gebhart/patrepeval huggingface dataset:
Sole brachytherapy of the tumor bed after conservative surgery for T1 breast cancer: Five‐year results of a phase I–II study and initial findings of a randomized phase III trial (2002)

Five-year results of our phase I-II study prove that sole HDR-BT of the tumor bed with careful patient selection and adequate quality assurance is a feasible alternative to WBRT. However, long-term results of phase III trials are required to determine the equivalence of TBRT alone, compared with WBRT in the management of selected patients with early breast cancer.
Reverse transcriptase from avian myeloblastosis virus (1979)

From lots of 20 to 30 g of avian myeloblastosis virus RNA-dependent DNA polymerase was obtained in preparations of purity greater than 95% by using a two-step column chromatographic procedure employing DEAE (DE 52) and carboxymethylcellulose (CM 52.). Yields of RNA-dependent DNA polymerase varied from approximately 20,000 to 35,000 U/g of virus. Specific activity of the enzyme was about 35,000 to 60,000 U/mg of protein. Free of detectable RNase activity, the product exhibited a molecular weight of about 160,000, an isoelectric point of 6.5, and approximately 2 mol of fatty acid per mol of enzyme.
Pharmacodynamics and tolerability of acetyl starch as a new plasma volume expander in patients undergoing elective surgery (2000)

ACS and HES are equally effective plasma volume expanders; ACS might be a new, alternative colloid solution with fewer coagulation side-effects than HES.
Power, performance, and cost comparisons of monolithic 3D ICs and TSV-based 3D ICs (2015)

Power, performance, area, and cost analysis of TSV, mini-TSV, and monolithic 3D ICs is presented. Power savings for TSV, mini-TSV, and monolithic 3D ICs are 21%, 25%, and 37%, respectively, compared to that of a 2D IC. It is shown that monolithic 3D can deliver one node PPC benefit, whereas TSV 3D or mini-TSV 3D can only achieve a half node PPC advantage.
Evidence for a strong sulfur–aromatic interaction derived from crystallographic data (2000)

We have uncovered new evidence for a significant interaction between divalent sulfur atoms and aromatic rings. Our study involves a statistical analysis of interatomic distances and other geometric descriptors derived from entries in the Cambridge Crystallographic Database (F. H. Allen and O. Kennard, Chem. Design Auto. News, 1993, Vol. 8, pp. 1 and 31–37). A set of descriptors was defined sufficient in number and type so as to elucidate completely the preferred geometry of interaction between six-membered aromatic carbon rings and divalent sulfurs for all crystal structures of nonmetal-bearing organic compounds present in the database. In order to test statistical significance, analogous probability distributions for the interaction of the moiety X–CH2–X with aromatic rings were computed, and taken a priori to correspond to the null hypothesis of no significant interaction. Tests of significance were carried our pairwise between probability distributions of sulfur–aromatic interaction descriptors and their CH2–aromatic analogues using the Smirnov–Kolmogorov nonparametric test (W. W. Daniel, Applied Nonparametric Statistics, Houghton-Mifflin: Boston, New York, 1978, pp. 276–286), and in all cases significance at the 99% confidence level or better was observed. Local maxima of the probability distributions were used to define a preferred geometry of interaction between the divalent sulfur moiety and the aromatic ring. Molecular mechanics studies were performed in an effort to better understand the physical basis of the interaction. This study confirms observations based on statistics of interaction of amino acids in protein crystal structures (R. S. Morgan, C. E. Tatsch, R. H. Gushard, J. M. McAdon, and P. K. Warme, International Journal of Peptide Protein Research, 1978, Vol. 11, pp. 209–217; R. S. Morgan and J. M. McAdon, International Journal of Peptide Protein Research, 1980, Vol. 15, pp. 177–180; K. S. C. Reid, P. F. Lindley, and J. M. Thornton, FEBS Letters, 1985, Vol. 190, pp. 209–213), as well as studies involving molecular mechanics (G. Nemethy and H. A. Scheraga, Biochemistry and Biophysics Research Communications, 1981, Vol. 98, pp. 482–487) and quantum chemical calculations (B. V. Cheney, M. W. Schulz, and J. Cheney, Biochimica Biophysica Acta, 1989, Vol. 996, pp.116–124; J. Pranata, Bioorganic Chemistry, 1997, Vol. 25, pp. 213–219)—all of which point to the possible importance of the sulfur–aromatic interaction. However, the preferred geometry of the interaction, as determined from our analysis of the small-molecule crystal data, differs significantly from that found by other approaches. © 2000 John Wiley & Sons, Inc. Biopoly 53: 233–248, 2000
The wavelength add/drop multiplexer for lightwave communication networks (2002)

