gebhart/patrepeval huggingface dataset:
An Efficient Transaction Commit Protocol for Composite Web Services (2006)

Transaction commit protocols have widely been used to ensure the correctness and reliability of distributed applications. This paper investigates into the performance of such protocols within the context of composite web services. It presents a new commit protocol which aims to improve the performance of composite web services transactions. The proposed protocol is tested through various analytical experiments. These experiments reveal that the proposed protocol significantly improves the performance in committing a composite web service transaction. The experiments also exhibit the processing overhead of the proposed protocol in the case of unsuccessful execution of a web service transaction
Pharmacogenetics in clinical pharmacology and toxicology (1995)

This subject was particularly important to discuss in the presence of Werner Kalow, 77 years young, who is considered as one of the grandfathers of this unique combination of medical research fields. It has become increasingly appreciated that dozens of human drug metabolism polymorphisms exist. The interindividual variabilities in drug metabolism discussed at this symposium do not represent small differences such as 50% or 3-fold but, rather, represent 10- to greater than 1000-fold differences. When attributed to a single gene, dramatic differences can be seen among family members, just as blue and brown eyes can occur in siblings. These differences can result in acute drug toxicity. In addition, there are chronic effects: over one's lifetime, striking differences in the metabolism of drugs, occupationally hazardous chemicals, and other environmental pollutants can lead to interindividual differences in the buildup of DNA damage (e.g., mutations, chromosomal breaks, rearrangements) leading to toxicity and tumor initiation, as well as leading to a buildup in nongenotoxic signals (signal transduction pathways without DNA damage) important for toxicity, tumor promotion, and tumor progression. The human UDP glucuronosyltransferase (UGT superfamily is known to comprise more than 10 genes in humans, and probably in other mammalian species. Breakthroughs in UGT gene mutations responsible for the Crigler-Najjar syndrome and Gilbert's disease have recently been reported. The human cytochrome P450 termed CYP3A4 is a major P450 enzyme in the liver and gastrointestinal tract, and the full impact of the CYP3A4 polymorphism has yet to be fully appreciated.(ABSTRACT TRUNCATED AT 250 WORDS)
All (animal) models (of neurodegeneration) are wrong. Are they also useful? (2018)

Richard M. Ransohoff, Entrepreneur-in-Residence at Third Rock Ventures and Visiting Scientist at Harvard Medical School, provides his personal opinion on using animal models to address current challenges and opportunities in drug development for neurodegeneration.
Adoptive Cell Therapy in Hepatocellular Carcinoma: Biological Rationale and First Results in Early Phase Clinical Trials (2021)

The mortality of hepatocellular carcinoma (HCC) is quickly increasing worldwide. In unresectable HCC, the cornerstone of systemic treatments is switching from tyrosine kinase inhibitors to immune checkpoints inhibitors (ICI). Next to ICI, adoptive cell transfer represents another promising field of immunotherapy. Targeting tumor associated antigens such as alpha-fetoprotein (AFP), glypican-3 (GPC3), or New York esophageal squamous cell carcinoma-1 (NY-ESO-1), T cell receptor (TCR) engineered T cells and chimeric antigen receptors (CAR) engineered T cells are emerging as potentially effective therapies, with objective responses reported in early phase trials. In this review, we address the biological rationale of TCR/CAR engineered T cells in advanced HCC, their mechanisms of action, and results from recent clinical trials.
Cytomegalovirus Quantitation by Real-Time PCR Is Unaffected by Delayed Separation of Plasma from Whole Blood (2004)

A previous study suggested that delayed sample preparation can cause a false-positive plasma cytomegalovirus (CMV) PCR. We evaluated 78 samples submitted for CMV testing, and we report that a 24-h delay in plasma separation did not affect viral quantitation by real-time PCR. Laboratories should evaluate specimen handling requirements for their own PCR technology.
P3E-4 Transducer Design for Liquid Custody Transfer Ultrasonic Flowmetering (2007)

