gebhart/patrepeval huggingface dataset:
Endobronchial ultrasound-guided sampling can be used for successful molecular sampling in routine clinical practice (2012)

Treatment in oncology is becoming increasingly driven by tumour genetics and biomarker status. In non-small cell lung cancer, mutations within the gene encoding for the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) are associated with improved response to tyrosine kinase inhibitors. This has led to need for genetic analysis for this mutation in lung cancer patients. Initial studies assessed EGFR status in surgical biopsies. Many patients have advanced disease at presentation and there is a requirement to be able to perform this analysis on fine needle aspirates. Whilst studies have shown cytological samples specifically prepared are suitable for this analysis, few studies have assessed the ability to perform molecular analysis on routine samples. We hypothesised that molecular analysis would be possible from routine samples collected at our institution. All procedures performed between 2008 and 2011 were reviewed. Using patient and pathology records, data was collected on patient demographics, adequacy of samples, cytological diagnosis and molecular analyses performed. Cancer was diagnosed in 352 out of 741 cases (48%). Molecular analysis was performed in 70 cases (20% cancer cases). Molecular analysis included PCR, flow cytometry and FISH and occurred in varying cancer diagnoses including: lymphoma (B cell and Hodgkins), melanoma, sarcoma and lung and breast cancer. In a subgroup, EGFR analysis was possible in 87% (47/54) of cases with mutations present in 34% (16/47). Samples from EBUS-TBNA can be used for molecular analysis in routine clinical practice. Their use extends not only to lung but other metastatic cancers of the thorax.
Molecular Biology of the 230-kD Bullous Pemphigoid Antigen (1994)

The 230-kD bullous pemphigoid antigen is a hemidesmosomal protein of the cutaneous basement membrane zone. We have previously cloned overlapping cDNAs corresponding to the human 230-kD bullous pemphigoid antigen gene (BPAG1), located at the human chromosomal locus 6p11-12. Utilizing the cDNA clones, a genomic DNA lambda FIX II phage library was screened. Seven over-lapping genomic clones, spanning approximately 20 kb, were isolated. These clones were shown to contain the entire approximately 9-kb coding sequence of BPAG1, and it consisted of 22 separate exons which varied from 78 to 2,810 bp in size. Elucidation of 2.6 kb of 5'-flanking DNA was found to contain several putative transcriptional response elements, and development of promoter chloramphenicol acetyltransferase (CAT) reporter gene constructs allowed identification of putative cis-elements which confer keratinocyte-specific expression to the gene. In particular, a putative AP2-binding sequence (KRE2) in the position -(1,786-1778) was shown to be responsible for marked enhancement of the endogenous promoter, as well as of a heterologous thymidine kinase/CAT construct, activity in normal human keratinocytes. Normal human keratinocyte nuclear extracts contained a protein, designated as KTP1, which complexed with the KRE2 oligomer by gel mobility shift assays. UV cross-linking and Southwestern analysis suggested that KTP1 is a DNA-binding protein clearly distinct from AP2, and this protein may be responsible for the basal keratinocyte-specific expression of the BPAG1 gene.
Cross-coupling reactions of nucleoside triphosphates followed by polymerase incorporation. Construction and applications of base-functionalized nucleic acids (2008)

Construction of functionalized nucleic acids (DNA or RNA) via polymerase incorporation of modified nucleoside triphosphates is reviewed and selected applications of the modified nucleic acids are highlighted. The classical multistep approach for the synthesis of modified NTPs by triphosphorylation of modified nucleosides is compared to the novel approach consisting of direct aqueous cross-coupling reactions of unprotected halogenated nucleoside triphosphates. The combination of cross-coupling of NTPs with polymerase incorporation gives an efficient and straightforward two-step synthesis of modified nucleic acids. Primer extension using biotinylated templates followed by separation using streptavidine-coated magnetic beads and DNA duplex denaturation is used for preparation of modified single stranded oligonucleotides. Examples of using this approach for electrochemical DNA labelling and bioanalytical applications are given.
The Proposed TRIUMF Accelerator Mass Spectrometer (1985)