Lightwave systems are progressing toward optical networks capable of manipulating data paths by optical means rather than by traditional electronic switching. This is facilitated by wavelength multiplexed transmission, in which narrow bandwidth optical filters can be used to remove specific channels and reinsert new ones anywhere in the optical link. Wavelength add/drop multiplexers performing this optical channel processing can range in capability from providing dedicated add/drop of a single channel to having fully reconfigurable add/drop of many, if not all, of the wavelength division multiplexed (WDM) channels. Careful placement of wavelength add/drop multiplexers can dramatically improve a network's flexibility and robustness while providing significant cost advantages. This paper summarizes the rationale for incorporating wavelength add/drop multiplexers in modern optical networks, outlines their logical and optical characteristics, and introduces the predominant technology choices.
Production of transgenic soybean plants using Agrobacterium-mediated DNA transfer (1988)

Transgenic soybean plants have been produced using an Agrobacterium-mediated gene transfer system. This procedure relied on a regeneration protocol in which shoot organogenesis was induced on cotyledons of soybean genotypes selected for susceptibility to Agrobacterium. Cotyledon explants were inoculated with Agrobacterium tumefaciens pTiT37-SE harboring pMON9749 (conferring kanamycin resistance and β-glucuronidase “GUS” activity) or pTiT37-SE∷pMON894 (conferring kanamycin resistance and glyphosate tolerance) and cultured on shoot induction medium containing kanamycin. Plantlets were tested for gene insertion 3–4 months post-inoculation. Approximately 6% of the shoots (8 plants to date) produced on the kanamycin-selected cotyledons were transgenic based on assays for GUS expression, kanamycin resistance or glyphosate tolerance. Progeny from two of these plants demonstrated co-segregation of kanamycin resistance and either GUS expression or glyphosate tolerance in a 3:1 ratio indicating a single insert inherited in a Mendelian fashion.
Characterization of the Epitope Region of F1-2 and F1-5, Two Monoclonal Antibodies to Botulinum Neurotoxin Type A (2009)

F1-2 and F1-5 are mouse IgG1 monoclonal antibodies that bind the heavy chain of Botulinum neurotoxin serotype A (BoNT/A). To characterize the epitopes of F1-2 and F1-5, three complementary experimental approaches were selected. First, recombinant peptide fragments of BoNT/A heavy-chain were used in Western blots to identify the epitope regions. Second, a peptide phage display library was used to identify specific amino acids bound by F1-2 and F1-5, and these amino acids were mapped onto the three-dimensional structure of BoNT/A. Third, selected amino acids were mutated to alanine and the effects of the mutations on F1-2 and F1-5 binding were evaluated. Data from recombinant peptide fragment binding experiments suggested that the epitopes for antibodies F1-2 and F1-5 are located between amino acids R564 and S793 on the toxin heavy chain. Furthermore, elimination of amino acids from the amino terminus (R564-K595), or from the carboxyl terminus (N759-S793) of this fragment abolished binding of both F1-2 and F1-5, suggesting a conformational epitope for these antibodies. Peptide sequences deduced from antibody binding to the peptide phage display library suggested that tyrosine residues located at positions 748, 750, and 753 might form a significant part of the F1-2 and F1-5 epitope motif. Mutation of Y750 or Y753 to alanine significantly reduced binding of either antibody, while mutation of Y748 to alanine had no effect on antibody binding. The nucleotide and deduced amino acid sequences of the variable regions of the heavy chains of F1-2 and F1-5 are reported. The complementarity determining regions (CDRs) of the heavy chains were found to be 78% identical. It is possible that F1-2 and F1-5 bind the same epitope via the common amino acids within their CDRs.
Materials, Process, and Manufacturing Considerations for Lipid-Based Hard-Capsule Formats (2007)