Liquid custody transfer (LCT) monitoring demands accurate measurement of flow at a relatively wide temperature range. Transit-time ultrasonic flowmeters, built as a one-piece "drop-in" flowcell with wetted transducers (i.e., transducers that are in contact with fluids), have provided a solution. In the applications of ultrasonic flowmetering to LCT, the desired accuracy and potential exposure to harsh environments impose challenges to ultrasonic transducer design in terms of sensitivity, bandwidth, safety and temperature tolerance. This paper concerns the above design aspects of ultrasonic transducers, including both transducer elements and passive buffers, for transit-time ultrasonic flowmetering in the context of LCT applications. Two types of transducer elements have been investigated in combination with potential backings and buffers. In order to achieve the desired high accuracy across a wide temperature range, the real time-of-flight in the buffers is measured via the so-called pulse-echo technique and is used for compensation to realize an exact time-of-flight in the liquid path. Both solid buffer design and bundled waveguide buffer design have been proposed and compared. MHz-range ultrasonic transducers have been designed for transit-time ultrasonic flowmetering with a high accuracy of 0.15% in flow measurement and an exposure to fluid temperature applications of -40degC to 140degC The performance of the transducers is theoretically modeled and optimized. Prototypes have been built and tested in water. Pulse-echo with a high signal-to-noise ratio (SNR) of more than 20dB has been achieved in ultrasonic buffers by properly designing the dimensions and mechanical features.
Effect of laser power and powder flow rate on dilution rate and surface finish produced during laser metal deposition of Titanium alloy (2017)

The influence of processing parameters on the resulting properties of laser metal deposition process cannot be overemphasized. In this research, the influence of laser power and powder flow rate on the dilution and surface roughness value produced are critically studied.. The laser power was set between 1.8 kW and 3.0 kW, while the powder flow rate was set between 2.88 and 5.76 g/min. The scanning speed and the gas flow rate were maintained at constant values of 0.05m/s and 4l/min respectively. The study revealed that, as the laser power was increased, the degree of dilution increases but the average surface roughness value decreases. Also, as the powder flow rate was increased, the dilution decreases and the average surface roughness increases. The study shows that it is important to keep the powder flow rare low so as to achieve a better surface finished and also not to use too high laser power as this will result in higher dilution, which is not desirable in the laser additive manufacturing process because it will affect the dimensional accuracy of the part under processing.
Ultra-sensitive polyaniline–iron oxide nanocomposite room temperature flexible ammonia sensor (2015)

We report for the first time a room temperature smart NH<sub>3</sub>sensor based on PAni–Fe<sub>2</sub>O<sub>3</sub>nanocomposite loading on flexible PET substrate by<italic>in situ</italic>chemical oxidative polymerization method.
Characterization of Leaf Senescence and Pod Development in Soybean Explants (1983)

Excised soybean (Glycine max [L.] Merrill) cv Anoka leaf discs tend to remain green even after the corresponding intact leaves have turned yello on fruiting plants. We have found that explants which include a leaf along with a stem segment (below the node) and one or more pods (maintained on distilled H(2)O) show similar but accelerated leaf yellowing and abscission compared with intact plants. In podded explants excised at pre-podfill, the leaves begin to yellow after 16 days, whereas those excised at late podfill begin to yellow after only 6 days. Although stomatal resistances remain low during the first light period after excision, they subsequently increase to levels above those in leaves of intact plants. Explants taken at mid to late podfill with one or more pods per node behave like intact plants in that pod load does not affect the time lag to leaf yellowing. Explant leaf yellowing and abscission are delayed by removal of the pods or seeds or by incubation in complete mineral nutrient solution or in 4.6 micromolar zeatin. Like chorophyll breakdown, protein loss is accelerated in the explants, but minerals or especially zeatin can retard the loss. Pods on explants show rates and patterns of color change (green to yellow to brown) similar to those of pods on intact plants. These changes start earlier in explants on water than in intact plants, but they can be delayed by adding zeatin. Seed dry weight increased in explants, almost as much as in intact plants. Explants appear to be good analogs of the corresponding parts of the intact plant, and they should prove useful for analyzing pod development and mechanisms of foliar senescence. Moreover, our data suggest that the flux of minerals and cytokinin from the roots could influence foliar senescence in soybeans, but increased stomatal resistance does not seem to cause foliar senescence.
Insights into the Origin of High Activity and Stability of Catalysts Derived from Bulky, Electron-Rich Monophosphinobiaryl Ligands in the Pd-Catalyzed C−N Bond Formation (2003)

