gebhart/patrepeval huggingface dataset:
Review article: bacterial flora and pathogenesis in hepatic encephalopathy (2007)

The aetiology of hepatic encephalopathy has not been conclusively established, but it is widely agreed that ammonia derived primarily from enteric bacterial flora plays a central role. Recent research on the pathogenesis of hepatic encephalopathy reinforces previous findings, supporting an integral role of bacteria-derived ammonia and reveals other potential mechanisms by which bacterial flora and pathogens may be pathophysiologically important. This review discusses this research and considers its implications for the therapeutic management of hepatic encephalopathy. Besides producing ammonia, the enteric flora generates other neurotoxic products, such as phenols and mercaptans, that may potentiate the effects of ammonia. Bacteria may also constitute a primary source of the benzodiazepine-like compounds implicated in neuropsychiatric symptoms in patients with liver disease. New evidence suggests that acute bacterial infections, long recognized as important precipitants of hepatic encephalopathy, may mediate clinical worsening through effects on systemic inflammatory responses. Considered together, these data suggest wide-ranging pathophysiological contributions of bacteria to hepatic encephalopathy and underline the potential for an integral role of antibiotics and other bactericidal agents in its management.
DICER/AGO-dependent epigenetic silencing of D4Z4 repeats enhanced by exogenous siRNA suggests mechanisms and therapies for FSHD (2015)

Facioscapulohumeral muscular dystrophy (FSHD) is caused by the aberrant expression of the DUX4 transcription factor in skeletal muscle. The DUX4 retrogene is encoded in the D4Z4 macrosatellite repeat array, and smaller array size or a mutation in the SMCHD1 gene results in inefficient epigenetic repression of DUX4 in skeletal muscle, causing FSHD1 and FSHD2, respectively. Previously we showed that the entire D4Z4 repeat is bi-directionally transcribed with the generation of small si- or miRNA-like fragments and suggested that these might suppress DUX4 expression through the endogenous RNAi pathway. Here we show that exogenous siRNA targeting the region upstream of the DUX4 transcription start site suppressed DUX4 mRNA expression and increased both H3K9 methylation and AGO2 recruitment. In contrast, similarly targeted MOE-gapmer antisense oligonucleotides that degrade RNA but do not engage the RNAi pathway did not repress DUX4 expression. In addition, knockdown of DICER or AGO2 using either siRNA or MOE-gapmer chemistries resulted in the induction of DUX4 expression in control muscle cells that normally do not express DUX4, indicating that the endogenous RNAi pathway is necessary to maintain repression of DUX4 in control muscle cells. Together these data demonstrate a role of the endogenous RNAi pathway in repeat-mediated epigenetic repression of the D4Z4 macrosatellite repeat, and show that enhancing the activity of this pathway by supplying exogenous siRNA oligonucleotides represents a potential therapeutic approach to silencing DUX4 in FSHD.
Induction of Ovulation and Multiple Ovulations in Seasonally Anovulatory and Ovulatory Mares with an Equine Pituitary Extract (1977)

A crude equine pituitary extract (EE) was used to induce single and multiple ovulations in seasonally anovulatory pony mares. Six control mares received saline vehicle only. Twelve mares were injected daily for 14 days with a total of 6.6 mg/kg body weight of EE (3.3 U NIH-FSH-S1). Six of the EE-treated mares were also treated with HCG (2,000 IU) on day 13, bred on days 13 and 15, and necropsied on day 17. The ovarian follicles were ≤10 mm in diameter at the beginning of treatment. The number of mares ovulating/group and the number of ovulations/mare were significantly greater following EE or EE+HCG than following saline vehicle administration (5/5, 1.6; 6/6, 1.8; 0/6, 0, respectively). The interval from day 13 (day of HCG treatment) to day of first subsequent ovulation was shorter (P<.05) in EE+ HCG-treated mares (2.3 days) than in EE-treated mares (4.4 days). A total of six fertilized and two recent, non-fertilized ova was recovered. A second experiment was designed to determine if EE treatment could induce multiple ovulations in seasonally ovulatory mares. Twenty-one cycling pony mares were assigned randomly to three groups (seven/group): 1) non-treated controls, 2) treatment during diestrus beginning on day 11 post-ovulation, and 3) treatment beginning on day one of estrus. Treated mares were given a total dose of 4 mg/kg body weight of EE (2 U NIH-FSH-S1) divided into six equal, daily subcutaneous injections. Number of mares with more than one ovulation was greater (P<.05) for mares in which treatment was initiated on day 11 post-ovulation (4/7) or on day 1 of estrus (3/7) than for controls (0/7). There were fewer (P<.01) mares showing estrus during the first post-treatment ovulatory period when mares were treated during diestrus compared to control mares (3/7, 7/7, respectively). Three of the mares that did not show estrus had multiple ovulations and one mare did not ovulate. There was a greater (P<.05) number of follicles ≥25 mm on the day of the first post-treatment ovulation when mares were treated during diestrus (3.2) or estrus (2.4) than when mares were untreated (0). Results of experiment 1 confirmed that EE can induce ovulation in mares during the anovulatory season and indicated that timing of ovulation can be improved with HCG and that ova from induced ovulations are fertilizable. Results of experiment 2 demonstrated that EE can induce follicular activity and multiple ovulations during the ovulatory season.
Internal Fingerprint Identification With Optical Coherence Tomography (2010)

