gebhart/patrepeval huggingface dataset:
Protein-Tyrosine Phosphatases: Biological Function, Structural Characteristics, and Mechanism of Catalysis (1998)

The protein-tyrosine phosphatases (PTPases) superfamily consists of tyrosine-specific phosphatases, dual specificity phosphatases, and the low-molecular-weight phosphatases. They are modulators of signal transduction pathways that regulate numerous cell functions. Malfunction of PTPases have been linked to a number of oncogenic and metabolic disease states, and PTPases are also employed by microbes and viruses for pathogenicity. There is little sequence similarity among the three subfamilies of phosphatases. Yet, three-dimensional structural data show that they share similar conserved structural elements, namely, the phosphate-binding loop encompassing the PTPase signature motif (H/V)C(X)5R(S/T) and an essential general acid/base Asp residue on a surface loop. Biochemical experiments demonstrate that phosphatases in the PTPase superfamily utilize a common mechanism for catalysis going through a covalent thiophosphate intermediate that involves the nucleophilic Cys residue in the PTPase signature motif. The transition states for phosphoenzyme intermediate formation and hydrolysis are dissociative in nature and are similar to those of the solution phosphate monoester reactions. One strategy used by these phosphatases for transition state stabilization is to neutralize the developing negative charge in the leaving group. A conformational change that is restricted to the movement of a flexible loop occurs during the catalytic cycle of the PTPases. However, the relationship between loop dynamics and enzyme catalysis remains to be established. The nature and identity of the rate-limiting step in the PTPase catalyzed reaction requires further investigation and may be dependent on the specific experimental conditions such as temperature, pH, buffer, and substrate used. In-depth kinetic and structural analysis of a representative number of phosphatases from each group of the PTPase superfamily will most likely continue to yield insightful mechanistic information that may be applicable to the rest of the family members.
The bulk of the peripheral B-cell pool in mice is stable and not rapidly renewed from the bone marrow. (1990)

We have reevaluated the in vivo lifespan of B lymphocytes based on incorporation of the thymidine analogue 5-bromo-2'-deoxyuridine into the DNA of dividing cells. To exclude potential alterations in the turnover of B-lineage cells due to the bromodeoxyuridine incorporation, we performed pulse-chase experiments comparing the appearance and disappearance of bromodeoxyuridine-labeled cells over long periods of time. The data consistently show that more than two-thirds of splenic B cells in adult (greater than 2 months old) mice have a lifetime of several weeks or months, whereas a more rapid turnover takes place in young (4 week old) mice. Thus, the peripheral B-cell pool is only slowly renewed after it has been initially built up early in life.
Frontotemporal lobar degeneration (1998)

The criteria ought to provide the foundation for research work into the neuropsychology, neuropathology, genetics, molecular biology, and epidemiology of these important clinical disorders that account for a substantial proportion of cases of primary degenerative dementia occurring before the age of 65 years.
Enhancer-trap targeting at the Broad-Complex locus of Drosophila melanogaster. (1995)

Here, we describe the exact replacement of a defective unmarked P element by an enhancer-trap transposon marked by the miniwhite gene and carrying lacZ as a reporter gene. The original defective P element was located in an intron of the Broad-Complex (BRC), a key gene involved in metamorphosis. Replacement events resulted from conversions induced by the P-element transposase from a donor enhancer-trap element located on another chromosome. Six independent conversion events were selected. In all converted chromosomes, the enhancer-trap transposon was in the same orientation as the original P element. From the pattern of X-gal staining observed, lacZ expression likely reflects the regulatory influence of BRC enhancers on the convertant transposon. Reversion to wild type was achieved by excision of the enhancer-trap transposon. The six convertants were analyzed in detail at the nucleotide level. The occurrence of a polymorphism at position 33 of the P-element sequences led us to propose a conversion mechanism involving homologous P sequences for repair. This is in contrast to previously analyzed P-element transposase-induced conversion events and proposed models relying on sequence identity between genomic Drosophila sequences. The lack of any homology requirement other than between P element sequences means that our findings can be easily generalized. Targeting a marked P-element derivative at a precise site without loss or addition of genetic information makes it possible to exploit the hundreds of defective P elements scattered throughout the Drosophila genome by replacing them with engineered P elements, already available.
Potentiometric quantification and speciation of oxygenated groups in humic substances using BEST7 software (2010)

