gebhart/patrepeval huggingface dataset:
MicroRNA expression profiling in cancer from a bioinformatics prospective (2007)

A new type of noncoding short single-stranded RNA molecules, microRNA (miRNA), has recently emerged as one of the most important new classes of cellular regulators. Recent advances in miRNA research have provided evidence that aberrant expression of specific miRNAs is associated with a broad spectrum of human diseases, such as cancer, diabetes, cardiovascular diseases, psychological disorders and others. Global microRNAome profiling has demonstrated drastic changes in expression of multiple miRNAs in many common human cancers. miRNA expression signatures have been shown to provide a more accurate method of classifying cancer subtypes than transcriptome profiling of an entire set of known protein-coding genes. miRNA profiling also allows classification of different stages in tumor progression and can predict disease outcome in some cases. Further characterization of these abnormal miRNA expression signatures and identification of the most significant and informative aberrantly expressed miRNAs could lead to the development of tissue- and biofluid-specific diagnostic markers, as well as a new type of oligonucleotide-based therapeutics. As researchers continue to study miRNA expression in cancer and focus on most relevant miRNAs, the further advancement of miRNA-detection technologies and bioinformatics algorithms is critical for successful identification of the most informative diagnostics markers among the tissue-specific miRNAs.
Phosphorothioate-containing RNAs show mRNA activity in the prokaryotic translation systems<i>in vitro</i> (1991)

Phosphorothioate-containing RNAs were generated by transcription of coliphage T7 DNA using the Sp diastereomers of ribonucleoside 5'-O-(1-thiotriphosphates) and T7 RNA polymerase. RNAs in which a single nucleotide was substituted by the corresponding nucleoside phosphorothioate functioned as mRNA in the cell-free translation systems prepared from Escherichia coli and from an extreme thermophilic bacterium, Thermus thermophilus. This substitution increased the efficiency of protein synthesis by stabilizing the mRNAs in these systems. As the proportion of substituted nucleotides was increased, their mRNA activity was decreased accordingly. As judged from the analysis by SDS-polyacrylamide gel-electrophoresis, the proteins synthesized using phosphorothioate-containing mRNAs as template were identical to those obtained with unsubstituted mRNAs. However, larger proteins which were barely detectable when unsubstituted mRNA was used were well represented when phosphorothioate-RNA was used instead. The advantages in using the phosphorothioate-mRNAs in the in vitro translation systems are discussed.
One-pot peptide and protein conjugation: a combination of enzymatic transamidation and click chemistry (2016)

Enzymatic transamidation and copper-catalyzed azide-alkyne cycloaddition (CuAAC) were combined to yield covalently conjugated peptides and proteins. The addition of glutathione preserved enzymatic activity in the presence of copper. Tuning the reaction kinetics was key to success, providing up to 95% conversion. This one-pot reaction allowed for targeted fluorescent protein labeling.
A Reinforcement Learning Approach to Online Clustering (1999)

A general technique is proposed for embedding online clustering algorithms based on competitive learning in a reinforcement learning framework. The basic idea is that the clustering system can be viewed as a reinforcement learning system that learns through reinforcements to follow the clustering strategy we wish to implement. In this sense, the reinforcement guided competitive learning (RGCL) algorithm is proposed that constitutes a reinforcement-based adaptation of learning vector quantization (LVQ) with enhanced clustering capabilities. In addition, we suggest extensions of RGCL and LVQ that are characterized by the property of sustained exploration and significantly improve the performance of those algorithms, as indicated by experimental tests on well-known data sets.
Plant regeneration from "Trovita" orange protoplasts. (1983)

Protoplasts isolated from nucellar callus of 'Trovita' orange (Citrus sinensis Osbeck) wvere cultured in a MURASHIGE and TUCKER'S medium containing 0.15 M sucrose, 0.45 M glucose, and 0.6% agar, but lacking phytohormones. Colonies with 26.3% plating efficiency were observed after 6 weeks culture. When the protoplasts were cultured in the presence of exogenous phytohormones, reduction in colony formation was observed. Some colonies developed to green embryoids, which eventually formed plants.
FPGA implementation of the ray tracing algorithm used in the XPATCH software (2002)

