REdiii: a pipeline for automated structure solution

High-throughput crystallographic approaches require integrated software solutions to minimize the need for manual effort. REdiii is a system that allows fully automated crystallographic structure solution by integrating existing crystallographic software into an adaptive and partly autonomous workflow engine. The program can be initiated after collecting the first frame of diffraction data and is able to perform processing, molecular-replacement phasing, chain tracing, ligand fitting and refinement without further user intervention. Preset values for each software component allow efficient progress with high-quality data and known parameters. The adaptive workflow engine can determine whether some parameters require modifications and choose alternative software strategies in case the preconfigured solution is inadequate. This integrated pipeline is targeted at providing a comprehensive and efficient approach to screening for ligand-bound co-crystal structures while minimizing repetitiveness and allowing a high-throughput scientific discovery process

Fokussieren und Kühlen neutraler Atome in starken Dipolpotentialen

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Transport and magnetic properties of La_(1-x)Ca_xMnO_3-films (0.1<x<0.9)

By laser ablation we prepared thin films of the colossal magnetoresistive compound La_(1-x)Ca_xMnO_3 with doping levels 0.1<x<0.9 on MgO substrates. X-ray diffraction revealed epitaxial growth and a systematic decrease of the lattice constants with doping. The variation of the transport and magnetic properties in this doping series was investigated by SQUID magnetization and electrical transport measurements. For the nonmetallic samples resistances up to 10^13 Ohm have been measured with an electrometer setup. While the transport data indicate polaronic transport for the metallic samples above the Curie temperature the low doped ferromagnetic insulating samples show a variable range hopping like transport at low temperature.Comment: 2 pages, 3 EPS figures, LT22 Proceedings to appear in Physica

Ein dediziertes Beschleuniger-Massenspektrometer für mittelschwere Radionuklide am Kölner FN-Tandembeschleuniger

In dieser Arbeit wurde erfolgreich ein Beschleuniger-Massenspektrometer für mittelschwere Radionuklide am Kölner FN-Tandembeschleuniger berechnet, aufgebaut und getestet. Mit diesem AMS-System konnten (53Mn/55Mn)-Isotopenverhältnisse im Bereich von 1e-9 bis 1e-10 mit einem Detektionslimit von 7,2e-13 erstmalig an einem 10MV Tandembeschleuniger gemessen werden. Das aufgebaute AMS-System ist dediziert für den Nachweis von mittelschweren Radionukliden. Es verfügt über einen achromatischen Injektor mit Fast-Injection-System sowie ein Hochenergie-Massenspektrometer mit einem 90°-Analysiermagneten (rho=1,1 m), hinter dem die Ionenströme der stabilen Nuklide in Offset-Farady-Cups gemessen werden. Die Isobarenunterdrückung kann über eine mehrstufige isotopenspezifische Energieverlust-Messung mit Kombinationen aus Siliziumnitrid-Folien, einem 30° elektrostatischen Analysierer (rho=3,5 m), einem 4 m Time-of-Flight-System sowie einem Gasionisationsdetektor erfolgen. Zusätzlich wurde das AMS-System für die Erhöhung der Transmission bei Radionuklidmessungen wie 60Fe um einen 135°-Magneten (rho=0,9 m) für den gasgefüllten Modus erweitert. Entscheidend sind bei allen AMS-Messungen die erreichbare Sensitivität und das Detektionslimit. Die hier gegebene Definition der fehlernormalisierten Sensitivität ermöglicht den Vergleich der Ergebnisse der (53Mn/55Mn)-Isotopenverhältnismessungen mit den Werten etablierter Labore. Das erreichte Detektionslimit ist trotz der niedrigen Ionenenergien mit anderen Forschungseinrichtungen vergleichbar, die über Tandembeschleuniger mit höherer Terminalspannung verfügen. Das gesamte AMS-System wurde mit Messungen von stabilen Isotopen und Isotopenverhältnissen überprüft. Bei den Testmessungen zu (41Ca/40Ca)-Isotopenverhältnissen wurde ohne passive Absorber ein Detektionslimit von <5,32e-13 erreicht. Bei den (53Mn/55Mn)-Isotopenverhältnismessungen wurde der hohe 53Cr Isobarentrennungsfaktor mit Siliziumnitrid-Folien und elektrostatischem Analysierer durch die Verwendung der optimalen Siliziumnitrid-Foliendicke erreicht. Die Foliendicke wurde unter Berücksichtigung der Beiträge der 53Cr Nachbarladungszustände berechnet. Eine weitere Unterdrückung des Isobars ohne starke Reduktion des Radionuklids konnte mit Schlitzen in der dispersiven Ebene vor dem elektrostatischen Analysierer erreicht werden. Die erreichte Isobarenunterdrückung mit Siliziumnitrid-Folien und dem 4 m Time-of-Flight-System ist nur hoch, wenn die Kernladungszahl des Isobars höher als die des Radionuklids ist. Die Isobarentrennung in einem 2-Anoden-Gasionisationsdetektor wurde mit den verschiedenen Kombinationen der mehrstufigen Energieverlustmessungen bestimmt. Durch die Verwendung des Gasionisationsdetektors direkt hinter dem elektrostatischen Analysierer konnte die Sensitivität der 53Mn-Messung gesteigert werden. Des Weiteren wurde das Isobarentrennungsvermögen von 53Cr/53Mn und 60Ni/60Fe über die Messung der charakteristischen Projektil-Röntgenenergien bestimmt. Dabei zeichnete sich der Messaufbau durch die intrinsische Kalibration des Energiespektrums über die M_alpha, L_alpha und L_beta Linien des Goldtargets aus