In this study the BEST7 software was employed to quantify different classes of functional groups and to model the proton titration behavior of humic substances. To illustrate the process, the Suwannee River fulvic acid of the IHSS (International Humic Substances Society) was used. Five categories – two classes of phenolic groups (phenol and cathecol), two classes of carboxylic groups (benzoic and phtalic) and the combination between them (salicylic) - of oxygenated groups were considered as being responsible for the potentiometric behavior of the sample and were quantitatively determined. The most and the least abundant groups were cathecol (3.300 0.010 mmol g-1) and phenol (1.225 0.070 mmol g-1), respectively. The estimated equilibrium constants were also determined and were in good agreement with the literature values for phenol and cathecol groups and for benzoic, phtalic and salicylic acids. Distribution diagrams of the species were generated with the software SPE and SPEPLOT.
Progress toward Noninvasive Prenatal Diagnosis (2011)

For decades, noninvasive analysis of the fetal genotype has been the holy grail of the field of prenatal diagnosis. Noninvasive prenatal diagnosis (NIPD)2 would use a sample source other than amniocentesis or chorionic villus sampling. The focus has been primarily on the use of maternal blood samples, with less attention given to the possibility of recovering fetal cells from maternal cervical samples (as would be collected for cervical cancer screening). The initial efforts focused on the presence of fetal cells in the maternal circulation, and evidence indicated as early as 1979 that fetal cells could be recovered via fluorescence-activated cell sorting. The elegant strategy of using antibodies to paternal HLA antigens to identify fetal cells was demonstrated. Attempts to recover fetal cells focused for a time on fetal nucleated red blood cells via analysis with fluorescence in situ hybridization and the PCR, but the disappointing results led to skepticism that NIPD would ever become a reality.

By 1996 there were reports of tumor DNA detected in the plasma of cancer patients, and Lo et al. first reported in 1997 the presence of fetal DNA in maternal plasma. The use of fetal DNA in the plasma has important advantages over the use of fetal cells in that fetal DNA can be obtained consistently in virtually 100% of pregnancies, whereas fetal cells are recovered much less consistently. In recent years, the use of fetal DNA in maternal plasma to detect fetal sex has become a well-established clinical test [see references in Lo et al. (1) for background on this test and other details]. In fact, determining whether any genotype present in the father but not the mother has been transmitted to the fetus is relatively straightforward. This approach has been used to determine whether a fetus is Rh negative or positive …
Expression and immunogenicity of pertussis toxin S1 subunit-tetanus toxin fragment C fusions in Salmonella typhi vaccine strain CVD 908 (1996)

Salmonella typhi vaccine strain CVD 908 can deliver heterologous antigens to the host immune system following mucosal immunization. Stable expression of foreign proteins in Salmonella cells often requires antigen-specific engineering strategies. Fusion of antigens to stabilizing proteins has proven to be a successful strategy for rescuing otherwise unstable proteins. We designed plasmids to allow the fusion of antigens to the amino terminus or carboxyl terminus of fragment C of tetanus toxin, separated by a 4-amino-acid hinge region. Towards the ultimate goal of developing a live oral diphtheria-pertussis-tetanus vaccine, we used these plasmids to stably express the S1 subunit of pertussis toxin in CVD 908. Driven by the anaerobically inducible nirB promoter, the S1 subunit alone was expressed poorly in Salmonella cytoplasm. In contrast, hybrid proteins with S1 fused to either the amino or carboxyl terminus of fragment C were expressed at a high level in CVD 908 and were recognized in Western blot (immunoblot) analysis by monoclonal antibodies directed to S1 and to fragment C. Mice were immunized by the oral or intranasal routes with CVD 908 derivatives harboring these recombinant plasmids. All fusion proteins elicited serum antibody responses to fragment C following intranasal immunization, whereas oral inoculation did not. The configuration of antigens constituting the fusion was critical; S1 fused to the amino terminus of fragment C was less effective than S1 fused to the carboxyl terminus in generating anti-fragment C antibodies. CVD 908 expressing truncated S1 fused to the carboxyl terminus of fragment C elicited neutralizing serum pertussis antitoxin following intranasal immunization of mice.
Loss of attachment to fibronectin with terminal human erythroid differentiation (1990)

