gebhart/patrepeval huggingface dataset:
Diffusion of peroxynitrite across erythrocyte membranes (1998)

Peroxynitrite anion (ONOO-) is a reactive species of increasingly recognized biological relevance that contributes to oxidative tissue damage. At present, however, there is limited knowledge about the mechanisms of peroxynitrite diffusion through biological compartments. In this work we have studied the diffusion of peroxynitrite across erythrocyte membranes. In solution, peroxynitrite rapidly reacts with oxyhemoglobin to yield methemoglobin, with k2 = (10.4 +/- 0.3) x 10(3) M-1.s-1 at pH 7.4 and 25 degrees C. Addition of peroxynitrite to intact erythrocytes caused oxidation of intracellular oxyhemoglobin to methemoglobin. Oxidation yields in red blood cells at pH 7.0 were approximately 40% of those obtained in solution, which results mostly from competition of other cytosolic components for peroxynitrite. Indeed, rather small differences were observed between oxidation yields in lysates compared with intact erythrocytes, in particular at acidic and neutral pH values, indicating that membrane was not precluding peroxynitrite diffusion. Incubation of erythrocytes at pH 7.0 with 4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid (DIDS), a specific inhibitor of anion exchange, resulted in up to 50% inhibition of oxyhemoglobin oxidation by peroxynitrite. More protection by DIDS was achieved at alkaline pH, while no effect was observed at pH 5.5, where 95% of peroxynitrite is in the acidic form, ONOOH (pKa = 6.8). In addition, peroxynitrite caused nitration of intracellular hemoglobin, in a process that was enhanced in thiol-depleted erythrocytes. Our results indicate that peroxynitrite is able to cross the erythrocyte membrane by two different mechanisms: in the anionic form through the DIDS-inhibitable anion channel, and in the protonated form by passive diffusion.
Biocellulose Membranes as Supports for Dermal Release of Lidocaine (2011)

Biocellulose (BC) is a highly pure form of cellulose, produced in the form of a swollen membrane, with several applications in the biomedical area. In this study, the behavior of BC membranes as systems for topical delivery of lidocaine was evaluated. The BC-lidocaine membranes were prepared and characterized in terms of structural and morphological properties. A uniform distribution of the drug inside the BC membranes was observed. In vitro diffusion studies with Franz cells were conducted using human epidermal membranes and showed that the permeation rate of the drug in BC membranes was slightly slower than that obtained with the conventional systems, which was attributed to the establishment of interactions between the lidocaine molecules and the BC membrane, as evidenced by FTIR and NMR analysis. These results indicate that this methodology can be successfully applied for the dermal administration of lidocaine regarding the release profile and ease of application.
Efficient gene transfer into myocardium by direct injection of adenovirus vectors. (1993)

Previous studies have established that gene transfer into myocardial cells in vivo is detectable after direct injection of plasmid DNA. Recently, adenovirus vectors have been shown to provide an efficient method for gene transfer into a wide range of tissues. Therefore, this study sought to assess the efficiency and stability of adenovirus-mediated gene transfer into myocardium and to compare this method with that using plasmid-based gene transfer techniques. Adult rats underwent myocardial injection via a subdiaphragmatic approach. Gene transfer efficiency was compared using direct injection of an adenovirus vector encoding for the marker gene beta-galactosidase (beta-gal), a control adenovirus vector encoding for the cystic fibrosis transmembrane conductance regulator gene, a plasmid encoding for beta-gal, or a control plasmid. Hearts infected with an adenovirus vector containing the beta-gal gene showed significantly increased beta-gal enzymatic activity compared with hearts injected with beta-gal plasmid. Histological examination revealed that cardiac myocytes were the target of adenovirus-mediated gene transfer. A time course of gene expression showed that beta-gal enzymatic activity peaked during the first week following injection. Adenovirus vectors provide an efficient but transient method for in vivo gene expression in myocardium.
Transformation of Haemophilus influenzae by plasmid RSF0885 containing a cloned segment of chromosomal deoxyribonucleic acid (1981)

