gebhart/patrepeval huggingface dataset:
Identification of Genes Associated with Dedifferentiation of Hepatocellular Carcinoma with Expression Profiling Analysis (2002)

To identify the genes associated with dedifferentiation of hepatocellular carcinoma (HCC), gene expression profiles of HCCs of well-and moderately differentiated grades were compared by means of oligonucleotide arrays. One tumor showed a nodule-in-nodule appearance (NIN), which is occasionally observed in the course of progression of HCC from well to less differentiated grade, when an inner, moderately differentiated tumor (MD) develops sequentially from the outer, well-differentiated tumor (WD). Seventy-six genes were identified to be up-regulated more than 3-fold and 33 genes were down-regulated in the inner nodule in NIN. By statistical analysis of the profiles from 10 individual additional liver tumors, 5 WDs and 5 MDs, we were able to identify 12 genes, LAMA3, PPIB, ADAR, PSMD4, NDUFS8, D9SVA, CCT3, GBAP, ARD1, RDBP, CSRP2, and TLE1, with significantly elevated expression, and 4 genes, CP, IL7R, CD48, and PLGL, with decreased expression in MD. These selected genes were further validated using another 12 tumors, 5 WDs and 7 MDs, with semi-quantitative RT-PCR. We also applied neighborhood analysis to list the genes with high predictability values as most closely correlated with WD-MD distinction. Seven genes, ADAR, PSMD4, D9SVA, CCT3, GBAP, RDBP, and CSRP2, whose expression was elevated and one gene, IL7R, whose expression was decreased, were included among the top 50 predictor genes. These genes are likely to be associated with dedifferentiation of HCC and their identification may help to elucidate the mechanism of liver cancer progression.
Inactivation of glutathione S-transferase P1 gene by promoter hypermethylation in human neoplasia. (1998)

Glutathione S-transferases (GSTs) are a family of isoenzymes that play an important role in protecting cells from cytotoxic and carcinogenic agents. The pi-class GST has been associated with preneoplastic and neoplastic changes. Recently, it has been reported that regulatory sequences near the GSTP1 gene, which encodes the human pi-class GST, are commonly hypermethylated in prostatic carcinomas. In the present study, we studied more than 300 primary human tumors originating in other organs for aberrant methylation of GSTP1 using methylation-specific PCR. GSTP1 hypermethylation was most frequent in breast and renal carcinoma, showing aberrant methylation in 30 and 20% of the cases, respectively. Other tumor types showed promoter methylation only rarely or not at all. Hypermethylation of GSTP1 was associated with loss of expression demonstrated by immunohistochemistry. Our results suggest that aberrant methylation of GSTP1 may contribute to the carcinogenetic process in breast and renal carcinomas.
The Data Deluge: An e‐Science Perspective (2003)

This chapter contains sections titled: Introduction The Imminent Scientific Data Deluge Scientific Metadata, Information and Knowledge Data Grids and Digital Libraries Open Archives and Scholarly Publishing Digital Preservation and Data Curation Concluding Remarks Acknowledgements References
Protocols for disease classification from mass spectrometry data (2003)

We report our results in classifying protein matrix-assisted laser desorption/ionization-time of flight mass spectra obtained from serum samples into diseased and healthy groups. We discuss in detail five of the steps in preprocessing the mass spectral data for biomarker discovery, as well as our criterion for choosing a small set of peaks for classifying the samples. Cross-validation studies with four selected proteins yielded misclassification rates in the 10-15% range for all the classification methods. Three of these proteins or protein fragments are down-regulated and one up-regulated in lung cancer, the disease under consideration in this data set. When cross-validation studies are performed, care must be taken to ensure that the test set does not influence the choice of the peaks used in the classification. Misclassification rates are lower when both the training and test sets are used to select the peaks used in classification versus when only the training set is used. This expectation was validated for various statistical discrimination methods when thirteen peaks were used in cross-validation studies. One particular classification method, a linear support vector machine, exhibited especially robust performance when the number of peaks was varied from four to thirteen, and when the peaks were selected from the training set alone. Experiments with the samples randomly assigned to the two classes confirmed that misclassification rates were significantly higher in such cases than those observed with the true data. This indicates that our findings are indeed significant. We found closely matching masses in a database for protein expression in lung cancer for three of the four proteins we used to classify lung cancer. Data from additional samples, increased experience with the performance of various preprocessing techniques, and affirmation of the biological roles of the proteins that help in classification, will strengthen our conclusions in the future.
Towards a high quality Finnish talking head (1999)

