gebhart/patrepeval huggingface dataset:
Grafting of paired 3-aminopropyltrialkoxy silanes onto mesoporous silica and adsorptions of isomers of benzenedialdehydes (2013)

A pair of 3-aminopropyltriethoxysilane molecules coupled with m- and p-benzenedialdehydes are grafted onto SBA-15 mesoporous silica, followed by the removal of benzenedialdehyde by hydrolysis. These paired 3-aminopropyl-grafted SBA-15, denoted (m)N- and (p)N-SBA-15, respectively, adsorb their own template benzenedialdehydes with a larger Langmuir constant K(L) than in other combinations of adsorbates and adsorbents. In addition, K(L) for the m-isomer is larger in the adsorption on (m)N-SBA-15 than on (p)N-SBA-15 and vice versa for the p-isomer. In contrast to this quadruple preference in the adsorption, a larger K(L) in the adsorption of the m-isomer onto the (m)N-adsorbent than onto the (p)N-adsorbent is the only adsorption preference that is observed in the case of Cab-O-sil M7D-based adsorbents prepared by the same procedure. The difference between the two kinds of silicas can be attributed to the surface curvature, concave or convex on a nanometre scale, which is supported by the evidence from spectroscopic analyses.
Real Time Deep Electrical Images, a Highly Visual Guide for Proactive Geosteering (2010)

For ideal well placement it is now possible to guide real time decisions with deep electrical images of<br>the surrounding geology. New azimuthal deep resistivity LWD sensors show images of approaching<br>boundaries long before they cross the well path. Clearly the earlier an approaching boundary is<br>detected and mapped in space, the longer the window of opportunity to change the course of the well<br>and to avoid exiting the reservoir. Because the geosteering engineer sees geological events from a<br>distance and makes decisions in advance of crossing reservoir boundaries, the geosteering operation is<br>said to be “proactive”.
Quantitative assessment of auditory cortex responses induced by imager acoustic noise (1999)

A clustered volume acquisition functional MRI pulse sequence was modified to assess the response to the acoustic noise of echo-planar imaging in the auditory cortex and to determine whether it is possible to obtain data which is relatively free of acoustic contamination. The spatial location and strength (percent signal change) of cortical responses to the imager noise were examined by introducing extra gradient readouts, without slice excitation, to provide acoustic stimulation immediately prior to acquisition of a cerebral volume. The duration of acoustic stimulation was controlled by varying the number of extra gradient readouts. Slice acquisitions were clustered at the end of the repetition time (TR) period to prevent a response from being induced by the volume acquisition itself ("Intra-Acquisition Response"). The cerebral volumes were acquired using a long TR in order to limit the integration of the cortical response across volume acquisitions ("Inter-Acquisition Response"). Cortical responses were observed to be largest and most significant on the medial two-thirds of Heschl's gyrus, the location of primary auditory cortex. Mean signal changes induced by the imager noise were observed to be as high as 0.95%. A 2 sec delay prior to onset of the BOLD response was empirically determined. These results demonstrate that clustered volume acquisitions may be utilized for up to 2 sec of volume acquisition without inducing an appreciable Intra-Acquisition Response and can be used, with a sufficiently long TR, to provide data which are similarly free of any Inter-Acquisition Response.
A Fast and Secure Pipelined Barrel Processor for Safety-Critical Applications for Real-Time Operating Systems (2019)

Security, reliability, and efficiency are crucial traits of the microprocessors used for safety and mission critical applications. Conventional microprocessors are typically not suitable for these applications, mainly because these processors do not support architectural-level protection including thread isolation, which in turn could lead to security vulnerabilities in embedded systems. In this case, a single erroneous thread could cause catastrophic failure of the whole system. Also, with conventional microprocessors, no specific defense mechanisms are provided to prevent foreign invaders such as viruses from attacking the system. This could become a significant problem especially for safety and mission critical applications that are typically real-time systems. In this paper, we introduce novel and unique pipeline barrel processor (PBP) architecture for safety and mission critical applications for real-time operating systems. Our PBP microprocessor is designed in such a way to alleviate the aforementioned issues, by comprising following features: fine-grained multi-tasking using single pipeline assembly, dynamic allocation of CPU cycles, memory partitioning at the architectural level, execution code regions at the hardware level, and global variables and stack protections. Experiments are performed to evaluate our PBP microprocessor, and to verify the correctness and functionality of the microprocessor design.
Using genetic algorithms and coupling measures to devise optimal integration test orders (2002)

