gebhart/patrepeval huggingface dataset:
Genome‐wide analysis of longevity in nutrient‐deprived Saccharomyces cerevisiae reveals importance of recycling in maintaining cell viability (2012)

Although typically cosseted in the laboratory with constant temperatures and plentiful nutrients, microbes are frequently exposed to much more stressful conditions in their natural environments where survival and competitive fitness depend upon both growth rate when conditions are favourable and on persistence in a viable and recoverable state when they are not. In order to determine the role of genetic heterogeneity in environmental fitness we present a novel approach that combines the power of fluorescence-activated cell sorting with barcode microarray analysis and apply this to determining the importance of every gene in the Saccharomyces cerevisiae genome in a high-throughput, genome-wide fitness screen. We have grown > 6000 heterozygous mutants together and exposed them to a starvation stress before using fluorescence-activated cell sorting to identify and isolate those individual cells that have not survived the stress applied. Barcode array analysis of the sorted and total populations reveals the importance of cellular recycling mechanisms (autophagy, pexophagy and ribosome breakdown) in maintaining cell viability during starvation and provides compelling evidence for an important role for fatty acid degradation in maintaining viability. In addition, we have developed a semi-batch fermentor system that is a more realistic model of environmental fitness than either batch or chemostat culture. Barcode array analysis revealed that arginine biosynthesis was important for fitness in semi-batch culture and modelling of this regime showed that rapid emergence from lag phase led to greatly increased fitness. One hundred and twenty-five strains with deletions in unclassified proteins were identified as being over-represented in the sorted fraction, while 27 unclassified proteins caused a haploinsufficient phenotype in semi-batch culture. These methods thus provide a screen to identifying other genes and pathways that have a role in maintaining cell viability.
Optimisation of the Production of VLP’s in 2 Lt Stirred Bioreactors (2006)

In this work the production of virus like particles (VLP’s) in insect cells was optimised for 2 Lt bioreactors. For this purpose the effects of pO2 and hydrodynamic conditions on product quality were evaluated. Although the pO2 did not show a significant effect upon cell growth in the range from 10 to 50%, cell infection and specific productivity were dramatically affected. The production was optimal at a pO2 of 25% and decreased up to two fold when the pO2 decreases to 10 or increases to 50%. The highest VLP titre was obtained at 96 hours post infection (hpi) and at pO2 of 25%. The effect of overcritical conditions upon productivity was also studied: cell infection is affected by agitation rates above 270 rpm or by aeration rates higher than 0.04 vvm, with a three fold decrease in VLP titre.
Versuche zur Stereochemie der im Pyrrolidinring Substituierten Tropanderivate (1957)

Abstract Im Rahmen weiterer Versuche zur Stereochemie von Teloidinon und seinen Derivaten wurde das Alkaloid Meteloidin in Scopolin umgewandelt. Aus dieser experimentellen Verknüpfung der Alkaloide Meteloidin und Scopolamin über Scopolin, die zugleich eine Totalsynthese des Scopolins darstellt, ergibt sich der räumliche Bau von Meteloidin. Das von K. Zeile und A. Heusner synthetisierte 6‐Hydroxy‐7‐methoxy‐tropinon hat sich sterisch als Monomethyläther des Teloidinons erwiesen.
Present and Future CCDs for UV and X-Ray Scientlfic Measurements (1985)

Significant advances in CCD performance are reported. Specifically, interacting quantum efficiency of ⩾ 50% is demonstrated throughout the spectral range of 600-9,000 Å, with comparable sensitivity expected to continue to wavelengths as short as a few Angstroms. Non-dispersive X-ray spectra, throughout the 250-8000 eV range, have been obtained with an FWHM spectral resolution of 200-250 eV. At present, both spatial and spectral resolution is limited, at some energies, by the diffusion of photo-generated charge into more than one picture element. A detailed model of this diffusion is described and evaluated on the basis of measured performance.
Emergence of hierarchical structural complexities in nanoparticles and their assembly (2016)

