gebhart/patrepeval huggingface dataset:
Fed‐batch cultivation of animal cells using different medium design concepts and feeding strategies (1994)

In animal cell cultivation, cell density and product concentration are often low due to the accumulation of toxic end-products such as ammonia and lactate and/or the depletion of essential nutrients. A hybridoma cell line (CRL-1606) was cultivated in T-flasks using a newly devised medium feeding strategy. The goals were to decrease ammonia and lactate formation by the design of an initial medium which would provide a starting environment to achieve optimal cell growth. This was followed by using a stoichiometric equation governing animal cell growth and then designing a supplemental medium for feeding strategy used to control the nutritional environment. The relationship between the stoichiometric demands for glutamine and nonessential amino acids was also studied. Through stoichiometric feeding, nutrient concentrations were controlled reasonably well. Consequently, the specific production rate of lactate was decreased by fourfold compared with conventional fed-batch culture and by 26-fold compared with conventional batch culture. The specific production rate of ammonia was decreased by tenfold compared with conventional fed-batch culture and by 50-fold compared with conventional batch culture. Most importantly, total cell density and monoclonal antibody concentration were increased by five- and tenfold respectively, compared with conventional batch culture. (c) 1994 John Wiley & Sons, Inc.
The Effect of Carvedilol on Morbidity and Mortality in Patients with Chronic Heart Failure (1996)

Carvedilol reduces the risk or death as well as the risk of hospitalization for cardiovascular causes in patients with heart failure who are receiving treatment with digoxin, diuretics, and an angiotensin-converting-enzyme inhibitor.
A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes (2016)

The genetic code is the cellular translation table for the conversion of nucleotide sequences into amino acid sequences. Changes to the meaning of sense codons would introduce errors into almost every translated message and are expected to be highly detrimental. However, reassignment of single or multiple codons in mitochondria and nuclear genomes, although extremely rare, demonstrates that the code can evolve. Several models for the mechanism of alteration of nuclear genetic codes have been proposed (including "codon capture," "genome streamlining," and "ambiguous intermediate" theories), but with little resolution. Here, we report a novel sense codon reassignment in Pachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons, we show that Pachysolen translates CUG codons as alanine and not as the more usual leucine. The Pachysolen tRNACAG is an anticodon-mutated tRNA(Ala) containing all major alanine tRNA recognition sites. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by a tRNA loss driven codon reassignment mechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is not part of the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects.
Allele frequency estimation from data on relatives. (1991)

Given genetic marker data on unrelated individuals, maximum-likelihood allele-frequency estimates and their standard errors are easily calculated from sample proportions. When marker phenotypes are observed on relatives, this method cannot be used without either discarding a subset of the data or incorrectly assuming that all individuals are unrelated. Here, I describe a method for allele frequency estimation for data on relatives that is based on standard methods of pedigree analysis. This method makes use of all available marker information while correctly taking into account the dependence between relatives. I illustrate use of the method with family data for a VNTR polymorphism near the apolipoprotein B locus.
From Oil-Prone Source Rock to Gas-Producing Shale Reservoir – Geologic and Petrophysical Characterization of Unconventional Shale-Gas Reservoirs (2010)

Abstract Many currently producing shale-gas reservoirs are overmature oil-prone source rocks. Through burial and heating these reservoirs evolve from organic-matter-rich mud deposited in marine, lacustrine, or swamp environments. Key characterization parameters are: total organic carbon (TOC), maturity level (vitrinite reflectance), mineralogy, thickness, and organic matter type. Hydrogen-to-carbon (HI) and oxygen-to-carbon (OI) ratios are used to classify organic matter that ranges from oil-prone algal and herbaceous to gas-prone woody/coaly material. Although organic-matter-rich intervals can be hundreds of meters thick, vertical variability in TOC is high (&amp;lt;1–3 meters) and is controlled by stratigraphic and biotic factors. In general, the fundamental geologic building block of shale-gas reservoirs is the parasequence, and commonly 10's to 100's of parasequences comprise the organic-rich formation whose lateral continuity can be estimated using techniques and models developed for source rocks. Typical analysis techniques for shale-gas reservoir rocks include: TOC, X-ray diffraction, adsorbed/canister gas, vitrinite reflectance, detailed core and thin-section descriptions, porosity, permeability, fluid saturation, and optical and electron microscopy. These sample-based results are combined with full well-log suites, including high resolution density and resistivity logs and borehole images, to fully characterize these formations. Porosity, fluid saturation, and permeability derived from core can be tied to log response; however, several studies have shown that the results obtained from different core analysis laboratories can vary significantly, reflecting differences in analytical technique, differences in definitions of fundamental rock and fluid properties, or the millimeter-scale variability common in mudstones that make it problematic to select multiple samples with identical attributes. Porosity determination in shale-gas mudstones is complicated by very small pore sizes and, thus, large surface area (and associated surface water); moreover, smectitic clays that are commonly present in mud have interlayer water, but this clay family tends to be minimized in high maturity formations due to illitization. Finally, SEM images of ion-beam-milled samples reveal a separate nano-porosity system contained within the organic matter, possibly comprising &amp;gt;50% of the total porosity, and these pores may be hydrocarbon wet, at least during most of the thermal maturation process. A full understanding of the relation of porosity and gas content will result in development of optimized processes for hydrocarbon recovery in shale-gas reservoirs.
Synthesis of luminescent silicon clusters by spark ablation (1993)

