Our results indicated that the usage of probability scores was the main source of this improvement, and that the location of observed field abnormalities and spatial modelling were other important factors. Candidate methods which did not properly combine spatial and normative analyses resulted in false positive defects in the mid-periphery and/or underestimated paracentral glaucomatous field defects. Similar approaches based on classification of visual field results in terms of significances, and on recognition of specific spatial patterns of field loss could be used for other groups of diseases having visual field abnormality as an important diagnostic sign.(ABSTRACT TRUNCATED AT 400 WORDS)
EspP, a Type V-secreted serine protease of enterohaemorrhagic<i>Escherichia coli</i>O157:H7, influences intestinal colonization of calves and adherence to bovine primary intestinal epithelial cells (2007)

Enterohaemorrhagic Escherichia coli (EHEC) comprise a group of zoonotic diarrhoeal pathogens of worldwide importance. Cattle are a key reservoir; however the molecular mechanisms that promote persistent colonization of the bovine intestines by EHEC are ill-defined. The large plasmid of EHEC O157:H7 encodes several putative virulence factors. Here, it is reported that the pO157-encoded Type V-secreted serine protease EspP influences the intestinal colonization of calves. To dissect the basis of attenuation, a bovine primary rectal epithelial cell line was developed. Adherence of E. coli O157:H7 to such cells was significantly impaired by espP mutation but restored upon addition of highly purified exogenous EspP. Data of this study add to the growing body of evidence that cytotoxins facilitate intestinal colonization by EHEC.
First tests of a liquid xenon multiwire drift chamber for PET (2002)

The prototype of a recently proposed liquid xenon drift chamber for PET with simultaneous detection of scintillation and ionization signal has been built. First tests of the chamber under irradiation by 511 keV /spl gamma/-photons are reported.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Identification of Smyd4 as a Potential Tumor Suppressor Gene Involved in Breast Cancer Development (2009)

To identify genes involved in breast tumorigenesis, we applied the retroviral LoxP-Cre system to a nontumorigenic mouse mammary epithelial cell line NOG8 to create random chromosome deletion/translocation. We found that the disruption of one allele of Smyd4 (SET and MYND domain containing 4) gene through chromosome translocation led to tumorigenesis. The expression of Smyd4 was markedly decreased in tumor cells. Re-expression of Smyd4 resulted in growth suppression of tumor cells and inhibition of tumor formation in nude mice. Furthermore, the RNA interference-mediated suppression of Smyd4 expression in human MCF10A mammary epithelial cells caused their growth in soft agar. Microarray studies revealed that platelet-derived growth factor receptor alpha polypeptide (Pdgfr-alpha) was highly expressed in tumor cells compared with NOG8 cells. Re-expression of Smyd4 significantly reduced the expression of Pdgfr-alpha in tumor cells. In human breast cancers, reverse transcription-PCR results revealed that Smyd4 expression was totally silenced in 2 of 10 specimens. These findings indicate that Smyd4, as a potential tumor suppressor, plays a critical role in breast carcinogenesis at least partly through inhibiting the expression of Pdgfr-alpha, and could be a novel target for improving treatment of breast cancer.
A crossed polaroid-pinhole device. (1986)

The study describes the use of a pinhole device in which the light-absorbing area surrounding the holes is varied by polarizing filters. The study demonstrates that a pinhole aperture of 1.6-1.8 mm in diameter with polaroids crossed at 90 degrees will allow a visual acuity equal to or better than 20/40 in the face of refractive errors of 1, 2, and 3 diopters. The study next evaluates the effects of pinholes of different sizes and the polarizing components crossed at angles less than 90 degrees. The study concludes by showing that polaroids crossed at between 75 degrees and 85 degrees allow a greater depth of focus, a larger visual field, and greater illumination than traditional pinhole devices.
STRUCTURE DETERMINATION OF<font>TpRu</font>(<font>PPh</font><sub>3</sub>){κ<sup>2</sup>-N, O-<font>NH</font>=<font>C</font>(<font>Ph</font>)<font>N</font>=<font>C</font>(<font>Ph</font>)<font>O</font>}: A STORY OF HOW COMPUTATIONAL STUDIES CONTRIBUTE TO THE STRUCTURAL CHARACTERIZATION PROCESS (2009)

In this paper, we described the process involved in the structure determination of TpRu ( PPh 3 ){κ 2 -N, O- NH = C ( Ph ) N = C ( Ph ) O } and demonstrated the tremendous help of computational chemistry in the molecular structure elucidation.
Introduction (2006)