Ray tracing is one of the most popular and powerful image synthesis technique for creating photo-realistic images. In this research, we focus on the time critical application of ray tracing in the XPATCH software for high-resolution radar simulation and detection. Of particular interest to us is the ray/box intersection algorithm employed in the XPATCH ray tracer for achieving faster execution time. The ray/box algorithm is used to determine whether a ray hits or misses the target enclosed in a rectangular bounded volume.
Ring finger motif of Arabidopsis thaliana COP1 defines a new class of zinc-binding domain. (1993)

Zinc Binding of the Ring Finger Motif 19627 in to recover the COPl start codon and ligated to SmaI-and HindIIIdigested pMal-c (New England Biolabs) to give pM-COP1.The junction between the two coding regions was confirmed by sequencing.pM-COP1 encodes the protein M-COPl, a fusion between the E. coli maltose-binding protein (MBP)' and COP1.The XbaI site at codon position 393 of COPl in pM-COP1 was filled in, creating a stop codon and, after religation, forming plasmid pM-COP1 N. A 65residue deletion of the ring finger motif between residues 39 and 105 of COPl was generated by inverse polymerase chain reaction of the COPl coding sequence excluding the ring finger using the oligonucleotides 5' CCA ATC TCG AGA CCG CCG CT 3' and 5' TTT CTT GCT CGA GAA GCT AT 3'.Reinsertion of the modified COPl sequence into pMal-c resulted in pM-COPlAZ.The XbaI site in pM-COPlAZ was filled in as described above and the plasmid religated to give pM-COP1 NAZ.The COPl coding region in pM-COP1 NAZ was sequenced completely and the designed structure confirmed.pMal-c itself will produce a fusion protein consisting of the maltosebinding protein and a short peptide derived from @-galactosidase.For this reason, pMal-c is here referred to as pM-BGal.To create pN287 an EcoRI/HincII fragment containing the N-terminal 287 codons of COPl was excised from pBSCOPl and inserted into the pET3aderived vector ~P 0 -9 .~ This fusion created an open reading frame consisting of six NHp-terminal codons of phage T7 gene 10, 287 codons representing the NHz-terminal half of COP1, and 22 COOHterminal codons derived from the pP0-9 vector.Expression and Purification of M-COP1 Fusion Proteins-E. coli strain DH5a was used as the host for overexpression of "COP1 fusion proteins.Expression of the fusion protein was induced by addition of 0.1 mM isopropyl-1-thio-@-galactopyranoside.Two hours after induction, cells were harvested on ice, washed once with TN buffer (200 mM NaC1, 50 mM Tris, pH 7.5) and lysed by sonication in TN, containing 1 mM phenylmethylsulfonyl fluoride, 5 pg/ml leupeptin, 1 mM benzamidine, 1 pg/ml phosphoramidone, and 1 pg/ ml bestatin (Boehringer Mannheim).The fusion protein was purified from the soluble fraction by affinity chromatography over amyloseresin (New England Biolabs) as recommended by the manufacturer.The preparations contained over 95% fusion proteins as judged by SDS-PAGE and staining with Coomassie Brilliant Blue (Fig. 2).Some heterogeneity of the final product "COP1 N was probably caused by protease digestion in E. coli or during purification.This was confirmed by Western blot analysis with a COP1-specific antiserum and analysis of the digestion pattern of M-COP1 N with factor
Design and control of supernumerary robotic limbs (2016)

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2016.
Effects of Mannose and Fructose on the Synthesis and Secretion of Insulin (1989)

Synthesis-secretion coupling of insulin was determined in perfused pancreases stimulated for 3 h by various sugars. These monosaccharide stimuli included glucose alone at either 200 or 300 mg/dl; mannose or fructose alone at 1,200 mg/dl; or combinations of mannose and fructose or galactose and fructose at 600 mg/dl each. Glucose and mannose each promoted insulin synthesis and secretion. Mannose at 1,200 mg/dl produced synthesis-secretion coupling similar to glucose at 200 mg/dl. Fructose alone at 1,200 mg/dl failed to cause any significant release of insulin, but it did significantly increase beta cell insulin content. When mannose and fructose were combined at 600 mg/dl each, in the absence of glucose, they resulted in a synergistic effect on insulin secretion and an additive effect on insulinogenesis, which was in excess of, or equal to, the insulinotropic effect of glucose at 300 mg/dl. These results clearly establish that the synthesis and secretion of insulin can be uncoupled. Mannose primarily stimulates the putative beta cell glucoreceptor, and fructose signals the insulin biosynthetic pathway. When combined, these monosaccharides couple synthesis-secretion of insulin comparable to glucose. The data suggest that the uncoupling of insulin secretion and synthesis, which may contribute either independently or in combination to abnormalities in pancreatic function observed in various diabetic conditions can be studied using the isolated perfused pancreas model. Use of this relatively physiological experimental model should provide optimal opportunity to further investigate and identify cellular controlling signals regulating either insulin biosynthesis, insulin secretion, or the coupling of both mechanisms.
Current State of Preeclampsia Mouse Models: Approaches, Relevance, and Standardization (2021)