Existing biometric fingerprint devices show numerous reliability problems such as wet or fake fingers. In this letter, a secured method using the internal structures of the finger (papillary layer) for fingerprint identification is presented. With a frequency-domain optical coherence tomography (FD-OCT) system, a 3-D image of a finger is acquired and the information of the internal fingerprint extracted. The right index fingers of 51 individuals were recorded three times. Using a commercial fingerprint identification program, 95% of internal fingerprint images were successfully recognized. These results demonstrate that OCT imaging of internal fingerprints can be used for accurate and reliable fingerprint recognition.
Joint channel estimation and symbol detection for SFBC-OFDM systems via the EM algorithm (2004)

Joint channel estimation and symbol detection for space-frequency block coded OFDM (SFBC-OFDM) systems is considered. The expectation-maximization (EM) algorithm is employed to devise both soft-in-hard-out (SIHO) maximum likelihood (ML) iterative receivers and soft-in-soft-out (SISO) maximum a posteriori (MAP) iterative receivers for SFBC-OFDM systems. Besides the low computational complexity and fast convergence, the EM-based iterative receivers also have the ability of tracing the variation of fast fading channels, and thus provide quite satisfying performance and bandwidth efficiency even in high-vehicular-speed environment. Numerical results are provided to corroborate the theoretical designs.
Deletion analysis ofors12, a centromeric, early activated, mammalian origin of DNA replication (1997)

We have generated a panel of deletion mutants of ors12 (812-bp), a mammalian origin of DNA replication previously isolated by nascent strand extrusion from early replicating African Green monkey (CV-1) DNA. The deletion mutants were tested for their replication activity in vivo by the bromodeoxyuridine substitution assay, after transfection into HeLa cells, and in vitro by the Dpnl resistance assay, using extracts from HeLa cells. We identified a 215-bp internal fragment as essential for the autonomous replication activity of ors12. When subcloned into the vector pML2 and similarly tested, this subfragment was capable of autonomous replication in vivo and in vitro. Several repeated sequence motifs are present in this 215-bp fragment, such as TGGG(A) and G(A)AG (repeated four times each); TTTC, AGG, and CTTA (repeated 3 times each); the motifs CACACA and CTCTCT, and two imperfect inverted repeats. 22 and 16 bp long, respectively. The overall sequence of the 215-bp fragment is G/C-rich (50.2%), by comparison to the 186-bp (33.5% G/C-rich) minimal sequence required for the autonomous replication activity of ors8, another functional ors that was similarly isolated and characterized.
Object Detection using Dimensionality Reduction on Image Descriptors (2014)

The aim of object detection is to recognize objects in a visual scene. Performing reliable object detection is becoming increasingly important in the fields of computer vision and robotics. Various applications of object detection include video surveillance, traffic monitoring, digital libraries, navigation, human computer interaction, etc. The challenges involved with detecting real world objects include the multitude of colors, textures, sizes, and cluttered or complex backgrounds making objects difficult to detect.\nThis thesis contributes to the exploration of various dimensionality reduction techniques on descriptors for establishing an object detection system that achieves the best trade-offs between performance and speed. Histogram of Oriented Gradients (HOG) and other histogram-based descriptors were used as an input to a Support Vector Machine (SVM) classifier to achieve good classification performance. Binary descriptors were considered as a computationally efficient alternative to HOG. It was determined that single local binary descriptors in combination with Support Vector Machine (SVM) classifier don't work as well as histograms of features for object detection. Thus, histogram of binary descriptors features were explored as a viable alternative and the results were found to be comparable to those of the popular Histogram of Oriented Gradients descriptor.\nHistogram-based descriptors can be high dimensional and working with large amounts of data can be computationally expensive and slow. Thus, various dimensionality reduction techniques were considered, such as principal component analysis (PCA), which is the most widely used technique, random projections, which is data independent and fast to compute, unsupervised locality preserving projections (LPP), and supervised locality preserving projections (SLPP), which incorporate non-linear reduction techniques.\nThe classification system was tested on eye detection as well as different object classes. The eye database was created using BioID and FERET databases. Additionally, the CalTech-101 data set, which has 101 object categories, was used to evaluate the system. The results showed that the reduced-dimensionality descriptors based on SLPP gave improved classification performance with fewer computations.
‘Off–on’ fluorescent sensors for physiological levels of magnesium ions based on photoinduced electron transfer (PET), which also behave as photoionic OR logic gates (1994)

