gebhart/patrepeval huggingface dataset:
Presence of bifidobacteria in the rumen of calves fed different rations (1976)

A study was made on the numbers and species of bifidobacteria present in the rumen of calves fed high-roughage and high-concentrate diets. With the roughage ration the bifidobacteria were not detectable in a 10(-3) dilution, whereas with the concentrate ration their number was high, usually in the order of 10(8) to 10(9)/ml of rumen fluid. The species most represented, identified by means of deoxyribonucleic acid-deoxyribonucleic acid hybridization tests, included Bifidobacterium ruminale, Bifidobacterium globosum, and an apparently new species.
DigitEyes: vision-based hand tracking for human-computer interaction (2002)

Computer sensing of hand and limb motion is an important problem for applications in human-computer interaction (HCI), virtual reality, and athletic performance measurement. Commercially available sensors are invasive, and require the user to wear gloves or targets. We have developed a noninvasive vision-based hand tracking system, called DigitEyes. Employing a kinematic hand model, the DigitEyes system has demonstrated tracking performance at speeds of up to 10 Hz, using line and point features extracted from gray scale images of unadorned, unmarked hands. We describe an application of our sensor to a 3D mouse user-interface problem.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Assays for In Vitro and In Vivo Synergy (2003)

In the study of multi-modality therapy or combined chemotherapy, it is of interest to determine whether the combined effects of two agents are additive or whether their combination is substantially different from the sum of their parts (1,2). While controversy and discussion continue and new methodologies continue in development, two methods for the determination of synergy/additivity have emerged over the past 10 years as the main functional systems for the experimentalist and investigator in cancer. These are the median effect/combination index method and the isobologram method (3–14). This chapter will discuss these methods and provide examples, but will not delve into the mathematical derivations associated with each. Both methods have been applied widely. One or the other method may be more applicable to the drug interaction being studied, often this cannot be determined until after the experiment is done. Unfortunately, the method for determination of synergy/additivity must be selected before the experiment is performed since each method requires attention to experimental design. Some investigators have applied both the median effect/combination index and the isobologram analyses to their work.
An Aminated GDP-Fucose Analog Useful in the Fucosyltransferase Catalyzed Addition of Biological Probes onto Oligosaccharide Chains1 (1995)

Abstract An analog (1) of GDP-fucose, where C-6 is derivatized with an eight-atom spacer terminating in a primary amino group, was chemically synthesized. This amino group in sugar nucleotide 1 can be acylated using an N-hydroxysuccinimide ester of biotin and it can be coupled to another molecule that also contains an amino group using squaric acid diethyl ester as the coupling reagent. In this way, biotin and a blood group A-active trisaccharide were linked to C-6 of fucose in GDP-fucose. Both complex sugar nucleotides thus prepared were active as donors for a human milk fucosyltransferase, which transferred the derivatized α-linked fucose residue to a glycoside of N-acetyllactosamine, thus labeling this sequence with either biotin or the blood-group A trisaccharide. Compound 1 is proposed as a general and versatile reagent which should permit the addition of biological probes to the sugar chains of cell surface glycoproteins or glycolipids.
A conserved helical element is essential for internal initiation of translation of hepatitis C virus RNA (1994)

Translation of hepatitis C virus (HCV) RNA is initiated by cap-independent internal ribosome binding to the 5' noncoding region (NCR). To identify the sequences and structural elements within the 5' NCR of HCV RNA that contribute to the initiation of translation, a series of point mutations was introduced within this sequence. Since the pyrimidine-rich tract is considered a characteristic feature of picornavirus internal ribosome entry site (IRES) elements, our mutational analysis focused on two putative pyrimidine tracts (Py-I and Py-II) within the HCV 5' NCR. Translational efficiency of these mutant RNAs was examined by in vitro translation and after RNA transfection into liver-derived cells. Mutational analysis of Py-I (nucleotides 120 to 130), supported by compensatory mutants, demonstrates that the primary sequence of this motif is not important but that a helical structural element associated with this region is critical for HCV IRES function. Mutations in Py-II (nucleotides 191 to 199) show that this motif is dispensable for IRES function as well. Thus, the pyrimidine-rich tract motif, which is considered as an essential element of the picornavirus IRES elements, does not appear to be a functional component of the HCV IRES. Further, the insertional mutagenesis study suggests a requirement for proper spacing between the initiator AUG and the upstream structures of the HCV IRES element for internal initiation of translation.
Drilling a Medium-Radius Horizontal Well With Aerated Drilling Fluid: A Case Study (1991)

