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We present a software package designed to produce photometric light curves and measure rotation periods from full-frame images taken by the Transiting Exoplanet Survey Satellite (TESS), which we name ' tessilator '. tessilator is the only publicly available code that will run a full light curve and rotation period (⁠|$P_{\rm rot}$|⁠) analysis based on just a (list of) target identifier(s) or sky position(s) via a simple command-line prompt. This paper sets out to introduce the rationale for developing tessilator , and then describes the methods, considerations, and assumptions for: extracting photometry; dealing with potential contamination; accounting for natural and instrumental systematic effects; light-curve normalization and detrending; removing outliers and unreliable data; and finally, measuring the |$P_{\rm rot}$| value and several periodogram attributes. Our methods have been tuned specifically to optimize TESS light curves and are independent from the pipelines developed by the TESS Science Processing Operations Center (SPOC), meaning tessilator can, in principle, analyse any target across the entire celestial sphere. We compare tessilator |$P_{\rm rot}$| measurements with TESS -SPOC-derived light curves of 1560 (mainly solar-type and low-mass) stars across four benchmark open clusters (Pisces–Eridanus, the Pleiades, the Hyades, and Praesepe) and a sample of nearby field M-dwarfs. From a vetted subsample of 864 targets we find an excellent return of |$P_{\rm rot}$| matches for the first three open clusters (⁠|$\gt 85$|  per cent) and a moderate (⁠|$\sim 60$|  per cent) match for the 700 Myr Praesepe and MEarth sample, which validates tessilator as a tool for measuring |$P_{\rm rot}$|⁠. The tessilator code is available at https://github.com/alexbinks/tessilator. [ABSTRACT FROM AUTHOR]

The Cepheid AW Per is a component in a multiple system with a long-period orbit. The radial velocities of Griffin cover the 38 yr orbit well. An extensive program of interferometry with the Center for High Angular Resolution Astronomy array is reported here, from which the long-period orbit is determined. In addition, a Hubble Space Telescope high-resolution spectrum in the ultraviolet demonstrates that the companion is itself a binary with nearly equal-mass components. These data combined with a distance from Gaia provide a mass of the Cepheid (primary) of M 1 = 6.79 ± 0.85 M ⊙. The combined mass of the secondary is M S = 8.79 ± 0.50 M ⊙. The accuracy of the mass will be improved after the fourth Gaia data release, expected in approximately two years. [ABSTRACT FROM AUTHOR]

Terahertz (THz)-based electron acceleration has potential as a technology for next-generation cost-efficient compact electron sources. Although proof-of-principle demonstrations have proved the feasibility of many THz-driven accelerator components, THz-driven photoguns with sufficient brightness, energy and control for use in demanding ultrafast applications have yet to be achieved. Here we present a novel millimetre-scale multicell waveguide-based THz-driven photogun that exploits field enhancement to boost the electron energy, a movable cathode to achieve precise control over the accelerating phase as well as multiple cells for exquisite beam control. The short driving wavelength enables a peak acceleration gradient as high as ~3 GV m−1. Using microjoule-level single-cycle THz pulses, we demonstrate electron beams with up to ~14 keV electron energy, 1% energy spread and ~0.015 mm mrad transverse emittance. With a highly integrated rebunching cell, the bunch is further compressed by about ten times to 167 fs with ~10 fC charge. High-quality diffraction patterns of single-crystal silicon and projection microscopy images of the copper mesh are achieved. We are able to reveal the transient radial electric field developed from the charged particles on a copper mesh after photoexcitation with high spatio-temporal resolution, providing a potential scheme for plasma-based beam manipulation. Overall, these results represent a new record in energy, field gradient, beam quality and control for a THz-driven electron gun, enabling real applications in electron projection microscopy and diffraction. This is therefore a critical step and milestone in the development of all-optical THz-driven electron devices, validating the maturity of the technology and its use in precision applications. A terahertz-driven photogun with field gradients of 3 GV m−1 is demonstrated by using a few microjoules of single-cycle terahertz radiation. The emitted electrons are accelerated up to 14 keV and can be focused down to 90 μm. The electron bunch is further compressed to 167 fs. [ABSTRACT FROM AUTHOR]

For time-resolved diffraction studies of irreversible structural dynamics upon photoexcitation, there are constraints on the number of perturbation cycles due to thermal effects and accumulated strain, which impact the degree of crystal order and spatial resolution. This problem is exasperated for surface studies that are more prone to disordering and defect formation. Ultrafast electron diffraction studies of these systems, with the conventional stroboscopic pump–probe protocol, require repetitive measurements on well-prepared diffraction samples to acquire and average signals above background in the dynamic range of interest from few tens to hundreds of picoseconds. Here, we present ultrafast streaked low-energy electron diffraction (LEED) that demands, in principle, only a single excitation per nominal data acquisition timeframe. By exploiting the space–time correlation characteristics of the streaking method and high-charge 2 keV electron bunches in the transmission geometry, we demonstrate about one order of magnitude reduction in the accumulated number of the excitation cycles and total electron dose, and 48% decrease in the root mean square error of the model fit residual compared to the conventional time-scanning measurement. We believe that our results demonstrate a viable alternative method with higher sensitivity to that of nanotip-based ultrafast LEED studies relying on a few electrons per a single excitation, to access to all classes of structural dynamics to provide an atomic level view of surface processes. [ABSTRACT FROM AUTHOR]