Preeclampsia (PE) is a multisystemic, pregnancy-specific disorder and a leading cause of maternal and fetal death. PE is also associated with an increased risk for chronic morbidities later in life for mother and offspring. Abnormal placentation or placental function has been well-established as central to the genesis of PE; yet much remains to be determined about the factors involved in the development of this condition. Despite decades of investigation and many clinical trials, the only definitive treatment is parturition. To better understand the condition and identify potential targets preclinically, many approaches to simulate PE in mice have been developed and include mixed mouse strain crosses, genetic overexpression and knockout, exogenous agent administration, surgical manipulation, systemic adenoviral infection, and trophoblast-specific gene transfer. These models have been useful to investigate how biological perturbations identified in human PE are involved in the generation of PE-like symptoms and have improved the understanding of the molecular mechanisms underpinning the human condition. However, these approaches were characterized by a wide variety of physiological endpoints, which can make it difficult to compare effects across models and many of these approaches have aspects that lack physiological relevance to this human disorder and may interfere with therapeutic development. This report provides a comprehensive review of mouse models that exhibit PE-like symptoms and a proposed standardization of physiological characteristics for analysis in murine models of PE.
ANÁLISE CUSTO/VOLUME/LUCRO APLICADA NUMA PEQUENA PROPRIEDADE AGROPECUÁRIA DE CAMPOS DO GOYTACAZES/RJ (2013)

O artigo analisa sistematicamente uma pequena propriedade rural, chamada Sao Juliao, que cria gado leiteiro no municipio de Campos dos Goytacazes, situado no norte fluminense do estado do Rio de Janeiro. Para tanto, fez-se uma analise Custo/Volume/Lucro (CVL) nesta fazenda. Buscaram-se os dados in loco para calcular os parâmetros da ferramenta CVL, como os custos fixos, os custos variaveis, a margem de contribuicao unitaria e o ponto de equilibrio. O estudo de caso mostrou aos donos do negocio que o ponto de equilibrio da propriedade esta muito proximo da venda mensal de 5000 L de leite, fazendo com que a margem de contribuicao seja de R$0,17/L de leite e a margem de seguranca seja apenas 18%, consideradas baixas para a atividade. A demonstracao do resultado do exercicio – DRE do mes de abril de 2011 confirmou, pelo metodo do custeio variavel, o pouco retorno obtido no mes, R$142,82. Por fim, o uso da ferramenta Custo/Volume/Lucro permitiu que os proprietarios analisassem o modo que estavam administrando e tomando as decisoes em sua propriedade. Palavras-chave: agropecuaria leiteira, analise Custo/Volume/Lucro, ponto de equilibrio.
Floating OffShore Wind Turbines for Shallow waters (2003)

Bottom mounted Offshore wind turbines seem to have a promising future but they are restricted to shallow waters of Northern Europe. Many projects are planned or are in the phase of construction on the North Sea and the Baltic Sea. All projects that are planned have a water depth up to approximately 25 m. The project reported in this paper investigated the technical and economical feasibility of floating wind energy systems in deeper waters, approximately 50 m and deeper. It is assumed that at a certain water depth floating wind turbines will have better economics than bottom mounted wind turbines. Floating wind energy systems seem to have some advantages over bottom mounted wind energy systems, like e.g. â¢ lower cost installation (in a harbour); â¢ lower maintenance cost; â¢ lower removal cost. But floating wind energy systems have their own technical challenges, like â¢ dynamic interactions between floater and wind turbine; â¢ floater conceptual design including mooring system, taking into account restriction w.r.t. stability of floater and wind turbine, minimizing wave induced motion, water depth, etc.
The influence of SiO2 on the aluminum borate whisker reinforced aluminum phosphate wave-transparent materials (2012)

