gebhart/patrepeval huggingface dataset:
Statistical significance and statistical power in hypothesis testing (1990)

Experimental design requires estimation of the sample size required to produce a meaningful conclusion. Often, experimental results are performed with sample sizes which are inappropriate to adequately support the conclusions made. In this paper, two factors which are involved in sample size estimation are detailed--namely type I (alpha) and type II (beta) error. Type I error can be considered a "false positive" result while type II error can be considered a "false negative" result. Obviously, both types of error should be avoided. The choice of values for alpha and beta is based on an investigator's understanding of the experimental system, not on arbitrary statistical rules. Examples relating to the choice of alpha and beta are presented, along with a series of suggestions for use in experimental design.
Oxygen Tension Regulates the Expression of ANK (Progressive Ankylosis) in an HIF-1-Dependent Manner in Growth Plate Chondrocytes (2009)

The proximal promoter region of ANK, a gene that codes for a protein that regulates the transport of inorganic pyrophosphate, contains two hypoxia responsive elements (HREs); therefore, we studied the expression and function of ANK at different oxygen tensions. ATDC5 and N1511 clonal chondrocytic cells were cultured in either hypoxia (2% O(2)) or normoxia (21% O(2)). Transcript and protein levels of ANK were depressed in hypoxic conditions, as were levels of extracellular pyrophosphate (ePPi). To determine whether HIF-1 was involved in the oxemic response, Hif-1alpha knockdown cells were exposed to varying oxygen conditions and ANK expression was assessed. Knockdown of Hif-1alpha resulted in low levels of expression of ANK in hypoxia and normoxia. Chromatin immunoprecipitation (ChIP) assays explored the binding of Hif-1alpha to ANK HREs and showed that Hif-1alpha is able to bind to the HREs of ANK more avidly in normoxia than in hypoxia. Furthermore, functional studies of Hif-1alpha activity using luciferase reporter assays of wildtype and mutagenized HREs showed that only HRE-1 binds Hif-1alpha in normoxia. Expression of ANK in growth plate and articular cartilage was low in hypoxic regions of the tissues, and higher levels of ANK expression were observed in the synovium and meniscus in regions that have a normally higher oxygen tension. The data suggest that ANK expression and function in vitro and in vivo are repressed in hypoxic environments and that the effect is regulated by HIF-1.
Controlling threading dislocation densities in Ge on Si using graded SiGe layers and chemical-mechanical polishing (1998)

A method of controlling threading dislocation densities in Ge on Si involving graded SiGe layers and chemical-mechanical polishing (CMP) is presented. This method has allowed us to grow a relaxed graded buffer to 100% Ge without the increase in threading dislocation density normally observed in thick graded structures. This sample has been characterized by transmission electron microscopy, etch-pit density, atomic force microscopy, Nomarski optical microscopy, and triple-axis x-ray diffraction. Compared to other relaxed graded buffers in which CMP was not implemented, this sample exhibits improvements in threading dislocation density and surface roughness. We have also made process modifications in order to eliminate particles due to gas-phase nucleation and cracks due to thermal mismatch strain. We have achieved relaxed Ge on Si with a threading dislocation density of 2.1×106 cm−2, and we expect that further process refinements will lead to lower threading dislocation densities on the order of bulk Ge substrates.
Optimum pilot pattern for channel estimation in OFDM systems (2005)

The performance of channel estimation in orthogonal frequency division multiplexing (OFDM) systems significantly depends on the pilot signal, which is usually scattered in time and frequency domains. For a given pilot density, the authors optimally design the pilot pattern so as to minimize the mean squared error (MSE) of the channel estimate with the use of a general interpolator. The analytic results are verified by computer simulation.
A fully integrated wireless power supply for pinless active RFID-devices in 130nm CMOS (2007)

This paper presents the first fully integrated and pitiless wireless 0.5 V-power supply for RFID applications in 130 nm CMOS. It consists of an on-chip integrated dipole-antenna, a rectifier and storage capacitor. The system can generate 0.5 V from 36.4dBm E1RP at a distance of 0.5 m, the operating frequency being 10.35 GH <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">z</i> plusmn 1%. The integrated antenna is a dipole with a reflector underneath, to shield it from the lossy substrate. The rectifier uses a 20-stage voltage-doubler topology to rectify the incoming power. The die area is only 300 mum times 1500 mum.
Increased fragile sites and sister chromatid exchanges in bone marrow and peripheral blood of young cigarette smokers. (1987)