We describe how our Finnish talking head was improved by using a new auditory speech synthesis method based on neural networks and optimal synchronization of the facial speech animation and the audio signal. In our first version of the talking head, the user typed in text and synthesized auditory speech and synchronized facial animation were created automatically. We combine a 3D facial model with a commercial auditory text-to-speech synthetizer (TTS). The auditory speech is produced by concatenating pre-recorded samples of natural speech according to a set of rules. The quality of the current speech synthesis is not yet adequate. A new strategy has been developed to improve the TTS and to integrate auditory synthesizer synchronization, especially when hardware capabilities are limited. We are developing a new method to achieve an optimal synchronization, independent of the platform used. This method is based on predictive visual synthesis. The new synchronization method gives us better control over audio-visual speech synthesis in the time domain. Using the diphone duration, we can use a more realistic interpolation function between the visemes. Thus, we can also take into account coarticulation effects.
Social cognitive theory and physical activity: a systematic review and meta‐analysis (2014)

This review investigated three research questions (i) What is the utility of social cognitive theory (SCT) to explain physical activity (PA)?; (ii) Is the effectiveness of SCT moderated by sample or methodological characteristics? and (iii) What is the frequency of significant associations between the core SCT constructs and PA? Ten electronic databases were searched with no date or sample restrictions. Forty-four studies were retrieved containing 55 SCT models of PA. Methodological quality was assessed using a standardized tool. A random-effects meta-analysis revealed that SCT accounted for 31% of the variance in PA. However, methodological quality was mostly poor for these models. Methodological quality and sample age moderated the PA effect size, with increases in both associated with greater variance explained. Although self-efficacy and goals were consistently associated with PA, outcome expectations and socio-structural factors were not. This review determined that SCT is a useful framework to explain PA behaviour. Higher quality models explained more PA variance, but overall methodological quality was poor. As such, high-quality studies examining the utility of SCT to explain PA are warranted.
Homology Modeling of the Structure of Bacterial Acetohydroxy Acid Synthase and Examination of the Active Site by Site-Directed Mutagenesis (1996)

Acetohydroxy acid synthase (AHAS, EC 4.1.3.18) catalyzes the thiamin pyrophosphate (TPP)-dependent decarboxylation of pyruvate and condensation of the resulting two-carbon moiety with a second alpha-keto acid. It belongs to a family of homologous, TPP-dependent enzymes which catalyze different reactions which start from decarboxylation of alpha-keto acids. A model for the structure of Escherichia coli AHAS isozyme II, based on its homology with pyruvate oxidase and experimental testing of the model by site-directed mutagenesis, has been used here to study how AHAS controls the chemical fate of a decarboxylated keto acid. Because of the potential conformational freedom of the reacting substrates, residues interacting with the substrate could not be identified directly from the model of AHAS. Three residues were considered as candidates for involvement in the recognition of alpha-ketobutyrate, as the amino acids at these sites in a unique low-specificity AHAS are different from those in typical AHASs, which are highly specific for reaction with alpha-ketobutyrate as second substrate, in preference to pyruvate. These residues were altered in AHAS II by site-directed mutagenesis. Replacement of Trp464 lowers the specificity by at least 1 order of magnitude, with minor effects on the activity or stability of the enzyme, suggesting that Trp464 contributes > or = 1.3 kcal mol-1 to interaction with the "extra" methyl of alpha-ketobutyrate. Mutations of Met460 or Thr70 have small effects on specificity and do affect other properties of the protein. A model for enzyme-substrate interactions can be proposed on the basis of these results. The model of AHAS also explains previously reported spontaneous mutants of AHAS resistant to sulfonylurea herbicides, which probably bind in the narrow depression which provides access to the bound TPP. A role for the C terminus of the enzyme polypeptide in determination on the reaction pathway is also possible.
SEROLOGICALLY ACTIVE GLYCOLIPID FAMILIES FROM MYCOBACTERIUM BOVIS BCG (1974)

