gebhart/patrepeval huggingface dataset:
Mathematical models of ABE fermentation: review and analysis (2012)

Among different liquid biofuels that have emerged in the recent past, biobutanol produced via fermentation processes is of special interest due to very similar properties to that of gasoline. For an effective design, scale-up, and optimization of the acetone-butanol-ethanol (ABE) fermentation process, it is necessary to have insight into the micro- and macro-mechanisms of the process. The mathematical models for ABE fermentation are efficient tools for this purpose, which have evolved from simple stoichiometric fermentation equations in the 1980s to the recent sophisticated and elaborate kinetic models based on metabolic pathways. In this article, we have reviewed the literature published in the area of mathematical modeling of the ABE fermentation. We have tried to present an analysis of these models in terms of their potency in describing the overall physiology of the process, design features, mode of operation along with comparison and validation with experimental results. In addition, we have also highlighted important facets of these models such as metabolic pathways, basic kinetics of different metabolites, biomass growth, inhibition modeling and other additional features such as cell retention and immobilized cultures. Our review also covers the mathematical modeling of the downstream processing of ABE fermentation, i.e. recovery and purification of solvents through flash distillation, liquid-liquid extraction, and pervaporation. We believe that this review will be a useful source of information and analysis on mathematical models for ABE fermentation for both the appropriate scientific and engineering communities.
In Vivo Imaging of Quantum Dots Encapsulated in Phospholipid Micelles (2002)

Fluorescent semiconductor nanocrystals (quantum dots) have the potential to revolutionize biological imaging, but their use has been limited by difficulties in obtaining nanocrystals that are biocompatible. To address this problem, we encapsulated individual nanocrystals in phospholipid block-copolymer micelles and demonstrated both in vitro and in vivo imaging. When conjugated to DNA, the nanocrystal-micelles acted as in vitro fluorescent probes to hybridize to specific complementary sequences. Moreover, when injected into Xenopus embryos, the nanocrystal-micelles were stable, nontoxic (<5 x 10(9) nanocrystals per cell), cell autonomous, and slow to photobleach. Nanocrystal fluorescence could be followed to the tadpole stage, allowing lineage-tracing experiments in embryogenesis.
The T alpha 1 alpha-tubulin promoter specifies gene expression as a function of neuronal growth and regeneration in transgenic mice (1994)

We have previously demonstrated that one member of the alpha-tubulin multigene family, termed T alpha 1 in rats, is regulated as a function of neuronal growth and regeneration. To elucidate the molecular mechanisms responsible for coupling gene expression to morphological differentiation, we have isolated the T alpha 1 gene, have fused 1.1 kb of the 5' flanking region to a nuclear lacZ reporter gene, and have generated transgenic mice. Analysis of these transgenic mice demonstrated that marker gene expression was specific to the CNS and PNS, with expression in vivo at embryonic day 13.5 being similar to expression of the endogenous gene. Moreover, the induction of transgene expression was correlated temporally with neuronal commitment in developing neural crest-derived peripheral neurons and in the developing retina. Immunocytochemical analysis of mixed primary embryonic brain cultures confirmed that transgene expression was specific to neurons, with the majority of neurons, but not astrocytes or oligodendrocytes, expressing beta-galactosidase. Transgene expression in vivo was maintained in developing neurons until early in postnatal life, subsequent to which its expression decreased coincident with neuronal maturation. The transgene was then reinduced in regenerating facial motoneurons following unilateral axotomy of the facial nerve. Thus, 1.1 kb of 5' flanking sequence from the T alpha 1 gene contains the sequence elements responsible for specifying gene expression to embryonic neurons and for subsequently regulating gene expression in both developing and mature neurons as a function of morphological growth.
Cell Lineage Analysis of a Mouse Tumor (2008)