The sirtuins are NAD+‐dependent lysine deacylases, comprising seven isoforms (SIRT1–7) in humans, which are involved in the regulation of a plethora of biological processes, including gene expression and metabolism. The sirtuins share a common hydrolytic mechanism but display preferences for different ϵ‐N‐acyllysine substrates. SIRT7 deacetylates targets in nuclei and nucleoli but remains one of the lesser studied of the seven isoforms, in part due to a lack of chemical tools to specifically probe SIRT7 activity. Here we expressed SIRT7 and, using small‐angle X‐ray scattering, reveal SIRT7 to be a monomeric enzyme with a low degree of globular flexibility in solution. We developed a fluorogenic assay for investigation of the substrate preferences of SIRT7 and to evaluate compounds that modulate its activity. We report several mechanism‐based SIRT7 inhibitors as well as de novo cyclic peptide inhibitors selected from mRNA‐display library screening that exhibit selectivity for SIRT7 over other sirtuin isoforms, stabilize SIRT7 in cells, and cause an increase in the acetylation of H3 K18. [ABSTRACT FROM AUTHOR]

The sirtuins are NAD+‐dependent lysine deacylases, comprising seven isoforms (SIRT1–7) in humans, which are involved in the regulation of a plethora of biological processes, including gene expression and metabolism. The sirtuins share a common hydrolytic mechanism but display preferences for different ϵ‐N‐acyllysine substrates. SIRT7 deacetylates targets in nuclei and nucleoli but remains one of the lesser studied of the seven isoforms, in part due to a lack of chemical tools to specifically probe SIRT7 activity. Here we expressed SIRT7 and, using small‐angle X‐ray scattering, reveal SIRT7 to be a monomeric enzyme with a low degree of globular flexibility in solution. We developed a fluorogenic assay for investigation of the substrate preferences of SIRT7 and to evaluate compounds that modulate its activity. We report several mechanism‐based SIRT7 inhibitors as well as de novo cyclic peptide inhibitors selected from mRNA‐display library screening that exhibit selectivity for SIRT7 over other sirtuin isoforms, stabilize SIRT7 in cells, and cause an increase in the acetylation of H3 K18. [ABSTRACT FROM AUTHOR]

We performed molecular dynamics simulations of Reteplase in the presence of different excipients to study the stabilizing mechanisms and to identify the role of excipients during freeze drying. To simulate the freeze-drying process, we divided the process into five distinct steps: (i) protein–excipient formulations at room temperature, (ii) the ice-growth process, (iii)–(iv) the partially solvated and fully dried formulations, and (v) the reconstitution. Furthermore, coarse-grained (CG) simulations were employed to explore the protein-aggregation process in the presence of arginine. By using a coarse-grained representation, we could observe the collective behavior and interactions between protein molecules during the aggregation process. The CG simulations revealed that the presence of arginine prevented intermolecular interactions of the catalytic domain of Reteplase, thus reducing the aggregation propensity. This suggests that arginine played a stabilizing role by interacting with protein-specific regions. From the freeze-drying simulations, we could identify several protein-specific events: (i) collapse of the domain structure, (ii) recovery of the drying-induced damages during reconstitution, and (iii) stabilization of the local aggregation-prone region via direct interactions with excipients. Complementary to the simulations, we employed nanoDSF, size-exclusion chromatography, and CD spectroscopy to investigate the effect of the freeze-drying process on the protein structure and stability. [ABSTRACT FROM AUTHOR]

For improved control of biomaterial property design, a better understanding of complex coacervation involving anionic polysaccharides and proteins is needed. Here, we address the initial steps in condensate formation of β‐lactoglobulin A (β‐LgA) with nine defined alginate oligosaccharides (AOSs) and describe their multivalent interactions in structural detail. Binding of AOSs containing four, five, or six uronic acid residues (UARs), either all mannuronate (M), all guluronate (G), or alternating M and G embodying the block structural components of alginates, was characterized by isothermal titration calorimetry, nuclear magnetic resonance spectroscopy (NMR), and molecular docking. β‐LgA was highly multivalent exhibiting binding stoichiometries decreasing from five to two AOSs with increasing degree of polymerization (DP) and similar affinities in the mid micromolar range. The different AOS binding sites on β‐LgA were identified by NMR chemical shift perturbation analyses and showed diverse compositions of charged, polar and hydrophobic residues. Distinct sites for the shorter AOSs merged to accommodate longer AOSs. The AOSs bound dynamically to β‐LgA, as concluded from saturation transfer difference and 1H‐ligand‐targeted NMR analyses. Molecular docking using Glide within the Schrödinger suite 2016‐1 revealed the orientation of AOSs to only vary slightly at the preferred β‐LgA binding site resulting in similar XP glide scores. The multivalency coupled with highly dynamic AOS binding with lack of confined conformations in the β‐LgA complexes may help explain the first steps toward disordered β‐LgA alginate coacervate structures. [ABSTRACT FROM AUTHOR]

