gebhart/patrepeval huggingface dataset:
Genome fingerprinting as a typing method used on polyagglutinable Pseudomonas aeruginosa isolates from cystic fibrosis patients. (1991)

Phenotypical changes occur in the surface of Pseudomonas aeruginosa during the chronic lung infection of cystic fibrosis patients. It is difficult with the classical typing methods, such as serotyping, phage typing and pyocin typing, to decide if a patient has been colonized with a new strain or whether it is the same strain which has reappeared, for instance after chemotherapy in the lungs. This investigation was carried out to evaluate genome fingerprinting as a typing method and to see how it correlated with classical methods and with DNA probe typing. Forty Pseudomonas aeruginosa isolates, 34 polyagglutinable and six monoagglutinable, from 14 cystic fibrosis patients were analysed using genome fingerprinting. The bacterial chromosomes were digested with the restriction endonucleases Dra 1 and Xbal, and separated by field inversion gel electrophoresis. The results were compared with those of a previous work (Ojeniyi et al. 1990) concerning typing with a DNA probe, serotyping using both polyclonal and monoclonal sera, phage typing, pyocin typing and reverse phage typing. The results of genome fingerprinting and DNA probe typing showed the best correlation, followed by pyocin typing. The correlation between the results of genome typing and the other typing methods was low. The discriminatory effect of genome fingerprinting was higher than that of DNA probe typing, and genome fingerprinting was found to be the best single method for epidemiological investigations of polyagglutinable isolates from cystic fibrosis patients.
Culture and Health. What role does culture play in the development and the maintenance of social disparities in health (1991)

info:eu-repo/semantics/nonPublished
Mutations in the Nonstructural Protein 5a Gene and Response to Interferon in Patients with Chronic Hepatitis C Virus 1b Infection (1996)

In patients with chronic HCV-1b infection, there is a substantial correlation between responses to interferon and mutations in the NS5A gene.
Phase composition depth profiles using spatially resolved energy dispersive X-ray diffraction (2004)

Spatially resolved energy dispersive X-ray diffraction, using high-energy synchrotron radiation (∼35–80 keV), was used nondestructively to obtain phase composition profiles along the radii of cylindrical cement paste samples to characterize the progress of the chemical changes associated with sulfate attack on the cement. Phase distributions were acquired to depths of ∼4 mm below the specimen surface with sufficient spatial resolution to discern features less than 200 µm thick. The experimental and data analysis methods employed to obtain quantitative composition profiles are described. The spatial resolution that could be achieved is illustrated using data obtained from copper cylinders with a thin zinc coating. The measurements demonstrate that this approach is useful for nondestructively visualizing the sometimes complex transformations that take place during sulfate attack on cement-based materials. These transformations can be spatially related to microstructure as seen by computed microtomography.
Genomic profiling of intrahepatic cholangiocarcinoma: Refining prognostic determinants and identifying therapeutic targets. (2014)

210 Background: The molecular alterations that drive tumorigenesis in intrahepatic cholangiocarcinoma (ICC) remain poorly defined. We sought to define the incidence and prognostic significance of mutations associated with ICC among patients undergoing surgical resection. Methods: 138 patients who underwent resection at 6 centers in the United States and Europe were included in the cohort. Mutational profiling was performed using nucleic acids that were extracted from resected ICC tumor specimens; mutations were identified using a multiplexed mutational profiling platform. The frequency of mutations was ascertained and the impact on outcome determined. Results: Most patients had a solitary tumor (82%) and median tumor size was 6.0cm. Most patients had R0 resection (89%); 19% patients had N1 disease, while 15% had microscopic vascular invasion. A minority received adjuvant therapy (30%). The majority (55%) of patients had no genetic mutation identified. Among the 62 (45%) patients with a genetic mutation, only a small number of gene mutations were identified with a frequency of &gt;5%: IDH1 (17.4%), KRAS (8.7%), BRAF (5.8%), PIK3CA (5.1%). In contrast, other genetic mutations were identified in very low frequency: IDH2 (3.6%), NRAS (3.6%), TP53 (2.2%), MAP2K1 (1.5%), CTNNB1 (0.7%), and PTEN (0.7%). Approximately 7% of IDH1-mutant tumors were associated with a concurrent PIK3CA gene mutation, and to a much lower extent, a mutation in MAP2K1 (2%). No concurrent mutations in IDH1 and KRAS were noted. Compared with ICC tumors that had no identified mutation, IDH1-mutant tumors were more often bilateral (OR 3.46), while KRAS-mutant tumors were more likely to be associated with perineural invasion (OR 5.72)(both P&lt;0.05). While clinicopathological features such as tumor number and nodal status were associated with survival, no specific mutation was associated with prognosis. Conclusions: Most patients with resected ICC had no somatic mutation identified on multiplexed mutational profiling. IDH1 and KRAS were the most common mutations noted. While certain mutations were associated with ICC clinicopathological features, mutational status did not seemingly impact long-term prognosis.
Space and Time in the Nucleus: Developmental Control of Replication Timing and Chromosome Architecture (2010)

