gebhart/patrepeval huggingface dataset:
Human papillomavirus 6, 11, and 16 in laryngeal papillomas (1991)

Twenty-seven cases of benign laryngeal papillomas, both single and multiple variants, were analysed for human papillomavirus (HPV) by DNA slot-blot hybridization chiefly to determine the pattern of infection in Hong Kong Chinese. DNA was extracted from paraffin blocks of formalin-fixed tissue and probed separately for HPV 6, 11, 16, and 18. Sixteen cases (59 per cent) showed the presence of at least one of these four HPV genomes. Thirteen cases (48 per cent) were positive for HPV 11 only. Three other cases (11 per cent) showed triple positivity for HPV 6, 11, and 16. None were positive for HPV 18. The predominance of HPV 11 infection contrasts with other series which have shown either an almost equal distribution of HPV 6 and 11 or a predominance of HPV 6. The finding of HPV 16 in three cases was unexpected. Using the polymerase chain reaction (PCR) with primers complementary to the upstream regulatory region of the HPV 16 viral DNA, the presence of HPV 16 genome was confirmed in all three cases. As the number of HPV 16-positive cases in this study is small, analysis of more cases using fresh biopsy material and a wider range of HPV type-specific PCR primers is warranted to determine the relative incidence of HPV subtypes in these benign laryngeal papillomas.
Extracellular ATP Functions as an Endogenous External Metabolite Regulating Plant Cell Viability (2005)

ATP is a vital molecule used by living organisms as a universal source of energy required to drive the cogwheels of intracellular biochemical reactions necessary for growth and development. Animal cells release ATP to the extracellular milieu, where it functions as the primary signaling cue at the epicenter of a diverse range of physiological processes. Although recent findings revealed that intact plant tissues release ATP as well, there is no clearly defined physiological function of extracellular ATP in plants. Here, we show that extracellular ATP is essential for maintaining plant cell viability. Its removal by the cell-impermeant traps glucose-hexokinase and apyrase triggered death in both cell cultures and whole plants. Competitive exclusion of extracellular ATP from its binding sites by treatment with beta,gamma-methyleneadenosine 5'-triphosphate, a nonhydrolyzable analog of ATP, also resulted in death. The death response was observed in Arabidopsis thaliana, maize (Zea mays), bean (Phaseolus vulgaris), and tobacco (Nicotiana tabacum). Significantly, we discovered that fumonisin B1 (FB1) treatment of Arabidopsis triggered the depletion of extracellular ATP that preceded cell death and that exogenous ATP rescues Arabidopsis from FB1-induced death. These observations suggest that extracellular ATP suppresses a default death pathway in plants and that some forms of pathogen-induced cell death are mediated by the depletion of extracellular ATP.
ASCO 2011: Prostate Cancer in Older Adults: To Treat or Not to Treat? (2011)

At the session on Management of Prostate Cancer in Older Adults: To Treat or not to Treat, Anthony D’Amico, William Dale, and Shabbir Alibhai all lent their clinical expertise in treating prostate cancer to outline the latest recommendations for screening and treating men for prostate cancer.
Strained silicon on insulator substrates for fully depleted application (2012)

Smart Cut™ technology is used to manufacture Strained-SOI (sSOI) substrates. These substrates are proposed to boost performance for both planar and FinFET Fully Depleted SOI devices. To comply with tight transistor variability requirements, strong emphasis has been put on layer thickness control and low stress variation. A 1.2 Å RMS roughness and less than 10% stress fluctuation are already demonstrated for sSOI wafers.
Conversion of secretory proteins into membrane proteins by fusing with a glycosylphosphatidylinositol anchor signal of alkaline phosphatase (1994)

