The Heartland of the Democracy: Presidential Politics in Oley Township, Berks County, Pennsylvania, 1860-64

Oley Township, founded in 1740, in Berks County, Pennsylvania holds a special place in the commonwealth\u27s history because of its unique religious, political, and cultural history. With hundreds of historic buildings and its Pennsylvania German heritage, the heart of the Oley Valley continues to attract colonial and Pennsylvania German historians from great distances so that they are able to analyze and research its rich heritage. Indeed, the area was designated as a National Historic District by the National Register of Historic Places in 1983 and much of the farmland has been preserved through land trusts and historical preservation efforts. Many of the original settler\u27s descendants remain in Berks County and a large number of them live on or near the valley farmsteads which their ancestors built in the eighteenth and nineteenth centuries. Unfortunately, scholars have largely overlooked Oley\u27s antebellum and Civil War history. Throughout that period, the township (and larger county) maintained a strong allegiance to the Democratic Party. Oley, part of the Gibraltar of the Democracy, steadfastly voted for Democratic presidential candidates throughout the nineteenth century, including Southern Democrat John C. Breckinridge in 1860 and Gen. George B. McClellan in 1864. While Pennsylvania moved toward the new Republican Party, Oley and Berks County did not. Oley provides important insight into Democratic Party politics in the North during the Civil War

Using CRISPR interference to study genes in Staphylococcus aureus important for interaction with udder microbiome bacteria

Staphylococcus aureus er et av de hyppigste årsakene til utvikling av bovin mastitt, som er en av de mest utfordrende sykdommene hos melkekyr på verdensbasis. Mastitt forårsaker problemer som redusert helsetilstand hos kyrene, kostnader til behandling, økt antibiotikabruk, tidligere slakting, reduksjon i melkeproduksjon, dårlig melkekvalitet, redusert produktkvalitet og matsvinn. For å redusere disse store økonomiske tapene i meieriindustrien må nye effektive metoder for forebygging og behandling av mastitt utvikles. En bedre innsikt i infeksjonsprosessen til mastittpatogener i juret kan bidra på veien til dette. I dette arbeidet ble gener i S. aureus som er viktige for interaksjon med andre bakterier i jurmikrobiotaen studert ved bruk av CRISPR interferens (CRISPRi). Ved CRISPRi kan gener nedreguleres og endring av bakteriens fitness som følge av nedreguleringen kan bestemmes. For å kunne studere dette, ble det her utviklet en metode for kokultivering av et S. aureus CRISPRi-genomskalabibliotek med jurmikrobiotabakterier, før et kokultiveringsforsøk og CRISPRi-sekvensering (CRISPRi-seq) ble utført. CRISPRi-systemet ble vist å være funksjonelt i UHT-melk, et vekstmedium som likner miljøet i jurmikrobiotaen, som var en forutsetning for å kunne utføre kokultiveringsforsøket. I den utviklede kokultiveringsmetoden ble S. aureus CRISPRi-biblioteket dyrket sammen med jurmikrobiotabakterien Streptococcus dysgalactiae med en 1:8 inokuleringsratio av bakteriene. Genfitnessanalyse fra CRISPRi-seq viste to gener som var mer essensielle under kokultiveringen med S. dysgalactiae sammenliknet med S. aureus dyrket alene (glnR og pyrG), og to mindre essensielle gener (htsA og fhuC). glnR og pyrG assosieres med biosyntese og omdannelse av glutamin mens htsA og fhuC assosieres med jernopptak. CRISPRi-seq av kokultiveringsforsøket viste få gener med signifikant forskjell i genfitness for S. aureus dyrket alene og dyrket med S. dysgalactiae, noe som kan skyldes lite interaksjon mellom bakteriene. Dette tyder på at metoden utviklet her kan forbedres ved å bedre legge til rette for interaksjoner i kokultiveringen i fremtiden. CRISPRi-seq er en screening metode og i fremtiden bør også disse resultatene valideres med for eksempel vekstforsøk med ‘knockout’ mutanter eller ved å undersøke individuelle CRISPRi-stammer med de mer og mindre essensielle genene nedregulert av sgRNA. Dette vil danne grunnlag for å videre forstå hvordan S. aureus påvirkes ved kokultivering med S. dysgalactiae.Staphylococcus aureus is a major cause of bovine mastitis, which is one of the most challenging diseases in dairy cows worldwide. Mastitis leads to issues like reduced animal health, treatment costs, increase in usage of antibiotics, early culling, reduced milk production, reduced milk quality, reduced product quality and spoilage. New and more efficient methods to prevent and treat mastitis needs to be developed to reduce these major economic losses in the dairy industry. A better insight of the infection process of mastitis pathogens in the udder can contribute to this goal. In this work, S. aureus genes important for interaction with other bacteria in the udder microbiota was studied with the use of CRISPR interference (CRISPRi). Genes can be downregulated with CRISPRi, and change in fitness of the bacteria due to this downregulation can be determined. To be able to study this, a method for cocultivation of a S. aureus CRISPRi genome wide library with udder microbiota bacteria was developed, before a cocultivation experiment and a CRISPRi sequencing (CRISPRi-seq) was performed. The CRISPRi system was shown to be functional in UHT-milk, a growth medium that resembles that of the udder, with was a prerequisite to conduct the cocultivation experiment. In the designed cocultivation method the S. aureus CRISPRi library was cultivated with the udder microbiota bacteria Streptococcus dysgalactiae with a 1:8 inoculum ratio of the bacteria. A gene fitness analysis from CRISPRi-seq showed two genes that was more essential under cocultivation with S. dysgalactiae compared to S. aureus grown alone (glnR og pyrG), and two less essential genes (htsA og fhuC). glnR og pyrG is associated with biosynthesis and conversion of glutamine, while htsA og fhuC is associated with iron uptake. CRISPRi-seq of the coculture experiment showed few genes with significant differences in gene fitness of S. aureus grown as a monoculture and grown with S. dysgalactiae, which can be due to little interaction between bacteria. This suggests that the designed method can be improved in the future by better facilitating for interactions in the coculture. CRISPRi-seq is a screening method and in the future the results also need to be verified with for instance growth assays with knockout mutants or by examining individual CRISPRi strains with the significantly essential or less essential genes downregulated by sgRNA. This will form the basis of further understanding of how S. aureus is affected by being cultivated with S. dysgalactiae.M-K