All eukaryotic cells replicate segments of their genomes in a defined temporal sequence. In multicellular organisms, at least half of the genome is subject to changes in this temporal sequence during development. We now know that this temporal sequence and its developmentally regulated changes are conserved across distantly related species, suggesting that it either represents or reflects something biologically important. However, both the mechanism and the significance of this program remain unknown. We recently demonstrated a remarkably strong genome-wide correlation between replication timing and chromatin interaction maps, stronger than any other chromosomal property analyzed to date, indicating that sequences localized close to one another replicate at similar times. This provides molecular confirmation of long-standing cytogenetic evidence for spatial compartmentalization of early- and late-replicating DNA and supports our earlier model that replication timing is reestablished in each G(1) phase, coincident with the anchorage of chromosomal segments at specific locations within the nucleus (timing decision point [TDP]). Here, we review the evidence linking the replication program to the three-dimensional architecture of chromatin in the nucleus and discuss what such a link might mean for the mechanism and significance of a developmentally regulated replication program.
POSTHARVEST RIPENING BEHAVIOR OF NINE THAI MANGO CULTIVARS AND THEIR SUITABILITY FOR INDUSTRIAL APPLICATIONS (2004)

Postharvest ripening behavior and physical, chemical and nutritional properties of Thai mango cultivars were comprehensively characterized. Nine cultivars were harvested at mature green ripe stage and daily analyzed during postharvest ripening for pH, total soluble solids (TSS), titratable acidity (TA), color and firmness of mesocarp as well as color of peel. In fully ripe fruits, contents of β-carotene (provitamin A), pectin, fiber and total phenols were also considered. For individual characterization of the ripening behavior of the cultivars, quality parameters of the ripening fruits were related to each other, thus eliminating extrinsic effects on ripening kinetics. Acidity decreased with rising TSS/TA ratio following a power law relationship independent of cultivar. Decreasing mesocarp firmness and hue angle of flesh may be correlated with increasing TSS/TA ratio by analogy, but power law parameters were dependent on cultivar. From the ripening kinetics and the quality profile of fully ripe fruits, suitable processing applications could be deduced for each cultivar, such as for puree and nectar production requiring soft fruits at low TSS/TA ratio, accompanied by intense yellow-orange flesh color. Furthermore, provitamin A potential and susceptibility to enzymatic browning of the cultivars were discussed in this study.
On the Cost and Benefits of Building a High-Quality Institutional Repository (2009)

Much has been written about the difficulties of getting staff and students to contribute to an Institutional Repository (IR). The most difficult objections of staff to deal with are lack of time, and uncer-tainty about the benefits. We report on the measures that we have taken when building an IR to address those objections, indicating which were successful and which failed. We then propose a set of parameters to capture the quality, cost, and benefits of maintaining an IR in a quantitative manner, using the parameters to compare three IR. Our proposal is a first step towards a more objective ap-proach towards evaluating IR. 1.
Mass Transfer in Biology and Medicine (2009)

This overview of diffusion and separation processes brings unsurpassed, engaging clarity to this complex topic. Diffusion is a key part of the undergraduate chemical engineering curriculum and at the core of understanding chemical purification and reaction engineering. This spontaneous mixing process is also central to our daily lives, with importance in phenomena as diverse as the dispersal of pollutants to digestion in the small intestine. For students, Diffusion goes from the basics of mass transfer and diffusion itself, with strong support through worked examples and a range of student questions. It also takes the reader right through to the cutting edge of our understanding, and the new examples in this third edition will appeal to professional scientists and engineers. Retaining the trademark enthusiastic style, the broad coverage now extends to biology and medicine.
Aromatische Borheterocyclen: Erzeugung von 1 H -Borepin und Struktur von Tricarbonyl(1-phenylborepin)molybdÄn Diese Arbeit wurde von der Research Corporation und dem Petroleum Research Fund der American Chemical Society gefÖrdert. Professor William von E. Doering zum 75. Geburtstag gewidmet (1992)