Abstract Aluminum borate whisker reinforced aluminum phosphates composites with SiO2 additive were prepared by pressureless sintering. The influence of SiO2 on aluminum borate whisker aluminum phosphates ceramic wave-transparent materials was investigated. It was found that after the sintering at 1050°C for 1 h, the Vickers hardness of the composites with 5% SiO2 addition reaches 299 MPa, the flexural strength 153.8 MPa. The dielectric constantan and loss tangent of the composites are 2.8 and 0.03132 at 10 GHz, respectively.
Synchronization models for multimedia presentation with user participation (1993)

This paper addresses the key issue of providingflexible multimedia presentation with user participation and suggests synchronization models that can specify the user participation during the presentation. We study models like the Petrinet-based hypertext model and the object composition Petri nets (OCPN). We suggest adynamic timed Petri nets structure that can model pre-emptions and modifications to the temporal characteristics of the net. This structure can be adopted by the OCPN to facilitate modeling of multimedia synchronization characteristics with dynamic user participation. We show that the suggested enhancements for the dynamic timed Petri nets satisfy all the properties of the Petri net theory. We use the suggested enhancements to model typical scenarios in a multimedia presentation with user inputs.
Chemical structure and sweet taste of isocoumarins and related compounds synthesis of 5-hydroxyflavanones and related dihydrochalcones. (1977)

On the basis of the information obtained from our previous studies on relationship between structure and sweet taste of 3, 4-dihydroisocoumarins, 5-hydroxyflavanones and related dihydrochalcones were synthesized. Compounds (2, 3, 4, and 7) had a sweet taste while the others were tasteless. The relationship of structure-sweet taste of 5-hydroxy-flavanones was similar to that of 3, 4-dihydroisocoumarins.
Study of the Thermal Decomposition of 2-Azidoacetic Acid by Photoelectron and Matrix Isolation Infrared Spectroscopy (1997)

2-Azidoacetic acid (N3CH2CO2H) has been synthesized and characterized by a variety of spectroscopic techniques, and the thermal decomposition of this molecule studied by matrix isolation infrared spectroscopy and real-time ultraviolet photoelectron spectroscopy. The results are consistent with the vapor phase thermal decomposition following a pathway involving concerted ejection of molecular N2 and the simultaneous formation of CO2 and methanimine (CH2NH). No evidence was found for the presence of intermediates such as the nitrene NCH2CO2H or the imine HNCHCO2H. At higher temperatures, CH2NH further decomposes to give HCN and H2.
940-nm Broad Area Diode Lasers Optimized for High Pulse-Power Fiber Coupled Applications (2014)

Diode lasers with 400- μm stripe widths measured in pulsed-current mode are shown to reach peak (saturation) powers of 60 W for 1-ms pulses (60 mJ) and 189 W for 300-ns pulses ( ~ 55 μJ). Use of laterally structured contact and etched index guides at the stripe edges enables these devices to sustain stable lateral near- and far-field profiles to the highest bias, with a lateral beam parameter product of . Optical calculations are presented for an example system where arrays of these single emitters are incoherently coupled into a fiber with 1-mm core and numerical aperture of 0.22, extrapolating 5 kW in fiber for 1 ms (5 J) and 18 kW in fiber for 300-ns pulses ( ~ 5 mJ). Such sources would be well suited for pumping Yb:YAG crystals for applications needing high beam quality, or as direct sources.
Detection of Speaker Change Points in Conversational Speech (2007)

An important preprocessing step in many automatic speech segmentation and speaker clustering systems is the accurate detection of speaker change points, the times when one speaker stops talking and another begins. However, this becomes very difficult in conversational speech since utterance lengths can be extremely short, speaker changes occur frequently, speakers may talk over one another (co-channel interference), and the recording environment and/or communication channel is sub-optimal or degraded. Modern aviation systems can benefit from this research as a pre-processing stage in a variety of applications. Examples include automatic segmentation and clustering of pilot/air traffic controller communications, detection of a third or unauthorized speaker in commercial airline cockpits, and automatic transcription of cockpit audio recordings. This research presents an approach to detecting speaker change points using information obtained from voiced speech segments. This permits taking advantage of the facts that (1) speaker starting and stopping information should be contained between segments of voiced speech and (2) voiced speech contains the most useful speaker identifiable information. The technique presented here shows promise as an enhancement to currently available change point detection algorithms.
A Multi-Robotic System for Environmental Cleaning (2018)