Here, we propose an optimised protocol for controlling the initial water activity (aw) in organic reaction mixtures with soluble lipase to ensure reproducible and consistent enzyme activity measurements. Pre‐equilibration above saturated salt solutions was used to set aw of the reaction media, where aw was tracked with a hygrometer. Consistent stirring of the suspension and volume correction to compensate for solvent evaporation were found to be critical. The protocol was tested on Candida antarctica lipase B (CALB) in soluble and immobilised forms in three organic solvents (acetonitrile, methyl tert‐butyl ether, and hexane) at four different water activities ranging from 0.12 to 0.97. Soluble and immobilised CALB had similar aw‐profiles and showed the highest enzyme activity in hexane. The optimised protocol expands the possibility to study enzyme kinetics from immobilised enzymes to soluble enzymes. [ABSTRACT FROM AUTHOR]

Self-assembly and fibril formation play important roles in protein behaviour. Amyloid fibril formation is well-studied due to its role in neurodegenerative diseases and characterized by refolding of the protein into predominantly β-sheet form. However, much less is known about the assembly of proteins into other types of supramolecular structures. Using cryo-electron microscopy at a resolution of 1.97 Å, we show that a triple-mutant of the anti-microbial peptide plectasin, PPI42, assembles into helical non-amyloid fibrils. The in vitro anti-microbial activity was determined and shown to be enhanced compared to the wildtype. Plectasin contains a cysteine-stabilised α-helix-β-sheet structure, which remains intact upon fibril formation. Two protofilaments form a right-handed protein fibril. The fibril formation is reversible and follows sigmoidal kinetics with a pH- and concentration dependent equilibrium between soluble monomer and protein fibril. This high-resolution structure reveals that α/β proteins can natively assemble into fibrils. Here the authors report the cryo-EM structure of a triple-mutant of the anti-microbial peptide plectasin, PPI42, assembling in a pH- and concentration dependent manner into helical non-amyloid fibrils. The fibrils formation is reversible, and follows a sigmoidal kinetics. The fibrils adopt a right-handed helical superstructure composed by two protofilaments, stabilized by an outer hydrophobic ring and an inner hydrophobic centre. These findings reveal that α/β proteins can natively assemble into fibrils. [ABSTRACT FROM AUTHOR]

With increasing environmental concerns, the building sector must rethink the selection of building materials not only for structural members but also for connections. Densified wooden nails might become an alternative to metallic fasteners, at least in applications with lower structural requirements. However, their structural behaviour in timber-to-timber connections is not yet systematically studied. This paper presents a series of 90 shear tests to explore the shear capacity and slip modulus of timber-to-timber connections with wooden nails. Specimens with different nail dimensions, different nail orientations, and different nail arrangements were investigated. A typical three-member push-out test setup was adopted where the wooden nails were oriented perpendicular or inclined to the shear plane. Specimens with inclined nails exposed to shear and tensile forces showed a higher shear resistance due to the activated tensile capacity of the wooden nails. Failure of the wooden nails was predominantly observed when the nails were loaded in tension. This means that the interface between the wooden nails and the timber did not fail. Based on the results from the shear tests, an analytical model was developed to predict the load bearing capacity of timber-to-timber connections exposed to bending stresses. The analytical model was validated with experimental investigations. [ABSTRACT FROM AUTHOR]

Background: Histone acetylation and deacetylation seem processes involved in the pathogenesis of Ewing sarcoma (EwS). Here histone deacetylases (HDAC) class I were investigated. Methods: Their role was determined using different inhibitors including TSA, Romidepsin, Entinostat and PCI-34051 as well as CRISPR/Cas9 class I HDAC knockouts and HDAC RNAi. To analyze resulting changes microarray analysis, qRT-PCR, western blotting, Co-IP, proliferation, apoptosis, differentiation, invasion assays and xenograft-mouse models were used. Results: Class I HDACs are constitutively expressed in EwS. Patients with high levels of individual class I HDAC expression show decreased overall survival. CRISPR/Cas9 class I HDAC knockout of individual HDACs such as HDAC1 and HDAC2 inhibited invasiveness, and blocked local tumor growth in xenograft mice. Microarray analysis demonstrated that treatment with individual HDAC inhibitors (HDACi) blocked an EWS-FLI1 specific expression profile, while Entinostat in addition suppressed metastasis relevant genes. EwS cells demonstrated increased susceptibility to treatment with chemotherapeutics including Doxorubicin in the presence of HDACi. Furthermore, HDACi treatment mimicked RNAi of EZH2 in EwS. Treated cells showed diminished growth capacity, but an increased endothelial as well as neuronal differentiation ability. HDACi synergizes with EED inhibitor (EEDi) in vitro and together inhibited tumor growth in xenograft mice. Co-IP experiments identified HDAC class I family members as part of a regulatory complex together with PRC2. Conclusions: Class I HDAC proteins seem to be important mediators of the pathognomonic EWS-ETS-mediated transcription program in EwS and in combination therapy, co-treatment with HDACi is an interesting new treatment opportunity for this malignant disease. [ABSTRACT FROM AUTHOR]

