gebhart/patrepeval huggingface dataset:
Luminescent Ag7 and Ag8 Clusters by Interfacial Synthesis (2010)

Interfacial etching of silver nanoparticles and separation of the products by polyacrylamide gel electrophoresis afforded Ag8 and Ag7 clusters with red and blue-green fluorescence emission, respectively (see picture). The strongly temperature-dependent emission of the clusters suggests potential applications, whilst their facile phase transfer to organic media facilitates further studies. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
353 IN VITRO FERTILIZATION WITH FLOW-SORTED BUFFALO SPERM (2005)

Flow cytometrically sorted X and Y sperm have been successfully used for IVF and the production of offspring in cattle and sheep (Maxwell et al. 2004 Anim. Reprod. Sci. 82–83, 79–95).The objective of this study was to test the feasibility of flow sorted buffalo sperm used in IVF systems and to establish a suitable IVF system for sorted buffalo sperm. Oocytes were aspirated from 2–6 mm follicles on the buffalo ovaries from a slaughterhouse and matured for 22–24 h in a 1-mL dish containing TCM199 + 10% OCS + 3% BFF (bovine folliciular fluid) + hormones at 38.5°C, 5% CO2 in air with maximum humidity. Semen was sorted by a flow-sorter (Clontech, Mountain View, CA, USA) into X- and Y-chromosome bearing sperm at 90% accuracy and stored at 4°C for later use with IVF. Sorted sperm were prepared for IVF by centrifugation (700g, 20 min) through a Percoll gradient (90%:45%), and washed (centrifugation at 700g, 5 min) in mTALP-BSA. For IVF, groups of 10–15 oocytes were transferred to 40-µL drops of mTALP-BSA and incubated with motile sperm at a concentration of 2 × 106 sperm mL-1 in each fertilization drop for 8–10 h under mineral oil. Presumptive zygotes were cultured until Day 8 in 25-µL drops of TCM–199 supplemented with 0.33 mM pyruvate and 10% NCS with granulosa cells at 38.5°C under 5% CO2 in air. Cleavage and blastocyst rates per oocyte insemination were recorded on Day 2 and Days 6–8 after insemination, respectively. Data were analyzed by ANOVA procedures with replicates and treatments in the model. There were significant differences in cleavage rate (42.23% vs. 52.28%) and blastocyst rate (20.62% vs. 27.67%) between sorted and unsorted sperm, respectively (Table 1). There were no significant differences in the proportions of blastocyst development rates on Days 6, 7, or 8 after insemination with sorted and unsorted sperm. The results indicate that sorted buffalo sperm from two bulls have been successfully used in an IVF system to produce sex-controlled embryos. Table 1. Cleavage and blastocyst rates with different sperm types This research was supported by grants from the National Natural Science Foundation of China (30360073) and the Guangxi Department of Science and Technology (0330004–13). The authors (M. Z. and X.W. L.) contributed equally to this work.
Itaconate biosynthesis in Aspergillus terreus (1995)

Itaconate biosynthesis was studied in intact cells of high-yield (RC4') and low-yield (CM85J) strains of the fungus Aspergillus terreus by methods (tracers, nuclear magnetic resonance spectroscopy, and mass spectroscopy) that did not interfere with metabolism. Itaconate formation in RC4' required de novo protein biosynthesis. Krebs cycle intermediates increased in both strains during the production of itaconic acid. The Embden-Meyerhof-Parnas pathway and the Krebs cycle were shown to be involved in this biosynthesis by using 14C- and 13C-labelled substrates and nuclear magnetic resonance spectroscopy. A metabolic pathway for itaconate formation from glucose in A. terreus is proposed.
PI3K and STAT3: A New Alliance (2011)

The PI3K–TOR and STAT3 signaling pathways represent two distinct regulatory networks. The discovery of a functional link between these pathways is significant for our understanding of PI3K- and STAT3-driven oncogenic mechanisms and identifies the TEC kinase BMX as a new cancer target.
Time series filtering, smoothing and learning using the kernel kalman filter (2006)