Serological tests with serologically active glycolipids from Mycobacterium bovis BCG were investigated for their possible use in the diagonis of mycobacterioses. The results were positive with 95 percent of sera from patients with far advanced and moderately advanced tuberculosis, 80 percent of sera from patients with newly diagnosed tuberculosis and 75 percent of patients with atypical mycobacterial diseases. "False" positive serologic reactions were obtained from 4 percent or less. Furthermore, 39 percent of sera from recent tuberculin converters were positive compared with only 9 percent of sera from unselected PPD positive individuals.
Diagnosis and Staging of Chronic Graft-versus-Host Disease in the Clinical Practice (2010)

Based on expert opinion and retrospective data the National Institutes of Health (NIH) Consensus Development Project proposed criteria for diagnosis and staging of both overall severity as well as organ severity of chronic graft-versus-host disease (cGVHD) for use in clinical trials. In 2008, representatives of German and Austrian allogeneic hematopoietic stem cell transplant (HSCT) centers established a study group on cGVHD during the annual meeting of the German Working Group on Bone Marrow and Blood Stem Cell Transplantation (DAG-KBT) to intensify a dialog among HSCT physicians, pathologists, and medical consultants focusing on the usefulness of the NIH consensus criteria for patient care in clinical practice and to promote collaborations between HSCT centers as well as different medical specialities involved in HSCT. We first conducted a survey of current practices of diagnosis, staging, and overall grading of cGVHD in daily clinical routine by sending an electronic questionnaire to the heads of the HSCT centers. During 3 meetings in 2009, more representatives of allogeneic HSCT centers were included into the discussion process, resulting in 81% participation representing 88% of all allogeneic HSCT activities in Germany, Austria, and Switzerland. During the third consensus meeting held in Regensburg, Germany, from November 6 to November 7, 2009, important agreements were achieved among participant having a strong impact on care of patients with cGVHD. Areas of disagreement such as distinction between classical NIH cGVHD and overlap syndrome or assignment of liver GVHD after day 100 to acute or chronic category will be further assessed in prospective observational studies among participants in the near future.
Joint Optimization of Transceiver Matrices for MIMO-Aided Multiuser AF Relay Networks: Improving the QoS in the Presence of CSI Errors (2015)

This paper addresses the problem of amplify-and-forward (AF) relaying for multiple-input-multiple-output (MIMO) multiuser relay networks, where each source transmits multiple data streams to its corresponding destination with the assistance of multiple relays. Assuming realistic imperfect channel state information (CSI) of all the source-relay and relay-destination links, we propose a robust optimization framework for the joint design of the source transmit precoders (TPCs), relay AF matrices and receive filters. Specifically, two well-known CSI error models are considered, namely, the statistical and the norm-bounded error models. We commence by considering the problem of minimizing the maximum per-stream mean square error (MSE) subject to the source and relay power constraints (min-max problem). Then, the statistically robust and worst-case robust versions of this problem, which take into account the statistical and norm-bounded CSI errors, respectively, are formulated. Both of the resultant optimization problems are nonconvex (semi-infinite in the worst-case robust design). Therefore, algorithmic solutions having proven convergence and tractable complexity are proposed by resorting to the iterative block coordinate update approach along with matrix transformation and convex conic optimization techniques. We then consider the problem of minimizing the maximum per-relay power subject to the quality-of-service (QoS) constraints for each stream and the source power constraints (QoS problem). Specifically, an efficient initial feasibility search algorithm is proposed based on the relationship between the feasibility check and the min-max problems. Our simulation results show that the proposed joint transceiver design is capable of achieving improved robustness against different types of CSI errors when compared with nonrobust approaches.
Optical Holography (1996)