Purpose: Determination of absorbed dose is well established in many dosimetry protocols and considered to be highly reliable using ionization chambers under reference conditions. If dosimetry is performed under other conditions or using other detectors, however, open questions still remain. Such questions frequently refer to appropriate correction factors. A converted energy per mass (cema)‐based approach to formulate such correction factors offers a good understanding of the specific response of a detector for dosimetry under various measuring conditions and thus an estimate of pros and cons of its application. Methods: Determination of absorbed dose requires the knowledge of the beam quality correction factor kQ,Qo, where Q denotes the quality of a user beam and Qo is the quality of the radiation used for calibration. In modern Monte Carlo (MC)‐based methods, kQ,Qo is directly derived from the MC‐calculated dose conversion factor, which is the ratio between the absorbed dose at a point of interest in water and the mean absorbed dose in the sensitive volume of an ion chamber. In this work, absorbed dose is approximated by the fundamental quantity cema. This approximation allows the dose conversion factor to be substituted by the cema conversion factor. Subsequently, this factor is decomposed into a product of cema ratios. They are identified as the stopping power ratio water to the material in the sensitive detector volume, and as the correction factor for the fluence perturbation of the secondary charged particles in the detector cavity caused by the presence of the detector. This correction factor is further decomposed with respect to the perturbation caused by the detector cavity and that caused by external detector properties. The cema‐based formalism was subsequently tested by MC calculations of the spectral fluence of the secondary charged particles (electrons and positrons) under various conditions. Results: MC calculations demonstrate that considerable fluence perturbation may occur particularly under non‐reference conditions. Cema‐based correction factors to be applied in a 6‐MV beam were obtained for a number of ionization chambers and for three solid‐state detectors. Feasibility was shown at field sizes of 4 × 4 and 0.5 cm × 0.5 cm. Values of the cema ratios resulting from the decomposition of the dose conversion factor can be well correlated with detector response. Under the small field conditions, the internal fluence correction factor of ionization chambers is considerably dependent on volume averaging and thus on the shape and size of the cavity volume. Conclusions: The cema approach is particularly useful at non‐reference conditions including when solid‐state detectors are used. Perturbation correction factors can be expressed and evaluated by cema ratios in a comprehensive manner. The cema approach can serve to understand the specific response of a detector for dosimetry to be dependent on (a) radiation quality, (b) detector properties, and (c) electron fluence changes caused by the detector. This understanding may also help to decide which detector is best suited for a specific measurement situation. [ABSTRACT FROM AUTHOR]

Background: Histone acetylation and deacetylation seem processes involved in the pathogenesis of Ewing sarcoma (EwS). Here histone deacetylases (HDAC) class I were investigated. Methods: Their role was determined using different inhibitors including TSA, Romidepsin, Entinostat and PCI-34051 as well as CRISPR/Cas9 class I HDAC knockouts and HDAC RNAi. To analyze resulting changes microarray analysis, qRT-PCR, western blotting, Co-IP, proliferation, apoptosis, differentiation, invasion assays and xenograft-mouse models were used. Results: Class I HDACs are constitutively expressed in EwS. Patients with high levels of individual class I HDAC expression show decreased overall survival. CRISPR/Cas9 class I HDAC knockout of individual HDACs such as HDAC1 and HDAC2 inhibited invasiveness, and blocked local tumor growth in xenograft mice. Microarray analysis demonstrated that treatment with individual HDAC inhibitors (HDACi) blocked an EWS-FLI1 specific expression profile, while Entinostat in addition suppressed metastasis relevant genes. EwS cells demonstrated increased susceptibility to treatment with chemotherapeutics including Doxorubicin in the presence of HDACi. Furthermore, HDACi treatment mimicked RNAi of EZH2 in EwS. Treated cells showed diminished growth capacity, but an increased endothelial as well as neuronal differentiation ability. HDACi synergizes with EED inhibitor (EEDi) in vitro and together inhibited tumor growth in xenograft mice. Co-IP experiments identified HDAC class I family members as part of a regulatory complex together with PRC2. Conclusions: Class I HDAC proteins seem to be important mediators of the pathognomonic EWS-ETS-mediated transcription program in EwS and in combination therapy, co-treatment with HDACi is an interesting new treatment opportunity for this malignant disease. [ABSTRACT FROM AUTHOR]

Enzyme reactions, both in Nature and technical applications, commonly occur at the interface of immiscible phases. Nevertheless, stringent descriptions of interfacial enzyme catalysis remain sparse, and this is partly due to a shortage of coherent experimental data to guide and assess such work. In this work, we produced and kinetically characterized 83 cellulases, which revealed a conspicuous linear free energy relationship (LFER) between the substrate binding strength and the activation barrier. The scaling occurred despite the investigated enzymes being structurally and mechanistically diverse. We suggest that the scaling reflects basic physical restrictions of the hydrolytic process and that evolutionary selection has condensed cellulase phenotypes near the line. One consequence of the LFER is that the activity of a cellulase can be estimated from its substrate binding strength, irrespectively of structural and mechanistic details, and this appears promising for in silico selection and design within this industrially important group of enzymes. Enzyme reactions at interfaces are common in both Nature and industrial applications but no general kinetic framework exists for interfacial enzymes. Here, the authors kinetically characterize 83 cellulases and identify a scaling relationship between ligand binding strength and maximal turnover, a so-called linear free energy relationship, which may help rationalize cellulolytic mechanisms and guide the selection of technical enzymes. [ABSTRACT FROM AUTHOR]