A plasmid containing a single cloned insertion of Haemophilus influenzae chromosomal deoxyribonucleic acid that carried a novobiocin resistance marker was 2.6 times larger than the parent plasmid, RSF0885, which conferred ampicillin resistance. The most frequent type of transformation by this plasmid (designated pNov1) was the transfer of novobiocin resistance to the chromosome, with the loss of the plasmid from the recipient. In accord with this observation, after radioactively labeled pNov1 entered a competent cell, it lost acid-insoluble counts, as well as biological activity. The level of ampicillin transformation, which involved establishment of the plasmid, was almost two orders of magnitude lower than the level of novobiocin transformation. Both types of transformation were depressed profoundly in rec-1 and rec-2 mutants. Ampicillin transformants of wild-type cells always contained plasmids that were the same size as pNov1, although most of these transformants were not novobiocin resistant. Plasmid pNov1 in wild-type cells but not in rec-1 or rec-2 cells often recombined with the chromosome, causing a homologous region of the chromosome to be substituted for part of the plasmid, as shown by restriction and genetic analyses. Our data suggested that plasmid-chromosome recombination took place only around the time when the plasmid entered a cell, rather than after it became established.
Effects related to temperature changes during MR imaging (1992)

Magnetic resonance (MR) imaging has been proposed as a method of monitoring the interstitial laser heating of tissue for the clinical treatment of tumors (laser hyperthermia). The treatment causes considerable temperature changes over the time that image data are acquired, and therefore an analysis of the time-dependent effects of heating is required. The problem is expressed mathematically, and computer-simulated images are compared with those obtained from experimental heating and imaging of gel phantoms. Results show that at the rates of heating typical for laser hyperthermia and even with the relatively slow standard imaging techniques used, generation of artifact is not a major concern. It is also shown that a spatial spin signal magnitude distribution, evolving in time, is effectively sampled at the time to when the low-numbered phase-encoding steps are collected at to. It is noted, however, that substantial temperature changes during image data acquisition make accurate temperature determination difficult and place limits on MR imaging for quantitative spatial temperature mapping.
Identification of dynamic load for prosthetic structures (2017)

Dynamic load exists in numerous biomechanical systems, and its identification signifies a critical issue for characterizing dynamic behaviors and studying biomechanical consequence of the systems. This study aims to identify dynamic load in the dental prosthetic structures, namely, 3-unit implant-supported fixed partial denture (I-FPD) and teeth-supported fixed partial denture. The 3-dimensional finite element models were constructed through specific patient's computerized tomography images. A forward algorithm and regularization technique were developed for identifying dynamic load. To verify the effectiveness of the identification method proposed, the I-FPD and teeth-supported fixed partial denture structures were investigated to determine the dynamic loads. For validating the results of inverse identification, an experimental force-measuring system was developed by using a 3-dimensional piezoelectric transducer to measure the dynamic load in the I-FPD structure in vivo. The computationally identified loads were presented with different noise levels to determine their influence on the identification accuracy. The errors between the measured load and identified counterpart were calculated for evaluating the practical applicability of the proposed procedure in biomechanical engineering. This study is expected to serve as a demonstrative role in identifying dynamic loading in biomedical systems, where a direct in vivo measurement may be rather demanding in some areas of interest clinically.
TGF-β superfamily members and ovarian follicle development (2006)

