gebhart/patrepeval huggingface dataset:
Identification and Epidemiological Typing of Clinical and Environmental Isolates of the Genus Rhodococcus with Use of a Digoxigenin-Labeled rDNA Gene Probe (1992)

Rhodococcus species are ubiquitous in the environment, and several species have been reported to have pathogenic potential for humans. Rhodococcus equi, in particular, has been reported to cause infections in patients with AIDS. However, the identification of Rhodococcus species with use of conventional biochemical tests is problematic, and no simple and reproducible method exists for their rapid identification and differentiation. We found that the type strains of the 20 recognized species in the genus Rhodococcus could be clearly distinguished with use of a combination of the Pvu II and Pst I rRNA gene restriction endonuclease patterns and a digoxigenin-labeled Escherichia coli rDNA probe. Analysis of four clinical or environmental isolates confirmed as Rhodococcus bronchialis showed no interstrain variation of rRNA gene bands. Analysis of 15 isolates confirmed as R. equi from 13 patients showed 11 different rRNA gene patterns. No discernible difference was observed in the ribotype patterns between R. equi isolates from patients for whom AIDS had been diagnosed and those from patients who did not have AIDS, and there was no evidence of geographic clustering of R. equi ribotype patterns. Three of five Rhodococcus species isolates that could not be differentiated with use of conventional biochemical methods were identified with use of ribotype analysis. Therefore, ribotype analysis may provide an important adjunct to current biochemical identification of environmental and clinical isolates of Rhodococcus species.
Photoacoustic Probes for Nondestructive Testing and Biomedical Applications (2002)

Fiber-optic photoacoustic sources for nondestructive testing and biomedical applications are described. The photoacoustic sources consist of a pulsed laser, a fiber-optic cable, and a generation head. The generation head is a miniature hermetically sealed chamber, which can be embedded into solid structures or immersed in liquid media. The face of the chamber acts as a target for laser irradiation. Bulk ultrasonic waves generated inside of the target are transmitted into the medium. The proposed systems offer wide ultrasonic range (0.5-15 MHz), easy control over directivity of the ultrasonic beam, high efficiency of generation, and the ability to operate in a harsh environment. Sources with different radiation patterns with respect to the optical axis of the fiber, such as normal, sideways, as well as focused, have been devised. We present a proof-of-concept experiment using these sources in combination with fiber-optic ultrasonic receivers.
Optimized Quantification of Unculturable Candidatus Liberibacter Spp. in Host Plants Using Real-Time PCR (2008)

Citrus huanglongbing (HLB) is caused by the phloem-limited and psyllid-vectored Candidatus Liberibacter spp. and is a destructive disease of citrus that is rapidly increasing in importance. The disease was reported recently in the principle citrus-producing areas of São Paulo, Brazil in 2004 and in Florida in 2005. A variety of laboratory methods have been developed to confirm a symptom-based disease diagnosis or for the detection or identification of the pathogen; however, no quantitative information has been available on the pathogen titer in either host or vector interactions because the pathogen remains unculturable in artificial media. We previously developed a quantitative polymerase chain reaction (PCR)-based assay for detection of Ca. Liberibacter spp. and, in this study, we evaluated the effects of sample composition on quantification of the pathogen in citrus plants by TaqMan real-time PCR. Standard curves were established using cloned plasmids containing target DNA from the pathogen and with total DNA samples from field-grown HLB-infected citrus plants. Regression analysis showed that a standard curve established with DNA extracted from naturally infected field-grown plants was more accurate than the standard curve constructed from plasmids containing the amplification targets as cloned inserts. Nontarget DNA and putative PCR inhibitors from citrus plants decreased the sensitivity and the amplification efficiency of real-time PCR when plasmids provided the template target in "spiked" healthy citrus DNA extracts. This effect varied among plant tissue types, citrus species, and geographic locations. Based on these sample effects, a universal standard curve has been established for quantification of the pathogen in various citrus tissues of different citrus species planted in different geographic locations. Sample storage at 4°C for 2 months prior to PCR assay did not affect subsequent quantification of the pathogen. The validated quantitative real-time PCR method and the universal standard curve will be very useful for studies of host-pathogen interactions and epidemiology, and in the development of control strategies for the disease.
Bisantrene in Relapsed and Refractory Acute Myelogenous Leukemia (1993)