This 1996 book is a greatly expanded edition of what has become one of the best known introductions to the principles, techniques and applications of optical holography. Where necessary, existing sections have been updated, and two new chapters have been added. After presenting the theory of holographic imaging and the various types of holograms, practical aspects of holography are then covered, as are the production of holograms for display, colour holography and computer generated holograms. A variety of the applications of holography are then discussed in detail, such as high resolution imaging, information storage and processing, vibration analysis, and holographic interferometry. Containing more than 1000 selected references, this book will be invaluable to anyone wishing to learn more about optical holography, as well as to established researchers and engineers in this field.
Biodegradation of cresol isomers in anoxic aquifers (1987)

The biodegradation of o-, m-, and p-cresol was examined in material obtained from a shallow anaerobic alluvial sand aquifer. The cresol isomers were preferentially metabolized, with p-cresol being the most easily degraded. m-Cresol was more persistent than the para-isomer, and o-cresol persisted for over 90 days. Biodegradation of cresol isomers was favored under sulfate-reducing conditions (SRC) compared with that under methanogenic conditions (MC). Slurries that were acclimated to p-cresol metabolism transformed this substrate at 18 and 330 nmol/h per g (dry weight) for MC and SRC, respectively. Inhibition of electron flow to sulfate reduction with 2.0 mM molybdate reduced p-cresol metabolism in incubations containing sulfate. When methanogenesis was blocked with 5 mM bromoethanesulfonic acid in incubations lacking sulfate, p-cresol catabolism was retarded. Under SRC 3.4 mol of sulfate was consumed per mol of p-cresol metabolized. The addition of sulfate to methanogenic incubations stimulated p-cresol degradation. Simultaneous adaptation studies in combination with spectrophotometric and chromatographic analysis of metabolites indicated that p-cresol was oxidized under SRC to p-hydroxybenzoate via the corresponding alcohol and aldehyde. This series of reactions was inhibited under sulfate-limited or aerobic conditions. Therefore, the primary catabolic event for p-cresol decomposition under SRC appears to involve the hydroxylation of the aryl methyl group.
Buffer requirements of credit-based flow control when a minimum draining rate is guaranteed (2005)

Credit-based flow control (FQ offers significant advantages for data communication over networks such as ATM. One concern is the buffer memory requirement of credit FC, which is high when static, per-connection buffer allocation is used. The memory size can be reduced by dynamically sharing the buffer among the connections. We formulate and prove a new upper bound for the dynamically-shared buffer size, which applies when the downstream network guarantees that it will never throttle a connection down below a given minimum "draining" rate. This upper bound is inversely proportional to the minimum draining rate, and is independent of the number of connections. The minimum draining rate can be guaranteed by giving to the traffic arriving at a local area through long distance links priority over locally generated traffic in the use of a given fraction of the outgoing network capacity. In practical situations, the new upper bound can be made small, thus providing a new, additional method to reduce the buffer memory cost to a very small percentage of the link cost. Unlike other such methods, no link underutilization may occur and there is no rate ramp-up delay.
The Vitamin K-dependent Carboxylase (2002)