In this paper, we propose a new model, the kernel Kalman Filter, to perform various nonlinear time series processing. This model is based on the use of Mercer kernel functions in the framework of the Kalman filter or linear dynamical systems. Thanks to the kernel trick, all the equations involved in our model to perform filtering, smoothing and learning tasks, only require matrix algebra calculus whilst providing the ability to model complex time series. In particular, it is possible to learn dynamics from some nonlinear noisy time series implementing an exact expectation-maximization procedure.
Rapid Semiautomated Subtyping of Influenza Virus Species during the 2009 Swine Origin Influenza A H1N1 Virus Epidemic in Milwaukee, Wisconsin (2009)

In the spring of 2009, a novel influenza A (H1N1) virus (swine origin influenza virus [S-OIV]) emerged and began causing a large outbreak of illness in Milwaukee, WI. Our group at the Midwest Respiratory Virus Program laboratory developed a semiautomated real-time multiplex reverse transcription-PCR assay (Seasonal), employing the NucliSENS easyMAG system (bioMérieux, Durham, NC) and a Raider thermocycler (HandyLab Inc., Ann Arbor, MI), that typed influenza A virus, influenza B virus, and respiratory syncytial virus (RSV) and subtyped influenza A virus into the currently circulating H1 and H3 subtypes, as well as a similar assay that identified H1 of S-OIV. The Seasonal and H1 S-OIV assays demonstrated analytical limits of detection of <50 50% tissue culture infective doses/ml and 3 to 30 input copies, respectively. Testing of the analytical specificities revealed no cross-reactivity with 41 and 26 different common organisms and demonstrated outstanding reproducibility of results. Clinical testing showed 95% sensitivity for influenza A virus and influenza B virus and 95 and 97% specificity compared to tissue culture. Comparisons of results from other molecular tests showed levels of positive agreement with the Seasonal and H1 S-OIV assay results of 99 and 100% and levels of negative agreement of 98 and 100%. This study has demonstrated the use of a semiautomated system for sensitive, specific, and rapid detection of influenza A virus, influenza B virus, and RSV and subtyping of influenza A virus into human H1 and H3 and S-OIV strains. This assay/system performed well in clinical testing of regular seasonal influenza virus subtypes and was outstanding during the 2009 Milwaukee S-OIV infection outbreak. This recent outbreak of infection with a novel influenza A (H1N1) virus also demonstrates the importance of quickly distributing information on new agents and of having rapid influenza virus subtyping assays widely available for clinical and public health decisions.
An Analytical Comparison of Approaches to Personalizing PageRank (2003)

Abstract. PageRank, the popular link-analysis algorithm for ranking web pages, assigns a query and user independent estimate of “importance ” to web pages. Query and user sensitive extensions of PageRank, which use a basis set of biased PageRank vectors, have been proposed in order to personalize the ranking function in a tractable way. We analaytically compare three recent approaches to personalizing PageRank and discuss the tradeoffs of each one. 1
Development of an electrospray approach to deposit complex molecules on plasma modified surfaces (2003)

Two established techniques have been coupled to allow surfaces to be precision engineered. Electrospray ionization to bring large, complex, intact molecular ions into the gas phase has been interfaced with a radio frequency (rf) plasma reactor to treat surfaces making them receptive to the deposition of active biomolecules. The new instrument has been designed and used successfully to deposit a number of high molecular weight molecules including the polysaccharide, sodium hyaluronan (HA), that has an important role in a number of physiological functions. Substrate material is treated using a rf glow discharge plasma chamber, to clean and activate the surface in a controlled manner, then exposed to a beam of multiply charged ions in the gas phase that have been generated using electrospray techniques. The ions are deposited gently onto the substrate and become covalently bound. The molecular integrity and stability of HA surfaces prepared in this way was established using x-ray photoelectron spectroscopy, changes in the observed contact angle, time-of-flight secondary ion mass spectrometry, scanning electron microscopy, and a biological assay–platelet adhesion to the surface.
Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems (2011)

This article was reviewed by Malcolm White (nominated by Purficacion Lopez-Garcia), Frank Eisenhaber and Igor Zhulin. For the full reviews, see the Reviewers' Comments section.
Correlation of 99mTc-GSA hepatic scintigraphy with liver biopsies in patients with chronic active hepatitis type C. (1999)