Human erythroblastic progenitors (colony-forming unit-erythroid [CFU-E] and burst-forming unit-erythroid [BFU-E]) have been shown to attach to fibronectin (Fn), a property that might be involved in the local regulation of erythropoiesis. In this study, we have investigated changes in cell attachment to Fn upon terminal erythroid differentiation. We first purified CFU-E from human marrow by avidin- biotin immune rosetting. This negative selection procedure yielded a cell population containing approximately 80% blasts that, after characterization by colony-assays and electron microscopy, appeared to consist of CFU-E (10% to 15%) and their immediate progeny (85% to 90%), here defined as “preproerythroblasts.” In the presence of erythropoietin, purified cells differentiated into reticulocytes in 7 to 10 days. Cell attachment to Fn was inversely correlated to the stage of differentiation of the erythroid cell: more than 50% of the CFU-E population reproducibly adhered to Fn, whereas at most 30% of the preproerythroblasts had the same capacity. Adhesion was further lost at late maturation stages, and a constant finding was the inability of reticulocytes to adhere to Fn. Finally, CFU-E adhesion to Fn was blocked by polyclonal lgG raised against the Fn receptor and by a monoclonal antibody against VLA-5. These results demonstrate that adhesion to Fn is developmentally regulated during normal human erythropoiesis. Restriction of its expression to CFU-E and its first divisions strikingly correlates with the migratory capacity of these cells.
Increased urine phenylethylamine after methylphenidate treatment in children with ADHD (2002)

The urine levels of beta-phenylethylamine, 3-methoxy-4-hydroxyphenyl glycol, homovanillic acid, and 5-hydroxyindoleacetic acid were measured to clarify the neurochemical mechanism in attention deficit hyperactivity disorder. beta-Phenylethylamine levels were significantly lower in attention deficit hyperactivity disorder individuals (n = 37) than in controls (n = 21). The 22 children with attention deficit hyperactivity disorder were treated with methylphenidate, and they were further divided into methylphenidate responders (n = 18) and nonresponders (n = 4). beta-Phenylethylamine levels significantly increased after methylphenidate therapy in responders, whereas they did not increase in nonresponders.
Expression of the firefly luciferase gene in vaccinia virus: a highly sensitive gene marker to follow virus dissemination in tissues of infected animals. (1988)

We have introduced the firefly luciferase gene of Photinus pyralis into the vaccinia virus genome. This gene is expressed in a coordinate fashion during virus infection. Luminescence produced by the action of luciferase [Photinus-luciferin:oxygen 4-oxidoreductase(decarboxylating, ATP-hydrolyzing), EC 1.13.12.7] was easily detectable in infected cells in culture as well as in cells of tissues of infected mice. The limits of detection were about one infected cell in a background of a million noninfected cells. The luciferase assay was about 1000-fold more sensitive than that of beta-galactosidase. Our findings show that the luciferase assay can be conveniently used to follow viral gene expression and virus dissemination both in cell cultures and in tissues of infected animals.
Analysis of Multiconductor Transmission Lines (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
A comparative investigation of the metabolism of the herbicide glufosinate in cell cultures of transgenic glufosinate-resistant and non-transgenic oilseed rape (Brassica napus) and corn (Zea mays) (2002)