The pterin-dependent nonheme iron enzymes hydroxylate aromatic amino acids to perform the biosynthesis of neurotransmitters to maintain proper brain function. These enzymes activate oxygen using a pterin cofactor and an aromatic amino acid substrate bound to the FeII active site to form a highly reactive FeIV = O species that initiates substrate oxidation. In this study, using tryptophan hydroxylase, we have kinetically generated a pre-FeIV = O intermediate and characterized its structure as a FeII-peroxy-pterin species using absorption, Mössbauer, resonance Raman, and nuclear resonance vibrational spectroscopies. From parallel characterization of the pterin cofactor and tryptophan substrate-bound ternary FeII active site before the O2 reaction (including magnetic circular dichroism spectroscopy), these studies both experimentally define the mechanism of FeIV = O formation and demonstrate that the carbonyl functional group on the pterin is directly coordinated to the FeII site in both the ternary complex and the peroxo intermediate. Reaction coordinate calculations predict a 14 kcal/mol reduction in the oxygen activation barrier due to the direct binding of the pterin carbonyl to the FeII site, as this interaction provides an orbital pathway for efficient electron transfer from the pterin cofactor to the iron center. This direct coordination of the pterin cofactor enables the biological function of the pterin-dependent hydroxylases and demonstrates a unified mechanism for oxygen activation by the cofactor-dependent nonheme iron enzymes. [ABSTRACT FROM AUTHOR]

Cepheids in multiple systems provide information on the outcome of the formation of massive stars. They can also lead to exotic end-stage objects. This study concludes our survey of 70 galactic Cepheids using the Hubble Space Telescope (HST) Wide Field Camera 3 (WFC3) with images at two wavelengths to identify companions closer than 5″. In the entire WFC3 survey we identify 16 probable companions for 13 Cepheids. The 7 Cepheids having resolved candidate companions within 2″ all have the surprising property of themselves being spectroscopic binaries (as compared with a 29% incidence of spectroscopic binaries in the general Cepheid population). This is a strong suggestion that an inner binary is linked to the scenario of a third companion within a few hundred astronomical units. This characteristic is continued for more widely separated companions. Under a model where the outer companion is formed first, it is unlikely that it can anticipate a subsequent inner binary. Rather, it is more likely that a triple system has undergone dynamical interaction, resulting in one star moving outward to its current location. Chandra and Gaia data as well as radial velocities and HST/STIS and IUE spectra are used to derive properties of the components of the Cepheid systems. The colors of the companion candidates show a change in distribution at approximately 2000 au separations, from a range including both hot and cool colors for closer companions, to only low-mass companions for wider separations. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via the original article. [ABSTRACT FROM AUTHOR]

Background: Cellobiohydrolase from glycoside hydrolase family 7 is a major component of commercial enzymatic mixtures for lignocellulosic biomass degradation. For many years, Trichoderma reesei Cel7A (TrCel7A) has served as a model to understand structure–function relationships of processive cellobiohydrolases. The architecture of TrCel7A includes an N-glycosylated catalytic domain, which is connected to a carbohydrate-binding module through a flexible, O-glycosylated linker. Depending on the fungal expression host, glycosylation can vary not only in glycoforms, but also in site occupancy, leading to a complex pattern of glycans, which can affect the enzyme's stability and kinetics. Results: Two expression hosts, Aspergillus oryzae and Trichoderma reesei, were utilized to successfully express wild-types TrCel7A (WTAo and WTTr) and the triple N-glycosylation site deficient mutants TrCel7A N45Q, N270Q, N384Q (ΔN-glycAo and ΔN-glycTr). Also, we expressed single N-glycosylation site deficient mutants TrCel7A (N45QAo, N270QAo, N384QAo). The TrCel7A enzymes were studied by steady-state kinetics under both substrate- and enzyme-saturating conditions using different cellulosic substrates. The Michaelis constant (KM) was consistently found to be lowered for the variants with reduced N-glycosylation content, and for the triple deficient mutants, it was less than half of the WTs' value on some substrates. The ability of the enzyme to combine productively with sites on the cellulose surface followed a similar pattern on all tested substrates. Thus, site density (number of sites per gram cellulose) was 30–60% higher for the single deficient variants compared to the WT, and about twofold larger for the triple deficient enzyme. Molecular dynamic simulation of the N-glycan mutants TrCel7A revealed higher number of contacts between CD and cellulose crystal upon removal of glycans at position N45 and N384. Conclusions: The kinetic changes of TrCel7A imposed by removal of N-linked glycans reflected modifications of substrate accessibility. The presence of N-glycans with extended structures increased KM and decreased attack site density of TrCel7A likely due to steric hindrance effect and distance between the enzyme and the cellulose surface, preventing the enzyme from achieving optimal conformation. This knowledge could be applied to modify enzyme glycosylation to engineer enzyme with higher activity on the insoluble substrates. [ABSTRACT FROM AUTHOR]