No Abstract.
High-Resolution Mining of SARS-CoV-2 Main Protease Conformational Space: Supercomputer-Driven Unsupervised Adaptive Sampling (2020)

We provide a new unsupervised adaptive sampling strategy capable of producing microsecondtimescale molecular dynamics (MD) simulations using many-body polarizable force fields (PFF) on modern supercomputers. The global exploration problem is decomposed into a set of separate MD trajectories that can be restarted within an iterative/selective process to achieve sufficient phase-space sampling within large biosystems, while accurate statistical properties can be obtained through debiasing. With this pleasingly parallel setup, the Tinker-HP package can be powered by an arbitrary large number of GPUs (Graphics Processing Unit) cards available on pre-exascale supercomputers, reducing to days explorations that would have taken years. We applied the approach to the urgent problem of the modeling of the SARS–CoV–2 Main protease (Mpro) dimer. A 15.14 microsecond high-resolution all-atom simulation (AMOEBA PFF) of its apo state is provided and compared to other available long-timescale non-PFF data. Noticeable differences are found between clustering analysis of the simulations, the AMOEBA adaptive results exhibiting a richer conformational space. Overall, our high-resolution AMOEBA structural analysis captures key experimental observations concerning the stability of the oxyanion hole, a marker of activity through the stability of different stacking and salt bridge interactions. A dissymmetry is found between the enzyme protomers that exhibit different volumes. One of them appears fully inactive while the other is "activable", exhibiting some partial activity features. This activity evaluation can be further traced back to the large flexibility of the C terminal domain, fully captured by AMOEBA but not seen in X-rays due to insufficient electron densities related to the domain high mobility. The C–terminal region of the fully inactive protomer is shown to oscillate between several states, one of them interacting with the other protomer active site, therefore potentially modulating down its activity. Overall, these results reinforce the experimental hypothesis of a full inactivation of the apo state and clearly capture the asymmetric nature of protomers. Additional analysis show that the cavities volumes of the active and distal sites are found to be larger in the most active protomer with AMOEBA. To a larger extend, the PFF finds significantly larger cavities than those obtained with classical, non-polarizable simulations. The consequences on druggability are discussed as additional potential druggable cryptic pockets are found. All data produced within this research are fully accessible to the community for further analysis.
Front Cover: The Wild‐Type tRNA Adenosine Deaminase Enzyme TadA Is Capable of Sequence‐Specific DNA Base Editing (ChemBioChem 16/2023) (2023)

The directed evolution of the adenosine deaminase enzyme TadA from an RNA-editing enzyme to an efficient DNA-editing enzyme was crucial for the development of the adenine base editor (ABE). Previous experiments showed no detectable DNA-editing activity by an ABE utilizing wild-type TadA (ABE0.1), but here we show ABE0.1 is able to edit DNA strictly within TACG motifs. This sequence requirement is partially governed by the C-terminal α5 helix of TadA, which accumulated many mutations during the directed evolution of TadA. The evolution of TadA to better access adenines within a diverse range of sequences is reflective of the Galapagos finches, which evolved different beak shapes in order to better access the food that was available to them. This cover art shows the protein structures of ecTadA (PDB: 1Z3A) and the evolved TadA8e (PDB: 6VCA), along with two species of Galapagos finches using the different α5 helix structures to access a target adenine within different sequence contexts. More information can be found in the Research Article by A. C. Komor et al.
Comparative Histopathology of Grey‐Horse‐Melanoma and Human Malignant Melanoma (2004)