We describe an Accelerator Mass Spectrometer to be operated by TRIUMF Applied Programs for a consortium of earth scientists. The equipment will provide routine determinations of 14C, 10Be and 26Al in mg-sized samples derived from natural materials. The measurement system is designed around a used, but suitably upgraded, EN Tandem Van de Graaff accelerator. The design is an improved version of our first-generation AMS system which we currently operate at McMaster University.
Acid-Soluble Lost Circulation Material for Use in Large, Naturally Fractured Formations and Reservoirs (2017)

Abstract Lost circulation is an extremely difficult challenge to overcome in areas with large natural fractures. Few lost circulation materials (LCMs) are capableoftreatingsuch zones where severe to total losses occur, particularlyin the reservoir sections. Particulate-based LCMs are commonly used to help mitigate losses but mightnot contain the proper particle size distribution (PSD) or acid-solubility characteristicsfor useful application in production zones. This paper discusses a novel particulate-based LCMthat is an engineered composite solution (ECS) with a multimodal PSD comprised of acid-soluble components. The multimodal PSD provides the necessary particle sizes to seal a range of fracture widths, including large fractures where total losses canoccur. The acid solubility of the LCM can enable proper removal to help prevent hindering well production. Laboratory results are explained todemonstrate the potential effectiveness of the LCM forsealing large natural fractures. Acid solubility in a reservoir or production zone is important. LCMs used in these zones have tobe removed to permit maximum formation production. For large natural fractures, large particulates are necessaryto effectively mitigate losses. TheECS was designed to include particulates and fibers of various sizes and shapes to plug large-width fractures while retaining the ability to plug smaller- to intermediate-width fractures. This blend can plug laboratory simulated fractures up to 5,000micronsin width.When supplemented with an additional chip particulate, it can plug fractures up to 7,000 microns. The acid-soluble component of this blend is degradable in both 10% hydrochloric (HCl) and 10% formic acids. This paperdiscusses product specifications, such as PSD, recommended treatments, and laboratory performance test results, including acidizing treatment of anLCM plug contaminated with invert emulsion fluid.
cAMP-mediated Induction of Cyclin E Sensitizes Growth-arrested Adipose Stem Cells to DNA Damage–induced Apoptosis (2008)

The differentiation capacity of mesenchymal stem cells has been extensively studied, but little is known on cell cycle–related events in the proliferation and differentiation phases of these cells. Here, we demonstrate that exposure to cAMP-increasing agents inhibits proliferation of adipose stem cells (ASCs). This antiproliferative effect is associated with both reduced cdk2 activity and pRB phosphorylation. Concomitantly, however, the level of cyclin E markedly increases upon cAMP induction, indicating that cyclin E may have cdk2-independent functions in these cells besides its role as a cdk2 activator. Indeed, we found indications of a cdk2-independent role of cyclin E in DNA damage–induced apoptosis. 8-CPT-cAMP sensitizes ASCs to γ-irradiation–induced apoptosis, an effect abolished by knockdown of cyclin E. Moreover, cAMP induces early activation of ERK, leading to reduced degradation of cyclin E. The cAMP-mediated up-regulation of cyclin E was blocked by knockdown of ERK or by an inhibitor of the ERK kinase MEK. We conclude that cAMP inhibits cdk2 activity and pRB phosphorylation, leading to reduced ASC proliferation. Concomitant with this growth inhibition, however, cyclin E levels are increased in a MEK/ERK-dependent manner. Our results suggest that cyclin E plays an important, cdk2-independent role in genotoxic stress–induced apoptosis in mesenchymal stem cells.
Integrated widely tunable quantum cascade lasers with super-structure gratings (2014)

An integrated widely wavelength tunable mid-IR source is demonstrated. This three-section quantum cascade laser consists of a Fabry-Perot section placed between two super-structure grating (SSG) sections. The emission wavelength of the SSG-DBR QCL can be well controlled by varying the injection currents to the two grating sections of the device. The wavelength can be tuned from 4.58 μm to 4.77 μm (90 cm<sup>-1</sup>) with a supermode spacing of 30 nm. The SSG-DBR QCL can be a compact replacement for the external cavity QCL. It has great potential to achieve much further tuning ranges for many mid-IR sensing applications.
Knowledge-augmented Risk Assessment (KaRA): a hybrid-intelligence framework for supporting knowledge-intensive risk assessment of prospect candidates (2023)