Placental alkaline phosphatase (PLAP) is initially synthesized as a precursor (proPLAP) with a C-terminal extension. We constructed a recombinant cDNA which encodes a chimeric protein (alpha GL-PLAP) comprising rat alpha 2u-globulin (alpha GL) and the C-terminal extension of PLAP. Two molecular species (25 kDa and 22 kDa) were expressed in the COS-1 cell transfected with the cDNA for alpha GL-PLAP. Only the 22 kDa form was labelled with both [3H]stearic acid and [3H]ethanolamine. Upon digestion with phosphatidylinositol-specific phospholipase C the 22 kDa form was released into the medium, indicating that this form is anchored on the cell surface via glycosylphosphatidylinositol (GPI). A specific IgG raised against a C-terminal nonapeptide of proPLAP precipitated the 25 kDa form but not the 22 kDa form, suggesting that the 25 kDa form is a precursor retaining the C-terminal propeptide. When a mutant alpha GL-PLAP, in which the aspartic acid residue is replaced with tryptophan at a putative cleavage/attachment site, was expressed in COS-1 cells, the 25 kDa precursor was the only form found inside the cell and retained in the endoplasmic reticulum, as judged by immunofluorescence microscopy. In vitro translation programmed with mRNAs coding for the wild-type and mutant forms of alpha GL-PLAP demonstrated that the C-terminal propeptide was cleaved from the wild-type chimeric protein, but not from the mutant one. This gave rise to the 22 kDa form attached with a GPI anchor, suggesting that GPI is covalently linked to the aspartic acid residue (Asp159) of alpha GL-PLAP. Taken together, these results indicate that the C-terminal propeptide of PLAP functions as a signal to render alpha GL a GPI-linked membrane protein in vitro and in vivo in cultured cells, and that the chimeric protein constructed in this study may be useful for elucidating the mechanism underlying the cleavage of the propeptide and attachment of GPI, which occur in the endoplasmic reticulum.
Gene expression profiling of human HBV- and/or HCV-associated hepatocellular carcinoma cells using expressed sequence tags (2006)

Liver cancer is one of the leading causes of cancer death worldwide. To identify novel target genes that are related to liver carcinogenesis, we examined new genes that are differentially expressed in human hepatocellular carcinoma (HCC) cell lines and tissues based on the expressed sequence tag (EST) frequency. Eleven libraries were constructed from seven HCC cell lines and three normal liver tissue samples obtained from Korean patients. An analysis of gene expression profiles for HCC was performed using the frequency of ESTs obtained from these cDNA libraries. Genes were identified (n=120) as being either up- or down-regulated in human liver cancer cells. Among these, 14 genes (FTL, K-ALPHA1, LDHA, RPL4, ENO1, ANXA2, RPL9, RPL10, RPL13A, GNB2L1, AMBP, GC, A1BG, and SERPINC1), in addition to previously well-known liver cancer related genes, were confirmed to be differentially expressed in seven liver cancer cell lines and 17 HCC tissues by semi-quantitative RT-PCR. In addition, 73 genes, in which there was a significant difference (P>0.99) between HBV- and HCV-associated HCC cells, were selected. Of these, expression patterns of 14 (RPLP0, AKR1C, KRT8, GPX4, RPS15, ID1, RPS21, VIM, EEF1G, EIF4A1, HLA-C, FN1, CD44, and RPS10) were confirmed by semi-quantitative RT-PCR in four of HBV- and three of HCV-associated HCC cell lines. Among those genes, an immunohistochemical analysis for ANXA2 showed that it is expressed at high levels in HCC. Using an analysis of EST frequency, the newly identified genes, especially ANXA2, represent potential biomarkers for HCC and useful targets for elucidating the molecular mechanisms associated with HCC involving virological etiology.
A Label-Free Silicon Quantum Dots-Based Photoluminescence Sensor for Ultrasensitive Detection of Pesticides (2013)

Sensitive, rapid, and simple detection methods for the screening of extensively used organophosphorus pesticides and highly toxic nerve agents are in urgent demand. A novel label-free silicon quantum dots (SiQDs)-based sensor was designed for ultrasensitive detection of pesticides. This sensing strategy involves the reaction of acetylcholine chloride (ACh) with acetylcholinesterase (AChE) to form choline that is in turn catalytically oxidized by choline oxidase (ChOx) to produce betaine and H2O2 which can quench the photoluminescence (PL) of SiQDs. Upon the addition of pesticides, the activity of AChE is inhibited, leading to the decrease of the generated H2O2, and hence the PL of SiQDs increases. By measuring the increase in SiQDs PL, the inhibition efficiency of pesticide to AChE activity was evaluated. It was found that the inhibition efficiency was linearly dependent on the logarithm of the pesticides concentration. Consequently, pesticides, such as carbaryl, parathion, diazinon, and phorate, were determined with the SiQDs PL sensing method. The lowest detectable concentrations for carbaryl, parathion, diazinon, and phorate reached 7.25 × 10(-9), 3.25 × 10(-8), 6.76 × 10(-8), and 1.9 × 10(-7) g/L, respectively, which were much lower than those previously reported. The detecting results of pesticide residues in food samples via this method agree well with those from high-performance liquid chromatography. The simple strategy reported here should be suitable for on-site pesticides detection, especially in combination with other portable platforms.
Analysis and Improvement of MM-Wave GaAs MESFET's (1988)