The recognition of the potential of lipid-based formulations for improving the gastrointestinal absorption of poorly water-soluble drugs has been a major driver for the development of liquid-filled capsule technology (1-4). Lipid excipients possess a wide range of desirable characteristics, such as broad chemical compatibility, low melting points, surfactant or self-emulsifying properties, and suitability for large-scale manufacture. The increasing application of lipid-based formulations has prompted the production equipment and capsule manufacturers to develop new materials, processing systems, and product formats. Lipid-based capsule formulations are encountered not only in ethical pharmaceutical products but in consumer and “high-end” nutriceutical products as well. The market is therefore diverse and presents numerous technical challenges for the formulation and manufacture of these dosage forms.
Mapping disease genes: family-based association studies. (1995)

With recent rapid advances in mapping of the human genome, including highly polymorphic and closely linked markers, studies of marker associations with disease are increasingly relevant for mapping disease genes. The use of nuclear-family data in association studies was initially developed to avoid possible ethnic mismatching between patients and randomly ascertained controls. The parental marker alleles not transmitted to an affected child or never transmitted to an affected sib pair form the so-called AFBAC (affected family-based controls) population. In this paper, the theoretical foundation of the AFBAC method is proved for any single-locus model of disease and for any nuclear family-based ascertainment scheme. In a random-mating population, when there is a marker association with disease, the AFBAC population provides an unbiased estimate of the overall population (control) marker alleles when the recombination fraction (theta) between the marker and disease genes is sufficiently small that it can be taken as zero (theta = 0). With population stratification, only marker associations present in the subpopulations will be detected with family-based analyses. Of more importance, however, is the fact that, when theta not equal to 0, differences between transmitted parental (patient) marker allele frequencies and non- or never-transmitted parental marker allele frequencies (implying a marker association with disease) can only be observed for marker genes linked to a disease gene (theta < 1/2). Thus, associations of unlinked marker loci with disease at the population level, caused by population stratification, migration, or admixture, are eliminated. This validates the use of family-based association tests as an appropriate strategy for mapping disease genes.
Gonadectomy Affects Hormonal and Behavioral Responses to Repetitive Nociceptive Stimulation in Male Rats (2003)

Sex differences have been observed repeatedly in chronic pain syndromes in both humans and animals, with females showing a higher incidence; it is likely that the gonadal hormones are responsible for these differences. To examine the role of male gonadal hormones on repetitive nociceptive stimulation, we studied male rats, half of them gonadectomized (GDX) and half left intact (INT). Starting from the third week after gonadectomy, they were subjected to the formalin test once a week for 3 weeks (50 micro l formalin 5% injected s.c. in the dorsum of the hind paw: right, left, and right). Formalin-induced licking, flexing, and jerking of the injected paw were recorded and analyzed for each of the three trials. Analysis of variance showed significant differences between GDX and INT animals depending on the trial considered: Trial 1: the GDX and INT groups showed a similar amount of licking, flexing, and paw-jerk; Trials 2 and 3: these responses showed a sort of adaptation in INT animals, not present in the GDX ones, resulting in lower levels of pain responses in INT than GDX. Corticosterone was higher in GDX animals than in INT animals. Testosterone plasma levels were drastically decreased by gonadectomy, whereas estradiol was increased. These data indicate that male gonadal hormones play a key role in inhibiting the behavioral responses to repeated nociceptive stimulation. This suggests that the lower incidence of chronic pain syndromes in males could be caused by the presence of these hormones.
Cystatin E/M suppresses legumain activity and invasion of human melanoma (2010)

These results suggest that the level of cystatin E/M regulates legumain activity and hence the invasive potential of human melanoma cells.
Scale‐up analysis for a CHO cell culture process in large‐scale bioreactors (2009)