The synthesis of luminescent nanometer-scale Si clusters by spark ablation from a crystalline Si substrate is described. The cluster source, described in the text, generates clusters in a flowing Ar stream at atmospheric pressure. Electron microscopy reveals that the clusters have diameters in the 2–4 nm size range. The luminescence spectra of the clusters, similar to that of porous Si, are presented.
Approximating the head-related transfer function using simple geometric models of the head and torso (2002)

The head-related transfer function (HRTF) for distant sources is a complicated function of azimuth, elevation and frequency. This paper presents simple geometric models of the head and torso that provide insight into its low-frequency behavior, especially at low elevations. The head-and-torso models are obtained by adding both spherical and ellipsoidal models of the torso to a classical spherical-head model. Two different numerical techniques--multipole reexpansion and boundary element methods--are used to compute the HRTF of the models in both the frequency domain and the time domain. These computed HRTFs quantify the characteristics of elevation-dependent torso reflections for sources above the torso-shadow cone, and reveal the qualitatively different effects of torso shadow for sources within the torso-shadow cone. These effects include a torso bright spot that is prominent for the spherical torso, and significant attenuation of frequencies above 1 kHz in a range of elevations. Both torso reflections and torso shadow provide potentially significant elevation cues. Comparisons of the model HRTF with acoustic measurements in the horizontal, median, and frontal planes confirm the basic validity of the computational methods and establish that the geometric models provide good approximations of the HRTF for the KEMAR mannequin with its pinnae removed.
Specific Antibodies Reactive with the 22-Kilodalton Major Outer Surface Protein of Borrelia anserina Ni-NL Protect Chicks from Infection (1999)

An outer surface lipoprotein of 22 kDa was identified in the avian pathogen Borrelia anserina Ni-NL by using antibody preparations reactive with bacterial surface-exposed proteins. Amino acid sequence analysis of the 22-kDa protein demonstrated 90% identity with VmpA of B. turicatae, suggesting that the protein belongs to the family of 20-kDa outer surface proteins of the genus Borrelia. All of the 60 chicks intramuscularly treated with antibodies specifically reacting with the 22-kDa protein and infected with strain Ni-NL were completely protected from infection, since no spirochetemia was detected, and from death. Control chicks were treated with immune sera raised against apathogenic strain B. anserina Es, which expresses a prominent 20-kDa polypeptide that is also a member of the Vmp family but does not cross-react immunologically with the 22-kDa protein of the Ni-NL strain. These animals, infected with B. anserina Ni-NL, showed a high degree of spirochetemia 10 days after infection, and all died between 14 and 21 days after infection. The results showed that the 22-kDa surface protein of B. anserina Ni-NL is a determinant of the pathogenic potential of the strain and also confirmed that only strain-specific antibodies are protective against B. anserina infection.
Structural characteristics of the variable regions of immunoglobulin genes encoding a pathogenic autoantibody in murine lupus. (1990)

We have studied several monoclonal anti-double-stranded (ds) DNA antibodies for their ability to accelerate lupus nephritis in young NZB X NZW F1 female mice and to induce it in BALB/c mice. Two identified as pathogens in both strains have characteristics previously associated with nephritogenicity: expression of IgG2a isotype and IdGN2 idiotype. Both pathogenic antibodies used the combination of genes from the VHJ558 and VK9 subfamilies. Two weak pathogens failed to accelerate nephritis in young BW mice, but induced lupus nephritis in BALB/c mice. They both express IdGN2; one is cationic and an IgG3, the other is an IgG2a. Additional MAbs (some IgG2a, one IdGN2-positive) did not accelerate or induce nephritis. We have cloned and sequenced the variable regions of the immunoglobulin genes of one pathogenic autoantibody. No unique V, D, or J gene segments and no evidence of unusual mechanisms in generating diversity were used to construct this antibody. These data argue against use of unique abnormal Ig genes by systemic lupus erythematosus individuals to construct pathogenic autoantibody subsets. Instead, the major abnormality may be immunoregulatory.
The T7 RNA Polymerase Intercalating Hairpin Is Important for Promoter Opening during Initiation but Not for RNA Displacement or Transcription Bubble Stability during Elongation (2001)