Revealing the lineage relations among cancer cells can shed light on tumor growth patterns and metastasis formation, yet cell lineages have been difficult to come by in the absence of a suitable method. We previously developed a method for reconstructing cell lineage trees from genomic variability caused by somatic mutations. Here, we apply the method to cancer and reconstruct, for the first time, a lineage tree of neoplastic and adjacent normal cells obtained by laser microdissection from tissue sections of a mouse lymphoma. Analysis of the reconstructed tree reveals that the tumor initiated from a single founder cell, approximately 5 months before diagnosis, that the tumor grew in a physically coherent manner, and that the average number of cell divisions accumulated in cancerous cells was almost twice than in adjacent normal lung epithelial cells but slightly less than the expected figure for normal B lymphocytes. The cells were also genotyped at the TP53 locus, and neoplastic cells were found to share a common mutation, which was most likely present in a heterozygous state. Our work shows that the ability to obtain data regarding the physical appearance, precise anatomic position, genotypic profile, and lineage position of single cells may be useful for investigating cancer development, progression, and interaction with the microenvironment.
The effects of ketoconazole on the intestinal metabolism and bioavailability of cyclosporine* (1995)

The pharmacokinetics of cyclosporine were studied in the blood of five normal healthy volunteers (two men and three women) after each received oral and intravenous cyclosporine alone and with concomitant oral ketoconazole. Administration of ketoconazole caused a significant decrease in intravenous cyclosporine clearance (0.18 +/- 0.05 L/kg/hr versus 0.32 +/- 0.09 L/hr/kg) and a significant increase in cyclosporine oral bioavailability (56.4% +/- 11.7% versus 22.4% +/- 4.8%) compared with values before ketoconazole administration. Steady-state volume of distribution for intravenously administered cyclosporine was unchanged (1.26 +/- 0.44 L/kg versus 1.10 +/- 0.27 L/kg). Hepatic bioavailability (1 - hepatic extraction ratio) calculated for intravenous cyclosporine increased by 11% in the presence of ketoconazole (86.3% +/- 3.7% versus 75.2% +/- 6.6% without ketoconazole), which accounts for only one third of the observed increase in cyclosporine oral bioavailability. Because it is unlikely that ketoconazole had a significant effect on either cyclosporine absorption or hepatic blood flow, the increase in cyclosporine bioavailability observed in this study is most likely explained by inhibition of gastrointestinal cytochrome P450 enzymes.
Secondary Amines from the lron(II) Ion-Catalyzed Reaction of Amine Oxides: A General Method for the Dealkylation of Tertiary Amines (1985)

La desalkylation d'amines tertiaires se fait par une reaction «one pot»: oxydation d'amines tertiaires par l'acide m-chloroperbenzoique dans le dichloromethane suivie d'addition de FeCl 2 ; application a la synthese de (−)-methoxy-3 morphinanol-14, d'octahydroisoquinoleines, de derives de pyridine, etc
Mode of action and application of Scorpion primers to mutation detection (2000)

Scorpion primers can be used to detect PCR products in homogeneous solution. Their structure promotes a unimolecular probing mechanism. We compare their performance with that of the same probe sequence forced to act in a bimolecular manner. The data suggest that Scorpions indeed probe by a unimolecular mechanism which is faster and more efficient than the bimolecular mechanism. This mechanism is not dependent on enzymatic cleavage of the probe. A direct comparison between Scorpions, TaqMan and Molecular Beacons on a Roche LightCycler indicates that Scorpions perform better, particularly under fast cycling conditions. Development of a cystic fibrosis mutation detection assay shows that Scorpion primers are selective enough to detect single base mutations and give good sensitivity in all cases. Simultaneous detection of both normal and mutant alleles in a single reaction is possible by combining two Scorpions in a multiplex reaction. Such favourable properties of Scorpion primers should make the technology ideal in numerous applications.
Characteristics of crashes attributed to the driver having fallen asleep (1995)