Bioprocess scale-up is a fundamental component of process development in the biotechnology industry. When scaling up a mammalian cell culture process, it is important to consider factors such as mixing time, oxygen transfer, and carbon dioxide removal. In this study, cell-free mixing studies were performed in production scale 5,000-L bioreactors to evaluate scale-up issues. Using the current bioreactor configuration, the 5,000-L bioreactor had a lower oxygen transfer coefficient, longer mixing time, and lower carbon dioxide removal rate than that was observed in bench scale 5- and 20-L bioreactors. The oxygen transfer threshold analysis indicates that the current 5,000-L configuration can only support a maximum viable cell density of 7 x 10(6) cells mL(-1). Moreover, experiments using a dual probe technique demonstrated that pH and dissolved oxygen gradients may exist in 5,000-L bioreactors using the current configuration. Empirical equations were developed to predict mixing time, oxygen transfer coefficient, and carbon dioxide removal rate under different mixing-related engineering parameters in the 5,000-L bioreactors. These equations indicate that increasing bottom air sparging rate is more efficient than increasing power input in improving oxygen transfer and carbon dioxide removal. Furthermore, as the liquid volume increases in a production bioreactor operated in fed-batch mode, bulk mixing becomes a challenge. The mixing studies suggest that the engineering parameters related to bulk mixing and carbon dioxide removal in the 5,000-L bioreactors may need optimizing to mitigate the risk of different performance upon process scale-up.
Metabolic characterization of Lactococcus lactis deficient in lactate dehydrogenase using in vivo13C‐NMR (2000)

The metabolism of glucose by nongrowing cells of Lactococcus lactis strain FI7851, constructed from the wild-type L. lactis strain MG1363 by disruption of the lactate dehydrogenase (ldh) gene [Gasson, M.J., Benson, K., Swindel, S. & Griffin, H. (1996) Lait 76, 33-40] was studied in a noninvasive manner by 13C-NMR. The kinetics of the build-up and consumption of the pools of intracellular intermediates mannitol 1-phosphate, fructose 1,6-bisphosphate, 3-phosphoglycerate, and phosphoenolpyruvate as well as the utilization of [1-13C]glucose and formation of products (lactate, acetate, mannitol, ethanol, acetoin, 2,3-butanediol) were monitored in vivo with a time resolution of 30 s. The metabolism of glucose by the parental wild-type strain was also examined for comparison. A clear shift from typical homolactic fermentation (parental strain) to a mixed acid fermentation (lactate dehdydrogenase deficient; LDHd strain) was observed. Furthermore, high levels of mannitol were transiently produced and metabolized once glucose was depleted. Mannitol 1-phosphate accumulated intracellularly up to 76 mM concentration. Mannitol was formed from fructose 6-phosphate by the combined action of mannitol-1-phosphate dehydrogenase and phosphatase. The results show that the formation of mannitol 1-phosphate by the LDHd strain during glucose catabolism is a consequence of impairment in NADH oxidation caused by a highly reduced LDH activity, the transient production of mannitol 1-phosphate serving as a regeneration pathway for NAD+ regeneration. Oxygen availability caused a drastic change in the pattern of intermediates and end-products, reinforcing the key-role of the fulfilment of the redox balance. The flux control coefficients for the step catalysed by mannitol-1-phosphate dehydrogenase were calculated and the implications in the design of metabolic engineering strategies are discussed.
Stem‐cell plasticity and therapy for injuries of the peripheral nervous system (2004)

Numerous publications have investigated stem-cell biology and the possible therapeutic use of stem cells in a wide range of injuries and diseases. This interest has been fueled by recent reports suggesting that mesenchymal stem cells can show unorthodox plasticity, their being able to transdifferentiate into cells of different lineages, such as neuronal phenotypes. This capability has obvious implications for their potential application in tissue engineering and tissue regeneration. The peripheral nervous system has an inherent capacity for regeneration, but this is limited and not matched by the level of reinnervation of target organs, with a resulting loss of functional recovery. Several approaches have been attempted in order to overcome this deficiency, and transplant of cultured Schwann cells into bioengineered conduits has been shown to improve regeneration. An alternative may be the use of stem-cell technology, whereby cultured and differentiated stem cells can be transplanted to the site of injury in order to promote enhanced regeneration. The present review discusses the use of stem cells applied to the repair of peripheral nerve injury and their role in the regeneration process.
Chiral Gold Nanowires with Boerdijk–Coxeter–Bernal Structure (2014)

A Boerdijk-Coxeter-Bernal (BCB) helix is made of linearly stacked regular tetrahedra (tetrahelix). As such, it is chiral without nontrivial translational or rotational symmetries. We demonstrate here an example of the chiral BCB structure made of totally symmetrical gold atoms, created in nanowires by direct chemical synthesis. Detailed study by high-resolution electron microscopy illustrates their elegant chiral structure and the unique one-dimensional "pseudo-periodicity". The BCB-type atomic packing mode is proposed to be a result of the competition and compromise between the lattice and surface energy.
Monoclonal antibodies preventing leukocyte activation reduce experimental neurologic injury and enhance efficacy of thrombolytic therapy (1995)