We demonstrate that nanoparticle self-assembly can reach the same level of hierarchy, complexity, and accuracy as biomolecules. The precise assembly structures of gold nanoparticles (246 gold core atoms with 80 p-methylbenzenethiolate surface ligands) at the atomic, molecular, and nanoscale levels were determined from x-ray diffraction studies. We identified the driving forces and rules that guide the multiscale assembly behavior. The protecting ligands self-organize into rotational and parallel patterns on the nanoparticle surface via C-H⋅⋅⋅π interaction, and the symmetry and density of surface patterns dictate directional packing of nanoparticles into crystals with orientational, rotational, and translational orders. Through hierarchical interactions and symmetry matching, the simple building blocks evolve into complex structures, representing an emergent phenomenon in the nanoparticle system.
Suppression of beta 2 microglobulin by pentoxiphylline therapy in asymptomatic HIV infected individuals. (2001)

Pentoxiphylline, an inhibitor of tumor necrosis factor-alpha (TNF-alpha) has been used in the treatment of human immunodeficiency virus (HIV) infection. The inhibition of TNF-alpha results in decreased immune activation. Beta 2 microglobulin (beta 2 M) has been used as a surrogate marker to study the progression of HIV infection. The objective of this study was to see if use of pentoxiphylline resulted in any decline in beta 2 M levels. Twenty patients with HIV infection who were free of opportunistic infections at the time of inclusion in the study and 18 age and sex matched controls were studied. beta 2 M was measured using an enzyme immunoassay before and four weeks after the start of treatment with pentoxiphylline. Mean levels of beta 2 M before therapy were 1.51 +/- 0.77 mg/l (range 0.78-3.8 mg/l) and were significantly higher (P < 0.001) than the levels among controls [0.72 +/- 0.06 mg/l (range 0.46-0.88 mg/l)]. beta 2 M levels in patients declined to 0.85 +/- 0.22 mg/l (range 0.72-1.0 mg/l) after four weeks of therapy and this was statistically significant (P < 0.001). Use of pentoxiphylline for four weeks results in a significant decline in the levels of beta 2 M suggesting that the level of immune activation is reduced with the therapy.
Development of One Period of a Three-Dimensional Photonic Crystal in the 5-0 µm Wavelength Region by Wafer Fusion and Laser Beam Diffraction Pattern Observation Techniques (1998)

Due to a printing error, the title was incorrect. The title should read "Development of One Period of a Three-Dimensional Photonic Crystal in the 5-10 µm Wavelength Region by Wafer Fusion and Laser Beam Diffraction Pattern Observation Techniques"
Gonadal Activity in Male and Female Captive Fossas (Cryptoprocta ferox) During the Mating Season (2009)

The fossa is an endangered, mongoose-like carnivore species endemic to Madagascar with a breeding season (BS) in the southern hemisphere spring. For the present study, faecal samples of captive fossas were collected for over 1 year for five males and four non-pregnant females, and for two pregnant animals during the reproductive period. The goal was to assess gonadal activity using non-invasive hormone measurements of faecal testosterone (T) and gestagen metabolites using assays previously established in our laboratory and further validated in this study. All study animals were housed in northern hemisphere zoos. In males, the seasonal T metabolite profile revealed a peak in spring (March). High performance liquid chromatography (HPLC) analysis was used to characterize the faecal hormone metabolite composition. The highest immunoreactivity was detected in the position of dihydrotestosterone, whereas native T was not detected. In the two pregnant females, gestagen metabolite concentrations increased 4-9 days after the initial matings and remained elevated throughout gestation with concentrations dramatically higher than those of the non-pregnant females during the BS. In these females, gestagen metabolite analyses did not reveal a seasonal pattern similar to the males. The HPLC-analysis revealed that the major proportion of immunoreactivity was associated with an unknown metabolite, whereas native progesterone was undetectable. The seasonal hormone pattern of male fossas gives proof of the reproductive seasonality of this species. The elevated 5alpha-pregnan-3beta-ol-20-one levels in pregnant animals allows for the characterization of pregnancy in the fossa based on analysis of faecal steroid metabolite concentrations.
Culture time of vitrified/warmed zygotes before microinjection affects the production efficiency of CRISPR-Cas9-mediated knock-in mice (2017)