ABSTRACT Many formations throughout the world are sensitive to oil and water based drilling fluids and are best drilled with air as the drilling medium. However, positive displacement motors do not typically operate well with air. In addition, mud pulse telemetry MWD tools will not operate reliably in an air environment. In the second quarter of 1990, Marathon Oil Company successfully drilled a medium radius horizontal well in Jackson County, Michigan using an aerated mud system and an electromagnetic telemetry link MND tool. This paper will describe the pre-well planning and practical aspects of drilling the well with emphasis on the hydraulic system and drilling fluid mixture.
Lattice-based homomorphic encryption of vector spaces (2008)

In this paper we introduce a new probabilistic lattice-based bounded homomorphic encryption scheme. For this scheme the sum of two encrypted messages is the encryption of the sum of two messages and the scheme is able to preserve a vector spave structure of the message. The size of the public key is rather large ap 3 Mb but the encryption and the decryption operations are very fast (of the same speed order than NTRU). The homomorphic operation, i.e. the addition of ciphertexts is dramatically fast compared to homomorphic schemes based on group theory like Paillier or El Gamal.
A probabilistic approach to hybrid role mining (2009)

Role mining algorithms address an important access control problem: configuring a role-based access control system. Given a direct assignment of users to permissions, role mining discovers a set of roles together with an assignment of users to roles. The results should closely agree with the direct assignment. Moreover, the roles should be understandable from the business perspective in that they reflect functional roles within the enterprise. This requires hybrid role mining methods that work with both direct assignments and business information from the enterprise.
Incremental Eigenanalysis for Classification (1998)

Eigenspace models are a convenient way to represent sets of observations with widespread applications, including classification. In this paper we describe a new constructive method for incrementally adding observations to an eigenspace model. Our contribution is to explicitly account for a change in origin as well as a change in the number of eigenvectors needed in the basis set. No other method we have seen considers change of origin, yet both are needed if an eigenspace model is to be used for classification purposes. We empirically compare our incremental method with two alternatives from the literature and show our method is the more useful for classification because it computes the smaller eigenspace model representing the observations.
Dysregulated expression of fatty acid oxidation enzymes and iron‐regulatory genes in livers of Nrf2‐null mice (2012)

Nrf2 deletion dysregulates hepatic mRNA expression of β-oxidation enzymes and iron-related genes, possibly causing a trend for increased hepatic triglyceride and iron concentrations. Nrf2 may have roles in the progression of NASH.
Functional MASP2 single nucleotide polymorphism plays no role in psoriasis (2005)

We show that this mutant allele is not associated with psoriasis. There was no favoured transmission from parents to affected offspring. The calculated allele frequency in this psoriasis group (Scottish and English) was 0.0326, and in the unaffected group 0.0379.
National beef tenderness survey. (1991)

To determine the average tenderness and sensory ratings of beef subprimal cuts sold in retail cases across the United States, retail cuts were purchased through typical retail outlets in 14 metropolitan cities and transported to Texas A&M University for sensory and Warner-Bratzler shear analysis. The overall mean shear force for all cuts was 3.65 kg, and the mean shear force values for chuck, rib, loin, and round cuts were 3.72, 3.36, 3.17, and 4.31 kg, respectively. No difference (P greater than .05) in tenderness was detected among the cuts from the rib. Mean palatability ratings and shear force values of top loin steaks were similar to those of rib cuts. Top sirloin steaks were tougher (P less than .05) and received the lowest sensory ratings compared with other loin cuts. Approximately two to three times as many round and chuck steaks had shear force values in excess of 4.6 kg compared with their roast counterparts. In all cases, roasts tended to be more tender than steaks from the same subprimal source. USDA Choice chuck retail cuts, compared to Select and No-roll chuck cuts, had approximately 10% fewer cuts with shear force values in excess of 4.0 kg. More work is needed to improve meat tenderness, primarily for retail cuts from the round and chuck primals. Future research must investigate the interaction of antemortem and postmortem factors associated with variation in beef tenderness.
Syncytia Induction Enhances the Oncolytic Potential of Vesicular Stomatitis Virus in Virotherapy for Cancer (2004)