Most treatments are not sufficiently effective for you to tell whether or not they work based solely on clinical experience. You need statistical analysis!
Disruption of the Escherichia coli outer membrane permeability barrier by immobilized polymyxin B. (1977)

One of the apparent roles of the outer membrane system in gram-negative bacteria is to function as a selective permeability barrier. A number of antibiotics active against gram-positive bacteria are relatively ineffective against gram-negative bacteria presumably because of the implied barrier function of the outer membrane. This interpretation has been strengthened by studies demonstrating synergism between outer membrane perturbing agents such as EDTA or polymyxin B and specific antibiotics. In the case of polymyxin B, it is not totally clear that synergism with other antimicrobials is due to disruption of the outer membrane permeability barrier or to interactions with the inner membrane. In order to resolve this question, polymyxin B was covalently attached to agarose in order to limit interactions with the outer surface of E. coli. These studies demonstrate that immobilized polymyxin B acts synergistically with bacitracin, rifampicin, or lysozyme. It is proposed that synergistic effects exhibited by polymyxin B are due to its interaction with the outer membrane system.
Low voltage and high speed operating electrostatic wafer chuck using sputtered tantalum oxide membrane (1994)

An insulator figure of merit for an electrostatic wafer holder is introduced. A sputtered Ta2O5 membrane has a maximum figure of merit compared to other candidate dielectric coatings, e.g., Al2O3 and SiO2. The breakdown strength of sputtered Ta2O5 coatings can be optimized by controlling working gas pressure and oxygen concentration: a holding pressure that exceeds 30 gF/cm2 (2942 Pa), when 60 V dc is applied in atmosphere. The pressure is not influenced by the duration of the applied voltage. The residual pressure, after voltage is turned off, decreases to 1/50 of initial pressure within 1 s. The breakdown voltage for 60 cm2 area wafer holder exceeds ±290 V. A sputtered Ta2O5 coating can also be used to smooth relatively rough ceramic substrates. When a polished Al2O3 mixed with ZrO2 ceramic surface is coated with 10 μm thick sputtered Ta2O5 film, good substrate material for an electrostatic chuck is obtained. The sputter rate for the Ta2O5is much larger than that for the Al2O3 or SiO2.
Transfection With a Dominant-Negative Inhibitor of Monocyte Chemoattractant Protein-1 Gene Improves Cardiac Function After 6 Hours of Cold Preservation (2003)

Inhibition of MCP-1 with 7ND gene transfection reduced cytokine activation, attenuated myocardial damage, and improved cardiac function after 6 hours of preservation. These results show that MCP-1 plays an important role in ischemia-reperfusion injury.
A rapid screening procedure to identify mini-Tn10 insertion mutants of<i>Escherichia coli</i>K-12 with altered adhesion properties (1996)

A rapid screening procedure was developed for detection of Escherichia coli mutants with altered adhesion abilities using polystyrene 96-well microtiter plates as attachment surfaces. During this assay, bacterial strains grew and adhered simultaneously, and attached cells were measured after crystal violet staining. Starting with a total of 7000 W3110::Tn10 insertion mutants of E. coli K-12 W3110, 50 adhesion-deficient mutants were isolated which showed less than 40% attachment, and 22 mutants were found with an attachment of 40-75%. Motility assays were performed on these 72 mutants, and 34 displayed altered motility.
Emergency steer & brake assist: a systematic approach for system integration of two complementary driver assistance systems (2011)