Equine melanoma shows striking features particularly with regard to clinical development in grey horses: in contrast to malignant melanoma in humans and in solid coloured horses that are characterized by early onset of metastasis, pigment cell tumours display almost benign clinical features in ageing grey horses. Through evolution, grey horses appear to be in a favourable position in regard to the biological behaviour of melanomas. Yet unknown factors inhibiting or retarding early melanoma metastasis may be responsible for this phenomenon. In this study, immunostaining profiles and histopathologic patterns of equine vs. human melanotic tumours were compared. In addition, the expression of melanoma markers currently used in human melanoma detection and characterization were evaluated for their applicability in equine melanoma diagnosis. Immunohistopathologic investigations revealed that benign grey horse melanomas share common features with human blue nevi and with human malignant desmoplastic melanomas, whereas their resemblance to other types of human cutaneous malignant melanomas is less pronounced. Our data equally underline that S-100, proliferating cell nuclear antigen (PCNA), HMB-45, Ki-67, T-311 and CD44 can serve as reliable markers for horse melanomas. Further investigations aiming at identifying factors retarding metastasis in affected grey horses are needed, as they may contribute to the development of novel treatment strategies for human malignant melanoma.
Feasibility of magnetic resonance imaging-only rectum radiotherapy with a commercial synthetic computed tomography generation solution (2018)

Accurate MR-based dose calculations using a commercial sCT generation method were clinically feasible for treatment of rectal cancer patients. The accuracy of position verification was clinically acceptable. However, before clinical implementation future investigations will be performed to determine the origin of the systematic shift.
Protection against two spontaneous mouse leukemias conferred by immunogenic variants obtained by mutagenesis. (1983)

Two spontaneous mouse leukemias were adapted to culture. In agreement with most reported observations on spontaneous tumors, injection of irradiated cells of the malignant culture cell lines failed to protect mice against these leukemias. These cell lines were treated in vitro with the mutagen N-methyl-N'-nitro-N-nitrosoguanidine and stable immunogenic variants (tum-) were obtained, that failed to form progressive tumors in syngeneic CBA/Ht mice. Mice that had rejected tum- variants showed a significant degree of resistance to challenge not only with the original malignant cell line but also with the original transplantable tumor. No protection was observed against syngeneic tumor cells other than those of the parental tumor. These results indicate that these two spontaneous leukemias carry a specific transplantation antigen that can be the target of a rejection response by syngeneic mice. In confirmation of this, we found that lymphocytes of CBA/Ht mice that had rejected tum- variants could be restimulated in vitro so as to develop a cytolytic activity directed against an antigen that was specific for the original tumor cell line.
Low-stress nitride as oxidation mask for submicrometreLOCOS isolation (1995)

A large reduction in the LOCOS bird&apos;s beak is obtained by using a thick silicon nitride layer as an oxidation mask. Stress induced damage of the devices is avoided by using low-stress silicon-rich nitride.
Preliminary results of a phase I study of external beam radiation therapy (EBRT), oxaliplatin (OX), bevacizumab (BV), and capecitabine (CAP) for locally advanced or metastatic adenocarcinoma of the rectum (2006)

3543 Background: BV, a monoclonal antibody against vascular endothelial growth factor, increases survival when added to first and second line chemotherapy for metastatic colorectal cancer. Preclinical studies suggest BV may enhance tumoral radiation sensitivity. Preliminary studies of OX and 5-FU based chemoradiation therapy for rectal cancer have suggested improved pathologic CR rates compared to 5-FU/ radiation alone. CAP allows fluoropyrimidine treatment without the inconvenience of an infusion pump. We investigated CAP + BV + OX + EBRT for pts with rectal cancer to evaluate for the MTD and preliminary efficacy results. Methods: Pts with adenocarcinoma of the rectum and no prior pelvic irradiation received 5040 cGy EBRT (180 cGy/fx), CAP (625–825 mg/m 2 PO BID on EBRT days), BEV (15 mg/kg d1 and 10 mg/kg d8 and d22), and OX (50–75 mg/m 2 /week during radiation, weeks 1–5) in dose-escalating fashion. DLT was defined as any grade 3 heme tox ≥ 7d, grade 4 heme tox, grade 4 non-heme tox during chemoradiation, or inability to deliver &gt;85% of planned treatment. Pts eligible for surgical resection could have surgery 6–8 wks after treatment completion. After recovery from surgery, patients could be treated with CAP, BV, and OX. Results: 11 patients (5 men/6 women) have been enrolled. All have completed chemoradiation and resection. At dose level 1 (CAP 625 mg/m 2 BID, OX 50mg/m 2 ) there were no DLT’s in 3 pts. 1/3 pts had G3 subarachnoid hemorrhage during adjuvant chemotherapy. At dose level 2 (CAP 825 mg/m 2 , OX 50 mg/m 2 ) 2/2 pts had DLT (1 G4 diarrhea; 1 G2 rectal pain, causing treatment hold for study-defined DLT). 6 more pts were treated at dose level 1. 1pt had DLT of G3 diarrhea. G2 toxicities included diarrhea (3/11), fatigue (2/11), skin changes (2/11), and pain (2/11). 9/11 patients were downstaged. 2/11 patients had pCR at surgery and 2/11 microscopic disease only. Conclusions: CAP + BEV + OX + EBRT is a well-tolerated, active regimen for the treatment of rectal cancer. MTD was determined to be CAP 625 mg/m 2 BID + BEV 15 mg/kg d1 + 10 mg/kg d 8 and 22 + OX 50 mg/m 2 /week. Further study of efficacy at the MTD is warranted. [Table: see text]
ChemInform Abstract: Studies on the Synthesis of S5′,6‐Methano‐5′‐thiouridines. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Arachidonic acid increases MCF‐10A and MCF‐10CA1 motility dependent on PPAR‐gamma (2008)