Evaluating the potential of a prospective candidate is a common task in multiple decision-making processes in different industries. We refer to a prospect as something or someone that could potentially produce positive results in a given context, e.g., an area where an oil company could find oil, a compound that, when synthesized, results in a material with required properties, and so on. In many contexts, assessing the Probability of Success (PoS) of prospects heavily depends on experts' knowledge, often leading to biased and inconsistent assessments. We have developed the framework named KARA (Knowledge-augmented Risk Assessment) to address these issues. It combines multiple AI techniques that consider SMEs (Subject Matter Experts) feedback on top of a structured domain knowledge-base to support risk assessment processes of prospect candidates in knowledge-intensive contexts.
Mechanical recycling of cross-link polyethylene: Assessment of static and viscoplastic properties (2013)

Fundamentally, there are two recycling methods for plastics: material recycling (including primary, secondary, and tertiary recycling, i.e. hydrolysis and glycolysis) and energy recycling or quaternary recycling. Since the former method replenishes material resources, it is favored where it is possible, i.e. for none polluted or mixed product. At some point after repeated use, the material may commence to degrade, by then it is destined to energy conversion or total breakdown subjected to incineration, gasification or pyrolysis. This work considers the material recycling of LDPE. LDPE represents nearly of 8-10% of the total MSW waste received at the landfill. Initially thermal analysis based on Simultaneous Thermal Analysis (STA) and Differential Scanning Calorimetry (DSC) is carried out to observe the plastic thermal behavior of two successively molded samples. The samples are remolding using the thermosientific mini extruder and the HAAKE MiniJet II injected. The mechanical and thermomechancial properties are assessed using uniaxial static and dynamic tests under well controlled conditions. Mild variation is obtained in the thermal behavior to the two samples observed by the similarity in melting, extent of thermal stability, and onset and end of degradation. However, the mechanical behavior between the three samples clearly demonstrates the gain in total modulus and lower tan delta for the cross-linked product but with a reversion to original LDP behavior following the molding of the waste. This work support successive material recovery for cable plastics with an additional cross-linking to the rejected waste.
Alpha Hemoglobin Stabilizing Protein (AHSP) Is a Susceptibility Gene to Drug /Infection-Induced Hemolytic Anemia. (2005)

Abstract Approximately 500 patients are diagnosed as having congenital hemolytic anemia every year in Japan, and the etiology in 75% of these patients involves red cell membrane disorders. The remaining cases are categorized as congenital non-spherocytic hemolytic anemia (CNSHA) and only about 25 % of CNSHA patients are diagnosed as either unstable hemoglobinopathies or erythroenzymopathies. As a result, up to 100 subjects remained diagnosed as having idiopathic hemolytic anemia. Recently, α-hemoglobin stabilizing protein (AHSP) has been identified, and found to play an important role as molecular chaperones in the stabilization of unstable free α-globin. Intact α-globin monomer generates reactive oxygen species, resulting in damage to red cell protein and lipids. AHSP knockout mice showed compensated hemolysis with Heinz bodies. Genetic defects in protection against oxidative stress such as glucose-6-phosphate dehydrogenase deficiency may account for acute hemolysis only when subjects are exposed to either oxidative drugs or infection, but chronic hemolysis is not evident in those cases. These observations led us to hypothesize that AHSP gene defects might account for either Heinz body-positive or drug/infection-induced hemolytic anemia. We examined 25 CNSHA patients with unknown etiology: 6 cases showing Heinz body-positive red cells and 19 cases showing episodes of drug/infection-induced acute hemolysis. Erythroenzymopathies and unstable hemoglobinopathies were ruled out using red cell enzyme analysis, isopropanol stability tests and DNA sequencing of globin genes. Seven SNPs (single nucleotide polymorphisms) surrounding the AHSP gene (rs 4889672, rs 8046452, rs 8050390, rs 4296276, rs 17677, rs 10843, and a novel SNP at 92-bp upstream of rs 4889672) were examined, and compared with 100 control subjects. We found that a certain haplotype, 5′-GTCGA**-3′, was significantly prevalent in CNSHA cases (p=0.0086). Each SNP within the haplotype is located in the 5′-flanking region of AHSP gene, suggesting that the SNP(s) might account for decreased expression of AHSP gene. The reporter gene assay using K562 cells revealed that a construct containing 5′-GTCGA**-3′ had about 30% of transcriptional activity compared to a major haplotype 5′-ACCAG**-3′. Taken together, we conclude that the AHSP gene is correlated to disease-susceptibility in a group of hemolytic anemia with either Heinz body-positive or drug/infection-induced episodes.
Development and Experimental Characterization of a Small Scale Solar Powered Organic Rankine Cycle (ORC) (2016)