Fusion technology is widely used in protein-drug development to increase activity, stability, and bioavailability of protein therapeutics. Fusion proteins, like any other type of biopharmaceuticals, need to remain stable during production and storage. Due to the high complexity and additional intramolecular interactions, it is not possible to predict the behavior of fusion proteins based on the behavior the individual proteins. Therefore, understanding the stability of fusion proteins on the molecular level is crucial for the development of biopharmaceuticals. The current study on the albumin-neprilysin (HSA-NEP) fusion protein uses a combination of thermal and chemical unfolding with small angle X-ray scattering and molecular dynamics simulations to show a correlation between decreasing stability and increasing repulsive interactions, which is unusual for most biopharmaceuticals. It is also seen that HSA-NEP is not fully flexible: it is present in both compact and extended conformations. Additionally, the volume fraction of each conformation changes with pH. Finally, the presence of NaCl and arginine increases stability at pH 6.5, but decreases stability at pH 5.0. [ABSTRACT FROM AUTHOR]

Determining the requirements for efficient oxygen (O2) activation is key to understanding how enzymes maintain efficacy and mitigate unproductive, often detrimental reactivity. For the α-ketoglutarate (αKG)-dependent nonheme iron enzymes, both a concerted mechanism (both cofactor and substrate binding prior to reaction with O2) and a sequential mechanism (cofactor binding and reaction with O2 precede substrate binding) have been proposed. Deacetoxycephalosporin C synthase (DAOCS) is an αKG-dependent nonheme iron enzyme for which both of these mechanisms have been invoked to generate an intermediate that catalyzes oxidative ring expansion of penicillin substrates in cephalosporin biosynthesis. Spectroscopy shows that, in contrast to other αKG-dependent enzymes (which are six coordinate when only αKG is bound to the FeII), αKG binding to FeII-DAOCS results in ∼45% five-coordinate sites that selectively react with O2 relative to the remaining six-coordinate sites. However, this reaction produces an FeIII species that does not catalyze productive ring expansion. Alternatively, simultaneous αKG and substrate binding to FeII-DAOCS produces five-coordinate sites that rapidly react with O2 to form an FeIV=O intermediate that then reacts with substrate to produce cephalosporin product. These results demonstrate that the concerted mechanism is operative in DAOCS and by extension, other nonheme iron enzymes. [ABSTRACT FROM AUTHOR]

Serial X-ray crystallography at free-electron lasers allows to solve biomolecular structures from sub-micron-sized crystals. However, beam time at these facilities is scarce, and involved sample delivery techniques are required. On the other hand, rotation electron diffraction (MicroED) has shown great potential as an alternative means for protein nano-crystallography. Here, we present a method for serial electron diffraction of protein nanocrystals combining the benefits of both approaches. In a scanning transmission electron microscope, crystals randomly dispersed on a sample grid are automatically mapped, and a diffraction pattern at fixed orientation is recorded from each at a high acquisition rate. Dose fractionation ensures minimal radiation damage effects. We demonstrate the method by solving the structure of granulovirus occlusion bodies and lysozyme to resolutions of 1.55 Å and 1.80 Å, respectively. Our method promises to provide rapid structure determination for many classes of materials with minimal sample consumption, using readily available instrumentation. For conventional three-dimensional microcrystal electron diffraction (3D ED/MicroED), a crystal is slowly rotated under an electron beam, leading to inevitable accumulation of radiation damage during data collection. In this work, the authors present a serial electron diffraction method, where still diffraction patterns from many protein nanocrystals are rapidly recorded and merged, which minimises radiation damage and only requires a slightly modified standard scanning transmission electron microscope. [ABSTRACT FROM AUTHOR]

One of the most challenging tasks of companies with complex and discrete production systems is to determine an appropriate production control strategy (PCS). The PCS is crucial, as it influences inventory, costs, and service. We propose a framework to address the most important questions of PCS engineering: limiting work in process, positioning the order penetration point (OPP), and coping with demand uncertainty upstream the OPP. Thereby, uncertain advance demand information in the form of forecasts is considered and desirable characteristics of push and pull strategies are combined. A serial manufacturing system with multiple products, variable processing times, and uncertain advance demand information is examined. The model is formulated as a queuing network model and solved numerically by discrete-event simulation. The framework and a resulting hybrid control strategy are applied to a case study from electronics manufacturing, where a significant improvement potential is identified. [ABSTRACT FROM PUBLISHER]

We describe a method for extending radial distribution functions obtained from molecular simulations of pure and mixed molecular fluids to arbitrary distances. The method allows total correlation function integrals to be reliably calculated from simulations of relatively small systems. The long-distance behavior of radial distribution functions is determined by requiring that the corresponding direct correlation functions follow certain approximations at long distances. We have briefly described the method and tested its performance in previous communications [R. Wedberg, J. P. O'Connell, G. H. Peters, and J. Abildskov, Mol. Simul. 36, 1243 (2010); Fluid Phase Equilib. 302, 32 (2011)], but describe here its theoretical basis more thoroughly and derive long-distance approximations for the direct correlation functions. We describe the numerical implementation of the method in detail, and report numerical tests complementing previous results. Pure molecular fluids are here studied in the isothermal-isobaric ensemble with isothermal compressibilities evaluated from the total correlation function integrals and compared with values derived from volume fluctuations. For systems where the radial distribution function has structure beyond the sampling limit imposed by the system size, the integration is more reliable, and usually more accurate, than simple integral truncation. [ABSTRACT FROM AUTHOR]