Vesicular stomatitis virus (VSV) selectively replicates in tumor but not in normal cells and is being developed as an oncolytic agent for cancer therapy. Here we report the construction of a recombinant VSV capable of inducing syncytia formation between tumor cells through membrane fusion at neutral pH, which led to enhanced oncolytic properties against multifocal hepatocellular carcinoma (HCC) in the livers of immunocompetent rats. Recombinant VSV vectors were constructed by insertion into their genome a transcription unit expressing a control or fusion protein derived from Newcastle disease virus. In vitro characterization of the recombinant fusogenic VSV vector on human and rat HCC cells showed extensive syncytia formation and significantly enhanced cytotoxic effects. In vivo, administration of fusogenic VSV into the hepatic artery of Buffalo rats bearing syngeneic multifocal HCC lesions in their livers resulted in syncytia formation exclusively within the tumors, and there was no collateral damage to the neighboring hepatic parenchyma. The fusogenic VSV also conferred a significant survival advantage over a nonfusogenic control virus in the treated animals (P = 0.0078, log-rank test). The results suggest that fusogenic VSV can be developed into an effective and safe therapeutic agent for cancer treatment in patients, including those with multifocal HCC in the liver.
Lysenin, a Novel Sphingomyelin-specific Binding Protein (1998)

Lysenin, a novel 41-kDa protein purified from coelomic fluid of the earthworm Eisenia foetida, induced erythrocyte lysis. Preincubation of lysenin with vesicles containing sphingomyelin inhibited lysenin-induced hemolysis completely, whereas vesicles containing phospholipids other than sphingomyelin showed no inhibitory activity, suggesting that lysenin bound specifically to sphingomyelin on erythrocyte membranes. The specific binding of lysenin to sphingomyelin was confirmed by enzyme-linked immunosorbent assay, TLC immunostaining, and liposome lysis assay. In these assays, lysenin bound specifically to sphingomyelin and did not show any cross-reaction with other phospholipids including sphingomyelin analogs such as sphingosine, ceramide, and sphingosylphosphorylcholine, indicating that it recognized a precise molecular structure of sphingomyelin. Kinetic analysis of the lysenin-sphingomyelin interaction by surface plasmon resonance measurements using BIAcoreTM system showed that lysenin associated with membrane surfaces composed of sphingomyelin (kon = 3.2 x 10(4) M-1 s-1) and dissociated extremely slowly (koff = 1.7 x 10(-4) s-1), giving a low dissociation constant (KD = 5.3 x 10(-9) M). Incorporation of cholesterol into the sphingomyelin membrane significantly increased the total amount of lysenin bound to the membrane, whereas it did not change the kinetic parameters of the lysenin-membrane interaction, suggesting that lysenin specifically recognized sphingomyelin and cholesterol incorporation changed the topological distribution of sphingomyelin in the membranes, thereby increasing the accessibility of sphingomyelin to lysenin. Immunofluorescence staining of fibroblasts derived from a patient with Niemann-Pick disease type A showed that lysenin stained the surfaces of the fibroblasts uniformly, whereas intense lysosomal staining was observed when the cells were permeabilized by digitonin treatment. Preincubation of lysenin with vesicles containing sphingomyelin abolished lysenin immunostaining. This study demonstrated that lysenin bound specifically to sphingomyelin on cellular membranes and should be a useful tool to probe the molecular motion and function of sphingomyelin in biological membranes.
Cross-Talk between Fatty Acid and Cholesterol Metabolism Mediated by Liver X Receptor- (2000)