Solar thermal power plants have been widely studied in recent years as solar energy is clean, affordable and largely available. The possibility of converting solar thermal energy into electricity with small scale (lower than 10 kWe) Organic Rankine Cycle (ORC) plants operating at low temperature (lower than 130 °C), seems today a viable option. In this paper, the design and development of a prototypal small scale ORC plant (< 10 kWe) is presented. The ORC, equipped with a scroll expander and installed in Florence, Italy, is powered by parabolic trough solar collectors (PTC) with collector surface area of 100 m2. In the first part of the paper the experimental data collected during the lab tests are presented. Then, the data collected during the field test are presented and discussed. A gross electrical efficiency up to 8% has been achieved. The value of net efficiency is dependent on the power absorbed by the auxiliary components that have not been optimized yet.
Functional Mimetics of the HIV-1 CCR5 Co-Receptor Displayed on the Surface of Magnetic Liposomes (2015)

Chemokine G protein coupled receptors, principally CCR5 or CXCR4, function as co-receptors for HIV-1 entry into CD4+ T cells. Initial binding of the viral envelope glycoprotein (Env) gp120 subunit to the host CD4 receptor induces a cascade of structural conformational changes that lead to the formation of a high-affinity co-receptor-binding site on gp120. Interaction between gp120 and the co-receptor leads to the exposure of epitopes on the viral gp41 that mediates fusion between viral and cell membranes. Soluble CD4 (sCD4) mimetics can act as an activation-based inhibitor of HIV-1 entry in vitro, as it induces similar structural changes in gp120, leading to increased virus infectivity in the short term but to virus Env inactivation in the long term. Despite promising clinical implications, sCD4 displays low efficiency in vivo, and in multiple HIV strains, it does not inhibit viral infection. This has been attributed to the slow kinetics of the sCD4-induced HIV Env inactivation and to the failure to obtain sufficient sCD4 mimetic levels in the serum. Here we present uniquely structured CCR5 co-receptor mimetics. We hypothesized that such mimetics will enhance sCD4-induced HIV Env inactivation and inhibition of HIV entry. Co-receptor mimetics were derived from CCR5 gp120-binding epitopes and functionalized with a palmitoyl group, which mediated their display on the surface of lipid-coated magnetic beads. CCR5-peptidoliposome mimetics bound to soluble gp120 and inhibited HIV-1 infectivity in a sCD4-dependent manner. We concluded that CCR5-peptidoliposomes increase the efficiency of sCD4 to inhibit HIV infection by acting as bait for sCD4-primed virus, catalyzing the premature discharge of its fusion potential.
Tapered backfire helical antenna with loaded termination (1982)

In order to improve the radiation characteristics of a backfire bifilar helical antenna, a means of terminating the arm ends with a resistor is numerically and experimentally investigated. Owing to the reduction of reflected current, the present backfire helix realises an excellent front-to-back ratio and axial ratio, while maintaining inherent absolute gain.
Monte Carlo simulation of electron transport in the III-nitride wurtzite phase materials system: binaries and ternaries (2001)

We present a comprehensive study of the transport dynamics of electrons in the ternary compounds, Al/sub x/Ga/sub 1-x/N and In/sub x/Ga/sub 1-x/N. Calculations are made using a nonparabolic effective mass energy band model. Monte Carlo simulation that includes all of the major scattering mechanisms. The band parameters used in the simulation are extracted from optimized pseudopotential band calculations to ensure excellent agreement with experimental information and ab initio band models. The effects of alloy scattering on the electron transport physics are examined. The steady state velocity field curves and low field mobilities are calculated for representative compositions of these alloys at different temperatures and ionized impurity concentrations. A field dependent mobility model is provided for both ternary compounds AlGaN and InGaN. The parameters for the low and high field mobility models for these ternary compounds are extracted and presented. The mobility models can be employed in simulations of devices that incorporate the ternary III-nitrides.
The Effect of the Dynamics of Revolving Gates on the Kinetics of Molecular Encapsulation—The Activity/Selectivity Relationship (2011)