"gesund leben lernen" - Hebammen als Gesundheitscoach von Frauen. Ein Forschungsprozess der Annäherung

Das Forschungsinteresse dieser Dissertation ist auf das berufliche Feld von Hebammen in Deutschland in der Gegenwart gerichtet und fragt danach, wie der Sinn-Container „gesund leben lernen“ gefüllt und Lernprozesse, die damit in Verbindung stehen, gesehen werden. Es geht um Erkenntnisse zu feldspezifischen Sichtweisen und einen Forschungsprozess der Annäherung mit forschendem Lernen und in lernendem Forschen. Das Forschungsprojekt ist konzipiert als qualitativer Forschungsprozess mit empirischen Bausteinen. Als Materialien sind beispielhaft bereits vorhandene Textdokumente zum strukturellen Rahmen des Berufs von Hebammen und Familienhebammen sowie im Forschungsprojekt erzeugte Textdokumente aus Interviews mit Hebammen bzw. Familienhebammen und aus Interviews mit Supervisor_innen, die berufliche Erfahrung mit Supervisionsprozessen von Hebammen bzw. Familienhebammen haben, einbezogen worden. In jeweils separater Auswertung werden diese Dokumente interpretiert. In einem weiteren Schritt sind daraus resultierende Erkenntnisse der Forscherin in eine Fokusgruppe mit Hebammen eingebracht worden. Mit theoretischen Bezügen auf Pierre Bourdieu, Ralf Bohnsack und Hartmut Rosa werden anschließend Verbindungslinien zu „gesund leben lernen“ aufgezeigt und Aspekten struktureller Logik im beruflichen Feld von Hebammen nachgegangen. In unterschiedlichen Auswertungsprozessen verdichten sich Sichtweisen auf „gesund leben lernen“ in einer Doppelorientierung als professionelle Partnerin für andere Frauen in einer Umbruchssituation des Mutter-Werdens und als berufstätige Frau im Hebammenberuf

Survey Protocols to Investigate the Information Habits and Needs of Engineering and Engineering Technology Students and Practicing Engineers

This .pdf document contains two survey protocols created in 2016 to study the information literacy experiences and needs of undergraduate engineering and technology students and practicing engineers

How do professional engineers use information compared to undergradutes, and how can libraries prepare students and support engineers for future success?