Because of the lack of standard treatment in refractory and relapsed acute myelogenous leukemia (AML) several new drugs have been employed alone to evaluate their efficacy in this peculiar category of patient. Bisantrene, a new anthracene bishydrazone derivative, has shown antileukemic effect in phase I and II clinical trials with acceptable extrahaematological toxicity. Seven patients (six males and one female, median age 41.8 years) received Bisantrene (250 mg/sqm/daily 1-7) as a single agent in relapsed or refractory leukemia. 5 out of 7 patients achieved complete remission, one attained partial remission and one was resistant. However, haematological toxicity was severe with prolonged myelosuppression. Hepatic toxicity was the main extrahaematological side effect and occurred in 3 of 7 patients, however all of them recovered within 40 days. No cardiovascular dysfunction occurred although all the patients had been heavily previously treated with anthracyclines. Our data confirm that Bisantrere is active in relapsed and refractory AML and suggest the need for larger clinical trials to better evaluate its efficacy.
A critique of ANSI SQL isolation levels (1995)

ANSI SQL-92 [MS, ANSI] defines Isolation Levels in terms of phenomena: Dirty Reads, Non-Repeatable Reads, and Phantoms. This paper shows that these phenomena and the ANSI SQL definitions fail to properly characterize several popular isolation levels, including the standard locking implementations of the levels covered. Ambiguity in the statement of the phenomena is investigated and a more formal statement is arrived at; in addition new phenomena that better characterize isolation types are introduced. Finally, an important multiversion isolation type, called Snapshot Isolation, is defined.
Identification of residues in the human DNA repair enzyme HAP1 (Ref-1) that are essential for redox regulation of Jun DNA binding. (1993)

The DNA binding activity of the c-jun proto-oncogene product is inhibited by oxidation of a specific cysteine residue (Cys-252) in the DNA binding domain. Jun protein inactivated by oxidation of this residue can be efficiently reactivated by a factor from human cell nuclei, recently identified as a DNA repair enzyme (termed HAP1 or Ref-1). The HAP1 protein consists of a core domain, which is highly conserved in a family of prokaryotic and eukaryotic DNA repair enzymes, and a 61-amino-acid N-terminal domain absent from bacterial homologs such as Escherichia coli exonuclease III. The eukaryote-specific N-terminal domain was dispensable for the DNA repair functions of the HAP1 protein but was essential for reactivation of the DNA binding activity of oxidized Jun protein. Consistent with this finding, exonuclease III protein could not reactive Jun. A minimal 26-residue region of the N-terminal domain proximal to the core of the HAP1 enzyme was required for redox activity. By site-directed mutagenesis, cysteine 65 was identified as the redox active site in the HAP1 enzyme. In addition, it is proposed that cysteine 93 interacts with the redox active site, probably via disulfide bridge formation. It is concluded that the HAP1 protein has evolved a novel redox activation domain capable of regulating the DNA binding activity of a proto-oncogene product which is not essential for its DNA repair functions. Identification of a putative active site cysteine residue should facilitate analysis of the mechanism by which the HAP1 protein may alter the redox state of a wide range of transcription factors.
Lab-in-a-Tube: Detection of Individual Mouse Cells for Analysis in Flexible Split-Wall Microtube Resonator Sensors (2010)

We report a method for the precise capturing of embryonic fibroblast mouse cells into rolled-up microtube resonators. The microtubes contain a nanometer-sized gap in their wall which defines a new type of optofluidic sensor, i.e., a flexible split-wall microtube resonator sensor, employed as a label-free fully integrative detection tool for individual cells. The sensor action works through peak sharpening and spectral shifts of whispering gallery modes within the microresonators under light illumination.
Muscle water and electrolytes following varied levels of dehydration in man (1976)