The fluorescence of molecules 1–3 is enhanced by factors of up to 67 in the presence of magnesium and calcium ions in neutral water which allows the selective monitoring of magnesium ions under simulated physiological conditions and permits the construction of truth tables with OR logic when these molecules are viewed as ion input–photon output molecular devices.
A let-7 microRNA-binding site polymorphism in the KRAS 3' UTR is associated with reduced survival in oral cancers (2009)

MicroRNA (miRNA)-binding site polymorphisms that could contribute to disease risk and prognosis are rapidly being identified and investigated as this genetic variation may have a potentially profound impact on human health. A recently described variant allele in the KRAS 3' untranslated region that arises in the let-7 miRNA complementary site (KRAS-LCS6) and leads to increased KRAS expression in lung cancer was examined for its association with the occurrence of head and neck squamous cell carcinoma (HNSCC). We examined the prevalence of the KRAS-LCS6 variant allele in a population-based case-control study of HNSCC to determine if this KRAS-LCS6 genotype was associated with disease occurrence and patient survival. Although the KRAS-LCS6 variant genotype was not associated with the overall risk of HNSCC, cases with the KRAS-LCS6 variant genotype had significantly reduced survival [hazard ratio (HR), 1.6; 95% confidence interval (CI), 1.0-2.5] in models controlled for confounders of survival. This risk was greatest in cases of oral cavity carcinoma (HR, 2.7; 95% CI, 1.4-5.3). These data demonstrate that cases with the KRAS-LCS6 variant have significantly reduced survival time and suggest that this variant may alter the phenotype or therapeutic response of this disease.
Bounds and analysis of aliasing errors in linear feedback shift registers (1988)

Aliasing errors in linear feedback shift registers (LFSRs) used as signature analysis registers in self-testing networks are considered. A bound on aliasing is established by a straightforward algebraic analysis of LFSRs. It is calculated as a function of p, the probability of an error occurring at an output of the network under test. This bound is robust but is only good for p close to 1/2. To investigate the question of what happens to aliasing errors in general, the function of LFSRs is modeled by a Markov process and a solution is obtained by the z-transform. It is shown that for p>1/2 the aliasing probability for primitive polynomials converges much faster to the final steady-state value than for nonprimitive polynomials. For values of p<1/2, aliasing probability for primitive polynomials is always less than for nonprimitive ones. These results indicate that, in general, primitive polynomials are much better with respect to aliasing than nonprimitive polynomials. Simulation results for aliasing errors for these polynomials give insight to how aliasing occurs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Wnt/β-Catenin Is Essential for Intestinal Homeostasis and Maintenance of Intestinal Stem Cells (2007)

The Wnt signaling pathway is deregulated in over 90% of human colorectal cancers. beta-Catenin, the central signal transducer of the Wnt pathway, can directly modulate gene expression by interacting with transcription factors of the TCF/LEF family. In the present study we investigate the role of Wnt signaling in the homeostasis of intestinal epithelium by using tissue-specific, inducible beta-catenin gene ablation in adult mice. Block of Wnt/beta-catenin signaling resulted in rapid loss of transient-amplifying cells and crypt structures. Importantly, intestinal stem cells were induced to terminally differentiate upon deletion of beta-catenin, resulting in a complete block of intestinal homeostasis and fatal loss of intestinal function. Transcriptional profiling of mutant crypt mRNA isolated by laser capture microdissection confirmed those observations and allowed us to identify genes potentially responsible for the functional preservation of intestinal stem cells. Our data demonstrate an essential requirement of Wnt/beta-catenin signaling for the maintenance of the intestinal epithelium in the adult organism. This challenges attempts to target aberrant Wnt signaling as a new therapeutic strategy to treat colorectal cancer.
Registration of 2D C-Arm and 3D CT Images for a C-Arm Image-Assisted Navigation System for Spinal Surgery (2015)