Cigarette smoking is considered to be the single most important acquired cause of cancer mortality. Studies of chromosome aberrations, sister chromatid exchanges, and fragile sites in peripheral blood or bone marrow are useful methods to detect the effects of the environmental mutagens or carcinogens found in cigarette smoke. The effects of smoking on the immature cells in the bone marrow have not been studied. Here, we examine the peripheral blood and bone marrow in 18 smokers (15 females and 3 males) with a median age of 25 years (range, 21-40) and an average cigarette use corresponding to 6 pack years. In both bone marrow cells and peripheral blood lymphocytes, we were able to show a significantly increased frequency of sister chromatid exchanges in smokers with a 5 or more cigarette pack year history, but not in those who smoked less than 5 pack years. We also found a higher frequency of sister chromatid exchanges in peripheral blood lymphocytes than in bone marrow cells. In addition, the peripheral lymphocytes of smokers demonstrated (a) a significantly higher frequency of fragile sites, (b) an increased number of metaphases with extensive breakage; and (c) elevated expression of fragile sites at the cancer breakpoints 3p14.2, 11q13.3, 22q12.2, and 11p13-p14.2 and at the oncogene sites bcl 1, erb B, erb A, and sis. Our results suggest that chromosomal DNA of peripheral blood lymphocytes is sensitive to cigarette smoking. Studies of the chromosomal changes in these cells provide an index of the mutagenic damage caused by these exogenous agents in individual patients and the ability of individuals to repair that damage, and might predict susceptibility to malignant events.
Earthquakes in Victoria (2008)

Report presented describes an activity to identify the earthquake affected areas in Victoria through maps and an article. Based on the article some questions are presented for purpose of discussion and analysis.
Stoffwechselprodukte von Mikroorganismen 143. Mitteilung. Echinocandin B, ein neuartiges Polypeptid‐Antibioticum aus Aspergillus nidulans var. echinulatus: Isolierung und Bausteine (1974)

From a strain of Aspergillus nidulans var. echinulatus , A 32204, echinocandin, a novel polypeptide antibiotic complex with high and specific anti‐yeast activity was isolated. The main component, echinocandin B, was separated by counter‐current distribution. A tentative molecular formula C 52 H 81 N 7 O 18 is discussed. The antibiotic is characterized by its IR. and NMR. spectra and by its characteristic hydrolytic degradation products: linoilic acid, L ‐4‐hydroxyproline, L ‐4‐oxoproline, (2 S , 3 S , 4 S )‐4‐methyl‐3‐hydroxy‐proline, L ‐threonine (2 mols), and 1‐( p ‐hydroxyphenyl)‐3‐amino‐propan‐2‐one.
Comparing calpain- and caspase-3-mediated degradation patterns in traumatic brain injury by differential proteome analysis (2006)

A major theme of TBI (traumatic brain injury) pathology is the over-activation of multiple proteases. We have previously shown that calpain-1 and -2, and caspase-3 simultaneously produced alphaII-spectrin BDPs (breakdown products) following TBI. In the present study, we attempted to identify a comprehensive set of protease substrates (degradome) for calpains and caspase-3. We further hypothesized that the TBI differential proteome is likely to overlap significantly with the calpain- and caspase-3-degradomes. Using a novel HTPI (high throughput immunoblotting) approach and 1000 monoclonal antibodies (PowerBlottrade mark), we compared rat hippocampal lysates from 4 treatment groups: (i) naïve, (ii) TBI (48 h after controlled cortical impact), (iii) in vitro calpain-2 digestion and (iv) in vitro caspase-3 digestion. In total, we identified 54 and 38 proteins that were vulnerable to calpain-2 and caspase-3 proteolysis respectively. In addition, the expression of 48 proteins was down-regulated following TBI, whereas that of only 9 was up-regulated. Among the proteins down-regulated in TBI, 42 of them overlapped with the calpain-2 and/or caspase-3 degradomes, suggesting that they might be proteolytic targets after TBI. We further confirmed several novel TBI-linked proteolytic substrates, including betaII-spectrin, striatin, synaptotagmin-1, synaptojanin-1 and NSF (N-ethylmaleimide-sensitive fusion protein) by traditional immunoblotting. In summary, we demonstrated that HTPI is a novel and powerful method for studying proteolytic pathways in vivo and in vitro.
Design and magnetics optimization of LLC resonant converter with GaN (2017)