The confinement analysis from bulk structure (CABS) approach [Y. Wang et al., J. Chem. Phys. 128, 124904 (2008)] is extended to determine the depletion profiles of dilute polymer solutions confined to a slit or near an inert wall. We show that the entire spatial density distributions of any reference point in the polymer chain (such as the center of mass, middle segment, and end segments) can be computed as a function of the confinement size solely based on a single sampling of the configuration space of a polymer chain in bulk. Through a simple analysis based on the CABS approach in the case of a single wall, we prove rigorously that (i) the depletion layer thickness δ is the same no matter which reference point is used to describe the depletion profile and (ii) the value of δ equals half the average span (the mean projection onto a line) of the macromolecule in free solution. Both results hold not only for ideal polymers, as has been noticed before, but also for polymers regardless of details in molecular architecture and configuration statistics. [ABSTRACT FROM AUTHOR]

We present a new framework for the description of macromolecules subject to confining geometries. The two main ingredients are a new computational method and the definition of a new molecular size parameter. The computational method, hereafter referred to the confinement analysis from bulk structures (CABS), allows the computation of equilibrium partition coefficients as a function of confinement size solely based on a single sampling of the configuration space of a macromolecule in bulk. Superior in computational speed to previous computational methods, CABS is capable of handling slits, channels, and box confining geometries for all molecular architectures. The new molecular size parameter, hereafter referred to the steric exclusion radius Rs, is explicitly defined and computed for a number of rigid objects and flexible polymers. We suggest that Rs is the relevant molecular size parameter for characterization of spatial confinement effects on macromolecules. Results for the equilibrium partition coefficient in the weak confinement regime depend only on the ratio of Rs to the confinement size regardless of molecular details. [ABSTRACT FROM AUTHOR]

In printed circuit board (PCB) assembly, collect-and-place machines, which use a revolver-type placement head to mount electronic components onto the board, represent one of the most popular types of assembly machinery. The assignment of feeders to slots in the component magazine and the sequencing of the placement operations are the main optimisation problems for scheduling the operations of an automated placement machine. In this paper, we present different genetic algorithms (GAs) for simultaneously solving these highly interrelated problems for collect-and-place machines in PCB assembly. First we consider single-gantry machines as the basic type of machinery. In the conventional GA approach all placement operations and the feeder-slot assignment are represented by a single chromosome. In order to increase the efficiency of the genetic operators, we present a novel GA approach, which integrates a clustering algorithm for generating sub-sections of the PCB and grouping the corresponding placement operations. It is shown that the proposed GAs can be extended to schedule dual-gantry placement machines, which are equipped with two independent placement heads and two dedicated component magazines. Hence, component feeders have to be allocated between the two magazines. To solve this allocation problem, two different heuristic strategies are proposed. Finally, detailed numerical experiments are carried out to evaluate the performances of the proposed GAs. [ABSTRACT FROM AUTHOR]

Balancing setup effort and actual production time is an important issue in medium-variety, medium-volume printed circuit board (PCB) assembly. By grouping batches of similar PCB types to be processed with a common machine setup, the total time required for setting up the component feeders in the magazine of the placement machine can be reduced. On the other hand, the assembly times per PCB increase, since it is no longer possible to optimise the feeder locations in the magazine for each PCB type individually. In order to balance the savings in setup time and the increase in assembly time and to minimise the global makespan, we propose efficient grouping procedures which include machine-specific algorithms for fine-tuning the machine operations for a group of PCBs. Hence, the actual placement times are reflected much more accurately, compared with conventional grouping procedures which merely analyse the component similarity between pairs of PCBs. Two different agglomerative clustering techniques are proposed. One is based on average linkage clustering, the other on a novel hierarchical clustering approach using an inclusion tree representation of the PCB types. Both take the limited capacity of the component magazine into account. We demonstrate the effectiveness of our approach in an extensive numerical investigation of a single-gantry collect-and-place machine equipped with a rotary placement head and an interchangeable feeder trolley. Compared to conventional methodologies, the proposed group setup strategies reduce the global makespan for a given number of batches significantly. [ABSTRACT FROM AUTHOR]

In the industrial application environment considered, different variants of a basic product type are produced using the same resources and following the same basic process plan. To support production planning and scheduling for this type of production system, the concept of block planning is introduced, which has gained considerable attention, particularly in the consumer goods industry. A block represents a pre-defined sequence of production orders of variable size. In order to demonstrate the practical applicability of the proposed block planning concept, we consider the production system of a major producer of hair dyes as a case study. We present two different implementations of the block planning concept. One utilizes the Production Planning/Detailed Scheduling module of the SAP APO © software. The other approach is based on a mixed-integer linear programming formulation. In contrast to the academic literature, a continuous representation of time is chosen. Thus, the number of variables and constraints could be considerably reduced. The approach suggested is computationally very efficient and provides the flexibility to model a variety of application specific features. [ABSTRACT FROM AUTHOR]