C-Arm image-assisted surgical navigation system has been broadly applied to spinal surgery. However, accurate path planning on the C-Arm AP-view image is difficult. This research studies 2D-3D image registration methods to obtain the optimum transformation matrix between C-Arm and CT image frames. Through the transformation matrix, the surgical path planned on preoperative CT images can be transformed and displayed on the C-Arm images for surgical guidance. The positions of surgical instruments will also be displayed on both CT and C-Arm in the real time. Five similarity measure methods of 2D-3D image registration including Normalized Cross-Correlation, Gradient Correlation, Pattern Intensity, Gradient Difference Correlation, and Mutual Information combined with three optimization methods including Powell's method, Downhill simplex algorithm, and genetic algorithm are applied to evaluate their performance in converge range, efficiency, and accuracy. Experimental results show that the combination of Normalized Cross-Correlation measure method with Downhill simplex algorithm obtains maximum correlation and similarity in C-Arm and Digital Reconstructed Radiograph (DRR) images. Spine saw bones are used in the experiment to evaluate 2D-3D image registration accuracy. The average error in displacement is 0.22 mm. The success rate is approximately 90% and average registration time takes 16 seconds.
Enzymatic method for assaying calcium in serum with Ca++-ATPase (2003)

A kinetic assay for total calcium in serum was developed which is based on the activation of Ca(++)-ATPase by free Ca(++) [Ca(++)](f) maintained by EGTA in the reaction mixture. The concentration of Ca(++)(f) was dependent on total reference calcium added or serum calcium. Ca(++)-ATPase activity was coupled to the reduction of NADH by pyruvate kinase (PK) and lactate dehydrogenase (LDH) and monitored by change in absorbance at 340 nm. The calcium in normal serum was 10.08 +/- 0.24 mg/dl (n = 35) by our method while with o-cresolphthalein complexone (CPC) method, the total calcium in the same 35 serum samples was 10.14 +/- 0.54 mg/dl. The range of within-run coefficient of variations (CVs) by this method was 0.9-2.87% at 8-12 mg/dl and day-to-day CVs were 0.72-3.17%. The presence of other ions and standard clinical interfering agents did not affect this assay system. The correlation between values obtained with our method (y) and CPC method (x) for normal serum was: y = 1.064x-0.580 mg/dl (r = 0.912, n = 59).
Microwave Electromagnetic Characteristics of New Substituted M-Hexaferrites BaFe<sub>12-2x</sub>A<sub>x</sub>Me<sub>x</sub>O<sub>19</sub>(A = Ru, Ir ; Me = Co, Zn) (1997)

The substitution of x(Ti-Co) for 2x Fe cations reduces the strong axial anisotropy of the BaM-hexaferrite, which becomes in-plane for x = 1.3. Then M(Ti-Co) substituted hexaferrite have been extensively investigated as promising material for magnetic recording or hyperfrequency wave absorption. But saturation magnetization and ordering temperature are unfortunately reduced in proportion to the substitution ratio. Doping barium hexaferrite with A-Me elements (A = Ru, Ir ; Me = Co, Zn) produces the same effects for a much smaller substitution ratio. Ordering temperature and saturation magnetization are consequently much higher. Large saturation magnetization associated with in-plane magnetic anisotropy allows to obtain high magnetic permeability values on a wide frequency range at high values of some GHz. Complex electromagnetic characteristics : μ', μ", ε' and ε" of these new M(A-Me) substituted hexaferrites have been simustaneously measured at high frequency (0.5 to 18 GHz) using coaxial wire device on ceramic samples. The ferromagnetic resonance observed in these ceramics strongly depends on both their magnetic and microstrucutral properties. Results are discussed in terms of substitution ratio and microstructure depending on preparation conditions.
Oil mining field test to start in East Texas (1996)

Before year-end 1996, PetroTech Resources Corp. (PRC) of Fort Worth, Texas, will begin mobilizing for construction of a non-conventional quaternary-oil-recovery project in Corsicana field, in Navarro County, Texas, some 50 miles SSE of Dallas. The project will involve construction of large-diameter vertical and horizontal access shafts for people and equipment to some 70 feet below the bottom of the 820-ft deep reservoir, then upward drilling of multiple oil production boreholes into the reservoir and collection of oil moving to a subterranean manifold by gravity drainage. PRC calls the process Mining-Assisted Petroleum Development (MAPD). Project background and the developer`s objectives are explained here, along with an overview of principal features of the proprietary process and basic equipment to be used by several contractors.
Introduction to Galectins. (1997)