This paper presents the design and magnetics optimization of 1-kW regulated LLC resonant converter with GaN FETs. By adopting the GaN FETs for primary side switches, the gate driver loss and turn-off loss are significantly reduced. A new structure of integrated transformer with stacked planar cores, shaped windings and synchronous rectifier MOSFET proposed to reduce the core loss and winding loss. The proposed integrated transformer has highly compact structure including transformer, resonant inductor, SR MOSFET and output capacitor. A regulated 1-kW LLC resonant converter prototype is designed and tested. The peak efficiency can reach 97.4%.
Multilayer Formation of Copper Ions (Cu2+) Deposited onto Self-Assembled Monolayers of Alkanedithiols on Au (111) Surfaces (2000)

Self-assembled monolayers (SAMs) of 1,5-pentanedithiol and 1,9-nonanedithiol on Au (111) surfaces were used to adsorb copper ions (Cu 2+ ) from an ethanolic solution of cupric chloride (CuCl 2 ) by chemical interaction of thiol groups and copper ions assembling multilayer structures. Ellipsometry, contact angle measurement and X-ray photoelectron spectroscopy (XPS) confirmed that the alkanedithiol molecules formed SAMs with only one-ended thiol groups attached to the gold surface, leaving the other-ended thiol groups free, which is supported by the molecular mechanics calculation. XPS and X-ray Auger electron spectroscopy (XAES) not only indicate that copper ions deposited onto SAMs from the solution by the chemical reaction of copper ions with ended free thiol groups of SAMs, but more importantly demonstrate that copper is present in the +1 oxidation state in the multilayer system. Atomic force microscopy (AFM) was used to observe SAMs and multilayer structures.
Effects of Perhexiline on Coronary Hemodynamic and Myocardial Metabolic Responses to Tachycardia (1974)

Coronary hemodynamic and myocardial metabolic responses before and after perhexiline administration were studied in 21 patients with coronary heart disease during pacing-induced angina pectoris. Perhexiline increased the threshold to tachycardia-induced angina pectoris in 16 of the 21 patients (HR 123 ± 3 to 134 ± 3 beats/min, P &lt; 0.01). Anaerobic myocardial lactate extraction was reduced by –6.1 ± 6.3 to 10.7 ± 4% after perhexiline, although lactate extraction declined in four patients and ST segment depression was not significantly changed. Myocardial oxygen extraction was enhanced, 64 ± 2 to 69 ± 2% ( P &lt; 0.05). Coronary flow as reflected by coronary sinus blood flow was not altered (165 ± 24 to 173 ± 26 cc/min) as left ventricular oxygen utilization was increased (18.9 ± 4 to 20.9 ± 4 ml/min, P &lt; 0.05). These findings are interpreted to indicate decreased myocardial ischemia in certain patients on perhexiline.
Use of adhesion-defective mutants of Staphylococcus aureus to define the role of specific plasma proteins in promoting bacterial adhesion to canine arteriovenous shunts (1995)