LXR alpha (liver X receptor, also called RLD-1) is a nuclear receptor, highly expressed in tissues that play a role in lipid homeostasis. In this report we show that fatty acids are positive regulators of LXR alpha gene expression and we investigate the molecular mechanisms underlying this regulation. In cultured rat hepatoma and primary hepatocyte cells, fatty acids and the sulfur-substituted fatty acid analog, tetradecylthioacetic acid, robustly induce LXR alpha (up to 3.5- and 7-fold, respectively) but not LXR beta (also called OR-1) mRNA steady state levels, with unsaturated fatty acids being more effective than saturated fatty acids. RNA stability and nuclear run-on studies demonstrate that changes in the transcription rate of the LXR alpha gene account for the major part of the induction of LXR alpha mRNA levels. A similar induction of protein level was also seen after treatment of primary hepatocytes with the same fatty acids. Consistent with such a transcriptional effect, transient transfection studies with a luciferase reporter gene, driven by 1.5 kb of the 5'-flanking region of the mouse (m)LXR alpha gene, show a peroxisome proliferator-activated receptor-alpha-dependent increase in luciferase activity upon treatment with tetradecylthioacetic acid and the synthetic peroxisome proliferator-activated receptor-alpha activator, Wy 14.643, suggesting that the mLXR alpha 5'-flanking region contains the necessary sequence elements for fatty acid responsiveness. In addition, in vivo LXR alpha expression was induced by fatty acids, consistent with the in vitro cell culture data. These observations demonstrate that LXR alpha expression is controlled by fatty acid signaling pathways and suggest an important cross-talk between fatty acid and cholesterol regulation of lipid metabolism.
A combinatorial approach to content-based music selection (2000)

Accessing large digital music catalogues raises a problem for both users and content providers. We propose a novel approach to music selection called RecitalComposer, which is based on computing coherent sequences of music titles. This amounts to solving a combinatorial pattern generation problem by using constraint satisfaction techniques.
Identification of a Novel Antibody Associated with Autoimmune Pancreatitis (2009)

The antibody that we identified was detected in most patients with autoimmune pancreatitis but also in some patients with pancreatic cancer, making it an imperfect test to distinguish between these two conditions.
Clinical effect of danazol in patients with IgA nephropathy. (1987)

A multi-center study on the clinical effect of danazol in patients with IgA nephropathy is described. Two different doses of oral administration, including 200 mg or 300 mg per day, were employed in the present study. Urinalysis and measurements of complement components, i.e. C3 and C4, were performed before, and in the eighth and 20th week after the administration of danazol. It was demonstrated that 200 or 300 mg of danazol administration was effective in reducing the amount of proteinuria and in increasing the levels of serum complement components in the patients. It is concluded that the administration of danazol may be useful for treatment of patients with IgA nephropathy.
Oncogenic ALK regulates EMT in non-small cell lung carcinoma through repression of the epithelial splicing regulatory protein 1 (2016)

A subset of Non-Small Cell Lung Carcinoma (NSCLC) carries chromosomal rearrangements involving the Anaplastic Lymphoma Kinase (ALK) gene. ALK-rearranged NSCLC are typically adenocarcinoma characterized by a solid signet-ring cell pattern that is frequently associated with a metastatic phenotype. Recent reports linked the presence of ALK rearrangement to an epithelial-mesenchymal transition (EMT) phenotype in NSCLC, but the extent and the mechanisms of an ALK-mediated EMT in ALK-rearranged NSCLC are largely unknown. We found that the ALK-rearranged H2228 and DFCI032, but not the H3122, cell lines displayed a mesenchymal phenotype. In these cell lines, oncogenic ALK activity dictated an EMT phenotype by directly suppressing E-cadherin and up-regulating vimentin expression, as well as expression of other genes involved in EMT. We found that the epithelial splicing regulatory protein 1 (ESRP1), a key regulator of the splicing switch during EMT, was repressed by EML4-ALK activity. The treatment of NSCLC cells with ALK tyrosine kinase inhibitors (TKIs) led to up-regulation of ESRP1 and E-cadherin, thus reverting the phenotype from mesenchymal to epithelial (MET). Consistently, ESRP1 knock-down impaired E-cadherin up-regulation upon ALK inhibition, whereas enforced expression of ESRP1 was sufficient to increase E-cadherin expression. These findings demonstrate an ALK oncogenic activity in the regulation of an EMT phenotype in a subset of NSCLC with potential implications for the biology of ALK-rearranged NSCLC in terms of metastatic propensity and resistance to therapy.
Towards the Development of an Integrative Framework for Technology Mediated Learning (2008)