The only known biological function of Vitamin K (Fig. 1) in animals is as a required cofactor for the production of the unusual amino acid, -carboxyglutamate (Gla). This amino acid has a profound role in human blood coagulation. Several blood proteins require the presence of nine to thirteen Gla residues for normal function; these are the socalled Vitamin K-dependent (VKD) proteins. While some of the VKD blood proteins have a pro-coagulant function (prothrombin, and factors VII, IX, and X), others primarily serve anti-coagulant roles (proteins C, S, and Z). For all of the VKD blood proteins, however, the Gla residues are located in a homologous ≈ 45 residue amino-terminal “Gla” domain (1-3). The presence of multiple Gla residues in this domain allow it to adopt a calcium-dependent conformation that promotes binding to a membrane surface (4, 5), such as found on damaged vascular endothelial cells or activated platelets. This interaction allows the localization of the VKD blood protein near the site of vascular injury, where it participates in reactions that either promote or regulate clotting (6-8). The importance of Gla in the catalytic function of these proteins is emphasized by the effect that administration of Vitamin K antagonists (e. g. coumadins, such as warfarin sodium) has on humans. Warfarin decreases the concentration of vitamin K in the tissues, which, in turn, results in the production of VKD proteins that contain a decreased number (or a complete absence) of Gla. The Gla domain of these under-carboxylated blood proteins cannot adopt its natural conformation and, as a result, the VKD blood proteins have poor affinity for phospholipid surfaces. For this reason, the reactions that involve these proteins are significantly damped, and efficient clotting no longer occurs (9-11). Gla is synthesized in mammals by post-translational modification of glutamate. The enzyme that catalyzes the conversion of glutamate to Gla is the vitamin K-dependent -glutamyl carboxylase (12). In addition to a glutamate-containing substrate, this enzyme requires carbon dioxide, reduced Vitamin K, and molecular oxygen as reactants. The products of the carboxylase-catalyzed reaction are Gla, Vitamin K 2,3 epoxide, and water (13) (Fig. 2). The enzyme is found not only in liver (where the VKD blood proteins are produced and secreted), but also in a variety of other tissues, such as skin, lung, and kidney (13, 14). The widespread tissue distribution of carboxylase in humans suggests the presence of additional Gla-containing proteins of diverse function. To date, fourteen VKD proteins have been identified in humans, seven of which are the blood proteins mentioned above. Two other proteins (bone-gla and matrix-gla protein) are involved in bone metabolism (15), while another (Gas6) is involved in cell signaling (16, 17). Screenings of human nucleotide-based databases for sequences with homology to Gla domain sequences have identified four additional putative VKD proteins of unknown function: PRGP1, PRGP2, TMG3 and TMG4 (18, 19).
Electronic microrefrigerator based on a normal-insulator-superconductor tunnel junction (1994)

We present measurements on a novel electronic microrefrigerator that can cool conduction electrons significantly below the lattice temperature. A normal-insulator-superconductor tunnel junction is used to extract electrons from the normal metal electrode whose energy is higher than the Fermi energy. Electrons with an average energy equal to the Fermi energy are returned to the metal by a superconducting contact. Consequently, the high-energy thermal excitations are removed from the normal metal, thus cooling the electrons. For lattice temperatures higher than 100 mK the data can be explained by a simple theory incorporating the BCS density of states in the superconducting electrode and the coupling between electrons and phonons. At lower temperatures our measurement suggests that the electron energies in the normal electrode depart strongly from an equilibrium distribution.
B Cell-Activating Factor Belonging to the TNF Family (BAFF)-R Is the Principal BAFF Receptor Facilitating BAFF Costimulation of Circulating T and B Cells (2004)

BAFF (B cell-activating factor belonging to the TNF family) is a cell survival and maturation factor for B cells, and overproduction of BAFF is associated with systemic autoimmune disease. BAFF binds to three receptors, BAFF-R, transmembrane activator and calcium modulator and cyclophilin ligand interactor (TACI), and B cell maturation Ag (BCMA). Using specific mAbs, BAFF-R was found to be the predominant BAFF receptor expressed on peripheral B cells, in both humans and mice, and antagonist mAbs to BAFF-R blocked BAFF-mediated costimulation of anti- micro responses. The other BAFF receptors showed a much more restricted expression pattern, suggestive of specialized roles. BCMA was expressed by germinal center B cells, while TACI was expressed predominantly by splenic transitional type 2 and marginal zone B cells, as well as activated B cells, but was notably absent from germinal center B cells. BAFF was also an effective costimulator for T cells, and this costimulation occurs entirely through BAFF-R. BAFF-R, but not TACI or BCMA, was expressed on activated/memory subsets of T cells, and T cells from BAFF-R mutant A/WySnJ mice failed to respond to BAFF costimulation. Thus, BAFF-R is important not only for splenic B cell maturation, but is the major mediator of BAFF-dependent costimulatory responses in peripheral B and T cells.