Robust reproductive engineering techniques are required for the efficient and rapid production of genetically modified mice. We have reported the efficient production of genome-edited mice using reproductive engineering techniques, such as ultra-superovulation, <i>in vitro</i> fertilization (IVF) and vitrification/warming of zygotes. We usually use vitrified/warmed fertilized oocytes created by IVF for microinjection because of work efficiency and flexible scheduling. Here, we investigated whether the culture time of zygotes before microinjection influences the efficiency of producing knock-in mice. Knock-in mice were generated using clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system and single-stranded oligodeoxynucleotide (ssODN) or PITCh (Precise Integration into Target Chromosome) system, a method of integrating a donor vector assisted by microhomology-mediated end-joining. The cryopreserved fertilized oocytes were warmed, cultured for several hours and microinjected at different timings. Microinjection was performed with Cas9 protein, guide RNA(s), and an ssODN or PITCh donor plasmid for the ssODN knock-in and the PITCh knock-in, respectively. Different production efficiencies of knock-in mice were observed by changing the timing of microinjection. Our study provides useful information for the CRISPR-Cas9-based generation of knock-in mice.
Grundlagen von Datenbanksystemen (2005)

Das in der dritten und stark uberarbeiteten Auflage vorliegende Buch zahlt zu den international renommiertesten und bewahrtesten Lehrbuchern zum Thema Datenbanken. Der im Originalbuch behandelte Stoff geht weit uber den Rahmen einer einfuhrenden Vorlesung hinaus und behandelt auch fortgeschrittene Themen und Fragestellungen. Diese im Vergleich zum Original gekurzte und an die hiesige Lehre angepasste Bachelorausgabe stellt unterschiedliche Datenmodelle und Datenbanksprachen vor und behandelt die fur jeden Studenten wichtigen Grundlagen des Datenbankentwurfs.Zudem befassen sich die Autoren mit verschiedenen praxisrelevanten Aspekten des Mehrnutzerbetriebs. Alle Themenbereiche werden grundlich vertieft und so umfassend dargestellt, dass das Buch als Vorlesungsgrundlage ebenso geeignet ist wie zum spateren Nachschlagen und zum Selbststudium. Wiederholungsfragen und Ubungsaufgaben zu jedem Kapitel erleichtern die Uberprufung des Lernerfolgs. Die Losungen zu den Aufgaben und zusatzliche Kapitel der Originalubersetzung zu weiterfuhrenden Themen stehen auf der Companion Website zum Buch zur Verfugung. Hier finden Sie Downloads zu diesem Titel.
Effect of initial-learning dataset on etching profile optimization using machine learning in plasma etching (2023)

Abstract Machine learning (ML) was applied to optimize the etching profile for a line and space pattern sample in plasma etching. To investigate the effect of different initial-learning datasets on the optimization of the etching profile, high-, medium-, and low-quality datasets were prepared. The high-quality dataset was composed of etching results relatively close to a target etching profile. The low-quality dataset was composed of etching results relatively far from the target etching profile. The medium-quality dataset was intermediate between the high- and low-quality datasets. For the ML, the kernel ridge regression method was used. After six learning cycles, better etching results were obtained from the medium- and low-quality datasets than from the whole initial-learning dataset. However, the etching results from the high-quality dataset did not exceed those from the whole initial-learning dataset. These results indicate that an initial-learning dataset that has etching results far from the target profile can be useful for optimizing etching profiles.
Investment in a natural gas economy: The future of the Marcellus Shale and Southwestern Pennsylvania (2011)

The Marcellus Shale Formation is the largest natural gas play within the United States. Spanning along the Appalachian basin, the Marcellus reaches from New York State to Virginia. Given advances in drilling technology, the Marcellus Shale is now situated as one of the most promising known domestic natural resource endowments. The Marcellus Systems Synthesis Project Team (MSSPT) examines how Southwestern Pennsylvania (SWPA) can position itself to develop regional energy generating capacity through investment in natural gas fired power plants (NGFPP). The Project Team has developed a framework for evaluating this investment decision via an assessment of key impact areas and key stakeholders involved in the investment process. This framework is the result of a review of scholarly literature along with recent news publications to develop an accurate characterization of the current state of operations within Marcellus Shale. Building off of this framework, a network matrix has been created to demonstrate how regional actors align around different impact areas. Mapping out a network matrix allows for a better understanding of the subsequent results from an initiative to expand the use of NGFPPs.
Synthesis of new aza- and thia-crown ethers and their metal ion templates synthesis as model case study (2014)