We used an ex vivo canine arteriovenous shunt model, previously developed to study plasma protein adsorption and thrombogenesis on polymeric biomaterials, to define the role of host proteins in promoting adhesion of Staphylococcus aureus. Either polyethylene or polyvinyl chloride tubings were exposed to canine blood for 5, 15, or 60 min at a flow rate of 300 ml/min and then were flushed in phosphate-buffered saline (PBS), cut into 1.5-cm segments, and stored at -70 degrees C. After thawing, each segment was preincubated in 0.5% albumin in PBS to prevent nonspecific staphylococcal attachment to surfaces that were not exposed to blood. Each segment was then incubated with 4 x 10(6) CFU of [3H]thymidine-labelled S. aureus per ml for 60 min at 37 degrees C in an in vitro adhesion assay. Two site-specific mutants of S. aureus were tested: one specifically defective in adhesion to surface-bound fibronectin (FnAd-def) and the other defective in adhesion to fibrinogen (FgAD-def) [corrected]. Compared with their respective parental strains, the FgAd-def, but not the FnAd-def, mutant of S. aureus showed a strong (> 80%) decrease in attachment to ex vivo tubings. The adhesion of each strain of S. aureus onto polyethylene was consistently more than twofold higher than the adhesion onto polyvinyl chloride segments exposed to flowing blood for 5 or 15 min, but adhesion became similar to that on polyvinyl chloride after 60 min of exposure. In conclusion, the specific adhesion-defective mutants of S. aureus suggested that fibrinogen was the most active adhesion-promoting protein in a short-term blood-material interaction. The experimental approach described in this study should prove useful for screening materials thought to be resistant to protein-mediated staphylococcal adhesion and colonization.
The relationship between the metabolism of 2,4-dichloro-6-phenylphenoxyethylamine (DPEA) and related compounds and their activities as microsomal mono-oxygenase inhibitors. (1974)

2,4-Dichloro-6-phenylphenoxyethylamine and 2-chloro-6-phenylphenoxyethylamine are effective, long-acting in vivo inhibitors of microsomal mono-oxygenases. Plasma and liver half-lives were found to be in the range of 110-130 min. Distribution studies show that DPEA1 and MPEA concentrate in liver, principally in the microsomal fraction, as unmetabolized amines. These observations offer an explanation for the long duration of action of DPEA and MPEA. They are relatively inactive substrates for the microsomal enzyme system and are excreted principally in the bile as unchanged amine (25-30%) or as an N-glucuronide conjugate (40-60%). The in vitro formation of deaminated metabolites (alcohol, acid, or aldehyde) required NADPH and oxygen as cofactors and microsomes as the enzyme source. α-Methyl-MPEA, an ineffective inhibitor of microsomal mono-oxygenases but an excellent substrate for microsomal deamination, yielded not only alcohol and ketone as metabolites but also the oxime of the ketone. Incorporation of isotope from 182 into the alcohol and ketone (74 atom %) and oxime (96-99 atom % 18O) support the hypothesis that the microsomal deamination of primary amines occurs via an unstable carbinolamine intermediate.
Overview: Assays for Studying Integrin-Dependent Cell Adhesion (2011)

Interaction of the integrin receptors with ligands determines the molecular basis of integrin-dependent cell adhesion. Integrin ligands are typically large proteins with relatively low binding affinities. This makes direct ligand-binding kinetic measurements somewhat difficult. Here we examine several real-time methods, aimed to overcome these experimental limitations and to distinguish the regulation of integrin conformation and affinity. This chapter includes: the use of a small ligand-mimetic probe for studies of inside-out regulation of integrin affinity and unbending, real-time cell aggregation and disaggregation kinetics to probe integrin conformational states and the number of integrin-ligand bonds, as well as the real-time monitoring of ligand-induced epitopes under signaling through G-protein-coupled receptors, and others. Experimental data obtained using these novel methods are summarized in terms of the current model of integrin activation.
Purification and partial characterization of a cellular inhibitor of the interferon-induced protein kinase of Mr 68,000 from influenza virus-infected cells. (1990)

A number of eukaryotic viruses have evolved mechanisms to downregulate activity of the interferon-induced, double-stranded RNA-activated protein kinase (referred to as P68 based on its Mr of 68,000 in human cells). This control is essential because once activated, the P68 kinase phosphorylates its natural substrate, the alpha subunit of the eukaryotic protein synthesis initiation factor 2 (eIF-2), limiting functional eukaryotic protein synthesis initiation factor 2 available for protein synthesis initiation. We have previously shown that influenza virus encoded a specific mechanism to repress the autophosphorylation and activity of P68. Using in vitro assays for P68 inhibition, we now have purified, to near homogeneity, the P68 repressor from influenza virus-infected cells. The purified product inhibited both the autophosphorylation of P68 as well as phosphorylation of the alpha subunit of eukaryotic protein synthesis initiation factor 2 by the kinase. We tested for both protease and phosphatase activity but found neither activity associated with the purified inhibitor. Surprisingly we found the purified repressor, which had an apparent Mr of approximately 58,000, was a cellular and not a viral-encoded protein. Possible mechanisms by which influenza virus activates this cellular regulator of the protein kinase, thereby minimizing potential antiviral effects of interferon, are discussed.
Primary and secondary in vitro generation of cytolytic T lymphocytes in the murine sarcoma virus system (1975)