Abstract : A two-dimensional computer model, which takes into account the non- stationary conditions, is used to investigate several aspects of the GaAs submicron-gate MESFET. First, this model is used to evaluate the effects of carrier injection into the MESFET buffer-layer. It is shown that the carrier of injection reduces the transconductance and increases the output conductance. One of the ways to reduce the carrier injection is to introduce a potential-barrier between the active-layer and the substrate. Therefore, the MESFET grown on a P- substrate is studied. It is shown that a high acceptor concentration in the substrate depletes large part of the active-layer and greatly reduces the output current. A more flexible design can be obtained by introducing a thin P-layer between the active-layer and the semi-insulating substrate. This model is also used in investigating the traveling Gunn domain phenomenon in GaAs MESFET's. It is shown that traveling domains exist in MESFET's with relatively thick active- layers. The propagation characteristics of these domains are studied in detail. A new structure called Inverted-Gate FET (INGFET) is studied as well. This structure has equal input and output reactances. Hence, it relaxes the restriction on the device width which becomes very severe in the mm-wave range. Another structure that employs carrier injection over an N+i junction and possesses equal input and output reactances is analyzed. It is called Inverted- Gate-Injection FET (INGIFET). The potential characteristics of the INGIFET are compared with those of the INGFET as well as the coplanar MESFET.
Enhanced Fault-Tolerant Data Latches for Deep Submicron CMOS. (2005)

CMOS data latches used in critical applications must be immune to soft errors such as single event upsets. Existing designs protect the stored data against errors in the internal nodes, but may be vulnerable to transient faults in the control and data lines. The problem becomes more severe as feature sizes decrease. In this paper, we enhance the Dual Interlocked Storage Cell (DICE) to withstand soft errors at any node. We expand our scheme to encompass five fault-tolerant memory cells: one optimized for pipeline latches, and the others for SRAM. The designs have been verified through extensive layout simulations in 180-nm CMOS. Compared to the original DICE, the proposed cells can withstand a broader class of transient faults, but consume more energy during read and write operations. We explore the tradeoff between energy consumption and the number of redundant control lines required.
Mechanism of skin photosensitization by forucoumarins. Photoreactivity of various furocouma- rins with native DNA and with ribosomal RNA. (1970)

Abstract The photoreactions (by irradiation at 365 nm) between several furocoumarins and native DNA or rRNA have been studied. The initial rates of the photoreactions and the quantum yields were determined. Moreover some experiments have been performed in a manner suitable to give data of photoreactivity which could be directly compared with those previously obtained in determining the skin-photosensitizing activity of the same substances by irradiation at 365 nm. The results showing a close correlation between the capacity of the substances to photoreact with native DNA and that to produce skin photosensitization, offer valid evidence for the mechanism of action of furocoumarins on the skin. By contrast, the photoreactions with rRNA seem to be less (or not) connected with skin photosensitization.
Validation of the shake test for detecting freeze damage to adsorbed vaccines (2010)

The shake test had 100% sensitivity, 100% specificity and 100% positive predictive value in this study, which confirms its validity for detecting freeze damage to aluminium-based freeze-sensitive vaccines.
Paenibacillus lactis sp. nov., isolated from raw and heat-treated milk (2004)

Endospore-forming bacteria were recovered from individual packages from different processing lines in a dairy plant during a tenacious periodical contamination of their UHT-milk production. Two colony types were seen, one of which was identified as Bacillus sporothermodurans. Analysis of the 16S rRNA gene of the second colony type placed these isolates within the genus Paenibacillus, with Paenibacillus lautus as the closest known relative. Moreover, over 99 % similarity was observed to the 16S rDNA sequence of MB 2035, a strain isolated previously from raw milk during a survey at dairy farms for very heat-resistant spore-forming bacteria. Nine other potentially closely related strains among the dairy farm isolates were found using rep-PCR typing. The taxonomic positions of these 19 isolates were further investigated using 16S rRNA gene sequencing and DNA-DNA hybridizations of representative strains. All 19 isolates shared a high degree of phenotypic similarity and were easily distinguished from closely related members of the genus. Anteiso-C(15 : 0), C(16 : 0) and iso-C(15 : 0) were among the major fatty acids and the genomic DNA G+C content was 51.6-51.7 mol%. Therefore, based on their phenotypic, phylogenetic and genomic distinctiveness, these 19 strains, isolated from both raw and heat-treated milk, are placed in the genus Paenibacillus as Paenibacillus lactis sp. nov. The type strain is MB 1871(T) (=LMG 21940(T)=DSM 15596(T)).
Stability of spiral wave vortex filaments with phase twists (1998)