We present here an improved strategy to devise optimal integration test orders in object-oriented systems. Our goal is to minimize the complexity of stubbing during integration testing as this has been shown to be a major source of expenditure. Our strategy to do so is based on the combined use of inter-class coupling measurement and genetic algorithms. The former is used to assess the complexity of stubs and the latter is used to minimize complex cost functions based on coupling measurement. Using a precisely defined procedure, we investigate this approach in a case study involving a real system. Results are very encouraging as the approach clearly helps obtaining systematic and optimal results.
Activation of Vascular Endothelial Growth Factor A Transcription in Tumorigenic Glioblastoma Cell Lines by an Enhancer with Cell Type-specific DNase I Accessibility (2002)

Unregulated expression of vascular endothelial growth factor-A (VEGF-A) plays an important role in tumor growth. We have identified a cell type-specific enhancer, HS-1100, that contributes to VEGF-A transcriptional activation in tumorigenic glioblastoma cell lines. This enhancer exhibits increased accessibility to DNase I in glioblastoma cell lines that express high levels of VEGF-A but not in several other cell lines that express much lower levels of VEGF-A. HS-1100 contains a number of sequence elements that are highly conserved among human, mouse, and rat, including the hypoxia-response element (HRE). We show that the HRE contributes significantly to the cell type-specific enhancer activity of HS-1100 in U87MG glioblastoma cells. We use chromatin immunoprecipitation assays to show that endothelial PAS domain protein 1 (EPAS1) can efficiently bind to the endogenous HRE in U87MG cells but not in HEK293 cells in which the chromosomal HS-1100 is not accessible to DNase I. A dominant negative EPAS1 significantly reduces HS-1100 enhancer activity and VEGF-A levels in U87MG cells. Our results provide insight into the molecular mechanisms of VEGF-A up-regulation during cancer development.
Evaluation of the Rapidec Carba NP Test Kit for Detection of Carbapenemase-Producing Gram-Negative Bacteria (2015)

Recently, bioMérieux, France, introduced the Rapidec Carba NP test kit for rapid detection of carbapenemase-producing Gram-negative bacteria. This kit was evaluated in this study, and we report sensitivity, specificity, and positive and negative predictive values of 92.6%, 96.2%, 95.83%, and 92.6%, respectively. The test was easy to perform and interpret and relatively inexpensive ($5/Rs 300 per test) and provides a practical solution for early detection of carbapenemase-producing, multidrug-resistant Gram-negative bacteria.
TTV, a new human virus with single stranded circular DNA genome (2002)

TT virus (TTV) was found in 1997 from a hepatitis patient without virus markers. However, the real impact of TTV on liver diseases remains uncertain to date. Due to the lack of suitable cell systems to support the growth of TTV, the biology of TTV is still obscure. This review tries to summarise the current status of TTV on aspects other than the taxonomic diversity of TTV. TTV was the first human virus with a single stranded circular DNA genome. TTV was considered to be a member of Circoviridae, but others suggested it conformed to a new family. TTV is distinct from ambisense viruses in the genus Circovirus, since the former genome is negative stranded. The genome structure of TTV is more related to chicken anaemia virus in the genus Gyrovirus, however, the sequence similarity is minimal except for a short stretch at 3816-3851 of TA278. Currently the working group is proposing the full name for TTV as TorqueTenoVirus and the TTV-like mini virus as TorqueTenoMiniVirus (TTMV) in a new genus Anellovirus (ring). TTVs are prevalent in non-human primates and human TTV can cross-infect chimpanzees. Furthermore, TTV sequences have been detected in chickens, pigs, cows and sheep. TTV can be transmitted by mother-to-child infection. However, within a year after birth, the prevalence reaches the same level for children born to both TTV-positive and TTV-negative mothers even without breast-feeding. The non-coding region surrounding a short 113 nt GC-rich stretch and occupying approximately one-third of the genome is considered to contain the putative replication origin. Three mRNAs are expressed by TTV, 3.0 and 1.2 and 1.0 kb species. A protein translated from the 3.0 kb mRNA is considered to be the major capsid protein as well as replicase. The nature of the proteins translated by the other two mRNAs are still putative.
Re-evaluating high-frequency oscillation for ARDS: Would a targeted approach be successful? (2013)

