gebhart/patrepeval huggingface dataset:
High-throughput detection and multiplex identification of cell contaminations (2009)

Unnoticed cell culture contamination by viruses, Mycoplasma, or other cell lines is not uncommon and a threat to laboratory safety and the quality of scientific results. We developed and validated a novel high-throughput Multiplex cell Contamination Test (McCT), which is currently able to detect 37 contamination markers in a single reaction. The assay is based on multiplex PCR with target-specific primers and subsequent hybridization of amplimers to specific oligonucleotide probes. McCT proved to be highly specific, sensitive and robust, and allows to analyze more than 1000 cell lysates per week. In conclusion, the novel McCT assay is a powerful high-throughput tool in assessing cell line purity.
Performance improvement obtained for thin-film transistors fabricated in prepatterned laser-recrystallized polysilicon (1997)

Thin-film transistors (TFT's) are fabricated in polysilicon films that are laser recrystallized either before or after active-area definition. We find the the performance of TPT's fabricated in active areas that are prepatterned before laser recrystallization is dramatically improved. For example, the field-effect mobility is increased by a factor of three, the threshold voltage is reduced from 5.32 V to 0.07 V, and the subthreshold slope is cut in half for W/L = 10 μm/10 μm TFT's. All TFT's discussed utilize gas-immersion laser-doped source and drain junctions and are unhydrogenated.
Study on dissolution behavior of polymer-bound and polymer-blended photo-acid generator (PAG) resists (2013)

The requirements for the next generation resist materials are so challenging that it is indispensable for feasibility of EUV lithography to grasp basic chemistry of resist matrices in all stage of resist processes. Under such circumstances, it is very important to know dissolution characteristics of the resist film into alkaline developer though the dissolution of exposed area of resist films in alkaline developer to form a pattern is a complex reactive process. In this study, the influence of EUV and KrF exposure on the dissolution behavior of polymer bound PAG and polymer blended PAG was studied in detail using quartz crystal microbalance (QCM) methods. The difference in swelling formation between KrF and EUV exposure was observed. It is likely that difference of reaction mechanism induces the difference of these swelling. Also, it is observed that the swelling of polymer-bound PAG is less than that of polymer blended PAG in both KrF and EUV exposure. This result indicates that polymer-bound PAG suppresses swelling very well and showed an excellent performance. Actually, the developed polymer bound-PAG resist showed an excellent performance (half pitch 50 nm line and space pattern). Thus, polymer bound PAG is one of the promising candidate for 16 nm EUV resist.
TRIFLE DIFFERENCE APPROACH TO LOW EARTH ORBITER PRECISION ORBIT DETERMINATION (2003)

A precise kinematic orbit determination (P-KOD) procedure for Low Earth Orbiter(LEO) using the GPS ion-free triple differenced carrier phases is presented. Because the triple differenced observables provide only relative information, the first epoch's positions of the orbit should be held fixed. Then, both forward and backward filtering was executed to mitigate the effect of biases of the first epoch's position. p-KOD utilizes the precise GPS orbits and ground stations data from International GPS Service (IGS) so that the only unknown parameters to be solved are positions of the satellite at each epoch. Currently, the 3-D accuracy off-KOD applied to CHAMP (CHAllenging Min-isatellite Payload) shows better than 35 cm compared to the published rapid scientific orbit (RSO) solution from GFZ (GeoForschungsZentrum Potsdam). The data screening for cycle slips is a particularly challenging procedure for LEO, which moves very fast in the middle of the ionospheric layer. It was found that data screening using SNR (signal to noise ratio) generates best results based on the residual analysis using RSO. It is expected that much better accuracy are achievable with refined prescreening procedure and optimized geometry of the satellites and ground stations.
A comparison of high-power DC-DC soft-switched converter topologies (1996)