In an effort to assess the effects of dehydration on the content of water and electrolytes (Na+, K+, Cl-, and Mg2+) in plasma and muscle tissue, eight men exercised in the heat (39.5 degrees C, 25%). Blood urine, and muscle biopsy samples were obtained before exercise and after the subjects had reduced their body weight by 2.2, 4.1, and 5.8%. On the average, plasma and muscle water (H2Om) contents were found to decline 2.4 and 1.2% for each percent decrease in body weight. Muscle sodium (Na+m) and chloride (Cl-m) content remained unchanged with dehydration, while muscle magnesium (Mg2+m) declined 12% as a result of the 5.8% dehydration. In terms of intracellular concentrations, K+i increased 7.2 and 10.6% at the 2.2 and 4.1% dehydration levels, respectively. Calculations of the resting membrane potential suggest that the water and electrolyte losses observed in these studies do not significantly alter the excitability of the muscle cell membrane.
Fungal-plant interactions (1992)

Part 1 Fungal life-style: fungal morphogenesis and physiology fungal strategies. Part 2 Plants as an environment: living tissues as an environment effects of environmental conditions on plant health the plants' response to abiotic and biotic influences effects of fungi on plant health control of plant disease. Part 3 Fungal-plant confrontation: fungal invasion mechanisms of disease resistance. Part 4 Effects of pathogenic fungal invasion on host plant physiology: physiological changes in host plant tissues effects of invasion on cell growth. Part 5 Mutualistic symbioses: mycorrhizal symbioses lichens endophytic sybioses. Part 6 Biotechnology in the study of fungal-plant interaction: plant breeding for resistance to disease the study of disease resistance using tissue culture technique molecular biological techniques.
Corneal Wound Repair After Rose Bengal and Green Light Crosslinking: Clinical and Histologic Study (2017)

The healing response in corneas after RGX is very similar to that observed after DE alone, suggesting that, along with its short treatment time and limited effect on keratocytes, RGX displays good potential for clinical cornea stiffening.
Structure and evolution of insulins: Implications for receptor binding (1992)

Insulin is a member of a family of hormones, growth factors and neuropeptides which are found in both vertebrates and invertebrates. A common 'insulin fold' is probably adopted by all family members. Although the specificities of receptor binding are different, there is a possibility of co-evolution of polypeptides and their receptors.
PB2 and PA genes control the expression of the temperature-sensitive phenotype of cold-adapted B/USSR/60/69 influenza master donor virus (2009)

The cold-adapted (ca) and temperature-sensitive (ts) influenza master donor virus (MDV) B/USSR/60/69 was derived from its wild-type parental virus after successive passages in eggs at 32 degrees C and 25 degrees C. This strain is currently in use for preparing reassortant influenza B vaccine viruses which are used in the Russian trivalent live attenuated influenza vaccine. Vaccine viruses are obtained by classical reassortment of MDV and a currently circulating wild-type virus. The phenotypic properties cold adaptation and temperature sensitivity are inherited from the six genes encoding the internal proteins of the MDV. However, the role of the individual gene segments in temperature sensitivity and thus attenuation is not known. In this study, 35 reassortant viruses of B/USSR/60/69 MDV with current wild-type non-ts influenza B viruses were generated in eggs or MDCK cells and studied in order to identify the genes responsible for their ts phenotype. For each virus the exact genome composition was determined as well as its ts phenotype. The results demonstrated that the polymerase PB2 and PA gene segments of B/USSR/60/69 MDV independently controlled expression of the ts phenotype of B/USSR/60/69 MDV-based reassortant viruses. The other genes coding for internal proteins played no role in this respect. This suggests that mutations in the polymerase genes PB2 and PA play an essential role in attenuation of B/USSR/60/69 MDV-based reassortant influenza B vaccine viruses.
African American Study of Kidney Disease and hypertension (AASK)--clinical trial update. (1998)

African Americans are disproportionately afflicted with end-stage kidney failure (ESRD). Whereas they constitute approximately 12 percent of the US population, they comprise 32 percent of the prevalent ESRD population. Diabetes mellitus is the predominant cause of ESRD in the U.S. population. However, hypertension is the most frequently reported cause of ESRD in African Americans. In 1990, the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) of the National Institutes of Health launched an initiative to investigate the underlying cause, and to study mechanisms that could slow progression of hypertensive kidney disease in African Americans. An important component of this initiative is the clinical trial African American Study of Kidney Disease and Hypertension (AASK). This report provides an update on the Institute's initiative on hypertensive kidney disease in African Americans and, specifically, on the clinical trial.
A comparison of Gaussian and mean curvatures estimation methods on triangular meshes (2004)