A comparative kinetic examination of catalyst systems based on several monophosphinobiaryl ligands is reported. The bulk of the phosphine ligand controls the catalytic activity and the rate of catalyst activation with the catalyst based on 2-dicyclohexylphosphino-2',4',6'-triisopropylbiphenyl providing the greatest activity and fastest activation. In the case where catalyst activation is slow (i.e., use of the smaller ligands such as 2-dicyclohexylphosphino-2'-methylbiphenyl in combination with Pd(OAc)2) stirring the amine with the catalyst/base mixture prior to the commencement of the reaction increases the reaction rate along with the rate of catalyst activation. Kinetic isotope effects established that the catalyst activation process occurs through a beta-hydride elimination pathway.
Thermal Properties of Surface-Modified and Cross-Linked Boron Nitride/Polyethylene Glycol Composite as Phase Change Material (2021)

A thermally conductive phase change material (PCM) was fabricated using polyethylene glycol (PEG) and boron nitride (BN). However, the interfacial adhesion between the BN and the PEG was poor, hindering efficient heat conduction. Grafting polyvinyl alcohol (PVA) onto the surface of BN and cross-linking due to hydrogen bonding between the hydroxyl groups in PVA and oxygen atoms in PEG improved the wettability of fillers. By employing this strategy, we achieved a thermal conductivity value of 0.89 W/mK, a 286% improvement compared to the thermal conductivity of the pristine PEG (0.23 W/mK). Although the latent heat of composites decreased due to the mobility of the polymer chain, the value was still reasonable for PCM applications.
Microfluidics‐Enabled Multimaterial Maskless Stereolithographic Bioprinting (2018)

A stereolithography-based bioprinting platform for multimaterial fabrication of heterogeneous hydrogel constructs is presented. Dynamic patterning by a digital micromirror device, synchronized by a moving stage and a microfluidic device containing four on/off pneumatic valves, is used to create 3D constructs. The novel microfluidic device is capable of fast switching between different (cell-loaded) hydrogel bioinks, to achieve layer-by-layer multimaterial bioprinting. Compared to conventional stereolithography-based bioprinters, the system provides the unique advantage of multimaterial fabrication capability at high spatial resolution. To demonstrate the multimaterial capacity of this system, a variety of hydrogel constructs are generated, including those based on poly(ethylene glycol) diacrylate (PEGDA) and gelatin methacryloyl (GelMA). The biocompatibility of this system is validated by introducing cell-laden GelMA into the microfluidic device and fabricating cellularized constructs. A pattern of a PEGDA frame and three different concentrations of GelMA, loaded with vascular endothelial growth factor, are further assessed for its neovascularization potential in a rat model. The proposed system provides a robust platform for bioprinting of high-fidelity multimaterial microstructures on demand for applications in tissue engineering, regenerative medicine, and biosensing, which are otherwise not readily achievable at high speed with conventional stereolithographic biofabrication platforms.
AMP-Activated Protein Kinase-Regulated Activation of the PGC-1α Promoter in Skeletal Muscle Cells (2008)

The mechanisms by which PGC-1alpha gene expression is controlled in skeletal muscle remains largely undefined. Thus, we sought to investigate the transcriptional regulation of PGC-1alpha using AICAR, an activator of AMPK, that is known to increase PGC-1alpha expression. A 2.2 kb fragment of the human PGC-1alpha promoter was cloned and sequence analysis revealed that this TATA-less sequence houses putative consensus sites including a GC-box, a CRE, several IRSs, a SRE, binding sites for GATA, MEF2, p 53, NF-kappaB, and EBox binding proteins. AMPK activation for 24 hours increased PGC-1alpha promoter activity with concomitant increases in mRNA expression. The effect of AICAR on transcriptional activation was mediated by an overlapping GATA/EBox binding site at -495 within the PGC-1alpha promoter based on gel shift analyses that revealed increases in GATA/EBox DNA binding. Mutation of the EBox within the GATA/EBox binding site in the promoter reduced basal promoter activity and completely abolished the AICAR effect. Supershift analyses identified USF-1 as a DNA binding transcription factor potentially involved in regulating PGC-1alpha promoter activity, which was confirmed in vivo by ChIP. Overexpression of either GATA-4 or USF-1 alone increased the p851 PGC-1alpha promoter activity by 1.7- and 2.0-fold respectively, while co-expression of GATA-4 and USF-1 led to an additive increase in PGC-1alpha promoter activity. The USF-1-mediated increase in PGC-1alpha promoter activation led to similar increases at the mRNA level. Our data identify a novel AMPK-mediated regulatory pathway that regulates PGC-1alpha gene expression. This could represent a potential therapeutic target to control PGC-1alpha expression in skeletal muscle.
Characterisation, Origin and Repartition of Tar Mat in the Bul Hanine Field in Qatar (2007)

