gebhart/patrepeval huggingface dataset:
NET - A System for Extracting Web Data from Flat and Nested Data Records (2005)

Abstract. This paper studies automatic extraction of structured data from Web pages. Each of such pages may contain several groups of structured data records. Existing automatic methods still have several limitations. In this paper, we propose a more effective method for the task. Given a page, our method first builds a tag tree based on visual information. It then performs a post-order traversal of the tree and matches subtrees in the process using a tree edit distance method and visual cues. After the process ends, data records are found and data items in them are aligned and extracted. The method can extract data from both flat and nested data records. Experimental evaluation shows that the method performs the extraction task accurately. 1
Simultaneous Amplification of HER-2 (ERBB2) and Topoisomerase II&#945; (TOP2A) Genes - Molecular Basis for Combination Chemotherapy in Cancer (2006)

The HER-2 (also known as ERBB2/ErbB2/c-erbB2/HER-2/neu) oncogene is the most frequently amplified oncogene in breast cancer and is also amplified in other forms of cancer. Beside its important role in tumor induction, growth and progression, HER-2 is also a target for new therapeutic approaches such as Herceptin (trastuzumab), a recombinant antibody designed to block signaling through the HER-2 receptor. In addition to Herceptin, which is in a wide clinical use for HER-2 amplified breast cancer, a number of various HER-2 directed immunological and genetic strategies, either targeting the HER-2 receptor, its signaling pathways or both HER-2 and epidermal growth factor receptor (EGFR) simultaneously, have demonstrated promising pre-clinical activity in HER-2 amplified carcinomas. Moreover, the HER-2 amplicon is known to contain more than 30 genes with altered copy numbers that could be therapeutic targets for chemotherapy. The topoisomerase IIalpha gene, TOP2A, is located adjacent to the HER-2 oncogene at the chromosome location 17q12-q21 and is either amplified or deleted (with equal frequency) in a great majority of HER-2 amplified primary breast tumors and also in tumors without HER-2 amplification. Recent experimental as well as numerous, large, multi-center trials suggest that amplification (and/or deletion) of TOP2A may account for both sensitivity or resistance to commonly used cytotoxic drugs, i.e. topoII-inhibitors (anthracyclines etc.), depending on the specific genetic defect at the TOP2A locus. The understanding of HER-2 amplification and its role in the pathogenesis of cancer is expanding, and a number of therapeutic strategies targeting either the HER-2 or its signaling pathways in cancer therapy are being investigated. Combining HER-2 targeting therapies with conventional forms of cytotoxic chemotherapy, where additional diagnostic tests such as those ascertaining TOP2A status, may be helpful for the ideal selection of patients for the combination therapy of an HER-2 targeting drug together with a cytotoxic drug such as topoII-inhibitor especially in the case of TOP2A amplification.
Rice SPK, a Calmodulin-Like Domain Protein Kinase, Is Required for Storage Product Accumulation during Seed Development (2002)

Suc, an end product of photosynthesis, is metabolized by Suc synthase in sink organs as an initial step in the biosynthesis of storage products. Suc synthase activity is known to be regulated by reversible phosphorylation, but the details of this process are unclear at present. Rice SPK, a calcium-dependent protein kinase, is expressed uniquely in the endosperm of immature seed, and its involvement in the biosynthetic pathways of storage products was suggested. Antisense SPK transformants lacked the ability to accumulate storage products such as starch, but produced watery seed with a large amount of Suc instead, as the result of an inhibition of Suc degradation. Analysis of in vitro phosphorylation indicated that SPK phosphorylated specifically a Ser residue in Suc synthase that has been shown to be important for its activity in the degradation of Suc. This finding suggests that SPK is involved in the activation of Suc synthase. It appears that SPK is a Suc synthase kinase that may be important for supplying substrates for the biosynthesis of storage products.
The Uses of Duckweed (1978)

Among the various approaches to improving present technologies for waste-water treatment, several involve the use of plants, which can remove pollutants and provide materials useful as animal feeds or energy sources. Various aquatic plants are being proposed in such approaches, and the duckweeds in particular, an essentially unique group of higher aquatic plants, might be especially advantageous in such systems. Although this article focuses on only this one group of plants, it can nevertheless provide an introduction to issues that are both scientifically challenging and existentially inescapable.
Kinetic potentiometric determination of creatinine in serum with a picrate ion-selective membrane electrode. (1981)

We describe a new kinetic method for potentiometric determination of creatinine in serum, based on the creatinine--picrate reaction in alkaline medium (Jaffé reaction). The reaction is monitored with a picrate-selective electrode, and the increase in electrode potential during 270 s is measured and related directly to the creatinine concentration. Small cation-exchange columns are used to separate creatinine from interfering substances. Analytical recovery of creatinine added to serum was 100.7%. Results for a series of samples compared well with results obtained with a spectrophotometric method (r = 0.994).
The <i>sigA</i> Gene Which Is Borne on the <i>she</i> Pathogenicity Island of <i>Shigella flexneri</i> 2a Encodes an Exported Cytopathic Protease Involved in Intestinal Fluid Accumulation (2000)