As mandatory involvement requirements may not intrinsically motivate learners to achieve high quality learning, social factors under affective commitment are especially important determinants of TML success. This paper investigates an individualâs social and self identities as important determinants in developing affective commitment (identification) and intrinsic motivation (perceived enjoyment) to share knowledge by email in the TML environment. Furthermore, given the recent emphasis on gender in system adoption and socio-linguistic literature, this study investigates gender as a moderating variable in the proposed model. The integrative framework of e-learning in this study will help us understand the antecedents of effective knowledge sharing intervention in the TML environment, based on the integrated model of social identity theory, social influence theory, self determination theory, and socio-linguistic literature. Furthermore, IS practitioners will be able to understand the different roles of identity and gender in developing and designing TML and KM systems,
Automated delineation of organs-at-risk in head and neck CT images using multi-output support vector regression (2018)

Accurate segmentation of organs-at-risk (OAR) is essential for treatment planning of head and neck (HaN) cancers. A desire to shift from manual segmentation to automated processes allows for more efficient treatment planning. However, the technology of automated segmentation is hindered by complex and irregular morphology, poor soft tissue contrast, artifacts from dental fillings, variability of patient's anatomy, and inter-observer variability. In this study, we propose a state-of-the-art automated segmentation of OAR using a multi-output support vector regression (MSVR) machine learning algorithm to address these challenges under various selectable parameters. Shape image features were extracted using the histogram of oriented gradients and ground truth boundaries were obtained from physicians. Automated delineation of the OAR was performed on CT images from 56 subjects consisting of the brain stem, cochleae, esophagus, eye globes, larynx, lenses, lips, mandible, oral cavity, parotid glands, spinal cord, submandibular glands, and thyroid. Testing was done on previously unseen CT images. Model performance was evaluated using the dice similarity coefficient (DSC) and leave-one-subject- out strategy. Segmentation results varied from 66.9&percnt; DSC for the left cochlea to 93.8&percnt; DSC for the left eye globe. Analysis of the performance of a state-of-the-art algorithm reported in literature compared to MSVR demonstrated similar or superior performance on the segmentation of the OAR listed in this study. The proposed MSVR model accurately and efficiently segmented the OAR using a representative database of 56 HaN CT images. Thus, this model is an effective tool to aid physicians in reducing diagnostic and prognostic time.
Pulmonary response to intratracheal challenge with Pasteurella haemolytica and Pasteurella multocida. (1985)

Calves were inoculated intratracheally with 5 X 10(7), 5 X 10(8), or 5 X 10(9) colony forming units of either 18-hour stationary phase cultures or 4-hour log phase cultures of Pasteurella haemolytica. The log phase culture at all concentrations produced more severe clinical signs, hematological changes and pulmonary lesions at postmortem examination than did the corresponding stationary phase culture. More severe effects were seen with the larger doses especially with the log phase culture. Fibrinous bronchopneumonia with focal or multifocal necrosis was consistently produced by both the stationary and log phase cultures. To determine if this lesion was peculiar to P. haemolytica or whether it could be produced generally by rapidly growing Gram negative organisms, a 4-hour log phase culture of Pasteurella multocida was prepared in an identical manner to that used for the culture of P. haemolytica and given to calves intratracheally at the high bacterial dose (5 X 10(9]. The P. haemolytica produced more severe clinical, hematological and morphological changes than did the P. multocida. The lesions observed with P. multocida differed morphologically from those of P. haemolytica; there was a suppurative exudative component and minimal to no necrosis with P. multocida. It appears that an important pathogenic principle is produced by the rapidly growing P. haemolytica that causes it to produce a more severe clinical disease and more necrotizing pulmonary lesions than P. multocida.