Letter to the Editor Published in the Christian Intelligencer

A letter of this date to the editor was published December 8, 1859 in The Christian Intelligencer endorsed the Holland Academy. The writers are professors at the New Brunswick Theological Seminary. They conclude their letter by saying, In closing, the undersigned declare their strong conviction, that there have been as few errors of judgment in the management of the Holland Academy as could be expected in any business which fallible men managed. The signers are S[amuel] A. Van Vranken, W[illia]m H. Campbell, and S[amuel] M. Woodbridge.https://digitalcommons.hope.edu/vrp_1850s/1159/thumbnail.jp

Structure calculation, refinement and validation using CcpNmr Analysis

CcpNmr Analysis provides a streamlined pipeline for both NMR chemical shift assignment and structure determination of biological macromolecules. In addition, it encompasses tools to analyse the many additional experiments that make NMR such a pivotal technique for research into complex biological questions. This report describes how CcpNmr Analysis can seamlessly link together all of the tasks in the NMR structure-determination process. It details each of the stages from generating NMR restraints [distance, dihedral,hydrogen bonds and residual dipolar couplings (RDCs)],exporting these to and subsequently re-importing them from structure-calculation software (such as the programs CYANA or ARIA) and analysing and validating the results obtained from the structure calculation to, ultimately, the streamlined deposition of the completed assignments and the refined ensemble of structures into the PDBe repository. Until recently, such solution-structure determination by NMR has been quite a laborious task, requiring multiple stages and programs. However, with the new enhancements to CcpNmr Analysis described here, this process is now much more intuitive and efficient and less error-prone

Blockchain Technology in Business and Information Systems Research

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Probing interactions in mesoscopic gold wires

We have measured in gold wires the energy exchange rate between quasiparticles, the phase coherence time of quasiparticles and the resistance vs. temperature, in order to probe the interaction processes which are relevant at low temperatures. We find that the energy exchange rate is higher than expected from the theory of electron-electron interactions, and that it has a different energy dependence. The dephasing time is constant at temperatures between 8 K and 0.5 K, and it increases below 0.5 K. The magnetoresistance is negative at large field scales, and the resistance decreases logarithmically with increasing temperatures, indicating the presence of magnetic impurities, probably Fe. Whereas resistivity and phase coherence measurements can be attributed to magnetic impurities, the question is raised whether these magnetic impurities could also mediate energy exchanges between quasiparticles.Comment: latex pothier.tex, 12 files, 15 pages in: Proceedings of the NATO Advanced Research Workshop on Size Dependent Magnetic Scattering, Pesc, Hungary, May 28 - June 1st, 2000 Chandrasekhar V., Van Haesendonck C. eds (Kluwer, 2001) [SPEC-S00/083

Risk factor for footpad dermatitis and hock burns in broiler chickens

Footpad dermatitis (FPD) and hock burn (HB) are a major welfare concern in broiler chicken farming. In general, foot lesions are linked to poor environmental conditions. Ulcers caused by advanced lesions can negatively affect the gait of the birds, with effects on the welfare of animals, including, in the worst cases, inability to reach the feed or water. FPD and HB score data were collected manually at two broiler farms across Europe, during welfare assessments performed within the EU-PLF (Precision Livestock Farming) project, which is supported by the European Commission. This ongoing project aims to create "added value" for the farmer through the application of sensors and information technology at farm level. On those broiler farms, a number of variables such as temperature, relative humidity, ventilation rate, bird weight, light schedule, and feed and water consumption rates are measured automatically. The welfare of the chickens was assessed three times per cycle (at week 3, 4 and 5), scoring FPD, HB, gait score, cleanliness of the birds and litter quality. Data analysis was performed by combining data from the welfare assessments with environmental data collected by the automatic monitoring systems. The analysis showed that FPD and HB were more frequent when the flock was exposed to poor environmental conditions for prolonged periods of time. As environmental conditions can be measured continuously, and the risk factor for FPD and HB increases with poor environmental conditions, there is potential to develop a detection and control system for foot and hock lesions.</p

Rap1 binding and a lipid-dependent helix in talin F1 domain promote integrin activation in tandem.

Rap1 GTPases bind effectors, such as RIAM, to enable talin1 to induce integrin activation. In addition, Rap1 binds directly to the talin1 F0 domain (F0); however, this interaction makes a limited contribution to integrin activation in CHO cells or platelets. Here, we show that talin1 F1 domain (F1) contains a previously undetected Rap1-binding site of similar affinity to that in F0. A structure-guided point mutant (R118E) in F1, which blocks Rap1 binding, abolishes the capacity of Rap1 to potentiate talin1-induced integrin activation. The capacity of F1 to mediate Rap1-dependent integrin activation depends on a unique loop in F1 that has a propensity to form a helix upon binding to membrane lipids. Basic membrane-facing residues of this helix are critical, as charge-reversal mutations led to dramatic suppression of talin1-dependent activation. Thus, a novel Rap1-binding site and a transient lipid-dependent helix in F1 work in tandem to enable a direct Rap1-talin1 interaction to cause integrin activation