99mTc-DTPA-galactosyl human serum albumin (99mTc-GSA) liver scintigraphy was performed in 230 patients with chronic active hepatitis type C, and its quantitative indices were compared with histological findings. 99mTc-GSA findings correlated well with four indices of the histology activity index (HAI), especially with the fibrosis score. Ninety patients were given interferon treatments, and 99mTc-GSA findings were compared with the results of the treatments. We classified the effects of interferon treatment into three groups according to clinical outcome: group 1: good effect (HCV-RNA negative, n = 34), group 2: moderate effect (HCV-RNA positive, but the value of GPT was normal for six months after the end of treatment, n = 19) and group 3: no effect (n = 37). Quantitative indices of 99mTc-GSA showed significant differences between groups. Follow-up study with 99mTc-GSA scintigrams was obtained in eight patients. The results of 99mTc-GSA improved in three patients in group 1 and deteriorated in five patients in group 3. There is a possibility that 99mTc-GSA scintigraphy can be used to predict the clinical outcome of chronic active hepatitis type C after interferon treatment.
Expression of Biologically Active Human Vascular Endothelial Growth Factor in Yeast (1995)

Vascular endothelial growth factor (VEGF) is a glycoprotein consisting of two identical polypeptide chains linked by a disulfide bond. The unique biological activities of VEGF include its potent mitogenic and permeability inducing properties specific for the vascular endothelium. VEGF is implicated in tumor angiogenesis, wound healing, and the stimulation of collateral vessel formation at the site of arterial occlusion. Therefore, in order to produce large quantities of biologically active VEGF, a splice variant (VEGF165) was cloned and expressed in a yeast expression system. The coding region of VEGF165 was isolated from U937 cells by RT-PCR, sequenced and then cloned into the yeast expression vector pHILS1. VEGF165 was secreted into the medium as a dimer. Recombinant VEGF reacted to antibodies raised against the N-terminal and C-terminal synthetic polypeptides of human VEGF. As much as 35-40 mg/L of purified VEGF could be obtained from the yeast expression system. The recombinant protein was biologically active in inducing vascular endothelial cell proliferation in vitro and permeability changes in vivo.
Molecular Genetic Resources for Development of 1% Linolenic Acid Soybeans (2006)

Advanced plant breeding will incorporate the most efficient methods available to introgress new traits and develop improved crops. Molecular markers that are specifically targeted to desirable alleles are important molecular genetic resources for selection of traits. Reducing the amount of linolenic acid in soybeans [ Glycine max (L.) Merr.] is a desired breeding objective so that oxidatively stable soybean oil can be produced without the production of trans fatty acids. The objective of this work was to determine the molecular genetic basis for soybeans containing 1% (10 g kg −1 ) linolenic acid in the seed oil fraction and to develop molecular markers specific for identified alleles. Utilizing the soybean homologs of Arabidopsis FAD3 as candidate genes, mutations were discovered in all three GmFAD3 genes in the soybean line A29. The mutations were associated with the linolenic acid phenotype in segregating populations. Molecular markers specific for the mutant alleles enabled capture of the phenotype. Novel combinations of mutant alleles at the three GmFAD3 loci allowed the development of new germplasm containing 1% linolenic acid in the seed oil along with SNP‐based molecular markers that can be used in a backcross breeding strategy.
Effects of Some Environmental Factors on Flower Production and Reproductive Efficiency in Soybeans1 (1958)

Synopsis Percent flowers and pods shedding was increased both by high temperatures and long photoperiod in Clark and Midwest soybean varieties when grown under controlled temperatures and photoperiods. Shedding was not caused by a lack of viable pollen. Under field conditions varieties Mukden, T109, Acc. 2300–2, and Midwest shed 43, 73, 62, and 81% of flowers and pods combined, respectively. From one‐third to one‐half of total shedding was in the form of pods during various stages of development. Rising temperatures appeared to increase shedding.
Proteomics, pathway array and signaling network-based medicine in cancer (2009)