Advanced Driver Assistance Systems (ADAS) assist the driver during the driving task to improve the driving comfort and therefore indirectly traffic safety, ACC (Adaptive Cruise Control) is a typical example for a “Comfort ADAS” system. “Safety ADAS” directly target the improvement of safety, such as a forward collision warning or other systems which assist the driver during an emergency situation. A typical application for a “Safety ADAS” is EBA (Emergency Brake Assist), which additionally integrates information of surrounding sensors into the system function. While systems in the longitudinal direction, such as EBA, have achieved a high development status and are already available in the market (e.g. “City Safety” from Volvo), systems in the lateral direction are still in the predevelopment stage. The next logical development step in this case will be the system integration of the Emergency Brake and Steer function. This paper presents an approach to systematically combine longitudinal braking assistance and it’s complementary lateral dynamics into an integral advanced driver assistance system for collision avoidance or mitigation. The system assists the driver during emergency brake and/or steer maneuvers based on driver input, physical aspects and surrounding sensor information. The robust detection of the surrounding and the analysis of the driving situation play a major role regarding the discrimination of a hazard situation from normal driving. The level of assistance is based on the ability and robustness of the sensor to display the picture of the real surrounding and driving situation. The discussed system approach assists by preconditioning the chassis for the oncoming brake and/or evasion maneuver and – in the case of an emergency evasion maneuver initiated by the driver - gives a recommendation utilizing steering torque overlay to help the driver to steer along a calculated optimized trajectory. In this respect and beside all technical and physical aspects, the human factor plays a major role for the development of this integral assistance concept. Basis for the development of this assistance concept were subject driver vehicle tests to study the typical driver behavior in emergency situations. Objective was on the one hand to analyze the relevant parameters influencing the driver decision for brake and/or steer maneuvers. On the other hand the evaluation should result in a proposal for a preferable test setup, which can be used for use case evasion and/or braking tests to clearly evaluate the benefit of the system and the acceptance of normal drivers. Definition of assistance levels, warnings and intervention cascade, based on physical aspects and an analysis of driver behavior using objective and subjective data from vehicle tests with untrained drivers are presented.
Nanoscale investigation of surface potential distribution of Cu2ZnSn(S,Se)4 thin films grown with additional NaF layers (2014)

Abstract CZTS precursors [SLG/Mo (300 nm)/ZnS (460 nm)/SnS (480 nm)/Cu (240 nm)] were deposited by RF/DC sputtering, and then NaF layers (0, 15, and 30 nm) were grown by electron beam evaporation. The precursors were annealed in a furnace with Se metals at 590°C for 20 minutes. The final composition of the CZTSSe thin-films was of Cu/(Zn + Sn) ~ 0.88 and Zn/Sn ~ 1.05, with a metal S/Se ratio estimated at ~0.05. The CZTSSe thin-films have different NaF layer thicknesses in the range from 0 to 30 nm, achieving a ~3% conversion efficiency, and the CZTSSe thin-films contain ~3% of Na. Kelvin probe force microscopy was used to identify the local potential difference that varied according to the thickness of the NaF layer on the CZTSSe thin-films. The potential values at the grain boundaries were observed to increase as the NaF thickness increased. Moreover, the ratio of the positively charged GBs in the CZTSSe thin-films with an NaF layer was higher than that of pure CZTSSe thin-films. A positively charged potential was observed around the grain boundaries of the CZTSSe thin-films, which is a beneficial characteristic that can improve the performance of a device.
Prognostic Factors and Analysis of S100a4 Protein in Resected Pulmonary Metastases from Renal Cell Carcinoma (2009)

Abstract Background This study analyzes our experience with pulmonary resection for metastases from renal cell carcinoma. The goals were to search for factors influencing prognosis and to investigate the presence and the prognostic value of S100A4 protein in lung metastases and corresponding primary renal tumors. Methods Sixty‐five patients underwent surgical resection for renal and pulmonary lesions between 1992 and 2007. S100A4 protein expression was immunohistochemically examined in the peritumoral infiltrate of 64 lesions (32 metastases and the 32 corresponding primary carcinomas). Results Overall 3‐, 5‐, and 10‐year survival rates were 58, 46, and 25%, respectively. Univariate analysis revealed that surgical radicality ( p = 0.0039) and stratification into groups according to the International Registry of Lung Metastases classification ( p = 0.0137) were prognostic factors. Multivariate analysis confirmed that this classification was a significant prognostic factor ( p = 0.01). All metastases and the corresponding primary carcinomas expressed S100A4 protein. Twenty‐one metastases (66%) had weak expression and 11 (34%) had strong expression. Twelve (37.5%) primary lesions had weak expression and 20 (62.5%) had strong expression. The 5‐year survival rate for patients with strong expression in primary carcinoma was 41%, significantly lower than that of patients with weak expression (78%; p = 0.05). Conclusions Pulmonary resection in metastatic renal cell carcinoma results in long‐term survival. Complete resection and stratification into groups according to the International Registry of Lung Metastases classification were prognostic factors. Overexpression of S100A4 protein in primary tumors was correlated with a poor prognosis. If confirmed in larger studies this finding could be used to schedule adjuvant treatments in patients undergoing nephrectomy for renal cell carcinoma.