Abstract Cell‐mediated cytotoxic responses in vitro to surface antigens associated with murine sarcoma virus (MSV)‐induced tumors were investigated using mixed leukocyte‐tumor cell cultures (MLTC). The source of responding cells was either spleens from normal C57BL/6 mice (primary MLTC) or spleens of C57BL/6 mice carrying or having rejected a MSV‐induced tumor (secondary MLTC). Graffi virus‐induced GiL‐4 leukemia cells, Rauscher virus‐induced RBl‐5 leukemia cells, and MSV‐induced MSV‐B16 sarcoma cells were used as stimultating syngeneic tumor cells and/or target cells. Under appropriate culture conditions, cytolytic T lymphocytes (CTL) were generated in both primary and secondary MLTC. As assessed by a quantitative short‐term 51 Cr release assay system, CTL activity in secondary MLTC populations was at least 10‐fold higher than that in primary MLTC populations, and 100‐fold higher than that in spleen cells taken at the peak of the in vivo response of MSV‐infected mice. The ability of spleen cells to mount a secondary CTL response in vitro could be observed as early as 5 days after virus injection, increased up to the time of maximum tumor size and persisted long after tumor regression. This suggests the development of increased numbers of CTL progenitors and/or the formation of “memory” CTL in spleens of MSV‐injected mice.
AtUCP2: a Novel Isoform of the Mitochondrial Uncoupling Protein of Arabidopsis thaliana (1999)

Mitochondrial uncoupling proteins (UCPs) play a central role in adaptive thermogenesis in mammals. The UCPs dissipate the proton gradient formed through respiration without ATP synthesis, and the freed energy is readily converted to heat, helping the animals to maintain their body temperature in cold environments. Recently, it was found that UCPs also function in plant mitochondria. Subsequently, a cDNA clone encoding a UCP in potato was isolated. Whereas the UCP gene constitutes a multigene family in mammals, only a single cDNA sequence has been reported so far for the potato UCP. Moreover, it has been recently suggested that Arabidopsis has only a single nuclear gene for UCP. Here we report the existence of another UCP gene in the Arabidopsis genome, showing for the first time the occurrence of a multigene family for the protein in higher plants. A cDNA analysis of this gene showed that the novel isoform possesses all typical features reported for known UCPs. However, the new gene, unlike the other gene in Arabidopsis and the gene in potato, did not appear to respond to low temperature.
Structural analysis of human antibodies to proteinase 3 from patients with Wegener granulomatosis (1997)

Abstract We determined the structure of five IgM autoAbs to proteinase-3 (PR3). These Abs are highly specific for Wegener's granulomatosis (WG) and may be involved in the pathogenesis of vasculitis in WG. Five clonal lymphoblastoid cell lines secreting Abs to PR3 were derived from four patients' B cells. From 3 to 5% of supernatants from wells contained detectable anti-PR3 Abs, indicating that anti-neutrophil cytoplasmic Ab specificity represents a sizable part of the IgM B cell repertoire in patients with WG. Mu heavy chains of WG1, WG4-1, and WG4-2 clones belonged to the VH3 subgroup. WG4-1 and WG4-2 heavy chains were identical, indicating an oligoclonal expansion of autoreactive B cells in this patient. WG4-1 (and WG4-2) used the VH3-23 V(H) gene, the product of which was shown to directly bind PR3. Heavy chains of WG2 and WG3 derived from VH4-59 and VH1-2 genes, respectively. Comparison with germline sequences showed that three of the five V(H) genes from clonal lines were somatically mutated with a R:S ratio in complementarity-determining regions of 3:0, 5:1, and 5:1, respectively. Three kappa light chains derived from the Vkappa4 gene, and one derived from a Vkappa1 gene. In these four Vkappa genes, there were overall R:S ratios of mutation of 8:1 and 0:7 in complementarity-determining regions and framework regions, respectively. These data suggest that the production of these autoantibodies, which are increasingly important in the diagnosis and management of WG, are influenced by an Ag-driven process.