The recently described crystal structures of a T7RNAP-promoter complex and an initial transcription complex reveal a beta-hairpin which inserts between the template and nontemplate strands of the promoter [Cheetham, G. M., et al. (1999) Nature 399, 80; Cheetham, G. M., et al. (1999) Science 286, 2305]. A stacking interaction between the exposed DNA bases and a valine at the tip of this hairpin may be especially important for stabilizing the opened promoter during initiation. It has been suggested that this hairpin may also be important for holding the transcription bubble open during transcript elongation, and a proposed model for how the RNA exits the transcription complex implies that this hairpin may also help displace the RNA from the template strand. To test these hypotheses, we have characterized both point and deletion mutants of this element. We find that these mutants exhibit reduced activity on linear, double-stranded templates but not on supercoiled or partially single-stranded templates. Probing of promoter-polymerase complexes, initial transcription complexes, and elongation complexes with KMnO(4) and a single-strand specific endonuclease reveals that the mutants have greatly reduced promoter unwinding activity during initiation. However, the structure and stability of the transcription bubble during elongation are not altered in the mutant enzymes, and RNA displacement activity is also normal. Thus, the T7RNAP intercalating hairpin is important, though not essential, for stabilizing the opened promoter during initiation, but is not important for RNA displacement or for transcription bubble structure or stability during elongation.
The Five Worst (and Five Best) American Criminal Codes (2000)

Each American jurisdiction has a criminal code. Most jurisdictions have substantially restructured and improved their codes since 1962, when the American Law Institute first promulgated its Model Penal Code. Such reform efforts are worthwhile, especially in criminal law, because many advantages flow from the thoughtful codification of criminal law rules. By compiling all criminal rules in a single comprehensive source, codification makes access to these rules easier, increasing the chance that citizens will know what the criminal law commands. A codified rule has the advantage of increased precision, which is likely to increase the uniformity of its application. Uncodified rules--or, even worse, unenacted rules, such as common-law offenses--often suffer from vagueness and ambiguity, which increase the potential for bias, abuse, and arbitrariness in their application. The articulation of criminal law rules in an integrated code also makes it easier to detect internal inconsistencies and irrationalities among the rules because clear and unified legislative expression makes the specific demands and effects of each rule, and the relationship among the rules, apparent in a way that expression through judicial opinions or uncoordinated legislation cannot. Finally, requiring statutory enactment of criminal rules assures that the criminalization authority remains the province of the legislature, as is desirable in a democratic society. The absence of a statutory provision to control a significant component of the criminal law amounts to a de facto delegation of criminalization power to the courts.\nCrime and criminal justice are among the few perennially "hot" political issues to which legislatures are sure to pay frequent and close attention. But the virtues of codification are not always, or even usually, central to legislatures when they address these issues. No politician runs for office on a platform to "increase internal consistency within the criminal law." Thus, while criminal law attracts much legislative attention, criminal codes attract little. As a result, the advantages of codification commonly are realized only imperfectly in American codes.\nIndeed, many American criminal codes are not true codes at all, in the modern sense of cohesive, well-structured, and self-contained statutory schemes. Rather, they are mere collections of statutory provisions similar to the generalized legislative "codes" of the last century and before. In many instances, even states that adopted modern, systematic criminal codes-- typically during the recodification wave of the 1960s and 1970s--have since altered their codes through ad hoc amendment, making them dramatically less systematic and internally consistent. Often, the deterioration of a code results simply from ignorance of the structure and operation that the code's original drafters intended. In other cases, the deterioration is the product of politics, as interest groups of one sort or another arrange special provisions of one kind or another.\nAvailable for download at http://ssrn.com/abstract=183290
Characterization of nit-2, the major nitrogen regulatory gene of Neurospora crassa. (1987)