While it has been known for some time that crashes can result from the driver falling asleep at the wheel, this issue has received less attention in traffic safety programs than the role of alcohol or speed of the vehicle. The present study was done to investigate the characteristics of crashes attributed to the driver being asleep. The study utilized the database at the Highway Safety Research Center at the University of North Carolina that is based on the uniform crash reporting system in that state. Over the years 1990-1992, inclusive, there were 4333 crashes in which the driver was judged to be asleep but not intoxicated. The crashes were primarily of the drive-off-the-road type (78% of the total) and took place at higher speeds (62% in excess of 50 mph). The fatality rate was of similar magnitude to that in alcohol-related crashes with fatalities in 1.4% of such crashes (alcohol crashes had fatalities in 2.1%). The crashes occurred primarily at two times of day--during the nighttime period of increased sleepiness (midnight to 7.00 a.m.) and during the mid-afternoon "siesta" time of increased sleepiness (3.00 p.m.). These crashes occurred predominately in young people. Fifty-five percent of these were in individuals 25 years of age or younger, with a peak age of occurrence at age 20 years. Sleepiness may play a role in crashes other than those attributed by the police to the driver being asleep. Determining the magnitude of this role is a challenge to the traffic safety community.
LiF∕Co Nanocomposite as a New Li Storage Material (2006)

A nanocomposite consisting of both LiF and transition metal Co as general inactive electrochemical materials fabricated by pulsed laser deposition exhibits significant electrochemical activity. The charge and discharge measurement indicate that the first charge capacity of for the cell is found to release Li. The process of releasing Li from the as-deposited LiF–Co nanocomposite thin films is confirmed by ex situ high resolution transmission electron microscopy and selected area electron diffraction measurements. These results provide direct experimental evidence to support the decomposition of LiF driven by the transition metal Co. LiF–Co nanocomposite electrodes may be found to be a new good candidate for Li storage material.
Head-Worn Displays: The Future Through New Eyes (2009)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Jannick Rolland and Ozan Cakmakci, "Head-Worn Displays: The Future Through New Eyes," Optics & Photonics News 20(4), 20-27 (2009) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Necrotizing Fasciitis (2001)

Kovacs, Laszlo H. MD*; Kloeppel, Markus MD*; Papadopulos, Nikolaos A. MD*; Reeker, Wolfram MD†; Biemer, Edgar PhD* Author Information
Transduction of psychosocial stress into the neurobiology of recurrent affective disorder (1992)

Early clinical observations and recent systematic studies overwhelmingly document a greater role for psychosocial stressors in association with the first episode of major affective disorder than with subsequent episodes. The author postulates that both sensitization to stressors and episode sensitization occur and become encoded at the level of gene expression. In particular, stressors and the biochemical concomitants of the episodes themselves can induce the protooncogene c-fos and related transcription factors, which then affect the expression of transmitters, receptors, and neuropeptides that alter responsivity in a long-lasting fashion. Thus, both stressors and episodes may leave residual traces and vulnerabilities to further occurrences of affective illness. These data and concepts suggest that the biochemical and anatomical substrates underlying the affective disorders evolve over time as a function of recurrences, as does pharmacological responsivity. This formulation highlights the critical importance of early intervention in the illness in order to prevent malignant transformation to rapid cycling, spontaneous episodes, and refractoriness to drug treatment.
Expression of human choriogonadotropin in monkey cells using a single simian virus 40 vector. (1985)

We have inserted the cDNAs coding for both polypeptide subunits, alpha and beta, of human choriogonadotropin (hCG) into a single simian virus 40 expression vector in such a way that they replace the viral VP2 and VP1 coding sequences, respectively. Monkey cells infected with this virus and the appropriate helper virus produce dimeric hCG. hCG produced in this system was shown to chromatograph identically to standard hCG preparations on gel filtration and to be biologically active in the mouse uterine weight assay.
The Effect of Insulin Antibodies on the Metabolic Action of Inhaled and Subcutaneous Insulin (2005)

In patients with type 1 diabetes treated with inhaled insulin, development of high- or low-affinity IABs did not impair postprandial glucose tolerance, alter the time-action profile of insulin, or impact tolerability. No clinical relevance of IABs was identified in this study.
Adiponectin Inhibits Cell Proliferation by Interacting with Several Growth Factors in an Oligomerization-dependent Manner (2005)