Both core description and the log detection have evidenced the<br>presence of bitumen inside the Bul Hanine Field (figure 1),<br>which can be particularly abundant in some wells. This tar mat<br>severely impacts reservoir production behaviour because it<br>acts as a permeability reducer and a barrier to flow.
V<sub>H</sub> and V<sub>L</sub> region structure of antibodies that recognize the (NANP)<sub>3</sub> dodecapeptide sequence in the circumsporozoite protein of <i>Plasmodium falciparum</i> (1990)

The sporozoite form of Plasmodium falciparum displays on its surface the circumsporozoite (CS) protein. The central domain of this protein possesses a reiterated tetrapeptide sequence Asn-Ala-Asn-Pro (NANP), and greater than 90% of the sporozoite-specific antibodies obtained from individuals living in malaria endemic areas recognize epitopes within this repeat sequence. Considering the highly repetitive structure of this naturally occurring antigen and its immunodominance, we were interested in analyzing the structural diversity of antibodies that bind to the (NANP)3 sequence. Molecular characterization of immunoglobulin heavy and light chain mRNA was performed for five hybridomas that produce antibodies with binding specificity for the dodecapeptide (NANP)3. These hybridomas were produced in BALB/c mice by inoculation with whole P. falciparum sporozoites. Sequence analysis and Northern blotting showed that for heavy chain, three hybridomas used VH elements that belong to the VHIX family and two to the VHJ558 family. Four different V kappa subgroups were represented among the light chains. Different D and J kappa segments are also utilized, while four heavy chain gene rearrangements involved the JH4 segment. These results indicated that multiple VH-VL gene combinations can code for reactivity to the (NANP)3 sequence, demonstrating that the murine antibody response to this immunodominant region is structurally heterogeneous.
Low Levels of Cell-Free Circulating miR-361-3p and miR-625* as Blood-Based Markers for Discriminating Malignant from Benign Lung Tumors (2012)

The high mortality rate of lung cancer patients is mainly due to the late stage at which lung cancer is diagnosed. For effective cancer prevention programs and early diagnosis, better blood-based markers are needed. Hence, blood-based microarray profiling of microRNA (miR) expression was performed in preoperative serum of 21 non-small cell lung cancer (NSCLC) patients and 11 healthy individuals by microfluid biochips containing 1158 different miRs. Two out of the 30 most dysregulated miRs were further validated in serum of 97 NSCLC patients, 20 patients with benign lung diseases and 30 healthy individuals by TaqMan MicroRNA Assays. Microarray profiling showed that miR-361-3p and miR-625* were significantly down-regulated in serum of lung cancer patients. Their further evaluation by quantitative RT-PCR showed that the levels of miR-361-3p and miR-625* were lower in NSCLC than in benign disease (p = 0.0001) and healthy individuals (p = 0.0001, p = 0.0005, respectively). Moreover, the levels of miR-625* were significantly lower in patients with large cell lung cancer (LCLC, p = 0.014) and smoking patients (p = 0.030) than in patients with adenocarcinoma and non-smoking patients, respectively. A rise in the levels of both miRs was observed in the postoperative samples compared with the preoperative levels (p = 0.0001). Functional analyses showed that Smad2 and TGFß1 are not dysregulated by miR-361-3p and miR-625* in the lung cell line A549, respectively. Our present pilot study suggests that miR-361-3p and miR-625* might have a protective influence on the development of NSCLC, and the quantitative assessment of these miRs in blood serum might have diagnostic potential to detect NSCLC, in particular in smokers.
Pattern Density Effect on the Bottom-Up Fill during Damascene Copper Electrodeposition (2007)