ガレクチンファミリーに属するタンパク質は、β-ガラクトシドに対して親和性を持ち、一次配列上に保存された領域を持つ。哺乳類ではこれまでに10種類のガレクチンが知られており、他の種では、鳥類、両生類、魚類、線虫、海綿、菌類などでガレクチンが見つかっている。ガレクチンは他のレクチンと違って細胞質に存在する。細胞質からはゴルジ装置を介さない経路で分泌されるが、核や特異的な細胞内部位に移行することもある。細胞外コンパートメントにおけるガレクチンの役割が注目を集めている。β-ガラクトシドを含む複合糖質を架橋することにより、細胞の接着や情報伝達を調節しているらしい。しかし、細胞質や核でも働いている可能性がある。ゴルジ装置を介さないガレクチンの分泌経路自体も非常に興味が持たれるところであるが、ほとんど何もわかっていない。ガレクチンは当初はβ-ガラクトシド結合活性から発見されていたが、一次構造の特徴がわかるようになり、さらに分子生物学的手法が使えるようになったので、これまでとは異なった興味深い方法で発見され始めている。ガレクチン、ガレクチン阻害剤、抗ガレクチン抗体が、癌や炎症性疾患などで治療薬や診断薬として使える日が近い将来来るかもしれない。
An efficient cryptographic protocol verifier based on prolog rules (2005)

Abstract: We present a new automatic cryptographic protocol verifier based on a simple representation of the protocol by Prolog rules, and on a new efficient algorithm that determines whether a fact can be proved from these rules or not. This verifier proves secrecy properties of the protocols. Thanks to its use of unification, it avoids the problem of the state space explosion. Another advantage is that we do not need to limit the number of runs of the protocol to analyze it. We have proved the correctness of our algorithm, and have implemented it. The experimental results show that many examples of protocols of the literature, including Skeme [24], can be analyzed by our tool with very small resources: the analysis takes from less than 0.1 s for simple protocols to 23 s for the main mode of Skeme. It uses less than 2 Mb of memory in our tests.
Polyubiquitination of p53 by a Ubiquitin Ligase Activity of p300 (2003)

Rapid turnover of the tumor suppressor protein p53 requires the MDM2 ubiquitin ligase, and both interact with p300–CREB-binding protein transcriptional coactivator proteins. p53 is stabilized by the binding of p300 to the oncoprotein E1A, suggesting that p300 regulates p53 degradation. Purified p300 exhibited intrinsic ubiquitin ligase activity that was inhibited by E1A. In vitro, p300 with MDM2 catalyzed p53 polyubiquitination, whereas MDM2 catalyzed p53 monoubiquitination. E1A expression caused a decrease in polyubiquitinated but not monoubiquitinated p53 in cells. Thus, generation of the polyubiquitinated forms of p53 that are targeted for proteasome degradation requires the intrinsic ubiquitin ligase activities of MDM2 and p300.
A potent new class of .kappa.-receptor agonist: 4-substituted 1-(arylacetyl)-2-[(dialkylamino)methyl]piperazines (1993)

The synthesis of 4-substituted 1-(arylacetyl)-2-[(alkylamino)methyl]piperazines (10-22, 26, 27, and 30-33) and their activities as kappa-opioid receptor agonists are described. This includes a range of 4-acyl and 4-carboalkoxy derivatives with the latter series showing the greatest kappa-agonist activity. In particular, methyl 4-[(3,4-dichlorophenyl)acetyl]-3-[(1-pyrrolidinyl) methyl]-1-piperazinecarboxylate (18) displays exceptional potency and selectivity. It showed the following activities in functional in vitro assays: rabbit vas deferens (kappa-specific tissue) IC50 = 0.041 nM, rat vas deferens (mu-specific tissue) IC50 > 10,000 nM, and hamster vas deferens (delta-specific tissue) IC50 > 10,000 nM. Compound 18 is also a highly potent antinociceptive agent, as determined in the mouse acetylcholine-induced abdominal constriction test: ED50 = 0.000 52 mg/kg, sc. The activity of 18 resides solely in its 3(R)-enantiomer. The kappa-agonist activity in both the 4-acyl and the 4-carbamate series is sensitive to the size of the 4-substituent. In addition, it would appear that an appreciable negative electrostatic potential in this region of the molecule is an important requirement for optimal potency.