Adiponectin, an adipocyte-specific secretory protein, is present in serum as three oligomeric complexes. Apart from its roles as an anti-diabetic and anti-atherogenic hormone, adiponectin has been implicated as an important regulator of cell growth and tissue remodeling. Here we show that some of these functions might be mediated by the specific interactions of adiponectin with several important growth factors. Among six different growth factors examined, adiponectin was found to bind with platelet-derived growth factor BB (PDGF-BB), basic fibroblast growth factor (FGF), and heparin-binding epidermal growth factor-like growth factor (HB EGF) with distinct affinities. The bindings of adiponectin with these growth factors are oligomerization-dependent. PDGF-BB bound to the high molecular weight (HMW) and middle molecular weight (MMW) complexes, but not to the low molecular weight (LMW) complex of adiponectin. Basic FGF preferentially interacted with the HMW form, whereas HB EGF bound to all three forms with comparable affinities. These three growth factors did not compete with each other for their bindings to adiponectin, suggesting the involvement of distinct binding sites. The interactions of adiponectin with PDGF-BB, basic FGF, and HB EGF precluded the bindings to their respective membrane receptors and attenuated the DNA synthesis and cell proliferation induced by these growth factors. Small interfering RNA-mediated down-regulation of adiponectin receptors did not affect the suppressive effects of adiponectin on cell proliferation stimulated by these growth factors. These data collectively suggest that the oligomeric complexes of adiponectin can modulate the biological actions of several growth factors by controlling their bioavailability at a pre-receptor level and that this effect might partly account for the anti-atherogenic, anti-angiogenic, and anti-proliferative functions of adiponectin.
Dry etching of porous silicon in high density plasmas (2003)

Dry etching processes routinely used for plasma etching of crystalline Si (c-Si) are evaluated as potential means for removal of porous Si (PS). Etching rates for PS and the selectivity with respect to c-Si are determined for a variety of plasma conditions and material parameters. We find that PS etching rates depend on the plasma conditions, and more importantly on PS material properties such as porosity and degree of oxidization. In addition, the selectivity varies from high to very low values, depending on the porosity and the thermal treatment of PS. The developed dry etching processes are compatible with the fabrication of devices where PS is used both as a sacrificial layer and as a patternable active material.
Enantioselective Synthesis of the Ester Side Chain of Homoharringtonine (2003)

Abstract Details of the synthesis of the methyl ester of the side chain of homoharringtonine, a natural product with antileukemic properties, are reported below. The key tactical element involved a Michael addition between the known chiral imine 4 and 2‐acetoxyacrylonitrile ( 5 ), furnishing the adduct (2 R ,1′ R )‐ 6 with a high degree of regio‐ and stereoselectivity. This adduct was then converted into the target compound ( R )‐ 2 by a linear sequence of ten chemical operations, in 6.0% overall yield. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2003)
MASS CULTURE OF ALGAE FOR FOOD AND OTHER ORGANIC COMPOUNDS (1962)

Krauss, Robert W. (U. Maryland, College Park.) Mass culture of algae for food and other organic compounds. Amer. Jour. Bot. 49(4): 425–435. Illus. 1962.—Data are being collected which appear to support the use of unicellular algae for human food. Analyses of proteins, fats, carbohydrates, and vitamins indicate that unicellular green algae, especially Chlorella , should be excellent sources of these nutrients. The effectiveness of the algae for the support of growth of chickens, mice, rats, and rabbits has been found to be good. However, only limited studies have been done with humans. The problem of acceptability varies with the nationality of the subjects and the preparation of the food. Serious gaps still exist both in the technology of production and in the experimentation required to establish nutritional value. Nutrition studies using algae free of bacteria are urgently needed.
SO(4) symmetry and the static Jahn-Teller effect in icosahedral molecules (1989)

The G\ifmmode\times\else\texttimes\fi{}(g+h) Jahn-Teller problem, relevant to the instability of icosahedral molecules in fourfold-degenerate electronic states, is investigated. The stationary points of the resulting adiabatic potential energy surface are retrieved by the method of the isostationary function. This method takes advantage of the parent SO(4) symmetry of the G\ifmmode\times\else\texttimes\fi{}(g+h) problem under equal-coupling conditions. The structure of the surface depends on the relative strength of the coupling to fourfold- and fivefold-degenerate modes. If the G\ifmmode\times\else\texttimes\fi{}g coupling is predominant, five tetrahedral minima are found, forming the vertices of a four-dimensional tetrahedron. If the G\ifmmode\times\else\texttimes\fi{}h coupling is the more pronounced, ten trigonal minima are found at the vertices of a Petersen graph. The results are in agreement with the epikernel principle.
Role of KCNMA1 in the pathogenesis of GEPD syndrome. (2009)