Four new thia-and four new aza-crown ethers were synthesized using the reaction of ethylene glycols ditosylated with 1,1-(2,2-dihydroxynaphthyl)sulfide (DNS) and 2,6-bis(3hydroxyphenyl)-4-phenylpyridine in acetonitrile as solvent in the presence of bases (LiOH, NaOH, KOH and Cs2CO3). In the synthesis of macrocycles based on DNS, the template effects of alkaline metal ions; Li + , Na + , K + and Cs + on the reaction yields were investigated. Sodium template generally was more effective for the synthesis of all four macrocycles. Relatively, good yields of 15-and 18-membered macrocycles were obtained in the presence of all kinds of applied cations. K + Cation was more effective template ion than Na + in the formation of 18-membered macrocycles due to their larger cavity size compared to the 15-membered cycles. The structures of macrocycles were confirmed by CHN/O analysis, IR, 1 H NMR, 13 C NMR and mass spectrometry.
A schema-based approach to building a bioinformatics database federation (2002)

Developments in our ability to integrate and analyse the data held in existing heterogeneous data resources can lead to an increase in our understanding of biological function at all levels. However, supporting ad-hoc queries across multiple data resources and correlating the data retrieved from these is still difficult. To address this, we are building a mediator based on the functional data model database, P/FDM, which integrates access to heterogeneous, distributed biological databases, while making use of existing search engines and indexes, without infringing on the autonomy of the underlying databases. Central to our design philosophy is the use of schemas. We have adopted a federated architecture with a five-level schema, arising from the use of the ANSI-SPARC three-level schema to describe both the existing autonomous data resources and the mediator itself. We describe the use of mapping functions and list comprehensions in query splitting, producing execution plans, code generation and result fusion. We give an example of cross-database querying involving data held locally in P/FDM systems and external data in the Sequence Retrieval System (SRS).
Effects of intermolecular interactions on the stability of carbon nanotube&ndash;gold nanoparticle conjugates in solution (2016)

This work deals with the role of intermolecular interactions in the stability of a carbon nanotube (CNT) capped by functionalized gold nanoparticles (AuNPs). The importance of such a system is due to its potential application as a pH-controlled drug carrier. Our preliminary experimental studies showed that fabrication of such a nanobottle/nanocontainer is feasible and it is possible to encapsulate the anticancer drug cisplatin inside the inner space of a CNT and seal its ends by functionalized AuNPs. The expected behavior, that is, detachment of AuNPs at acidic pH and the release of cisplatin, was, however, not observed. On the other hand, our theoretical studies of chemically identical system led to the conclusion that the release of cisplatin at acidic pH should be observed. Therefore, in this work, a deeper theoretical analysis of various factors that could be responsible for the disagreement between experimental and theoretical results were performed. The study found that the major factor is a large dispersion interaction component acting between CNT and AuNP in solution in the case of the experimental system. This factor can be controlled to some extent by tuning the system size or the ratio between AuNP diameter and CNT diameter. Thus, such kind of a pH-sensitive drug carrier is still of great interest, but its structural parameters need to be properly adjusted.
Smectic Liquid Crystals from Supramolecular Guanidinium Alkanesulfonates (2005)

The thermotropic polymorphism of a series of guanidinium alkanesulfonates (6 < or = n < or = 18) was investigated by optical microscopy and differential scanning calorimetry. Hydrogen bonding was analyzed by infrared spectroscopy. Molecular volumes were measured by dilatometry. The structure of the crystal, smectic A, and ordered smectic phases observed were studied by X-ray diffraction and utilized to prove that the supramolecular arrangement of the molecules in the crystal survives in the smectic phases at high temperature.
Effects of high pressure on colour and texture of fish (2000)

Abstract The effect of high pressure on the colour of fish species was investigated to evaluate the range of high pressure treatments that did not influence the appearance of the fish. High pressure treatments during 5 minutes higher than 150-200MPa resulted in a cooked appearance of pollack (Pollachius virens), mackerel (Scomber scombrus), tuna (Thunnus thynnus), cod (Gadus morhua), salmon trout (Salmon trutta), carp (Cyprinus carpio), plaice (Pleuronectus platessa) and anglerfish (Lophius piscatorius). Only octopus (Octopus vulgaris) retained a raw appearance till 400-800MPa. The influence of high pressure on the texture of cod (Gadus morhua) was evaluated after frozen storage up to 6 months. The hardness increased as a result of high pressure processing at 200 and 400 MPa. During storage only minor changes of the hardness occurred. Even the non-pressurised sample showed only a small increase in the hardness during storage.
Overproduction of the free radical of ribonucleotide reductase in hydroxyurea-resistant mouse fibroblast 3T6 cells. (1981)