In recent years, exciting progress has been made towards unravelling the complex intraovarian control mechanisms that, in concert with systemic signals, coordinate the recruitment, selection and growth of follicles from the primordial stage through to ovulation and corpus luteum formation. A plethora of growth factors, many belonging to the transforming growth factor-beta (TGF-beta ) superfamily, are expressed by ovarian somatic cells and oocytes in a developmental, stage-related manner and function as intraovarian regulators of folliculogenesis. Two such factors, bone morphogenetic proteins, BMP-4 and BMP-7, are expressed by ovarian stromal cells and/or theca cells and have recently been implicated as positive regulators of the primordial-to-primary follicle transition. In contrast, evidence indicates a negative role for anti-Mullerian hormone (AMH, also known as Mullerian-inhibiting substance) of pre-granulosa/granulosa cell origin in this key event and subsequent progression to the antral stage. Two other TGF-beta superfamily members, growth and differentiation factor-9 (GDF-9) and BMP-15 (also known as GDF-9B) are expressed in an oocyte-specific manner from a very early stage and play key roles in promoting follicle growth beyond the primary stage; mice with null mutations in the gdf-9 gene or ewes with inactivating mutations in gdf-9 or bmp-15 genes are infertile with follicle development arrested at the primary stage. Studies on later stages of follicle development indicate positive roles for granulosa cell-derived activin, BMP-2, -5 and -6, theca cell-derived BMP-2, -4 and -7 and oocyte-derived BMP-6 in promoting granulosa cell proliferation, follicle survival and prevention of premature luteinization and/or atresia. Concomitantly, activin, TGF-beta and several BMPs may exert paracrine actions on theca cells to attenuate LH-dependent androgen production in small to medium-size antral follicles. Dominant follicle selection in monovular species may depend on differential FSH sensitivity amongst a growing cohort of small antral follicles. Changes in intrafollicular activins, GDF-9, AMH and several BMPs may contribute to this selection process by modulating both FSH- and IGF-dependent signalling pathways in granulosa cells. Activin may also play a positive role in oocyte maturation and acquisition of developmental competence. In addition to its endocrine role to suppress FSH secretion, increased output of inhibin by the selected dominant follicle(s) may upregulate LH-induced androgen secretion that is required to sustain a high level of oestradiol secretion during the pre-ovulatory phase. Advances in our understanding of intraovarian regulatory mechanisms should facilitate the development of new approaches for monitoring and manipulating ovarian function and improving fertility in domesticated livestock, endangered species and man.
Ephrin‐A1 stimulates migration of CD8+CCR7+ T lymphocytes (2007)

We have previously demonstrated that binding of ephrin-A1 to Eph receptors on human CD4+ T cells stimulates migration. Here, we show that a distinct population of CD8+ T lymphocytes, expressing the chemokine receptor CCR7, also binds ephrin-A1 and is stimulated to migrate after binding. The Eph receptor signaling pathway taking part in the migration event was here investigated. Induced tyrosine phosphorylation of several proteins was seen after ephrin-A1 binding. In particular, induced phosphorylation and kinase activity of the Src kinase family member Lck was observed. An Lck inhibitor inhibited ephrin-A1-induced migration, indicating the involvement of Lck in the migration event. In addition, we observed an induced association of the focal adhesion-like kinase proline-rich tyrosine kinase 2 (Pyk2) and the guanidine exchange factor Vav1 with Lck. PI3K inhibitors also inhibited migration, and studies in transfectants indicate an association of PI3K with EphA1. Further, ephrin-A1-induced migration could be related to the activation of Rho GTPases. This was also observed by using an inhibitor of the Rho-associated kinase ROCK, a downstream effector of Rho. Our results suggest that stimulation of Eph receptors on CD8+CCR7+ T cells leads to migration involving activation of Lck, Pyk2, PI3K, Vav1 and Rho GTPase.
HOXB7: An Oncogenic Gene in Breast Cancer Cells? (2003)

Abstract : Homeobox genes control anterioposterior body axis patterning during development. Although expressed primarily in developing embryos, a growing body of evidence shows that homeobox gene re-expression in adult tissues is associated with tumorigenesis. Earlier work has shown that introduction of HOXB7, one of the members of this gene family, into non-expressing breast cancer cells induced expression of a number of pro-angiogenic factors and formed tumors upon xenograft into nude mice. Since a growing body of evidence showed that HOXR7 may be involved in ovarian, skin and breast cancer, we wanted to investigate its expression levels in breast carcinomas and evaluate its oncogenic potential in this study. To characterized the role of HOXB7 in breast cancer, a number of HOXB7-interacting proteins in breast cancer cells were identified and binding to HOXB7 was confirmed in vivo. Interestingly, all of the HOXB7-associated proteins identified have well characterized roles in the non-homologous end joining (NHEJ) pathway for DNA double strand break (DSB) repair as well as a larger role in maintenance of genomic integrity. Cell survival experiments demonstrated that breast cancer cells stably transfected with HOXB7 survive better after induction Df DNA DSB with fewer chromosomal abnormalities following exposure to gamma radiation. In addition, transduction of HOXB7 into the normal immortalized mammary epithelial cell line, MCFlOA, induced anchorage independent growth that was dependent of PARP activity. These data have led us to propose that HOXB7 may serve a role in breast cancer tumorigenesis in which PARP shares a common pathway.
Freshwater flows affect the year-class strength of 'Barramundi lates calcarifer' in the Fitzroy River estuary, Central Queensland (2010)