Cancer is a multifaceted disease that results from dysregulated normal cellular signaling networks caused by genetic, genomic and epigenetic alterations at cell or tissue levels. Uncovering the underlying protein signaling network changes, including cell cycle gene networks in cancer, aids in understanding the molecular mechanism of carcinogenesis and identifies the characteristic signaling network signatures unique for different cancers and specific cancer subtypes. The identified signatures can be used for cancer diagnosis, prognosis, and personalized treatment. During the past several decades, the available technology to study signaling networks has significantly evolved to include such platforms as genomic microarray (expression array, SNP array, CGH array, etc.) and proteomic analysis, which globally assesses genetic, epigenetic, and proteomic alterations in cancer. In this review, we compared Pathway Array analysis with other proteomic approaches in analyzing protein network involved in cancer and its utility serving as cancer biomarkers in diagnosis, prognosis and therapeutic target identification. With the advent of bioinformatics, constructing high complexity signaling networks is possible. As the use of signaling network-based cancer diagnosis, prognosis and treatment is anticipated in the near future, medical and scientific communities should be prepared to apply these techniques to further enhance personalized medicine.
1,4-Disubstituted Anthracene Antitumor Agents (1997)

Three different types of 1,4-disubstituted anthracenes were synthesized, and their cytotoxicity in a panel of tumor cells was compared with that of the corresponding 9,10-disubstituted anthracenes. The panel contained human myeloma, melanoma, colon, and lung cancer cells and sensitive and multidrug-resistant murine L1210 leukemia cells. These compounds had [[(dimethylamino)ethyl]amino]methyl, N-[(dimethylamino)ethyl]carbamoyl, and carboxaldehyde (4,5-dihydro-1H-imidazol-2-yl)hydrazone side chains. The 1,4-diamide was more potent across the tumor panel than the corresponding 9,10-isomer, but the 1,4-diamine and the 1,4-hydrazone were less potent than their 9,10-isomers. Although the 1,4-hydrazone was active against P388 leukemia in mice, it was inactive against L1210 leukemia. Within each pair of compounds, the one with greater average potency against tumor cells gave a greater increase in the transition melt temperature of DNA.
A linkage study of chromosome 5q11.2-q13.3 in schizophrenia (1992)

Early studies investigating the inheritance of schizophrenia estimated that between 66% to 93% of the variance in the aetiology is genetic. However, segregation analysis studying the patterns of affected individuals within families has not been able to establish a common mode of transmission. Nevertheless linkage analysis of marker data obtained from families is considered to be the most efficient and robust approach to studying the genetic aetiology of schizophrenia. Linkage studies in schizophrenia can be directed towards regions of the genome where there is a priori grounds for the presence of a susceptibility locus. This study investigated chromosome 5 after a report of an association (though weak) between a partial trisomy of chromosome 5q 11.2-q13.3 and schizophrenia.
Progressive Expectation‐Maximization for Hierarchical Volumetric Photon Mapping (2011)

Abstract State‐of‐the‐art density estimation methods for rendering participating media rely on a dense photon representation of the radiance distribution within a scene. A critical bottleneck of such kernel‐based approaches is the excessive number of photons that are required in practice to resolve fine illumination details, while controlling the amount of noise. In this paper, we propose a parametric density estimation technique that represents radiance using a hierarchical Gaussian mixture. We efficiently obtain the coefficients of this mixture using a progressive and accelerated form of the Expectation‐Maximization algorithm. After this step, we are able to create noise‐free renderings of high‐frequency illumination using only a few thousand Gaussian terms, where millions of photons are traditionally required. Temporal coherence is trivially supported within this framework, and the compact footprint is also useful in the context of real‐time visualization. We demonstrate a hierarchical ray tracing‐based implementation, as well as a fast splatting approach that can interactively render animated volume caustics.
Vertical scaling of carbon nanotube field-effect transistors using top gate electrodes (2002)

We have fabricated single-wall carbon nanotube field-effect transistors (CNFETs) in a conventional metal–oxide–semiconductor field-effect transistor (MOSFET) structure, with gate electrodes above the conduction channel separated from the channel by a thin dielectric. These top gate devices exhibit excellent electrical characteristics, including steep subthreshold slope and high transconductance, at gate voltages close to 1 V—a significant improvement relative to previously reported CNFETs which used the substrate as a gate and a thicker gate dielectric. Our measured device performance also compares very well to state-of-the-art silicon devices. These results are observed for both p- and n-type devices, and they suggest that CNFETs may be competitive with Si MOSFETs for future nanoelectronic applications.
3. Neurocontrol of Systems with Friction (2002)