In this study, the sigA gene situated on the she pathogenicity island of Shigella flexneri 2a was cloned and characterized. Sequence analysis showed that sigA encodes a 139.6-kDa protein which belongs to the SPATE (serine protease autotransporters of Enterobacteriaceae) subfamily of autotransporter proteins. The demonstration that SigA is autonomously secreted from the cell to yield a 103-kDa processed form and possesses a conserved C-terminal domain for export from the cell were consistent with the autotransporter pathway of secretion. Functional analysis showed that SigA is a secreted temperature-regulated serine protease capable of degrading casein. SigA was cytopathic for HEp-2 cells, suggesting that it may be a cell-altering toxin with a role in the pathogenesis of Shigella infections. SigA was at least partly responsible for the ability of S. flexneri to stimulate fluid accumulation in ligated rabbit ileal loops.
Seismic Facies Identification and Classification Using Simple Statistics (2005)

Abstract The identification and mapping of rock facies is important to reliable reservoir characterization. Traditionally, facies identification and mapping is based on inspection of core data and/or well-log signatures, a procedure that has subjective aspects as it is relies on samples from only a very small portion of the reservoir. Such identification is also difficult to perform at the onset of the exploration stage due to lack of sufficient well data. This paper demonstrates a simple, practical approach to identify and classifiy facies from seismic amplitude data using basic statistical concepts. Within a geologic facies, measured properties (in this case acoustic impedance or AI) are assumed to differ mainly as a result of random additive events and are modeled by a normal distribution, as justified by the central limit theorem. The facies are identified by estimating the combination of facies volume fractions and distribution parameters (means and standard deviations of the facies probability density function), that best fit the population distribution of AI. A simple form of Bayes theorem is then used to compute the probability of occurrence of each of the facies at the measured locations. This generates a volume of facies probabilities corresponding to the seismic volume. Such a volume can be used to perform facies-specific petrophysical analysis or be a starting point to generate multiple realizations of petrophysical properties. The approach is easy and transparent to use with no significant computational requirements even on large data sets. We describe an application of the procedure to a synthetic reference data set and a Gulf of Mexico AI data set. Mapped probabilities of the individual facies show the spatial continuity and geologic character of the underlying depositional environment. Property values within the mapped regions are substantially less variable than the original data over the entire region. The within-facies semivariograms exhibit much less spatial correlation than across all facies. Since the facies are mapped over an exhaustive data volume, this approach considerably reduces the need for the geostatistical construction of property distributions within them as long as a high correlation exists between the seismic attribute and petrophysical properties.
Regulation of the Low Molecular Weight Phosphotyrosine Phosphatase by Phosphorylation at Tyrosines 131 and 132 (1997)

Activation of resting T lymphocytes is initiated by rapid but transient tyrosine phosphorylation of a number of cellular proteins. Several protein tyrosine kinases and protein tyrosine phosphatases are known to be important for this response. Here we report that normal T lymphocytes express the B isoform of low molecular weight protein tyrosine phosphatase B (LMPTP-B). The cDNA was cloned from Jurkat T cells, and an antiserum was raised against it. LMPTP immunoprecipitated from resting Jurkat T cells was found to be tyrosine phosphorylated. On stimulation of the cells through their T cell antigen receptor, the phosphotyrosine content of LMPTP-B declined rapidly. In co-transfected COS cells, Lck and Fyn caused phosphorylation of LMPTP, whereas Csk, Zap, and Jak2 did not. Most of the phosphate was located at Tyr-131, and some was also located at Tyr-132. Incubation of wild-type LMPTP with Lck and adenosine 5'-O-(thiotriphosphate) caused a 2-fold increase in the activity of LMPTP. Site-directed mutagenesis showed that Tyr-131 is important for the catalytic activity of LMPTP, and that thiophosphorylation of Tyr-131, and to a lesser degree Tyr-132, is responsible for the activation.
Improved Sensitivity in Patients with Peripheral Neuropathy (2005)