High-frequency oscillatory ventilation (HFOV) seems ideal for lung protection in acute respiratory distress syndrome, but randomized trials have not shown a mortality reduction. The initial oxygenation response to HFOV appears to be associated with survival. Here, we discuss the mechanisms of oxygenation response to increases in airway pressure and the interpretation of the oxygenation response observed in the present study.
LOST MERISTEMS genes regulate cell differentiation of central zone descendants in Arabidopsis shoot meristems (2010)

Meristems of seed plants continuously produce new cells for incorporation into maturing tissues. A tightly controlled balance between cell proliferation in the center and cell differentiation at the periphery of the shoot meristem maintains its integrity. Here, we describe the role of three GRAS genes, named LOST MERISTEMS genes, in shoot apical meristem maintenance and axillary meristem formation. Under short photoperiods, the lom1 lom2 and lom1 lom2 lom3 mutants have arrested meristems characterized by an over-proliferation of meristematic cells and loss of polar organization. They also show early arrest of axillary meristem development and formation of ectopic meristematic cell clusters within the stem. LOM1 and LOM2 transcripts accumulate in the peripheral and basal zones of the SAM and in vascular strands. We show that LOM1 and LOM2 promote cell differentiation at the periphery of shoot meristems and help to maintain their polar organization.
Oncogenic function and clinical implications of SLC3A2-NRG1 fusion in invasive mucinous adenocarcinoma of the lung (2016)

The neuregulin 1 (NRG1) fusion is a recently identified novel driver oncogene in invasive mucinous adenocarcinoma of the lung (IMA). After identification of a case of SLC3A2-NRG1 in a patient with IMA, we verified this fusion gene in a cohort of 59 patients with IMA. Targeted cancer panel sequencing and RT-PCR identified the possible coexistence of other driver oncogenes. Among 59 IMAs, we found 16 NRG1 fusions (13 SLC3A2-NRG1 and 3 CD74-NRG1). Of 16 patients with NRG1 fusions, concurrent KRAS codon 12 mutations were found in 10 cases. We also found concurrent NRAS Q61L mutation and EML4-ALK fusion in additional two cases with NRG1 fusions. When comparing overall survival (OS) according to the presence of NRG1 fusions showed that patients harboring NRG1 fusions had significantly inferior OS than those without NRG1 fusions (hazard ratio = 0.286; 95% confidence interval, .094 to .865). Ectopic expression of the SLC3A2-NRG1 fusion in lung cancer cells increased cell migration, proliferation and tumor growth in vitro and in xenograft models, suggesting oncogenic function for the fusion protein. We found that the SLC3A2-NRG1 fusion promoted ERBB2-ERBB3 phosphorylation and heteroduplex formation and activated the downstream PI3K/AKT/mTOR pathway through paracrine signaling. These findings suggested that the SLC3A2-NRG1 fusion was a driver in IMA with an important prognostic impact. SLC3A2-NRG1 should be considered a therapeutic target for patients with IMA.
Real-time plane extraction from depth images with the Randomized Hough Transform (2011)

Depth cameras, like the Microsoft Kinect system, are valuable sensors for mobile robotics since their data enables a highly detailed perception of the environmental structure. Certainly, their amount of data is often too high to be processed in real-time by the limited resources of mobile robots. One way of using these sensors is to reduce the amount of data by extracting features like planes from the raw depth images. In this work we present a method to extract planes from depth images based on the Randomized Hough Transformation, which is specially adapted to the properties of the Kinect sensor. Therefore we use a noise model of the sensor to solve the task of finding proper parameter metrics for the Randomized Hough Transform. As a result, our approach extracts the planes from a depth image in less than one millisecond on the platform of a mobile robot and is therefore real-time capable.
A Genomic Regulatory Network for Development (2002)

Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology. The network contains over 40 genes at present, and each node can be directly verified at the DNA sequence level by cis-regulatory analysis. Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time.
Enzyme-linked immunosorbent assay for detection of immunoglobulin G antibodies to Escherichia coli Vero cytotoxin 1 (1994)