In this paper we investigate the stability of a straight vortex filament with phase twist described by the three-dimensional complex Ginzburg-Landau equation (CGLE). The results of the linear stability analysis show that the straight filament is stable in a limited region of the two parameter space of the CGLE. The stable region is dependent on the phase twist imposed on the filament and shrinks in size as the phase twist is increased. It is also shown numerically that the nonlinear evolution of an unstable initial straight filament can lead to a helical filament.
Methods for Probing Lysosomal Membrane Permeabilization (2015)

Cell death triggered by lysosomal membrane permeabilization (LMP) is gaining increased interest as target for cancer therapy, but the death pathway also plays an important role in normal physiology (e.g., during involution of the mammary gland). LMP-induced cell death is triggered by release of hydrolases including cysteine cathepsin proteases from the lysosomal lumen into the cytosol. Limited release of proteases to the cytoplasm induces apoptosis or apoptosis-like cell death, whereas massive LMP results in rapid cellular necrosis. Here we introduce three complementary methods for quantifying and visualizing LMP: (i) monitoring LMP by immunocytochemistry, (ii) visualizing LMP by fluorescent dextran release, and (iii) quantification of LMP by activity measurements of lysosomal enzymes in digitonin-extracted cytosol.
Enzyme electrode for determining glucose in whole blood. (1988)

In this sensor for glucose in whole blood, glucose oxidase (EC 1.1.3.4) is directly coupled to a platinum electrode by a silane coupling agent and glutaraldehyde. This very thin catalytic layer is then coated with a thin rubber membrane. The response to glucose in whole blood varies linearly with glucose concentration to at least 6000 mg/L with a small positive intercept. The response time is a few minutes. The key factor in the success of this sensor is the unitized construction, with both membrane and enzyme chemibonded to the electrode. The compatibility with whole blood and the high oxygen permeability of the membrane also contribute to the good performance. The coefficient of variation in replication (glucose concentration 1 g/L, n = 13) is about 3%. The sensor is insensitive to hematocrit and has a lifetime of several days after initial use.
Congestion Aware High Level Synthesis Combined with Floorplanning (2008)

As VLSI gets large and complicated, routing congestion becomes more and more difficult to handle. In the traditional design flow, very little physical information is available at the high-level synthesis stage. To decrease the routing congestion and improve circuit’s performance, we propose a routing congestion aware high level synthesis method, which is based on simulated annealing (SA) algorithm. The method has two loops, the inner loop is a practical iteration, and the outer loop is a gradually cooling process. After the high level synthesis, we accept or reject the new result according to the cost function value which is obtained by fore-placement. Experimental results show that our method is more effective than traditional method and CRSF (Congestion driven re-synthesis after floorplanning ) algorithm.
Prevention of coronary artery reocclusion and reduction in late coronary artery stenosis after thrombolytic therapy in patients with acute myocardial infarction. A randomized study of maintenance infusion of recombinant human tissue-type plasminogen activator. (1988)