We evaluated the ability of monoclonal antibodies directed against leukocyte adhesion molecules (intercellular adhesion molecule-1 [ICAM-1], CD18) to enhance the efficacy of thrombolysis in a rabbit cerebral embolism stroke model. Both tissue-type plasminogen activator (tPA) and anti-CD18 (alpha-CD18) monoclonal antibody administered 5 minutes after embolization increased the quantity of clots required to produce neurologic damage, although the combination was no more effective than either substance alone. Neither alpha-CD18 nor anti-ICAM-1 (alpha-ICAM-1) improved neurologic outcome at postischemic delays of 15 or 30 minutes. However, the combination of alpha-ICAM-1 (15 minutes after embolization) and tPA (2 hours after embolization) significantly improved neurologic outcome even though neither substance was effective alone at these postembolization delays. These findings suggest that prevention of leukocyte adhesion increases the postischemic duration at which thrombolytic therapy remains effective.
Resveratrol Improves Cardiomyopathy in Dystrophin-deficient Mice through SIRT1 Protein-mediated Modulation of p300 Protein* (2013)

Cardiomyopathy is the main cause of death in Duchenne muscular dystrophy. Here, we show that oral administration of resveratrol, which leads to activation of an NAD(+)-dependent protein deacetylase SIRT1, suppresses cardiac hypertrophy and fibrosis and restores cardiac diastolic function in dystrophin-deficient mdx mice. The pro-hypertrophic co-activator p300 protein but not p300 mRNA was up-regulated in the mdx heart, and resveratrol administration down-regulated the p300 protein level. In cultured cardiomyocytes, cardiomyocyte hypertrophy induced by the α(1)-agonist phenylephrine was inhibited by the overexpression of SIRT1 as well as resveratrol, both of which down-regulated p300 protein levels but not p300 mRNA levels. In addition, activation of atrial natriuretic peptide promoter by p300 was inhibited by SIRT1. We found that SIRT1 induced p300 down-regulation via the ubiquitin-proteasome pathway by deacetylation of lysine residues for ubiquitination. These findings indicate the pathological significance of p300 up-regulation in the dystrophic heart and indicate that SIRT1 activation has therapeutic potential for dystrophic cardiomyopathy.
Electromagnetic fields influence NGF activity and levels following sciatic nerve transection (1999)

Pulsed electromagnetic fields (PEMF) have been shown to increase the rate of nerve regeneration. Transient post-transection loss of target-derived nerve growth factor (NGF) is one mechanism proposed to signal induction of early nerve regenerative events. We tested the hypothesis that PEMF alter levels of NGF activity and protein in injured nerve and/or dorsal root ganglia (DRG) during the first stages of regeneration (6-72 hr). Rats with a transection injury to the midthigh portion of the sciatic nerve on one side were exposed to PEMF or sham control PEMF for 4 hr/day for different time periods. NGF-like activity was determined in DRG, in 5-mm nerve segments proximal and distal to the transection site and in a corresponding 5-mm segment of the contralateral nonoperated nerve. NGF-like activity of coded tissue samples was measured in a blinded fashion using the chick DRG sensory neuron bioassay. Overall, PEMF caused a significant decrease in NGF-like activity in nerve tissue (P < 0.02, repeated measures analysis of variance, ANOVA) with decreases evident in proximal, distal, and contralateral nonoperated nerve. Unexpectedly, transection was also found to cause a significant (P=0.001) 2-fold increase in DRG NGF-like activity between 6 and 24 hr postinjury in contralateral but not ipsilateral DRG. PEMF also reduced NGF-like activity in DRG, although this decrease did not reach statistical significance. Assessment of the same nerve and DRG samples using ELISA and NGF-specific antibodies confirmed an overall significant (P < 0.001) decrease in NGF levels in PEMF-treated nerve tissue, while no decrease was detected in DRG or in nerve samples harvested from PEMF-treated uninjured rats. These findings demonstrate that PEMF can affect growth factor activity and levels, and raise the possibility that PEMF might promote nerve regeneration by amplifying the early postinjury decline in NGF activity.