The medical records of 1,047 patients (mean age, 73 years) with established peripheral neuropathy were examined to determine whether treatment with monochromatic infrared photo energy was associated with increased foot sensitivity to the 5.07 Semmes-Weinstein monofilament. The peripheral neuropathy in 790 of these patients (75%) was due to diabetes mellitus. Before treatment with monochromatic infrared photo energy, of the ten tested sites (five on each foot), a mean +/- SD of 7.9 +/- 2.4 sites were insensitive to the 5.07 Semmes-Weinstein monofilament, and 1,033 patients exhibited loss of protective sensation. After treatment, the mean +/- SD number of insensate sites on both feet was 2.3 +/- 2.4, an improvement of 71%. Only 453 of 1,033 patients (43.9%) continued to have loss of protective sensation after treatment. Therefore, monochromatic infrared photo energy treatment seems to be associated with significant clinical improvement in foot sensation in patients, primarily Medicare aged, with peripheral neuropathy. Because insensitivity to the 5.07 Semmes-Weinstein monofilament has been reported to be a major risk factor for diabetic foot wounds, the use of monochromatic infrared photo energy may be associated with a reduced incidence of diabetic foot wounds and amputations.
Resolution of organ fibrosis (2018)

Fibrosis is the excessive accumulation of extracellular matrix that often occurs as a wound healing response to repeated or chronic tissue injury, and may lead to the disruption of organ architecture and loss of function. Although fibrosis was previously thought to be irreversible, recent evidence indicates that certain circumstances permit the resolution of fibrosis when the underlying causes of injury are eradicated. The mechanism of fibrosis resolution encompasses degradation of the fibrotic extracellular matrix as well as elimination of fibrogenic myofibroblasts through their adaptation of various cell fates, including apoptosis, senescence, dedifferentiation, and reprogramming. In this Review, we discuss the present knowledge and gaps in our understanding of how matrix degradation is regulated and how myofibroblast cell fates can be manipulated, areas that may identify potential therapeutic approaches for fibrosis.
Efficacy of Iron Chelators on Campylobacter Concentrations in Turkey Semen (2006)

Campylobacter is a leading bacterial cause of human foodborne infections in the United States. Recent studies suggest that the organism is highly prevalent in poultry semen and may contribute to vertical transmission between the breeder hen and offspring. Because Campylobacter requires iron for its growth and survival, the objective of this study was to determine if the addition of natural and synthetic chelators such as ovotransferrin, desferrioxaime, EDTA, or 2,2'-dipyridyl could reduce or eliminate Campylobacter in turkey semen. In a preliminary study without semen, a commercial poultry semen extender was supplemented with various concentrations of ovotransferrin, desferrioxaime, EDTA, or 2,2'-dipyridyl and inoculated with an average of 10(8) cfu/mL of a wild-type Campylobacter coli turkey semen isolate. At 6 and 24 h of storage at 4 degrees C, a sample was taken from each treatment group and enumerated for Campylobacter. In all 3 trials, Campylobacter was undetectable (< 10(2)) in the commercial poultry semen extender supplemented with 20 mg/mL of 2,2'-dipyridyl. There were no differences observed in Campylobacter concentrations in the commercial poultry semen extender supplemented with ovotransferrin, desferrioxaime, or EDTA compared with unsupplemented controls. In a follow-up study, pooled semen samples were randomly collected from toms, diluted with a commercial poultry semen extender supplemented with 5, 10, or 20 mg/mL of 2,2'-dipyridyl and inoculated with an average of 10(8) cfu/mL of a wild-type C. coli turkey semen isolate. At 6 and 24 h of storage at 4 degrees C, samples were taken from each treatment group, enumerated for Campylobacter, and evaluated for sperm viability. In all 3 trials, supplementing the commercial poultry semen extender with 20 mg/mL of 2,2'-dipyryidyl significantly reduced (3 to 4 logs) Campylobacter concentrations when compared with the positive controls. Sperm viability was also reduced with this treatment, and, therefore, the use of 2,2'-dipyridyl may not be a practical treatment for reducing Campylobacter in poultry semen.
Investigation of electron-hole generation in mos capacitors on 4h sic (2003)

This paper investigates electron-hole generation in n-type MOS capacitors on 4H-SiC with the gate oxide directly grown in either 100% NO or 10% N/sub 2/O. High-temperature capacitance-transient measurements were used to determine and compare the contributions of carrier generation in the bulk and at the SiO/sub 2/-SiC interface. The effective generation rate in the bulk is similar in the MOS capacitors with either type of gate oxide, whereas the effective surface-generation rate is much lower in the case of oxides grown in 100% NO. Moreover, the effective surface-generation rate in these oxides is reduced to the level that is comparable to the effective bulk-generation rate. This result demonstrates the high quality of MOS capacitors with the gate oxide directly grown in 100% NO.
Kinetically Controlled Seeded Growth Synthesis of Citrate-Stabilized Gold Nanoparticles of up to 200 nm: Size Focusing versus Ostwald Ripening (2011)