The age-structure of the commercial catch of barramundi in the Fitzroy River estuary, central Queensland, was examined over fi ve consecutive years and used to estimate year-class strength (= index of recruitment). Barramundi year-class strength fl uctuated and was signifi cantly and positively correlated with freshwater flow and coastal rainfall in spring and summer. General linear models were used to identify relationships between year-class strength and freshwater variables, and explained between 85 and 90% of the variation in barramundi year-class strength. The results provide further evidence that recruitment variation in barramundi: (i) persists over time; and (ii) is signifi cantly correlated with the volume to freshwater flowing into the estuary. We reviewed the evidence in support of the three causal mechanisms currently proposed to explain the relationship between year-class strength and juvenile barramundi recruitment; and propose an additional mechanism, that of enhanced growth rates and thus increased survival of young-of-the-year. Freshwater flow is an important driver of barramundi recruitment, and reduction in flow, through water abstraction or climate change, will potentially reduce barramundi stock size available for human harvest. As such, fi shery stock assessments for barramundi should explicitly consider the impacts of variable flow on annual recruitment and stock dynamics.
Calcium Chloride in Neonatal Parenteral Nutrition: Compatibility Studies Using Laser Methodology (2014)

Maximum amounts of phosphate that could be added to parenteral nutrition solutions containing Trophamine and calcium chloride were about 7.5-10 mmol/L less for a given concentration of calcium based upon laser methodology compared to visual techniques to determine compatibility. There were minor differences in compatibility when adding calcium chloride and potassium phosphate to Premasol versus Trophamine.
Ultrasound Imaging–Guided Noninvasive Ultrasound Thrombolysis (2000)

External high-intensity focused ultrasound thrombolysis using optimal PW parameters for periods of </=300 seconds appears to be a safe and effective method to induce thrombolysis. The procedure can be guided by ultrasound imaging, thereby allowing the monitoring of therapy.
THE APPLICATION OF THE HAMMETT EQUATION TO ORTHO-SUBSTITUTED BENZENE REACTION SERIES (1960)

The Hammett equation is directly applicable to ortho-substituted benzene reaction series in which reaction site and benzene ring are separated by some group Z, apparently due to the absence of steric effects in these series. The σ p values are used in the correlations. Fourteen ortho-substituted benzene reaction series have been correlated. The electrical effect of a substituent in the ortho position is found to be about 0.75 times its effect in the para position. The effect of the side-chain Z in the transmission of substituent effects is OCH 2 &gt; SCH 2 &gt; CH = CH &gt; SeCH 2 &gt; CH 2 CH 2 .
Encapsidated adenovirus minichromosomes allow delivery and expression of a 14 kb dystrophin cDNA to muscle cells (1996)

Adenovirus-mediated gene transfer to muscle is a promising technology for gene therapy of Duchenne muscular dystrophy (DMD). However, currently available recombinant adenovirus vectors have several limitations, including a limited cloning capacity of approximately 8.5 kb, and the induction of a host immune response that leads to transient gene expression of 3-4 weeks in immunocompetent animals. Gene therapy for DMD could benefit from the development of adenoviral vectors with an increased cloning capacity to accommodate a full-length (approximately 14 kb) dystrophin cDNA. This increased capacity should also accommodate gene regulatory elements to achieve expression of transduced genes in a tissue-specific manner. Additional vector modifications that eliminate adenoviral genes, expression of which is associated with development of a host immune response, might greatly increase long-term expression of virally delivered genes in vivo. We have constructed encapsidated adenovirus minichromosomes theoretically capable of delivering up to 35 kb of non-viral exogenous DNA. These minichromosomes are derived from bacterial plasmids containing two fused inverted adenovirus origins of replication embedded in a circular genome, the adenovirus packaging signals, a beta-galactosidase reporter gene and a full-length dystrophin cDNA regulated by a muscle-specific enhancer/promoter. The encapsidated minichromosomes are propagated in vitro by trans-complementation with a replication-defective (E1 + E3 deleted) helper virus. We show that the minichromosomes can be propagated to high titer (> 10(8)/ml) and purified on CsCl gradients due to their buoyancy difference relative to helper virus. These vectors are able to transduce myogenic cell cultures and express dystrophin in myotubes. These results suggest that encapsidated adenovirus minichromosomes may be useful for gene transfer to muscle and other tissues.
Single-shot tomographic movies of evolving light-velocity objects (2014)