Sixty-eight patients with acute "transmural" myocardial infarction presenting within 6 hours (range, 1.3-5.8 hours) of onset of chest pain were given intravenous recombinant tissue-type plasminogen activator (rt-PA) at a dosage of 1 mg/kg during 90 minutes. Coronary angiography at 90 minutes revealed a patent infarct-related coronary artery in 52 patients (76%). These patients were randomized either to treatment by continuous infusion of heparin alone (27 patients) or to treatment by heparin and a maintenance infusion of rt-PA at a dosage of 0.8 mg/kg during 4 hours (25 patients). Coronary angiography was repeated 60 minutes after the start of the maintenance infusion and again after 8-14 days. Acute symptomatic reocclusion of the infarct-related artery occurred during the 1-hour observation period in five (19%) patients treated with heparin alone but in none of the patients treated with rt-PA (p = 0.05). The measured residual stenosis of the patent infarct-related coronary artery was similar in the heparin-treated and the rt-PA-treated groups at 90 minutes infusion: 66 +/- 14% versus 68 +/- 13% diameter stenosis, respectively (mean +/- SD) and 1.1 +/- 1.1 mm2 versus 0.82 +/- 0.7 mm2 area (p = 0.35). At 8-14 days after infusion, residual stenosis was unchanged in the heparin-treated group, but it improved to 55 +/- 17% (p = 0.001) and 1.6 +/- 1.2 mm2 (p = 0.003) in the rt-PA-treated group. At 90 minutes of infusion, residual intraluminal thrombus was observed in 29 of the 52 patients (56%) with a comparably measured distribution in the two groups (p = 0.43). At 150 minutes, however, the extent of intraluminal thrombus was significantly reduced in the rt-PA-treated group as compared with the heparin-treated group (p = 0.03). In-hospital ischemic events (symptomatic reocclusion, unstable angina, or cardiovascular death) occurred in 12 patients of the heparin-treated group but only in three patients of the rt-PA-treated group (p = 0.03). Fibrinogen levels decreased to 65 +/- 21% of baseline at 90 minutes of rt-PA infusion. During the rt-PA maintenance infusion, fibrinogen fell slightly from 63 +/- 26 to 57 +/- 28% (p = 0.18). This study shows that after successful reperfusion with 1 mg/kg rt-PA during 90 minutes, a maintenance infusion of 0.8 mg/kg rt-PA during 4 hours prevents acute symptomatic coronary artery reocclusion, and it reduces the frequency of ischemic events and the severity of residual coronary artery stenosis at hospital discharge.
Difficulties in Recruiting Participants for a Research Study on Immigrant Dementia Caregiver (2007)

(2007). Difficulties in Recruiting Participants for a Research Study on Immigrant Dementia Caregiver. Journal of Immigrant & Refugee Studies: Vol. 5, No. 4, pp. 103-108.
Gut Microbiota Dysbiosis Associated With Altered Production of Short Chain Fatty Acids in Children With Neurodevelopmental Disorders (2020)

While gut microbiota dysbiosis has been linked with autism, its role in the etiology of other neurodevelopmental disorders (NDD) is largely underexplored. To our knowledge this is the first study to evaluate gut microbiota diversity and composition in 36 children from the Republic of Serbia diagnosed with NDD and 28 healthy children. The results revealed an increased incidence of potentially harmful bacteria, closely related to <i>Clostridium</i> species, in the NDD patient group compared to the Control group: <i>Desulfotomaculum guttoideum</i> (<i>P</i> < 0.01), <i>Intestinibacter bartlettii</i> (<i>P</i> < 0.05), and <i>Romboutsia ilealis</i> (<i>P</i> < 0.001). On the other hand, significantly lower diversity of common commensal bacteria in the NDD group of patients was noticed. <i>Enterococcus faecalis</i> (<i>P</i> < 0.05), <i>Enterococcus gallinarum</i> (<i>P</i> < 0.01), <i>Streptococcus pasteurianus</i> (<i>P</i> < 0.05), <i>Lactobacillus rhamnosus</i> (<i>P</i> < 0.01) and <i>Bifidobacteria</i> sp. were detected in lower numbers of patients or were even absent in some NDD patients. In addition, butyrate-producing bacteria <i>Faecalibacterium prausnitzii</i> (<i>P</i> < 0.01), <i>Butyricicoccus pullicaecorum</i> (<i>P</i> < 0.05), and <i>Eubacterium rectale</i> (<i>P</i> = 0.07) were less frequent in the NDD patient group. In line with that, the levels of fecal short chain fatty acids (SCFAs) were determined. Although significant differences in SCFA levels were not detected between NDD patients and the Control group, a positive correlation was noted between number of rDNA amplicons obtained with universal primers and level of propionic acid, as well as a trend for levels of total SCFAs and butyric acid in the Control group. This correlation is lost in the NDD patient group, indicating that NDD patients' microbiota differs from the microbiota of healthy children in the presence or number of strong SCFA-producing bacteria. According to a range-weighted richness index it was observed that microbial diversity was significantly lower in the NDD patient group. Our study reveals that the intestinal microbiota from NDD patients differs from the microbiota of healthy children. It is hypothesized that early life microbiome might have an impact on GI disturbances and accompanied behavioral problems frequently observed in patients with a broad spectrum of NDD.