Here we develop a technique for control of industrial processes with friction using NNs. The NN appears in a feedback control loop and significantly improves the performance of the process by compensating for the deleterious effects of friction. The NN weights will be tuned in such a fashion that the NN learns about the friction nonlinearity on line. No preliminary offline learning is needed. First, we present an augmented form of NN that can be used to approximate functions with discontinuities, since friction has a jump discontinuity at the origin. 3.1 Neural network approximation of functions with discontinuities The friction nonlinearity appearing in industrial actuators was discussed in Chapter 2 and is shown in Figure 3.1.1. It is discontinuous at the origin. One of the most important properties of NNs for control purposes is the universal approximation property. Unfortunately, this property is generally proven for continuous functions. In most real industrial control systems, there are nonsmooth functions (e.g., piecewise continuous) for which approximation results in the literature are sparse. Examples include friction, deadzones, and backlash. It is found that attempts to approximate piecewise continuous functions using smooth activation functions require many NN hidden nodes and many training iterations, and they still do not yield very good results.
SOX9 is an intestine crypt transcription factor, is regulated by the Wnt pathway, and represses the CDX2 and MUC2 genes (2004)

TCF and SOX proteins belong to the high mobility group box transcription factor family. Whereas TCFs, the transcriptional effectors of the Wnt pathway, have been widely implicated in the development, homeostasis and disease of the intestine epithelium, little is known about the function of the SOX proteins in this tissue. Here, we identified SOX9 in a SOX expression screening in the mouse fetal intestine. We report that the SOX9 protein is expressed in the intestinal epithelium in a pattern characteristic of Wnt targets. We provide in vitro and in vivo evidence that a bipartite beta-catenin/TCF4 transcription factor, the effector of the Wnt signaling pathway, is required for SOX9 expression in epithelial cells. Finally, in colon epithelium-derived cells, SOX9 transcriptionally represses the CDX2 and MUC2 genes, normally expressed in the mature villus cells of the intestinal epithelium, and may therefore contribute to the Wnt-dependent maintenance of a progenitor cell phenotype.
DNA mismatch repair (MMR)‐dependent 5‐fluorouracil cytotoxicity and the potential for new therapeutic targets (2009)

The metabolism and efficacy of 5-fluorouracil (FUra) and other fluorinated pyrimidine (FP) derivatives have been intensively investigated for over fifty years. FUra and its antimetabolites can be incorporated at RNA- and DNA-levels, with RNA level incorporation provoking toxic responses in human normal tissue, and DNA-level antimetabolite formation and incorporation believed primarily responsible for tumour-selective responses. Attempts to direct FUra into DNA-level antimetabolites, based on mechanism-of-action studies, have led to gradual improvements in tumour therapy. These include the use of leukovorin to stabilize the inhibitory thymidylate synthase-5-fluoro-2'-deoxyuridine 5' monophoshate (FdUMP)-5,10-methylene tetrahydrofolate (5,10-CH(2)FH(4)) trimeric complex. FUra incorporated into DNA also contributes to antitumour activity in preclinical and clinical studies. This review examines our current state of knowledge regarding the mechanistic aspects of FUra:Gua lesion detection by DNA mismatch repair (MMR) machinery that ultimately results in lethality. MMR-dependent direct cell death signalling or futile cycle responses will be discussed. As 10-30% of sporadic colon and endometrial tumours display MMR defects as a result of human MutL homologue-1 (hMLH1) promoter hypermethylation, we discuss the use and manipulation of the hypomethylating agent, 5-fluorodeoxycytidine (FdCyd), and our ability to manipulate its metabolism using the cytidine or deoxycytidylate (dCMP) deaminase inhibitors, tetrahydrouridine or deoxytetrahydrouridine, respectively, as a method for re-expression of hMLH1 and re-sensitization of tumours to FP therapy.
Beneficial aspects of real time flow measurements for the management of acute right ventricular heart failure following continuous flow ventricular assist device implantation (2012)

Temporary mechanical circulatory support of the right ventricle was successfully performed. Real time flow measurement proved to be a useful tool for the diagnosis and ultimately for the management of right heart failure including the weaning from extracorporeal membrane oxygenation.