The frequency of Vero cytotoxin 1 (VT1)-neutralizing antibody (NAb) in serum specimens from 790 age-stratified (0 to 70 years) control individuals from Toronto was 61 of 790 (7.7%), with a peak of 19% in the 20- to 30-year-old age group and a second peak of 16.7% in the 60- to 70-year-old age group. A total of 568 serum specimens, including 538 from the 790 Toronto control subjects, 21 from patients from three outbreaks of VT-producing Escherichia coli (VTEC) infection, and 9 known VT1-NAb-positive serum specimens from patients with hemolytic-uremic syndrome (HUS), were then tested for the presence of anti-VT1 immunoglobulin G (IgG) by an enzyme-linked immunosorbent assay (ELISA). The mean ELISA values of 522 VT1-NAb-negative serum specimens and 46 VT1-NAb-positive serum specimens were 0.09 +/- 0.06 (range, 0 to 0.56) and 0.78 +/- 0.66 (range, 0.16 to 2.91), respectively (P < 0.001; Student's t test). With a breakpoint of 0.21 (mean ELISA value of the VT1-NAb-negative sera + 2 standard deviations), the sensitivity, specificity, positive predictive value, and negative predictive value of the VT1 IgG ELISA compared with those of the VT1-NAb assay were, respectively, 95.7, 98.7, 86.3, and 99.6%. There were nine discrepant serum specimens, of which seven were anti-VT1 IgG positive and VT1-NAb negative and two were anti-VT1 IgG negative and VT1-NAb positive. The ELISA was also used for testing 238 control serum specimens from The Netherlands, Japan, and India and acute- and convalescent-phase serum specimens from 42 Toronto patients with HUS. The frequencies of anti-VT1 IgG (with VT1-NAb frequencies in parantheses) in control sera from the Netherlands, Japan, and India were 6% (3%), 1.1% (0%), and 12% (10%), respectively, with no age clustering. The frequencies of anti-VT1 IgG seropositivity in HUS patients were 5 of 14 (35.7%) in patients with unknown toxin exposure, 2 of 22 (9.1%) in individuals with known exposure to VT1 plus VT2 or VT1 alone, and 0 of 6 (0%) in patients exposed to only VT2. Development of serum anti-VT1 IgG response appears to be the exception rather than the rule in sporadic HUS patients infected with VTEC expressing VT1. However, in two family outbreaks associated with VTEC strains expressing VT1 alone and VT1 plus VT2, respectively, the presence of anti-VT1 IgG in virtually all exposed individuals who remained symptom free suggests that the presence of antibody was associated with protection.
Liquid–crystalline aqueous clay suspensions (2006)

This article demonstrates the occurrence of a true isotropic/nematic transition in colloidal Brownian aqueous suspensions of natural nontronite clay. The liquid-crystalline character is further evidenced by polarized light microscopy and small-angle x-ray scattering experiments in the presence and absence of modest external magnetic fields. The complete phase diagram ionic strength/volume fraction then exhibits a clear biphasic domain in the sol region just before the gel transition in contrast with the situation observed for other swelling clays in which the sol/gel transition hinders the isotropic/nematic transition. Small-angle x-ray scattering measurements of gel samples reveal strong positional and orientational orders of the particles, proving unambiguously the nematic character of the gel and, thus, clearly refuting the still prevalent "house of cards" model, which explains the gel structure by means of attractive interactions between clay platelets. Such order also is observed in various other swelling clay minerals; therefore, this very general behavior must be taken into account to reach a better understanding of the rheological properties and phase behavior of these systems.
Hepatocellular carcinoma treated by percutaneous hot saline injection (2004)