There is a lot of waste in an industrial environment that could cause harmful effects to both the products and the workers resulting in product defects, itchy eyes or chronic obstructive pulmonary disease, etc. While automative cleaning robots could be used, the environment is often too big for one robot to clean alone in addition to the fact that it does not have adequate stored dirt capacity. We present a multi-robotic dirt cleaning system algorithm for multiple automatic iRobot Creates teaming to efficiently clean an environment. Moreover, since some spaces in the environment are clean while others are dirty, our multi-robotic system possesses a path planning algorithm to allow the robot team to clean efficiently by spending more time on the area with higher dirt level. Overall, our multi-robotic system outperforms the single robot system in time efficiency while having almost the same total battery usage and cleaning efficiency result.
Tobacco smoke induces CYP1B1 in the aerodigestive tract (2004)

Several members of the P450 family, including cytochrome P450 1B1 (CYP1B1), can convert tobacco smoke (TS) procarcinogens, including benzo[a]pyrene (B[a]P), to carcinogenic intermediates. In this study we investigated the effects of TS condensate and B[a]P on the expression of CYP1B1 in vitro and in vivo. CYP1B1 mRNA and protein were induced by both TS condensate and B[a]P in cell lines derived from the human aerodigestive tract. Treatment with TS condensate stimulated binding of the aryl hydrocarbon receptor (AhR) to an oligonucleotide containing a canonical xenobiotic response element (XRE) site and induced XRE-luciferase activity. These findings are consistent with prior evidence that polycyclic aromatic hydrocarbons, known ligands of the AhR, stimulate CYP1B1 transcription by an XRE-dependent mechanism. To determine whether these in vitro findings applied in vivo, both murine and human studies were carried out. Short-term exposure to TS induced CYP1B1 in the tongue, esophagus, lung and colon of experimental mice. In contrast, CYP1B1 was not induced by TS in the aorta of these mice. Levels of CYP1B1 mRNA were also elevated in the bronchial mucosa of human tobacco smokers versus never smokers (P < 0.05). Taken together, these results support a role for CYP1B1 in TS-induced carcinogenesis in the aerodigestive tract.
Iron-Corroding Methanogen Isolated from a Crude-Oil Storage Tank (2010)

Microbiologically influenced corrosion of steel in anaerobic environments has been attributed to hydrogenotrophic microorganisms. A sludge sample collected from the bottom plate of a crude-oil storage tank was used to inoculate a medium containing iron (Fe(0)) granules, which was then incubated anaerobically at 37 degrees C under an N(2)-CO(2) atmosphere to enrich for microorganisms capable of using iron as the sole source of electrons. A methanogen, designated strain KA1, was isolated from the enrichment culture. An analysis of its 16S rRNA gene sequence revealed that strain KA1 is a Methanococcus maripaludis strain. Strain KA1 produced methane and oxidized iron much faster than did the type strain of M. maripaludis, strain JJ(T), which produced methane at a rate expected from the abiotic H(2) production rate from iron. Scanning electron micrographs of iron coupons that had been immersed in either a KA1 culture, a JJ(T) culture, or an aseptic medium showed that only coupons from the KA1 culture had corroded substantially, and these were covered with crystalline deposits that consisted mainly of FeCO(3).
Electrostatic Deposition of Pesticide Spray onto Foliar Targets of Varying Morphology (1981)

ABSTRACT SPRAY deposition onto broccoli, corn, cotton and cab-bage foliage was measured for three distinct methods of application. In an air-carrier stream, charged vs. un-charged droplets provided 1.8-, 2.0-, 2.5- and 7.0-fold deposition increases, respectively. Charged vs. conven-tional spraying provided 1.9-, 2.9- and 4.4-fold increases on broccoli, cabbage and corn plants. A deposit limited condition was verified for electrostatic spraying of foliar targets exhibiting leaf point.