To obtain information on differences between the metabolic pathways of the herbicide glufosinate (trade names: BASTA, LIBERTY) in non-transgenic, glufosinate-sensitive plants and in transgenic, glufosinate-resistant plants, the metabolism of 14C-labeled glufosinate and its enantiomers L- and D-glufosinate was studied using cell cultures of oilseed rape and corn. Transformation of glufosinate in both sensitive and transgenic rape cells remained at a low rate of about 3-10% in contrast to corn cells, where 20% was transformed in sensitive and 43% in transgenic cells after 14 days of incubation, the rest remaining as unchanged glufosinate. In sensitive rape and corn cells the main metabolite was 4-methylphosphinico-2-oxo-butanoic acid (PPO) with 7.3 and 16.4%, respectively, together with low amounts of 3-methylphosphinicopropionic acid (MPP), 4-methylphosphinico-2-hydroxybutanoic acid (MHB), 4-methylphosphinicobutanoic acid (MPB) and 2-methylphosphinicoacetic acid (MPA). An additional metabolite formed in transgenic cell cultures was 2-acetamido-4-methylbutanoic acid (N-acetyl-L-glufosinate, NGA), which was formed at rates of 3.2% in rape and 16.1% in corn. A further minor metabolite, not yet identified, was detected in both cell types. The liberation of 0.2% 14CO2 indicates further metabolic steps prior to a limited mineralization in plant cell cultures. L-glufosinate was transformed into the same metabolites as the glufosinate racemate. D-glufosinate was not metabolized.
Manual and cognitive benefits of two-handed input (1998)

One of the recent trends in computer input is to utilize users' natural bimanual motor skills. This article further explores the potential benefits of such two-handed input. We have observed that bimanual manipulation may bring two types of advantages to human-computer interaction: manual and cognitive. Manual benefits come from increased time-motion efficiency, due to the twice as many degrees of freedom simultaneously available to the user. Cognitive benefits arise as a result of reducing the load of mentally composing and visualizing the task at an unnaturally low level which is imposed by traditional unimanual techniques. Area sweeping was selected as our experimental task. It is representative of what one encounters, for example, when sweeping out the bounding box surrounding a set of objects in a graphics program. Such tasks cannot be modeled by Fitts' Law alone and have not been previously studied in the literature. In our experiments, two bimanual techniques were compared with the conventional one-handed GUI approach. Both bimanual techniques employed the two-handed “stretchy” technique first demonstrated by Krueger in 1983. We also incorporated the “Toolglass” technique introduced by Bier et al. in 1993. Overall, the bimanual techniques resulted in significantly faster performance than the status quo one-handed technique, and these benefits increased with the difficulty of mentally visualizing the task, supporting our bimanual cognitive advantage hypothesis. There was no significant difference between the two bimanual techniques. This study makes two types of contributions to the literature. First, practically we studied yet another class of transaction where significant benefits can be realized by applying bimanual techniques. Furthermore, we have done so using easily available commercial hardware in the context to our understanding of why bimanual interaction techniques have an advantage over unimanual techniques. A literature review on two-handed computer input and some of the relevant bimanual human mototr control studies is also included.
Minireview: Transcriptional Control of Osteoblast Differentiation (2001)

The last 5 yr have witnessed major progress in skeleton biology. One of these areas of progress has been the partial elucidation of the transcriptional mechanisms of osteoblast differentiation and their conservation between mouse and human. Cbfal, or runx2, a homolog of the Drosophila Runt protein serves both as the earliest transcriptional regulator of osteoblast differentiation and as controller of bone formation by already differentiated osteoblast. Moreover, Cbfal is also a hypertrophic chondrocyte differentiation factor in several skeletal elements. Although other transcription factors are likely to be involved in osteoblast differentiation, Cbfal, by the multiplicity of the role that it plays, can be viewed as the central regulator of intramembranous and endochondral ossification.
VHF Single-Crystal Silicon Elliptic Bulk-Mode Capacitive Disk Resonators—Part I: Design and Modeling (2004)