Percutaneous ethanol injection therapy (PEI) is one of the local methods widely used for hepatocellular carcinoma (HCC) ablation. However, this method is limited by the toxicity of ethanol and severe pain derived from irritation of the peritoneum of the liver capsule. Therefore, we have focused on the heat coagulation necrosis effect of boiled hot saline and devised percutaneous hot water injection therapy (PHoT) as a new local treatment method. PHoT was performed in 17 patients with HCC (total 24 nodules: 11 nodules <2 cm in diameter, 10 nodules from 2-4 cm, and 3 nodules >4 cm). Changes in the AFP values, and both CT and ultrasonography (US) findings before and after treatment were investigated. All 24 tumors received 1 or more treatments (average, 3.3 treat-ments) of PHoT. The injection volume ranged from 3-26 ml (average, 11.2 ml). The total volume of the injection per tumor ranged from 10-37.2 ml (average, 37.2 ml). The AFP values decreased in all patients who initially showed high values. On CT scanning, all lesions receiving PHoT became hypodense. The disappearance of the tumor was also confirmed by contrast-enhanced CT. No severe complications, excluding mild abdominal pain and skin burning, were observed during the procedure. In conclusion, PHoT shows good anti-tumor effects despite a small number of punctures and holds promise as a curative local treatment method for small HCCs.
<title>Visual similarity analysis of Chinese characters and its uses in Japanese OCR</title> (1995)

Traditionally, a Chinese or Japanese optical character reader (OCR) has to represent each character category individually as one or more feature prototypes, or a structural description which is a composition of manually derived components such as radicals. Here we propose a new approach in which various kinds of visual similarities between different Chinese characters are analyzed automatically at the feature level. Using this method, character categories are related to each other by training on fonts; and character images from a text page can be related to each other based on the visual similarities they share. This method provides a way to interpret character images from a text page systematically, instead of a sequence of isolated character recognitions. The use of the method for post processing in Japanese text recognition is also discussed.
Embolic protection devices in saphenous percutaneous intervention. (2009)

Saphenous veins remain a source of conduit for use in surgical coronary bypass graft revascularisation procedures. Saphenous vein grafts have a progressive closure rate estimated to be 12% to 20% at the end of the first year, and approximately 50% by 10 years. Regarding secondary revascularisation in these cases, reoperation carries substantially increased morbidity and mortality rates, making saphenous coronary intervention, in particular stent implantation, a more attractive means of revascularisation. However, this procedure carries a significant risk of major adverse clinical events, predominantly myocardial infarction or reduced antegrade flow (non-reflow phenomenon), mainly due to distal embolisation of atherothrombotic debris and distal microvascular occlusion. Embolic protection devices are used to reduce the risk of distal embolisation. There are two different designs: filter and occlusion-aspiration devices. In this article we present the different systems of embolic protection devices in saphenous percutaneous intervention and the previously published information is reviewed.
Catalytic Dynamic Kinetic Resolutions with N‐Heterocyclic Carbenes: Asymmetric Synthesis of Highly Substituted β‐Lactones (2012)

New DKR type: An N-heterocyclic carbene (NHC)-catalyzed dynamic kinetic resolution of racemic α-substituted β-keto esters has been developed. This method relies on the epimerization of an NHC-enol intermediate before subsequent aldol/acylation events. Highly substituted β-lactones are produced in good yield with good to excellent selectivities (see scheme).
Vitamin C Facilitates Demethylation of the <i>Foxp3</i> Enhancer in a Tet-Dependent Manner (2016)

Demethylation of CpG motifs in the Foxp3 intronic element, conserved noncoding sequence 2 (CNS2), is indispensable for the stable expression of Foxp3 in regulatory T cells (Tregs). In this study, we found that vitamin C induces CNS2 demethylation in Tregs in a ten-eleven-translocation 2 (Tet2)-dependent manner. The CpG motifs of CNS2 in Tregs generated in vitro by TGF-β (iTregs), which were methylated originally, became demethylated after vitamin C treatment. The conversion of 5-methylcytosin into 5-hydroxymethylcytosin was more efficient, and the methyl group from the CpG motifs of Foxp3 CNS2 was erased rapidly in iTregs treated with vitamin C. The effect of vitamin C disappeared in Tet2(-/-) iTregs. Furthermore, CNS2 in peripheral Tregs in vivo, which were demethylated originally, became methylated after treatment with a sodium-dependent vitamin C transporter inhibitor, sulfinpyrazone. Finally, CNS2 demethylation in thymic Tregs was also impaired in Tet2(-/-) mice, but not in wild type mice, when they were treated with sulfinpyrazone. Collectively, vitamin C was required for the CNS2 demethylation mediated by Tet proteins, which was essential for Foxp3 expression. Our findings indicate that environmental factors, such as nutrients, could bring about changes in immune homeostasis through epigenetic mechanisms.