The purpose of this paper is to compare the properties of several soft-switching converter topologies when used to achieve DC-DC conversion at high-power and high-voltage levels. As an example, a 100 kW transformer isolated converter with 700-1400 Vdc input is designed with an estimated mass in the 90-kg range and an energy efficiency of 95%.
Fully digital feedforward delta-sigma modulator (2005)

A delta-sigma modulator using a fully digital feedforward path is proposed. The new modulator retains the conventional input feedforward structure advantages and adds to them the elimination of the analog adder at the quantizer input and improved signal-to-noise ratio. The new modulator requires an extra quantizer and digital adders.
Field-effect transistor made of individual V2O5 nanofibers (2000)

A field-effect transistor (FET) with a channel length of ∼100 nm was constructed from a small number of individual V2O5 fibers of the cross section 1.5 nm×10 nm. At low temperature, the conductance increases as the gate voltage is changed from negative to positive values, characteristic of a FET with n-type enhancement mode. The carrier mobility, estimated from the low-field regime, is found to increase from 7.7×10−5 cm2/V s at T=131 K to 9.6×10−3 cm2/V s at T=192 K with an activation energy of Ea=0.18 eV. The nonohmic current/voltage dependence at high electric fields was analyzed in the frame of small polaron hopping conduction, yielding a nearest-neighbor hopping distance of ∼4 nm.
The cloning and expression of Abl protein tyrosine kinase gene (2002)

Objective To obtain the recombinant protein tyrosine kinase (PTK) in order to identify the activity of PTK and screen the inhibitors of PTK.Methods To digest the target gene PTK from cloning plasmid containing PTK and clone into expression vector pGEX4T 2.The recombinant plasmid pGEX4T 2 PTK was identified with restriction analysis to choose the right recombinant transformant E.coli DH5a containing pGEX4T 2 PTK.The engineering E.coli pGEX4T 2 PTK/DH5a were induced to express by IPTG and the expressed products were analysed with SDS PAGE. Results Restriction analysis showed that the plasmid pGEX4T 2 PTK was constructed successfully. SDS PAGE analysis result showed that special band of the induced product was observed at the position of 58KD.Conclusion The fusion protein GST PTK is successfully expressed in E.coli . This study establishes a good foundation for the purification of PTK and identification of PTK inhibitors.
Different Circuits for ON and OFF Retinal Ganglion Cells Cause Different Contrast Sensitivities (2003)

The theory of "parallel pathways" predicts that, except for a sign reversal, ON and OFF ganglion cells are driven by a similar presynaptic circuit. To test this hypothesis, we measured synaptic inputs to ON and OFF cells as reflected in the subthreshold membrane potential. We made intracellular recordings from brisk-transient (Y) cells in the in vitro guinea pig retina and show that ON and OFF cells in fact express significant asymmetries in their synaptic inputs. An ON cell receives relatively linear input that modulates a single excitatory conductance; whereas an OFF cell receives rectified input that modulates both inhibitory and excitatory conductances. The ON pathway, blocked by L-AP-4, tonically inhibits an OFF cell at mean luminance and phasically inhibits an OFF cell during a light increment. Our results suggest that basal glutamate release is high at ON but not OFF bipolar terminals, and inhibition between pathways is unidirectional: ON --> OFF. These circuit asymmetries explain asymmetric contrast sensitivity observed in spiking behavior.
Lipid-Containing Eye Drops: A Step Closer to Natural Tears (1990)