Tomography--cross-sectional imaging based on measuring radiation transmitted through an object along different directions--enables non-invasive imaging of hidden stationary objects, such as internal bodily organs, from their sequentially measured projections. Here we adapt tomographic methods to visualize--in one laser shot--the instantaneous structure and evolution of a laser-induced object propagating through a transparent Kerr medium. We reconstruct 'movies' of a laser pulse's diffraction, self-focusing and filamentation from phase 'streaks' imprinted onto probe pulses that cross the main pulse's path simultaneously at different angles. Multiple probes are generated and detected compactly and simply, making the system robust, easy to align and adaptable to many problems. Our technique could potentially visualize, for example, plasma wakefield accelerators, optical rogue waves or fast ignitor pulses, light-velocity objects, whose detailed space-time dynamics are known only through intensive computer simulations.
Comparative Evolutionary Analysis of Chalcone Synthase and Alcohol Dehydrogenase Loci in Arabidopsis, Arabis, and Related Genera (Brassicaceae) (2000)

We analyzed sequence variation for chalcone synthase (Chs) and alcohol dehydrogenase (Adh) loci in 28 species in the genera Arabidopsis and Arabis and related taxa from tribe Arabideae. Chs was single-copy in nearly all taxa examined, while Adh duplications were found in several species. Phylogenies constructed from both loci confirmed that the closest relatives of Arabidopsis thaliana include Arabidopsis lyrata, Arabidopsis petraea, and Arabidopsis halleri (formerly in the genus Cardaminopsis). Slightly more distant are the North American n = 7 Arabis (Boechera) species. The genus Arabis is polyphyletic-some unrelated species appear within this taxonomic classification, which has little phylogenetic meaning. Fossil pollen data were used to compute a synonymous substitution rate of 1.5 x 10 substitutions per site per year for both Chs and Adh. Arabidopsis thaliana diverged from its nearest relatives about 5 MYA, and from Brassica roughly 24 MYA. Independent molecular and fossil data from several sources all provide similar estimates of evolutionary timescale in the Brassicaceae.
Cell Surface Expression of Biologically Active Influenza C Virus HEF Glycoprotein Expressed from cDNA (1999)

The hemagglutinin, esterase, and fusion (HEF) glycoprotein of influenza C virus possesses receptor binding, receptor destroying, and membrane fusion activities. The HEF cDNAs from influenza C/Ann Arbor/1/50 (HEF-AA) and influenza C/Taylor/1223/47 (HEF-Tay) viruses were cloned and expressed, and transport of HEF to the cell surface was monitored by susceptibility to cleavage by exogenous trypsin, indirect immunofluorescence microscopy, and flow cytometry. Previously it has been found in studies with the C/Johannesburg/1/66 strain of influenza C virus (HEF-JHB) that transport of HEF to the cell surface is severely inhibited, and it is thought that the short cytoplasmic tail, Arg-Thr-Lys, is involved in blocking HEF cell surface expression (F. Oeffner, H.-D. Klenk, and G. Herrler, J. Gen. Virol. 80:363-369, 1999). As the cytoplasmic tail amino acid sequences of HEF-AA and HEF-Tay are identical to that of HEF-JHB, the data indicate that cell surface expression of HEF-AA and HEF-Tay is not inhibited by this amino acid sequence. Furthermore, the abundant cell surface transport of HEF-AA and HEF-Tay indicates that their cell surface expression does not require coexpression of another viral protein. The HEF-AA and HEF-Tay HEF glycoproteins bound human erythrocytes, promoted membrane fusion in a low-pH and trypsin-dependent manner, and displayed esterase activity, indicating that the HEF glycoprotein alone mediates all three known functions at the cell surface.
Hidradenitis Suppurativa and Crohn's Disease: Response to Treatment with Infliximab (2001)

Cutaneous manifestations occur frequently in inflammatory bowel disease. The association between hidradenitis suppurativa (HS) and Crohn's disease (CD) has been reported. We present a new case supporting this association. A dramatic improvement after treatment with infliximab was achieved for both refractory fistulizing CD and axillary HS.