Gated molecular encapsulation: The relationship between the rate by which guest molecules enter/exit gated hosts and the rate by which gates revolve and thereby open/close the host were investigated. The results of kinetic measurements have indicated that more dynamic hosts are also more selective in trapping guests, thereby revealing an activity/selectivity relationship pertaining molecular recognition events (see figure). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Understanding the factors that influence breast reconstruction decision making in Australian women (2015)

A model using factors easily obtained on clinical history can be used to understand likelihood of reconstruction. This knowledge may help identify barriers to reconstruction, ultimately improving the clinicians' ability to appropriately educate mastectomy patients and ensure effective decision making around breast reconstruction.
An evaluation of PCR primer sets used for detection of <i>Propionibacterium acnes</i> in prostate tissue samples (2008)

Although the results of previous studies have shown that P. acnes is not the only organism potentially present in the prostates of prostate cancer patients, mismatches in PCR primer sets may have also influenced the sensitivity of P. acnes detection. When using PCR in determining the presence of P. acnes in the human prostate, care should be taken to establish the potential influence of exogenous contamination and, due to the sensitivity of the assay, samples exposed to the urethra during the collection process (prostatic secretions, TURP specimens) should not be used.
&lt;title&gt;Contrast-limited target acquisition: atmospheric and motion effects&lt;/title&gt; (1995)

In this paper, the incorporation of atmospheric aerosol and turbulence blur and motion blur into visible, near infrared, and thermal infrared target acquisition modeling is considered. Here, we show how the target acquisition probabilities and, conversely, the ranges at which objects can be detected are changed by the inclusion of these real-life environmental effects whose blur is often significantly greater than that of imaging system hardware. It is assumed that images are contrast-limited rather than noise-limited, as is indeed the case with most visible, near infrared (IR), and thermal IR sensors. For short focal lengths with low angular magnification, such environmental blur effects on target acquisition are negligible. However, for longer focal lengths with large angular magnification, resolution is limited by them and this has a strong adverse effect on target acquisition probabilities, times, and ranges. The considerable improvement possible with image correction for such environmental blur automatically in a fraction of a second is significant for contrast-limited imaging, and is discussed here too. Knowledge of such environmental MTF is essential to good system design and is also very useful in image restoration for any type of target or object.
Inhibition of early preneoplastic events in the rat liver by the somatostatin analog lanreotide (2007)

Hepatocellular carcinoma (HCC) is the third most common cause of cancer-related death, and its incidence is increasing worldwide. Due to the known risk factors (mainly hepatitis B and C viruses), we believe there is a rationale for a chemopreventive approach to treat HCC. Here, based on described in vitro data, we evaluated the preventive effects of lanreotide, a somatostatin analog, on the induction of early carcinogenic events. We monitored preneoplastic foci induced by a two-stage initiation/promotion model of hepatocarcinogenesis in male Wistar rats, using diethylnitrosamine and 2-acetylaminofluorene. Lanreotide was given starting the day after the first diethylnitrosamine injection. By quantitative morphometry, we showed that lanreotide significantly decreases the size of induced preneoplastic foci. Analysis of proliferation and apoptosis assessed by immunohistochemistry, showed decreased proliferation and increased cell death in rats treated with lanreotide. As these events were associated with a significant decreased expression of the cell cycle regulator cyclin D1 and an increased expression of the cyclin-dependent kinase inhibitor p27(kip1) compared to the non-treated group, it is tempting to speculate that these factors are involved in the favorable effect of lanreotide. In conclusion, lanreotide significantly decreases early carcinogenic transformation in a two-step rat model. As lanreotide has a low toxicity profile, we believe it would be interesting to evaluate its effect in chemoprevention of HCC.