Additives-assisted "bottom-up" fill during copper metallization of semiconductor interconnects is analyzed experimentally and by numerical modeling. The rate of the bottom-up growth is measured as a function of the "suppressor" additive concentration on specifically designed test structures that provide a highly nonuniform suppressor concentration distribution. These test structures include constant space–varying critical dimension (CD) structures that provide suppressor transport preferentially to the trenches at the periphery of trench clusters and (ii) constant CD–varying space structures that provide substantially enhanced suppressor transport to isolated trenches in comparison to trench clusters. Partial-fill experiments on these test structures indicate that the rate of bottom-up fill is diminished at locations such as isolated trenches or trenches located at the periphery of dense-feature clusters. Such locations are characterized by a relatively low surface area per unit volume for suppressor adsorption, and therefore, a localized zone with only a small suppressor concentration depletion is developed in their vicinity. Dense-feature clusters that develop a significantly large suppression depletion zone in their vicinity show accelerated bottom-up growth. The pattern-density-dependent modulation of the local suppressor concentration field and its subsequent impact on the bottom-up fill rate is illustrated by simple numerical modeling.
FORWARD SELECTION OF EXPLANATORY VARIABLES (2008)

This paper proposes a new way of using forward selection of explanatory variables in regression or canonical redundancy analysis. The classical forward selection method presents two problems: a highly inflated Type I error and an overestimation of the amount of explained variance. Correcting these problems will greatly improve the performance of this very useful method in ecological modeling. To prevent the first problem, we propose a two-step procedure. First, a global test using all explanatory variables is carried out. If, and only if, the global test is significant, one can proceed with forward selection. To prevent overestimation of the explained variance, the forward selection has to be carried out with two stopping criteria: (1) the usual alpha significance level and (2) the adjusted coefficient of multiple determination (Ra(2)) calculated using all explanatory variables. When forward selection identifies a variable that brings one or the other criterion over the fixed threshold, that variable is rejected, and the procedure is stopped. This improved method is validated by simulations involving univariate and multivariate response data. An ecological example is presented using data from the Bryce Canyon National Park, Utah, U.S.A.
Association of Vitamin D Receptor Gene Polymorphism and Parkinson's Disease in Koreans (2005)

1alpha,25-dihydroxyvitamin D3 (1,25(OH)2D3), which is the biologically active form of vitamin D, has anti-inflammatory effects and can prevent experimental Parkinson's disease (PD). 1,25(OH)2D3 exerts most of its actions only after it binds to its specific nuclear receptors. Eighty-five Korean patients with PD and 231 unrelated healthy individuals were evaluated to determine if vitamin D receptor gene (VDRG) BsmI polymorphisms were markers for the susceptibility to PD in Korean patients. Each polymorphism was detected using polymerase chain reaction (PCR)-based restriction analysis. In addition, the relationship between the BsmI polymorphisms and the clinical manifestations of PD was evaluated. Overexpression of the b allele (91.2 vs. 85.7%; p=0.069) and homozygote bb (84.7 vs. 72.7%; p=0.043) was found in the PD patients compared with the controls. These results show for the first time an association between PD and a VDRG polymorphism, which might be involved in the pathogenesis of PD, or in the linkage disequilibrium of the VDRG to another pathogenic gene locus.
The new stereological tools: Disector, fractionator, nucleator and point sampled intercepts and their use in pathological research and diagnosis (1988)

The new stereological methods for correct and efficient sampling and sizing of cells and other particles are reviewed. There is a hierarchy of methods starting from the simplest where even the microscopic magnification may be unknown to the most complex where typically both section thickness and the magnification must be known. Optical sections in suitably modified microscopes can be used to improve the ease and speed with which even the most demanding of these methods are performed. The methods are illustrated by practical examples of applications to a wide range of histological entities including synapses, neurons and cancer cells, glomerular corpuscles and ovarian follicles.