Recently, a high‐fat Western diet has been linked to an increase breast cancer risk. This high‐fat diet has an increased of omega‐6 (ω–6) poly‐unsaturated fatty acids (PUFAs) compared to omega‐3 (ω–3) PUFAs. We are investigating the role of one such ω‐6 PUFA, arachidonic acid (ArA), in breast cancer cell motility. ArA has been shown to be involved in increased cell motility and survival. Interestingly, ArA has also been shown to activate peroxisome‐proliferator activated receptor‐gamma (PPAR‐γ), a protein involved in adipocyte differentiation and plasminogen activator (PA) system regulation. We used two cell lines, MCF‐10CA1, an invasive carcinoma line and normal breast epithelial line, MCF‐10As, cells to study the effects of ArA. Chemotaxis to epidermal growth factor (EGF) was greatly increased in MCF‐10CA1 cells compared to the normal MCF‐10As. Arachidonic acid treatment increased chemotaxis in both cell lines about 2‐fold. Treatment with ArA increased uPA activity MCF‐10A cells, with a less dramatic increase in MCF‐10CA1 cells. To determine if ArA was acting on PPAR‐γ, we pretreated the cells with GW9662, a PPAR‐γ antagonist, and saw the ArA mediated increase in motility was abolished in both cell lines. This data suggests ArA increases cellular motility of normal and malignant cells through alterations in PA system components, through a PPAR‐γ dependent mechanism.
Estudo de compósitos magnéticos moles de ferro recoberto por suspensão de nanopartículas de alumina em vidro líquido (2017)

Tese (doutorado) - Universidade Federal de Santa Catarina, Centro Tecnológico, Programa de Pós-Graduação em Ciência e Engenharia de Materiais, Florianópolis, 2017.
Long-Lived Venus Lander Conceptual Design: How to Keep It Cool (2009)

Surprisingly little is known about Venus, our neighboring sister planet in the solar system, due to the challenges of operating in its extremely hot, corrosive, and dense environment. For example, after over two dozen missions to the planet, the longest-lived lander was the Soviet Venera 13, and it only survived two hours on the surface. Several conceptual Venus mission studies have been formulated in the past two decades proposing lander architectures that potentially extend lander lifetime. Most recently, the Venus Science and Technology Definition Team (STDT) was commissioned by NASA to study a Venus Flagship Mission potentially launching in the 2020- 2025 time-frame; the reference lander of this study is designed to survive for only a few hours more than Venera 13 launched back in 1981! Since Cytherean mission planners lack a viable approach to a long-lived surface architecture, specific scientific objectives outlined in the National Science Foundation Decadal Survey and Venus Exploration Advisory Group final report cannot be completed. These include: mapping the mineralogy and composition of the surface on a planetary scale determining the age of various rock samples on Venus, searching for evidence of changes in interior dynamics (seismometry) and its impact on climate and many other key observations that benefit with time scales of at least a full Venus day (Le. daylight/night cycle). This report reviews those studies and recommends a hybrid lander architecture that can survive for at least one Venus day (243 Earth days) by incorporating selective Stirling multi-stage active cooling and hybrid thermoacoustic power.