The nit-2 gene is the major nitrogen-regulatory gene of Neurospora crassa, and under conditions of nitrogen limitations, it turns on the expression of various unlinked structural genes which specify nitrogen-catabolic enzymes. The nit-2 gene was subcloned as a 6-kilobase (kb) DNA fragment from a cosmid that carried approximately a 40-kb N. crassa DNA insert. The nit-2 gene was localized in a DNA segment of approximately 3.5 kb and was shown to correspond to a unique DNA sequence located on linkage group 1. Several N. crassa nit-2 transformants were characterized and were found to possess significantly different levels of the regulated enzyme nitrate reductase. Northern blot analysis of RNA from various strains was carried out to determine whether the nit-2 gene was expressed constitutively or was itself subject to regulation. The results revealed that the nit-2 gene is transcribed to give a single large mRNA of approximately 3.5 kb. Expression of the nit-2 gene is regulated such that its transcript is present at a substantially higher level in cells which are limited for nitrogen than in cells growing under nitrogen-repressed conditions. However, the nit-2 gene is not controlled by autogenous regulation. The nit-2 gene was transcribed only at a low level in nmr-1 and in gln-1b, under both nitrogen-repressed and derepressed conditions, suggesting that these unlinked loci may exert a positive regulatory effect on nit-2.
Subcellular Metabolite Levels in Spinach Leaves (1987)

The alterations of subcellular metabolite levels during the day in spinach leaves have been investigated using nonaqueous density gradient centrifugation to separate chloroplasts, cytosol, and vacuole. The results provide direct evidence for the role of sucrose phosphate synthase and cytosolic fructose 1,6-bisphosphatase in regulating sucrose synthesis in leaves and also show that the phosphate translocator is kinetically limiting in vivo.
Purification and partial characterization of human lymphoblast interferon. (1979)

One component of human lymphoblastoid interferon obtained from Namalwa cultures induced by Newcastle disease virus has been purified to a specific activity of 2.5 x 10(8) interferon units per mg of protein (protein content based on amino acid analysis). A single polypeptide species with an apparent molecular weight of 18,500 comigrating with the antiviral activity was observed by sodium dodecyl sulfate/polyacrylamide gel electrophoresis. Preliminary amino-terminal sequencing results support the conclusion that the interferon species is essentially homogeneous.
Transmission Line Matrix (TLM) modelling of medical ultrasound (2001)

This thesis introduces TLM as a new method for modelling medical ultrasound wave propagation. Basic TLM theory is presented and how TLM is related to Huygens principle is discussed. Two dimensional TLM modelling is explained in detail and one dimensional and three dimensional TLM modelling are explained. Implementing TLM in single CPU computers and parallel computers is discussed and several algorithms are presented together with their advantages and disadvantages. Inverse TLM and modelling non linear wave propagation and different types of mesh are discussed. A new idea for modelling TLM as a digital filter is presented and removing the boundary effect based on digital filter modelling of TLM is discussed. Some modelling experiments such as : 1) Focusing mirror. 2) Circular mirror. 3) Array transducers. 4) Doppler effect. are presented and how to use TLM to model these experiments is explained. A new low sampling rate theory for TLM modelling is proposed and verified. This new theory makes the modelling of a much larger spaces practical on a given hardware platform.
Antifungal Agents: Mode of Action, Mechanisms of Resistance, and Correlation of These Mechanisms with Bacterial Resistance (1999)

The increased use of antibacterial and antifungal agents in recent years has resulted in the development of resistance to these drugs. The significant clinical implication of resistance has led to heightened interest in the study of antimicrobial resistance from different angles. Areas addressed include mechanisms underlying this resistance, improved methods to detect resistance when it occurs, alternate options for the treatment of infections caused by resistant organisms, and strategies to prevent and control the emergence and spread of resistance. In this review, the mode of action of antifungals and their mechanisms of resistance are discussed. Additionally, an attempt is made to discuss the correlation between fungal and bacterial resistance. Antifungals can be grouped into three classes based on their site of action: azoles, which inhibit the synthesis of ergosterol (the main fungal sterol); polyenes, which interact with fungal membrane sterols physicochemically; and 5-fluorocytosine, which inhibits macromolecular synthesis. Many different types of mechanisms contribute to the development of resistance to antifungals. These mechanisms include alteration in drug target, alteration in sterol biosynthesis, reduction in the intercellular concentration of target enzyme, and overexpression of the antifungal drug target. Although the comparison between the mechanisms of resistance to antifungals and antibacterials is necessarily limited by several factors defined in the review, a correlation between the two exists. For example, modification of enzymes which serve as targets for antimicrobial action and the involvement of membrane pumps in the extrusion of drugs are well characterized in both the eukaryotic and prokaryotic cells.