Librarians at Purdue University seek to develop engineering graduates who are effective information users. Similarly, information specialists at Caterpillar Inc. are concerned with how well new hires are prepared for the information landscape at work as practicing engineers. Librarians from Purdue University and Caterpillar partnered to create and disseminate a survey to compare how students and practicing engineers seek and use information in the research process. Within a framework that asked survey participants to think about information use in a recently completed project, responses highlighted several gaps in information literacy training, including the use of external standards and internal document storage systems, documentation practices, and resource awareness. We also explored information habits and frustrations of both user populations and found that, while students have more confidence in their abilities, they consult many fewer types of literature and utilize fewer strategies for organizing information effectively. Additionally, the findings suggest students tend to use more social media tools to keep abreast of developments in their field than practicing engineers, while engineers rely heavily on internal knowledge management systems to track information generated by the company that augments externally produced information. The goal of this project was to better understand both consistencies and gaps in university engineering education and industry expectations. This paper presents preliminary findings from this project and discusses how the authors plan to use the results to update undergraduate curricula and improve library services and resources for both populations

Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs

All-atom force fields are important for predicting thermodynamic, structural, and dynamic properties of RNA. In this paper, results are reported for thermodynamic integration calculations of free energy differences of duplex formation when CG pairs in the RNA duplexes r(CCGG)2, r(GGCC)2, r(GCGC)2, and r(CGCG)2 are replaced by isocytidine–isoguanosine (iCiG) pairs. Agreement with experiment was improved when ε/ζ, α/γ, β, and χ torsional parameters in the AMBER99 force field were revised on the basis of quantum mechanical calculations. The revised force field, AMBER99TOR, brings free energy difference predictions to within 1.3, 1.4, 2.3, and 2.6 kcal/mol at 300 K, respectively, compared to experimental results for the thermodynamic cycles of CCGG → iCiCiGiG, GGCC → iGiGiCiC, GCGC → iGiCiGiC, and CGCG → iCiGiCiG. In contrast, unmodified AMBER99 predictions for GGCC → iGiGiCiC and GCGC → iGiCiGiC differ from experiment by 11.7 and 12.6 kcal/mol, respectively. In order to test the dynamic stability of the above duplexes with AMBER99TOR, four individual 50 ns molecular dynamics (MD) simulations in explicit solvent were run. All except r(CCGG)2 retained A-form conformation for ≥82% of the time. This is consistent with NMR spectra of r(iGiGiCiC)2, which reveal an A-form conformation. In MD simulations, r(CCGG)2 retained A-form conformation 52% of the time, suggesting that its terminal base pairs may fray. The results indicate that revised backbone parameters improve predictions of RNA properties and that comparisons to measured sequence dependent thermodynamics provide useful benchmarks for testing force fields and computational methods

Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing

The crystal structure of the duplex formed by oligo(2′,3′-dideoxy-β-d-glucopyranosyl)nucleotides (homo-DNA) revealed strongly inclined backbone and base-pair axes [Egli,M., Pallan,P.S., Pattanayek,R., Wilds,C.J., Lubini,P., Minasov,G., Dobler,M., Leumann,C.J. and Eschenmoser,A. (2006) Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system. J. Am. Chem. Soc., 128, 10847–10856]. This inclination is easily perceived because homo-DNA exhibits only a modest helical twist. Conversely, the tight coiling of strands conceals that the backbone-base inclinations for A- (DNA and RNA) and B-form (DNA) duplexes differ considerably. We have defined a parameter ηB that corresponds to the local inclination between sugar-phosphate backbone and base plane in nucleic acid strands. Here, we show its biological significance as a predictive measure for the relative strand polarities (antiparallel, aps, or parallel, ps) in duplexes of DNA, RNA and artificial nucleic acid pairing systems. The potential of formation of ps duplexes between complementary 16-mers with eight A and U(T) residues each was investigated with DNA, RNA, 2′-O-methylated RNA, homo-DNA and p-RNA, the ribopyranosyl isomer of RNA. The thermodynamic stabilities of the corresponding aps duplexes were also measured. As shown previously, DNA is capable of forming both ps and aps duplexes. However, all other tested systems are unable to form stable ps duplexes with reverse Watson–Crick (rWC) base pairs. This observation illustrates the handicap encountered by nucleic acid systems with inclinations ηB that differ significantly from 0° to form a ps rWC paired duplex. Accordingly, RNA with a backbone-base inclination of −30°, pairs strictly in an aps fashion. On the other hand, the more or less perpendicular orientation of backbone and bases in DNA allows it to adopt a ps rWC paired duplex. In addition to providing a rationalization of relative strand polarity with nucleic acids, the backbone-base inclination parameter is also a determinant of cross-pairing. Thus, systems with strongly deviating ηB angles will not pair with each other. Nucleic acid pairing systems with significant backbone-base inclinations can also be expected to display different stabilities depending on which terminus carries unpaired nucleotides. The negative inclination of RNA is consistent with the higher stability of duplexes with 3′- compared to those with 5′-dangling ends