Estimating intrinsic geometric properties of a surface from a polygonal mesh obtained from range data is an important stage of numerous algorithms in computer and robot vision, computer graphics, geometric modeling, industrial and biomedical engineering. This work considers different computational schemes for local estimation of intrinsic curvature geometric properties. Five different algorithms and their modifications were tested on triangular meshes that represent tessellations of synthetic geometric models. The results were compared with the analytically computed values of the Gaussian and mean curvatures of the non-uniform rational B-spline (NURBs) surfaces, these meshes originated from. This work manifests the best algorithms suited for that indeed different algorithms should be employed to compute the Gaussian and mean curvatures.
Pretreatment with NMDA antagonists limits release of excitatory amino acids following traumatic brain injury (1992)

After central nervous system (CNS) trauma, there are marked elevations in the extracellular levels of excitatory amino acids (EAA), which are believed to contribute to delayed tissue damage. Administration of N-methyl-D-aspartate (NMDA) receptor antagonists reduces injury severity after brain or spinal cord trauma, presumably by blocking the postsynaptic NMDA receptor. In the present studies, levels of extracellular amino acids were monitored by microdialysis during, and after, a moderately severe fluid-percussion brain injury to rats. Pretreatment (15 min prior to injury) with the non-competitive NMDA antagonist dextrorphan or the competitive NMDA antagonist CGS 19755 significantly attenuated the post-traumatic increase in extracellular glutamate. Pretreatment with dextrorphan attenuated the post-traumatic increase in extracellular levels of aspartate; although these differences did not reach significance when examined as absolute values, they were significant when analyzed as percent increase over pre-trauma baseline levels. These results are consistent with recent experiments and suggest that NMDA antagonists may limit the release of glutamate and aspartate after trauma through a presynaptic mechanism.
A structural perspective of CTD function (2005)

The C-terminal domain (CTD) of RNA polymerase II (Pol II) integrates nuclear events by binding proteins involved in mRNA biogenesis. CTD-binding proteins recognize a specific CTD phosphorylation pattern, which changes during the transcription cycle, due to the action of CTD-modifying enzymes. Structural and functional studies of CTD-binding and -modifying proteins now reveal some of the mechanisms underlying CTD function. Proteins recognize CTD phosphorylation patterns either directly, by contacting phosphorylated residues, or indirectly, without contact to the phosphate. The catalytic mechanisms of CTD kinases and phosphatases are known, but the basis for CTD specificity of these enzymes remains to be understood.
Osteoblast function on synthetic biodegradable polymers (1994)

Rat osteoblasts were cultured on films of biodegradable poly(L-lactic acid) (PLLA), 75:25 poly(DL-lactic-co-glycolic acid) (PLGA), 50:50 PLGA, and poly(glycolic acid) (PGA) for up to 14 days. Osteoblasts attached equally well to all the polymer substrates after 8 h in culture. By day 4 in culture, osteoblasts had exceeded confluency numbers, and their proliferation leveled off by day 7. An increase in alkaline phosphatase (ALP) activity from 1.92 (+/- 0.47) x 10(-7) for day 7 to 5.75 (+/- 0.12) x 10(-7) mumol/cell per min for day 14 was reported for osteoblasts cultured on 75:25 PLGA, which was comparable to that observed for tissue culture polystyrene (TCPS) controls. The ALP activities expressed by osteoblasts cultured on PLLA, 50:50 PLGA, and PGA films did not significantly increase over time. Collagen synthesis for osteoblasts cultured on all polymer substrates was similar to that of TCPS and did not vary with time. The morphology of cultured osteoblasts was not affected by the continuous degradation of the polymer substrates. These results demonstrate that poly(alpha-hydroxy esters) can provide a suitable substrate for osteoblast culture and hold promise in bone regeneration by osteoblast transplantation.
Functional Analysis of Burkitt's Lymphoma Mutant c-Myc Proteins (1996)