The coexistence of generalized epilepsy and paroxysmal dyskinesia within the same individual is an increasingly recognized neurological syndrome, with both sporadic and familial cases reported.The basic pathophysiology underlying GEPD is unknown, and no specific genes have been identified for it.In order to identify genes associated with GEPD, a genome-wide linkage scan was carried out in a Caucasian family affected by GEPD.A disease locus was mapped on chromosome 10q22 and a mutation was identified in KCNMA1 encoding the pore-forming -subunit of the large conductance calcium-activated potassium channel (BK channel).The mutant BK channel showed a markedly greater macroscopic current and an increase in calcium sensitivity.We propose that enhancement of BK channels in vivo leads to increased excitability by inducing rapid repolarization of action potentials, resulting in GEPD by allowing neurons to fire at a faster rate.These results identify a gene that is mutated in GEPD and support the role of ion channels in the pathogenesis of this syndrome.
A Survey on Metamorphic Testing (2016)

A test oracle determines whether a test execution reveals a fault, often by comparing the observed program output to the expected output. This is not always practical, for example when a program's input-output relation is complex and difficult to capture formally. Metamorphic testing provides an alternative, where correctness is not determined by checking an individual concrete output, but by applying a transformation to a test input and observing how the program output “morphs” into a different one as a result. Since the introduction of such metamorphic relations in 1998, many contributions on metamorphic testing have been made, and the technique has seen successful applications in a variety of domains, ranging from web services to computer graphics. This article provides a comprehensive survey on metamorphic testing: It summarises the research results and application areas, and analyses common practice in empirical studies of metamorphic testing as well as the main open challenges.
Isolation of Sterol-resistant Chinese Hamster Ovary Cells with Genetic Deficiencies in Both Insig-1 and Insig-2 (2005)

Insig-1 and Insig-2, a pair of endoplasmic reticulum (ER) membrane proteins, mediate feedback control of cholesterol synthesis through their sterol-dependent binding to the following two polytopic ER membrane proteins: sterol regulatory element-binding protein (SREBP) cleavage-activating protein (SCAP) and 3-hydroxy-3-methylglutaryl-coenzyme A reductase. Sterol-induced binding of Insigs to SCAP prevents the proteolytic processing of SREBPs, membrane-bound transcription factors that enhance the synthesis of cholesterol, by retaining complexes between SCAP and SREBP in the ER. Sterol-induced binding of Insigs to reductase leads to the ubiquitination and ER-associated degradation of the enzyme, thereby slowing a rate-controlling step in cholesterol synthesis. Here we report the isolation of a new line of mutant Chinese hamster ovary cells, designated SRD-15, deficient in both Insig-1 and Insig-2. The SRD-15 cells were produced by gamma-irradiation of Insig-1-deficient SRD-14 cells, followed by selection in high levels of the oxysterol, 25-hydroxycholesterol. Sterols neither inhibit SREBP processing nor promote reductase ubiquitination/degradation in SRD-15 cells. Sterol regulation of SREBP processing and reductase ubiquitination/degradation is fully restored in SRD-15 cells when they are transfected with expression plasmids encoding either Insig-1 or Insig-2. These results demonstrate an absolute requirement for Insig proteins in the regulatory system that mediates lipid homeostasis in animal cells.
A low-phase-noise 5-GHz CMOS quadrature VCO using superharmonic coupling (2003)

A new concept for quadrature coupling of LC oscillators is introduced and demonstrated on a 5-GHz CMOS voltage-controlled oscillator (VCO). It uses the second harmonic of the outputs to couple the oscillators. The technique provides quadrature over a wide tuning range without introducing any increase in phase noise or power consumption. The VCO is tunable between 4.57 and 5.21 GHz and has a phase noise lower than -124 dBc/Hz at 1-MHz offset over the entire tuning range. The worst-case measured image rejection is 33 dB. The circuit draws 8.75 mA from a 2.5-V supply.