Monodisperse citrate-stabilized gold nanoparticles with a uniform quasi-spherical shape of up to ∼200 nm and a narrow size distribution were synthesized following a kinetically controlled seeded growth strategy via the reduction of HAuCl(4) by sodium citrate. The inhibition of any secondary nucleation during homogeneous growth was controlled by adjusting the reaction conditions: temperature, gold precursor to seed particle concentration, and pH. This method presents improved results regarding the traditional Frens method in several aspects: (i) it produces particles of higher monodispersity; (ii) it allows better control of the gold nanoparticle size and size distribution; and (iii) it leads to higher concentrations. Gold nanoparticles synthesized following this method can be further functionalized with a wide variety of molecules, hence this method appears to be a promising candidate for application in the fields of biomedicine, photonics, and electronics, among others.
Enhancement of in Vitro and in Vivo Function of Agarose-Encapsulated Porcine Islets by Changes in the Islet Microenvironment (2013)

The transplantation of porcine islets of Langerhans to treat type 1 diabetes may provide a solution to the demand for insulin-producing cells. Porcine islets encapsulated in agarose-agarose macrobeads have been shown to function in nonimmunosuppressed xenogeneic models of both streptozotocin-induced and autoimmune type 1 diabetes. One advantage of agarose encapsulation is the ability to culture macrobeads for extended periods, permitting microbiological and functional assessment. Herein we describe optimization of the agarose matrix that results in improved islet function. Porcine islets (500 IEQs) from retired breeding sows were encapsulated in 1.5% SeaKem Gold (SG), 0.8% SG, or 0.8% Litex (Li) agarose, followed by an outer capsule of 5% SG agarose. Insulin production by the encapsulated islets exhibited an agarose-specific effect with 20% (0.8% SG) to 50% (0.8% Li) higher initial insulin production relative to 1.5% SG macrobeads. Insulin production was further increased by 40-50% from week 2 to week 12 in both agarose types at the 0.8% concentration, whereas islets encapsulated in 1.5% SG agarose increased insulin production by approximately 20%. Correspondingly, fewer macrobeads were required to restore normoglycemia in streptozotocin-induced diabetic female CD(SD) rats that received 0.8% Li (15 macrobeads) or 0.8% SG (17 macrobeads) as compared to 1.5% SG (19 macrobeads). Islet cell proliferation was also observed during the first 2 months postencapsulation, peaking at 4 weeks, where approximately 50% of islets contained proliferative cells, including β-cells, regardless of agarose type. These results illustrate the importance of optimizing the microenvironment of encapsulated islets to improve islet performance and advance the potential of islet xenotransplantation for the treatment of type 1 diabetes.
Quantum dynamics of simple systems : the Forty-Fourth Scottish Universities Summer School in Physics, Stirling, August 1994 (1996)

Introduction to models on constant negative curvature surfaces, Eugene B. Bogomolny cavity quantum electrodynamics, Michel Brune and Serge Haroche coherent interactions of two trapped ions, Ralph DeVoe two-photon decay of metastable atomic hydrogen and Bell's inequality, Alan J. Duncan studies of fundamental interactions using molecules, Ed A. Hinds quantum fluctuations and applications of squeezed light, H.J. Kimble and G.-L. Oppo quantum superpositions in dissipative environments - decoherence and deconstruction, Peter L. Knight and Barry M. Garraway optical physics of quantum wells, David A.B. Miller simple quantum dynamics, Stig Stenholm atomic hydrogen in magnetostatic traps, Jook T.M. Walraven.
The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota (2017)

The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.
Serum levels of the c-erbB-2 (HER2/neu) encoded oncoprotein fragment p105 in normal pregnancies. (1997)

The c-erbB-2 encoded oncoprotein p185 is overexpressed in fetal epithelial cells, in the placenta, and in several human carcinomas. Elevated serum levels of the 105 kD extracellular part are found in cancer patients and in pregnancy. Our purpose was to examine whether there is a characteristic development of p105 serum levels in the course of normal pregnancy. Using ELISA, we measured the p105 serum concentrations in nonpregnant women, women with normal pregnancy in the 1st, 2nd, and 3rd trimester and pueperas. Compared to nonpregnant women, we found a significant decrease in p105 in the 1st and 2nd trimester, followed by a significant increase in the 3rd trimester. Post partum serum values returned to the levels found in nonpregnant women. The clinical judgment of female p105 serum values requires comparison with the normal range of random samples, and the consideration of pregnancy and the age of gestation as in vivo influencing factors.
The Structure and Functions of Cetacean Schools. (1979)

Contents: Food Related Activity; Reproduction and Growth; Social Integration and Communication; Learning, Protective Behavior; and Responses to Environmental Cycles.
A Novel Sm(II)-Induced Route to Highly Substituted Benzannulated Cyclooctanol Derivatives (1997)

Siloxycyclopropane derivatives 3 with a suitable styrene side chain can effectively be ring opened to precursors 2 which undergo reductive ring closure with SmI2 to furnish benzannulated cyclooctanols 1 or lactones 7 derived thereof. Tricyclic lactone 7c can be further substituted by conversion into a bridgehead enolate and reactions with electrophiles.