The c-myc gene encodes a sequence-specific DNA binding protein that activates transcription of cellular genes. Transcription activation by Myc proteins is regulated by phosphorylation of serine and threonine residues within the transactivation domain and by complex formation with the retinoblastoma-related protein p107. In Burkitt's lymphoma, missense mutations within the c-Myc transactivation domain have been found with high frequency. It has been reported that mutant c-Myc proteins derived from Burkitt's lymphoma cell lines are resistant to inhibition by p107, thus providing a rationale for the increased oncogenic activity of these mutant c-Myc proteins. It has been suggested that these mutant c-Myc proteins resist down-modulation by p107 because they lack cyclin A-cdk2-dependent phosphorylation. Here, we have examined three different Burkitt's lymphoma mutant c-Myc proteins found in primary Burkitt's lymphomas and one mutant c-Myc protein detected in a Burkitt's lymphoma cell line. All four have an unaltered ability to activate transcription and are sensitive to inhibition of transactivation by p107. Furthermore, we provide evidence that down-modulation of c-Myc transactivation by p107 does not require phosphorylation of the c-Myc transactivation domain by cyclin A-cdk2. Our data indicate that escape from p107-induced suppression is not a general consequence of all Burkitt's lymphoma-associated c-Myc mutations, suggesting that other mechanisms exist to deregulate c-Myc function.
Development of the algorithm of adaptive construction of hierarchical neural network classifiers (2017)

This paper presents the development of the algorithm for adaptive construction of hierarchical neural network classifiers based on automatic modification of the desired response of a perceptron with a small number of neurons in a single hidden layer. Improved versions of the algorithm are tested on standard benchmark problems Vowels and MNIST. A discussion of the results, strengths and weaknesses of the algorithm, directions of further work on its testing and improvement, is provided.
Purification and Characterization of an Acetyl Xylan Esterase fromBacillus pumilus (1998)

ABSTRACT Bacillus pumilus PS213 was found to be able to release acetate from acetylated xylan. The enzyme catalyzing this reaction has been purified to homogeneity and characterized. The enzyme was secreted, and its production was induced by corncob powder and xylan. Its molecular mass, as determined by gel filtration, is 190 kDa, while sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed a single band of 40 kDa. The isoelectric point was found to be 4.8, and the enzyme activity was optimal at 55°C and pH 8.0. The activity was inhibited by most of the metal ions, while no enhancement was observed. The Michaelis constant ( K m ) and V max for α-naphthyl acetate were 1.54 mM and 360 μmol min −1 mg of protein −1 , respectively.
Animal Models of Neuropathic Pain (2003)

Despite its prevalence, nerve injury-related (neuropathic) pain in humans is not well understood and, as such, remains difficult to manage (, , ). A variety of clinical conditions can lead to neuropathic pain, which contributes to our lack of understanding of this phenomenon. Although there is substantial etiological heterogeneity among neuropathic pain conditions, commonalities exist. For example, most patients present with combinations of spontaneous and stimulus-evoked pain, the latter of which is characterized by a hypersensitivity to previously innocuous tactile or thermal stimuli (allodynia). To improve our understanding of neuropathic pain, the challenge for basic scientists has been twofold: 1) to develop animal models of persistent pain that more closely mimic clinical pain in humans; and 2) to ensure high reproducibility, within and between animals, across different investigators and laboratories.
Oxidative Stress and the Pathogenesis of Muscular Dystrophies (2002)

The muscular dystrophies represent a diverse group of diseases differing in underlying genetic basis, age of onset, mode of inheritance, and severity of progression, but they share certain common pathologic features. Most prominent among these features is the necrotic degeneration of muscle fibers. Although the genetic basis of many of the dystrophies has been known for over a decade and new disease genes continue to be discovered, the pathogenetic mechanisms leading to muscle cell death in the dystrophies remain a mystery. This review focuses on the oxidative stress theory, which states that the final common pathway of muscle cell death in these diseases involves oxidative damage.