Electron Dephasing in Mesoscopic Metal Wires

The low-temperature behavior of the electron phase coherence time, $\tau_{\phi}$, in mesoscopic metal wires has been a subject of controversy recently. Whereas theory predicts that $\tau_{\phi}(T)$ in narrow wires should increase as $T^{-2/3}$ as the temperature $T$ is lowered, many samples exhibit a saturation of $\tau_{\phi}$ below about 1 K. We review here the experiments we have performed recently to address this issue. In particular we emphasize that in sufficiently pure Ag and Au samples we observe no saturation of $\tau_{\phi}$ down to our base temperature of 40 mK. In addition, the measured magnitude of $\tau_{\phi}$ is in excellent quantitative agreement with the prediction of the perturbative theory of Altshuler, Aronov and Khmelnitskii. We discuss possible explanations why saturation of $\tau_{\phi}$ is observed in many other samples measured in our laboratory and elsewhere, and answer the criticisms raised recently by Mohanty and Webb regarding our work.Comment: 14 pages, 3 figures; to appear in proceedings of conference "Fundamental Problems of Mesoscopic Physics", Granada, Spain, 6-11 September, 200

Dephasing of Electrons in Mesoscopic Metal Wires

We have extracted the phase coherence time $\tau_{\phi}$ of electronic quasiparticles from the low field magnetoresistance of weakly disordered wires made of silver, copper and gold. In samples fabricated using our purest silver and gold sources, $\tau_{\phi}$ increases as $T^{-2/3}$ when the temperature $T$ is reduced, as predicted by the theory of electron-electron interactions in diffusive wires. In contrast, samples made of a silver source material of lesser purity or of copper exhibit an apparent saturation of $\tau_{\phi}$ starting between 0.1 and 1 K down to our base temperature of 40 mK. By implanting manganese impurities in silver wires, we show that even a minute concentration of magnetic impurities having a small Kondo temperature can lead to a quasi saturation of $\tau_{\phi}$ over a broad temperature range, while the resistance increase expected from the Kondo effect remains hidden by a large background. We also measured the conductance of Aharonov-Bohm rings fabricated using a very pure copper source and found that the amplitude of the $h/e$ conductance oscillations increases strongly with magnetic field. This set of experiments suggests that the frequently observed ``saturation'' of $\tau_{\phi}$ in weakly disordered metallic thin films can be attributed to spin-flip scattering from extremely dilute magnetic impurities, at a level undetectable by other means.Comment: 16 pages, 11 figures, to be published in Physical Review

Solution structure of the inner DysF domain of myoferlin and implications for limb girdle muscular dystrophy type 2b

Mutations in the protein dysferlin, a member of the ferlin family, lead to limb girdle muscular dystrophy type 2B and Myoshi myopathy. The ferlins are large proteins characterised by multiple C2 domains and a single C-terminal membrane-spanning helix. However, there is sequence conservation in some of the ferlin family in regions outside the C2 domains. In one annotation of the domain structure of these proteins, an unusual internal duplication event has been noted where a putative domain is inserted in between the N- and C-terminal parts of a homologous domain. This domain is known as the DysF domain. Here, we present the solution structure of the inner DysF domain of the dysferlin paralogue myoferlin, which has a unique fold held together by stacking of arginine and tryptophans, mutations that lead to clinical disease in dysferlin

The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries

Several pilot experiments have indicated that improvements in older NMR structures can be expected by applying modern software and new protocols (Nabuurs et al. in Proteins 55:483–186, 2004; Nederveen et al. in Proteins 59:662–672, 2005; Saccenti and Rosato in J Biomol NMR 40:251–261, 2008). A recent large scale X-ray study also has shown that modern software can significantly improve the quality of X-ray structures that were deposited more than a few years ago (Joosten et al. in J. Appl Crystallogr 42:376–384, 2009; Sanderson in Nature 459:1038–1039, 2009). Recalculation of three-dimensional coordinates requires that the original experimental data are available and complete, and are semantically and syntactically correct, or are at least correct enough to be reconstructed. For multiple reasons, including a lack of standards, the heterogeneity of the experimental data and the many NMR experiment types, it has not been practical to parse a large proportion of the originally deposited NMR experimental data files related to protein NMR structures. This has made impractical the automatic recalculation, and thus improvement, of the three dimensional coordinates of these structures. We here describe a large-scale international collaborative effort to make all deposited experimental NMR data semantically and syntactically homogeneous, and thus useful for further research. A total of 4,014 out of 5,266 entries were ‘cleaned’ in this process. For 1,387 entries, human intervention was needed. Continuous efforts in automating the parsing of both old, and newly deposited files is steadily decreasing this fraction. The cleaned data files are available from the NMR restraints grid at http://restraintsgrid.bmrb.wisc.edu