Differential Base Stacking Interactions Induced by Trimethylene Interstrand DNA Cross-Links in the 5′-CpG-3′ and 5′-GpC-3′ Sequence Contexts

Synthetically derived trimethylene interstrand DNA cross-links have been used as surrogates for the native cross-links that arise from the 1,N 2-deoxyguanosine adducts derived from R,β-unsaturated aldehydes. The native enal-mediated cross-linking occurs in the 5′-CpG-3 ′ sequence context but not in the 5′-GpC-3 ′ sequence context. The ability of the native enal-derived 1,N 2-dG adducts to induce interstrand DNA cross-links in the 5′-CpG-3 ′ sequence as opposed to the 5′-GpC-3 ′ sequence is attributed to the destabilization of the DNA duplex in the latter sequence context. Here, we report higher accuracy solution structures of the synthetically derived trimethylene cross-links, which are refined from NMR data with the AMBER force field. When the synthetic trimethylene cross-links are placed into either the 5′-CpG-3′ or the 5′-GpC-3 ′ sequence contexts, the DNA duplex maintains B-DNA geometry with structural perturbations confined to the cross-linked base pairs. Watson-Crick hydrogen bonding is conserved throughout the duplexes. Although different from canonical B-DNA stacking, the cross-linked and the neighbor base pairs stack in the 5′-CpG-3 ′ sequence. In contrast, the stacking at the cross-linked base pairs in the 5′-GpC-3 ′ sequence is greatly perturbed. The π-stacking interactions between the crosslinked and the neighbor base pairs are reduced. This is consistent with remarkable chemical shift perturbations of the C 5 H5 and H6 nucleobase protons that shifted downfield by 0.4-0.5 ppm. In contrast

Swarm Learning for decentralized and confidential clinical machine learning

Fast and reliable detection of patients with severe and heterogeneous illnesses is a major goal of precision medicine1,2. Patients with leukaemia can be identified using machine learning on the basis of their blood transcriptomes3. However, there is an increasing divide between what is technically possible and what is allowed, because of privacy legislation4,5. Here, to facilitate the integration of any medical data from any data owner worldwide without violating privacy laws, we introduce Swarm Learning—a decentralized machine-learning approach that unites edge computing, blockchain-based peer-to-peer networking and coordination while maintaining confidentiality without the need for a central coordinator, thereby going beyond federated learning. To illustrate the feasibility of using Swarm Learning to develop disease classifiers using distributed data, we chose four use cases of heterogeneous diseases (COVID-19, tuberculosis, leukaemia and lung pathologies). With more than 16,400 blood transcriptomes derived from 127 clinical studies with non-uniform distributions of cases and controls and substantial study biases, as well as more than 95,000 chest X-ray images, we show that Swarm Learning classifiers outperform those developed at individual sites. In addition, Swarm Learning completely fulfils local confidentiality regulations by design. We believe that this approach will notably accelerate the introduction of precision medicine

Sequence-Dependent Fluorescence of Cyanine Dyes on Microarrays

Cy3 and Cy5 are among the most commonly used oligonucleotide labeling molecules. Studies of nucleic acid structure and dynamics use these dyes, and they are ubiquitous in microarray experiments. They are sensitive to their environment and have higher quantum yield when bound to DNA. The fluorescent intensity of terminal cyanine dyes is also known to be significantly dependent on the base sequence of the oligonucleotide. We have developed a very precise and high-throughput method to evaluate the sequence dependence of oligonucleotide labeling dyes using microarrays and have applied the method to Cy3 and Cy5. We used light-directed in-situ synthesis of terminally-labeled microarrays to determine the fluorescence intensity of each dye on all 1024 possible 5′-labeled 5-mers. Their intensity is sensitive to all five bases. Their fluorescence is higher with 5′ guanines, and adenines in subsequent positions. Cytosine suppresses fluorescence. Intensity falls by half over the range of all 5-mers for Cy3, and two-thirds for Cy5. Labeling with 5′-biotin-streptavidin-Cy3/-Cy5 gives a completely different sequence dependence and greatly reduces fluorescence compared with direct terminal labeling