Hydroxyurea inhibits the activity of ribonucleotide reductase (ribonucleoside-diphosphate reductase; 2'-deoxy-ribonucleoside-diphosphate:oxidized-thioredoxin 2'-oxidoreductase, EC 1.17.4.1) in bacteria and mammalian cells. The reductase from Escherichia coli consists of two nonidentical subunits (B1 and B2) and hydroxyurea acts by specifically destroying a tyrosine free radical of B2 required for enzyme activity. The mammalian enzyme also consists of two nonidentical subunits (M1 and M2), only one of which (M1) has been obtained in pure form. By continuous culture at stepwise increasing drug concentrations, we have now obtained a 3T6 mouse fibroblast cell line with a 100-fold increased resistance to hydroxyurea. Extracts from resistant cells showed a 3- to 15-fold increase in reductase activity. The amount of M1 protein was not increased. The amount of M2 protein could not be measured directly, but the M2 activity in extracts from resistant cells (but not normal cells) showed an EPR spectrum very similar to that of the tyrosine radical of the bacterial B2 subunit. We propose that resistance to hydroxyurea is caused either by overproduction of the complete M2 subunit or by increased generation of the tyrosine radical within the M2 protein. It seems that either alternative mirrors a possible normal regulatory mechanism for the activity of the reductase.
Advanced Nano-analysis of High-k Dielectric Stacks (2006)

Analytical electron microscopy techniques are used to investigate elemental distributions across high-k dielectric stacks with metal gates. Electron energy loss spectroscopy results from Si(100)/SiO2/HfO2/TiN and Si (100)/SiO2/HfO2/TiN/poly-Si gate stacks show evidence of interface reactions having occurred at the TiN/poly-Si interface and possibly at the HfO2/TiN interfaces. As such, this technique offers unique capabilities to further improve understanding of the work function behavior of metal gate electrode/dielectric stacks to be used in future CMOS technologies.
Shape Descriptor Based Document Image Indexing and Symbol Recognition (2009)

In this paper we present a novel shape descriptor based on shape context, which in combination with hierarchical distance based hashing is used for word and graphical pattern based document image indexing and retrieval. The shape descriptor represents the relative arrangement of points sampled on the boundary of the shape of object. We also demonstrate the applicability of the novel shape descriptor for classification of characters and symbols. For indexing, we provide anew formulation for distance based hierarchical locality sensitive hashing. Experiments have yielded promising results.
Paper #259: High Activity Level and Return to Sports Following Knee Osteotomy in Young Athletic Patients (2017)

Knee osteotomies in young patients resulted in 95% return to sports of which 60% could return to their pre-injury main sports, which included high-impact activities in 74%, suggesting that it might not be the realignment osteotomy that prevents returning to pre-injury levels of sport, but rather other reasons such as the disease state of the knee.
Rapid Hydrolysis of Penicillin Antibiotics Mediated by Adsorbed Zinc on Goethite Surfaces (2019)

The soil environment is an important sink for penicillin antibiotics released from animal manure and wastewater, but the mineral-catalyzed transformation of penicillins in soil has not been well studied. To simulate this environmental process, we systematically investigated the behavior of penicillin G and amoxicillin, the two most widely-used penicillin antibiotics, in the presence of goethite and metal ions. The results demonstrated that Zn ions significantly promoted the hydrolysis of penicillins in goethite suspensions, as evidenced by the degradation rate nearly 3 orders of magnitude higher than that of the non-Zn-containing control. The spectroscopic analysis indicated that the specific complexation between penicillins, adsorbed Zn, and goethite was responsible for the enhanced degradation. Metastable interactions, involving hydrogen bonds between carbonyl groups in the β-lactam ring and the double/triple hydroxyl groups on goethite surface, and coordination bonding between carboxyl groups and surface irons were proposed to stabilize the ternary reaction intermediates. Moreover, the surface zinc-hydroxide might act as powerful nucleophile to rapidly rupture the β-lactam ring in penicillins. This study is among the first to identify the synergic roles of Zn ion and goethite in facilitating penicillin degradation and provides insights into β-lactam antibiotics to assess their environmental risk in soil.