Low Incidence of Community-Acquired Pneumonia among Human Immunodeficiency Virus-Infected Patients after Interruption of Pneumocystis carinii Pneumonia Prophylaxis

We compared the incidence of bacterial pneumonia among 336 patients who discontinued trimethoprim-sulfamethoxazole (TMP-SMX) as prophylaxis against Pneumocystis carinii pneumonia (PCP) with that among 75 patients who fulfilled the criteria for discontinuation but continued receiving prophylaxis. The difference in the overall incidence rates for the 2 groups (1.2 events per 100 person-years) was not statistically significant. Discontinuation of TMP-SMX prophylaxis against PCP is not associated with a significant increase in the incidence of bacterial pneumonia among patients with a sustained CD4 cell count increase to >200 cells/μ

Urinary proteome pattern in children with renal Fanconi syndrome

Background. The renal Fanconi syndrome (FS) is characterized by renal glucosuria, loss of electrolytes, bicarbonate and lactate, generalized hyperaminoaciduria and low-molecular-weight proteinuria. We studied the urinary low-molecular-weight proteome to identify excreted peptides indicative of a pathogenetic mechanism leading to tubular dysfunction. Methods. We established a urinary proteome pattern using capillary electrophoresis mass spectrometry (CE-MS) of 7 paediatric patients with cystinosis and 6 patients with ifosfamide-induced FS as the study group, and 54 healthy volunteers and 45 patients suffering from other renal diseases such as lupus nephritis (n = 8), focal segmental glomerulosclerosis (n = 27), minimal change disease (n = 7) and membranous glomerulonephritis (n = 3) as controls. Consequently, we conducted a blinded study consisting of 11 FS patients and 9 patients with renal disease other than FS. Additionally, we applied this pattern to 294 previously measured samples of patients with different renal diseases. Amino acid sequences of some marker proteins were obtained. Results. Specificity for detecting FS was 89% and sensitivity was 82%. The marker peptides constituting the proteome pattern are fragments derived from osteopontin, uromodulin and collagen alpha-1. Conclusions. CE-MS can be used to diagnose FS in paediatric patients and might be a future tool for the non-invasive diagnosis of FS. The reduced amount of the marker proteins osteopontin and uromodulin indicates loss of function of tubular excretion in all patients suffering from FS regardless of the underlying cause. In addition, the six different fragments of the collagen alpha-1 (I) chain were either elevated or reduced in the urine. This indicates a change of proteases in collagen degradation as observed in interstitial fibrosis. These changes were prominent irrespectively of the stages of FS. This indicates fibrosis as an early starting pathogenetic reason for the development of renal insufficiency in FS patient

Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity

Nucleic acid editing enzymes are essential components of the immune system that lethally mutate viral pathogens and somatically mutate immunoglobulins, and contribute to the diversification and lethality of cancers. Among these enzymes are the seven human APOBEC3 deoxycytidine deaminases, each with unique target sequence specificity and subcellular localization. While the enzymology and biological consequences have been extensively studied, the mechanism by which APOBEC3s recognize and edit DNA remains elusive. Here we present the crystal structure of a complex of a cytidine deaminase with ssDNA bound in the active site at 2.2 A. This structure not only visualizes the active site poised for catalysis of APOBEC3A, but pinpoints the residues that confer specificity towards CC/TC motifs. The APOBEC3A-ssDNA complex defines the 5\u27-3\u27 directionality and subtle conformational changes that clench the ssDNA within the binding groove, revealing the architecture and mechanism of ssDNA recognition that is likely conserved among all polynucleotide deaminases, thereby opening the door for the design of mechanistic-based therapeutics

Discrepancies Between Planned and Actual Operating Room Turnaround Times at a Large Rural Hospital in Germany

Objectives: While several factors have been shown to influence operating room (OR) turnaround times, few comparisons of planned and actual OR turnaround times have been performed. This study aimed to compare planned and actual OR turnaround times at a large rural hospital in Northern Germany. Methods: This retrospective study examined the OR turnaround data of 875 elective surgery cases scheduled at the Marienhospital, Vechta, Germany, between July and October 2014. The frequency distributions of planned and actual OR turnaround times were compared and correlations between turnaround times and various factors were established, including the time of day of the procedure, patient age and the planned duration of the surgery. Results: There was a significant difference between mean planned and actual OR turnaround times (0.32 versus 0.64 hours; P <0.001). In addition, significant correlations were noted between actual OR turnaround times and the time of day of the surgery, patient age, actual duration of the procedure and staffing changes affecting the surgeon or the medical specialty of the surgery (P <0.001 each). The quotient of actual/planned OR turnaround times ranged from 1.733–3.000. Conclusion: Significant discrepancies between planned and actual OR turnaround times were noted during the study period. Such findings may be potentially used in future studies to establish a tool to improve OR planning, measure OR management performance and enable benchmarking

Combinations of Host- and Virus-Targeting Antiviral Drugs Confer Synergistic Suppression of SARS-CoV-2

Three directly acting antivirals (DAAs) demonstrated substantial reduction in COVID-19 hospitalizations and deaths in clinical trials. However, these agents did not completely prevent severe illness and are associated with cases of rebound illness and viral shedding. Combination regimens can enhance antiviral potency, reduce the emergence of drug-resistant variants, and lower the dose of each component in the combination. Concurrently targeting virus entry and virus replication offers opportunities to discover synergistic drug combinations. While combination antiviral drug treatments are standard for chronic RNA virus infections, no antiviral combination therapy has been approved for SARS-CoV-2. Here, we demonstrate that combining host-targeting antivirals (HTAs) that target TMPRSS2 and hence SARS-CoV-2 entry, with the DAA molnupiravir, which targets SARS-CoV-2 replication, synergistically suppresses SARS-CoV-2 infection in Calu-3 lung epithelial cells. Strong synergy was observed when molnupiravir, an oral drug, was combined with three TMPRSS2 (HTA) oral or inhaled inhibitors: camostat, avoralstat, or nafamostat. The combination of camostat plus molnupiravir was also effective against the beta and delta variants of concern. The pyrimidine biosynthesis inhibitor brequinar combined with molnupiravir also conferred robust synergistic inhibition. These HTA+DAA combinations had similar potency to the synergistic all-DAA combination of molnupiravir plus nirmatrelvir, the protease inhibitor found in paxlovid. Pharmacodynamic modeling allowed estimates of antiviral potency at all possible concentrations of each agent within plausible therapeutic ranges, suggesting possible in vivo efficacy. The triple combination of camostat, brequinar, and molnupiravir further increased antiviral potency. These findings support the development of HTA+DAA combinations for pandemic response and preparedness. IMPORTANCE Imagine a future viral pandemic where if you test positive for the new virus, you can quickly take some medicines at home for a few days so that you do not get too sick. To date, only single drugs have been approved for outpatient use against SARS-CoV-2, and we are learning that these have some limitations and may succumb to drug resistance. Here, we show that combinations of two oral drugs are better than the single ones in blocking SARS-CoV-2, and we use mathematical modeling to show that these drug combinations are likely to work in people. We also show that a combination of three oral drugs works even better at eradicating the virus. Our findings therefore bode well for the development of oral drug cocktails for at home use at the first sign of an infection by a coronavirus or other emerging viral pathogens.Peer reviewe