Disturbances of the lipid composition can, like mucin or fluid deficiency, cause 'dry eye'. The substitution of the lipids of the tear fluid has previously been unsatisfactory since eye ointments containing fats can lead to a considerable deterioration of the visual acuity due to the film of ointment resulting from an irregular spreading behavior. We proposed the introduction of physiological lipids that are normally present in tear fluid, such as phospholipids, saturated and unsaturated fatty acids and triglycerides, to provide lipid-containing eye drops. These best correspond to 'natural tears' and, due to the small size of the lipid particles, avoid a disturbance of the spreading behavior of the lipid layer. With lipid-containing eye drops of this kind, we carried out the following examinations: inquiry of patients' symptoms based on a standardized interview; Schirmer test under local anesthesia; break-up time (BUT); biomicroscopic evaluation of the lipid film, and stability tests as pH, gas chromatographic analysis of the fatty acid pattern and thin-layer chromatographic analysis of the lipid pattern. Schirmer test, BUT measurement and questioning about symptoms were undertaken after 1 week and then again after 3 weeks of treatment. All three parameters finally showed an improvement with a high statistical significance (p less than 0.001). The stability tests have shown that pH, lipid particle size, fatty acid and lipid composition of the examined lipid-containing eye drops were nearly unchanged till 4 months after preparation.
Morphology, yield and functional integrity of islet-like cell clusters in tissue culture of human fetal pancreata obtained after different means of abortion (1988)

Morphology, yield and function were studied in cultured islet-like cell clusters (ICC) from 140 human fetal pancreata obtained after abortions of different types performed at 11-23 weeks of gestation (12 by hysterotomy, 75 by mechanical dilation and extraction, and 53 induced with prostaglandin). After collagenase digestion and culture in medium supplemented with 10% human serum, up to 2000 free-floating ICC were formed from a single pancreas. Randomly scattered insulin- and glucagon-immunoreactive cells were found in the medullary part of the ICC. More than 100 ICC developed in 100% of the hysterotomies and 87% of the mechanical abortions, but in only 53% of the prostaglandin-induced abortions. Insulin and glucagon levels in the culture medium decreased rapidly during the first 7 days of culture, but then remained stable for at least 31 days. The hysterotomy-derived ICC responded to 10 mmol/l theophylline plus 20 mmol/l glucose by a 12.2 +/- 3.1 (SEM, N = 7) fold increase in insulin release, as compared with a 5.4 +/- 0.9 fold response of the prostaglandin ICC (N = 16; P less than 0.02). Despite the low proportion of B-cells, (pro)insulin biosynthesis accounted for 10% of the total protein biosynthesis in low (2 mmol/l) glucose. In conclusion, the yield and viability of the ICC were clearly better, if prostaglandin had not been used for the induction of the abortion.
A juxtamembrane autophosphorylation site in the Eph family receptor tyrosine kinase, Sek, mediates high affinity interaction with p59fyn. (1996)

The large subfamily of receptor tyrosine kinases (RTKs) for which EPH is the prototype have likely roles in intercellular communication during normal mammalian development, but the biochemical signalling pathways utilised by this family are poorly characterised. We have now identified two in vitro autophosphorylation sites within the juxtamembrane domain of the Eph family member Sek, and a candidate binding protein for the activated Sek kinase. Specific antibodies defined Sek as a 130 kDa glycoprotein with protein kinase activity expressed in keratinocytes, whilst a bacterially expressed gst-Sek kinase domain fusion protein autophosphorylated exclusively on tyrosine residues, confirming that Sek encodes an authentic protein tyrosine kinase. Two dimensional phosphopeptide mapping and site-directed mutagenesis defined juxtamembrane residue Y602 as a major site of in vitro autophosphorylation in Sek, whilst Y596 was phosphorylated to a lower stoichiometry. Complimentary approaches of in vitro binding assays and BIAcore analysis revealed a high affinity association between the Y602 Sek autophosphorylation site and the cytoplasmic tyrosine kinase p59fyn, an interaction mediated through the SH2 domain of this intracellular signalling molecule. Moreover, these data identify the novel phosphotyrosyl motif pYEDP as mediating high affinity association with fyn-SH2, extending the previously defined consensus motif for this interaction. The extensive conservation of this fyn-binding motif within the juxtamembrane domain of Eph family RTKs suggests that signalling through fyn, or fyn-related, tyrosine kinases may be utilised by many members of this large subclass of transmembrane receptors.
A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family (2009)