This work, the first of two parts, presents the design and modeling of VHF single-crystal silicon (SCS) capacitive disk resonators operating in their elliptical bulk resonant mode. The disk resonators are modeled as circular thin-plates with free edge. A comprehensive derivation of the mode shapes and resonant frequencies of the in-plane vibrations of the disk structures is described using the two-dimensional (2-D) elastic theory. An equivalent mechanical model is extracted from the elliptic bulk-mode shape to predict the dynamic behavior of the disk resonators. Based on the mechanical model, the electromechanical coupling and equivalent electrical circuit parameters of the disk resonators are derived. Several considerations regarding the operation, performance, and temperature coefficient of frequency of these devices are further discussed. This model is verified in part II of this paper, which describes the implementation and characterization of the SCS capacitive disk resonators.
Review: ATM: the protein encoded by the gene mutated in the radiosensitive syndrome ataxia-telangiectasia (1999)

ATM is involved in DNA damage recognition and cell cycle control in response to ionizing radiation damage. There is evidence that ATM may also have a more general signalling role.
On the origin of the 1602 cm–1 Raman band of yeasts; contribution of ergosterol (2012)

The 1602 cm(-1) Raman signature, which we call the "Raman spectroscopic signature of life" in yeasts, is a marker Raman band for cell metabolic activity. Despite the established fact that its intensity sensitively reflects the metabolic status of the cell, its molecular origin remained unclear. In this work, we propose ergosterol as the major contributor of the 1602 cm(-1) Raman signature. The theoretical isotope shift calculation for ergosterol agreed with previous observations. Furthermore, experiments showed that the Raman spectrum of ergosterol corresponds very well with the depleting spectral component in yeast that behaves together with the 1602 cm(-1) signature when the cells are under stress. This work implies that the 1602 cm(-1) Raman signature could serve as an intrinsic ergosterol marker in yeasts for the study of sterol metabolism in vivo and in a label-free manner, which could not be done by any other techniques at the current stage.
A Critical Role for p38 Mitogen-Activated Protein Kinase in the Maturation of Human Blood-Derived Dendritic Cells Induced by Lipopolysaccharide, TNF-α, and Contact Sensitizers (2001)

Abstract We investigated the involvement of mitogen-activated protein kinases (MAPKs) in the maturation of CD83− dendritic cells (DC) derived from human blood monocytes. Maturating agents such as LPS and TNF-α induced the phosphorylation of members of the three families of MAPK (extracellular signal-regulated kinase l/2, p46/54 c-Jun N-terminal kinase, and p38 MAPK). SB203580, an inhibitor of the p38 MAPK, but not the extracellular signal-regulated kinase l/2 pathway blocker PD98059, inhibited the up-regulation of CD1a, CD40, CD80, CD86, HLA-DR, and the DC maturation marker CD83 induced by LPS and TNF-α. In addition, SB203580 inhibited the enhancement of the allostimulatory capacity and partially prevented the down-regulation of FITC-dextran uptake induced by LPS and TNF-α. Likewise, SB203580 partially prevented the up-regulation of IL-1α, IL-1β, IL-lRa, and TNF-α mRNA upon stimulation with LPS and TNF-α, as well as the release of bioactive TNF-α induced by LPS. DC maturation induced by the contact sensitizers 2,4-dinitrofluorobenzene and NiSO4, as seen by the up-regulation of CD80, CD86, and CD83, was also coupled to the phosphorylation of p38 MAPK, and was inhibited by SB203580. The irritants SDS and benzalkonium chloride that do not induce DC maturation did not trigger p38 MAPK phosphorylation. Together, these data indicate that phosphorylation of p38 MAPK is critical for the maturation of immature DC. These results also suggest that p38 MAPK phosphorylation in DC may become useful for the identification of potential skin contact sensitizers.