Conformational ensembles are increasingly recognized as a useful representation to describe fundamental relationships between protein structure, dynamics and function. Here we present an ensemble of ubiquitin in solution that is created by sampling conformational space without experimental information using "Backrub" motions inspired by alternative conformations observed in sub-Angstrom resolution crystal structures. Backrub-generated structures are then selected to produce an ensemble that optimizes agreement with nuclear magnetic resonance (NMR) Residual Dipolar Couplings (RDCs). Using this ensemble, we probe two proposed relationships between properties of protein ensembles: (i) a link between native-state dynamics and the conformational heterogeneity observed in crystal structures, and (ii) a relation between dynamics of an individual protein and the conformational variability explored by its natural family. We show that the Backrub motional mechanism can simultaneously explore protein native-state dynamics measured by RDCs, encompass the conformational variability present in ubiquitin complex structures and facilitate sampling of conformational and sequence variability matching those occurring in the ubiquitin protein family. Our results thus support an overall relation between protein dynamics and conformational changes enabling sequence changes in evolution. More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics.
Hsa-miR-520d induces hepatoma cells to form normal liver tissues via a stemness-mediated process (2014)

The human ncRNA gene RGM249 regulates the extent of differentiation of cancer cells and the conversion of 293FT cells to hiPSCs. To identify the factors underlying this process, we investigated the effects of lentivirally inducing miR-520d expression in 293FT and HLF cells in vitro. Subsequently, we evaluated tumor formation in a xenograft model. Transformed HLF cells were Oct4 and Nanog positive within 24 h, showed p53 upregulation and hTERT downregulation, and mostly lost their migration abilities. After lentiviral infection, the cells were intraperitoneally injected into mice, resulting in benign teratomas (6%), the absence of tumors (87%) or differentiation into benign liver tissues (7%) at the injection site after 1 month. We are the first to demonstrate the loss of malignant properties in cancer cells in vivo through the expression of a single microRNA (miRNA). This miRNA successfully converted 293FT and hepatoma cells to hiPSC-like cells. The regulation of malignancy by miR-520d appears to be through the conversion of cancer cells to normal stem cells, maintaining p53 upregulation.
Brusella epididimo-orşitleri Ağrı Bölgesinde saptanan 4 olgunun sunumu (2006)

Introduction: Brucellosis is transmitted to humans from infected animals or their products mainly through gastrointestinal tract. Epididymo-orchitis is described in 2-20% of patients with brucellosis
Epigenetic Regulation of Cancer-Associated Genes in Ovarian Cancer (2011)

The involvement of epigenetic aberrations in the development and progression of tumors is now well established. However, most studies have focused on the epigenetic inactivation of tumor suppressor genes during tumorigenesis and little is known about the epigenetic activation of cancer-associated genes, except for the DNA hypomethylation of some genes. Recently, we reported that the overexpression of cancer-promoting genes in ovarian cancer is associated with the loss of repressive histone modifications. This discovery suggested that epigenetic derepression may contribute to ovarian tumorigenesis by constituting a possible mechanism for the overexpression of oncogenes or cancer-promoting genes in tumors. The emerging importance of epigenetic aberrations in tumor initiation and in the regulation of cancer-initiating cells, suggests that epigenetically regulated genes may be promising therapeutic targets and biomarkers. Given that the current challenges in ovarian cancer include the identification of biomarkers for early cancer detection and the discovery of novel therapeutic targets for patients with recurrent malignancies undergoing chemotherapy, understanding the epigenetic changes that occur in ovarian cancer is crucial. This review looks at epigenetic mechanisms involved in the regulation of cancer-associated genes, including the contribution of epigenetic derepression to the activation of cancer-associated genes in ovarian cancer. In addition, possible epigenetic therapies targeting epigenetically dysregulated genes are discussed. A better understanding of the epigenetic changes in ovarian cancer will contribute to the improvement of patient outcomes.
Using Permanent and Temporary Polyimide Adhesives in 3D-TSV Processing to Avoid Thin Wafer Handling (2010)

3D chip integration processes use thinned silicon wafers in conjunction with through silicon vias. Polyimide adhesives are evaluated for use as temporary and permanent adhesives to enable handling of thinned wafers and subsequent bonding into 3D stacks. These adhesives are found to have a combination of thermal and mechanical properties and processing capabilities required for 3D chip integration applications.
Smarter clustering methods for SNP genotype calling (2008)

The R code for the family-based genotype calling methods (SNPCaller) is available to be downloaded from the following website: http://watson.hgen.pitt.edu/register.
Education of adult patients at an "asthma school": effects on quality of life, knowledge and need for nursing (1990)

The effect of education of adult asthma patients at a special "asthma school" was studied with regard to knowledge of the disease and its treatment and quality of life measured by leisure activities, social interaction and psychological well being. We also studied if there were any differences in number of days in hospital and emergency visits before and one year after the asthma-school. Patients were randomised to an intervention group (7 men and 13 women) and a control group (7 men and 11 women). The age-range was 22-66 yrs. Both groups answered the same standardized and quantified questionnaires on three occasions, before the start of the asthma school, after five months and after twelve months. Both groups increased their knowledge of the disease and how to treat it, with slightly better results in the intervention group. The self-assessments all showed that patients in the intervention group felt better than those in the control group. The number of days in hospital as well as acute visits to out patients clinics were reduced significantly after the asthma school. The intervention did not influence spirometric variables.
Analysis and design of digital transmission systems (1979)

The analysis of baseband digital transmission systems is reviewed. Modifications to the standard methods are proposed, which lead to fairly simple algebraic expressions for system performance in a number of important cases. These results are used to investigate the relations between system performance and design parameters, and the conditions under which optimum performance may be obtained are investigated.
Comportamiento de derivados de isoxazol frente a hidruros metalicos complejos y compuestos organoaluminicos (1984)

Las reacciones de sales de isoxazolio 3 5-disustituidas con borohidruro sodico e hidruro de aluminio y litio proporcionan 4-isoxazolinas. Por otra parte los 3 5-dimetilisoxazoles 4-funcionalizados con grupos electroaceptores originan frente a los mismos hidruros las correspondientes 2-isoxazolinas. Por ultimo las sales de 3 5-dimetilisoxazolio 4-funcionalizadas reaccionan con hidruros metalicos complejos y conducen a mezclas facilmente separables de 3- y 4-isoxazolinas. Ademas las sales de isoxazolio 3 5-disustituidas frente al hidruro de diisobutilaluminio y el trietilaluminio originan 4-isoxazolinas mientras que los 4-nitro-y 4-ciano-isoxazoles 3 5-disustituidos en su reaccioncon trietilaluminio conducen respectivamente a las correspondientes 5-etil-2- y 3-isoxazolinas.
PDCD2 functions in cancer cell proliferation and predicts relapsed leukemia (2013)

PDCD2 is an evolutionarily conserved eukaryotic protein with unknown function. The Drosophlia PDCD2 ortholog Zfrp8 has an essential function in fly hematopoiesis. Zfrp8 mutants exhibit marked lymph gland hyperplasia that results from increased proliferation of partially differentiated hemocytes, suggesting Zfrp8 may participate in cell growth. Based on the above observations we have focused on the role of PDCD2 in human cancer cell proliferation and hypothesized that aberrant PDCD2 expression may be characteristic of human malignancies. We report that PDCD2 is highly expressed in human acute leukemia cells as well as in normal hematopoietic progenitors. PDCD2 knockdown in cancer cells impairs their proliferation, but not viability relative to parental cells, supporting the notion that PDCD2 overexpression facilitates cancer cell growth. Prospective analysis of PDCD2 in acute leukemia patients indicates PDCD2 RNA expression correlates with disease status and is a significant predictor of clinical relapse. PDCD2's role in cell proliferation and its high expression in human malignancies make it an attractive, novel potential molecular target for new anti-cancer therapies.