In the production of perishable products such as dairy, meat or bakery goods, the consideration of shelf life in production planning is of particular importance. Retail customers with relatively low inventory turns can benefit significantly from longer product shelf life as wastage and out-of-stock rates decrease. However, in today's production planning and control systems, shelf-life issues with regard to specific products or customers are only seldom accounted for. Therefore, the objective of this paper is to develop Mixed-Integer Linear Programming (MILP) models that integrate shelf-life issues into production planning and scheduling. The research is based on an industrial case study of yoghurt production. Relying on the principle of block planning, three different MILP models for weekly production planning are presented that apply a combination of a discrete and continuous representation of time. Overnight production and, hence, the necessity for identifying two different shelf-life values for the same production lot is included in the model formulation. Numerical experiments show that near-optimal solutions can be obtained within reasonable computational time. [ABSTRACT FROM AUTHOR]

Structural and dynamic properties of water confined between two parallel, extended, either hydrophobic or hydrophilic crystalline surfaces of n-alkane C36H74 or n-alcohol C35H71OH, are studied by molecular dynamics simulations. Electron density profiles, directly compared with corresponding experimental data from x-ray reflectivity measurements, reveal a uniform weak de-wetting characteristic for the extended hydrophobic surface, while the hydrophilic surface is weakly wetted. These microscopic data are consistent with macroscopic contact angle measurements. Specific water orientation is present at both surfaces. The ordering is characteristically different between the surfaces and of longer range at the hydrophilic surface. Furthermore, the dynamic properties of water are different at the two surfaces and different from the bulk behavior. In particular, at the hydrophobic surface, time-correlation functions reveal that water molecules have characteristic diffusive behavior and orientational ordering due to the lack of hydrogen bonding interactions with the surface. These observations suggest that the altered dynamical properties of water in contact with extended hydrophobic surfaces together with a partial drying of the surfaces are more indicative of the hydrophobic effect than structural ordering, which we suggest to be independent of surface topology. [ABSTRACT FROM AUTHOR]

In automated printed circuit board (PCB) assembly, modular placement machines represent the most recent type of machinery. Similar to assembly lines they require the workload between their modules to be balanced in order to achieve the desired output rate. To optimize the operations of this type of machinery, we present an integer programming (IP) model and two different heuristic solution procedures. In the first stage of both heuristics, a feasible solution with respect to the limited component magazine capacity at each module of the placement machine is determined. Priority rules are used for generating an initial assignment of components to the various modules of the machine. In the second stage, the workload of the modules is balanced in order to minimize the resulting cycle time. Two alternative approaches are offered. The first one uses priority rules in order to de-bottleneck the workload by reassigning assembly operations to other modules of the machine, whereas the second one determines an exact solution to this sub-problem by solving an IP. The approaches presented are especially designed to consider the technological constraints arising from the design of modular placement machines. Numerical investigations reveal that optimal solutions can be obtained for all but a few extreme and hypothetical cases within short CPU times. In a case study investigation, it could be shown that the output rate of a modular placement machine is considerably increased compared with solutions applied in industry. [ABSTRACT FROM AUTHOR]

Due to the high degree of automation in modern printed circuit board (PCB) assembly, production planning and scheduling in this industry relies heavily on the accuracy of the underlying models of the automated machinery. In this paper, the derivation of such mathematical models is exemplified for one of the most wide-spread machine types (the so-called chip shooter). Moreover, a simulation system for practical use in the electronics assembly is presented which incorporates various types of assembly machines. It serves as a tactical production planning aid as well as a test field for the analysis of the kinematic processes of PCB assembly machines. Such simulation, tailored to the specifics of a production environment, gives reliable estimates of the achievable production volume. Considerable deviations between the performance figures provided by the machine supplier and the actual result can thus be explained, and potential assembly system configurations be compared by drawing on reliable measures. Since the equipment is modelled at a level which takes precise account of its specific kinematics, a detailed analysis of the operations of the individual machine can also be performed revealing potential bottlenecks in its design. These insights are used to optimize machine design and control. Methods based on graph theory as well as on modern numerical search algorithms have been developed for the latter purpose. They lead to considerable performance improvements. [ABSTRACT FROM AUTHOR]

A mixed-integer linear programming (MILP) model for scheduling chemical batch processes is presented. Since computational times are prohibitive for most problems of realistic size, a two-stage solution procedure is suggested. In the first stage, an initial solution is derived by use of a LP-based heuristic. The proposed heuristic defines a time grid that includes only a limited number of feasible periods in which a processing task is allowed to start. Thus, the size of the original multi-period MILP model is reduced in a controlled manner and optimal solutions to the relaxed model are obtained within reasonable computational time. The second stage consists of an improvement step that aims to compress the initial schedule by left-shifting operations over the time-axis. In order to evaluate the applicability of the heuristics a number of numerical experiments were performed. It is shown that near-optimal solutions are obtained for largesize problems with only modest computational effort. [ABSTRACT FROM AUTHOR]

Purpose: Data on the output correction factor for small photon beam dosimetry of the microDiamond detector manufactured by the company PTW can be found in a variety of papers. Referring either to measurements or to Monte Carlo (MC) calculations, they show substantial disagreements particularly at very small fields. This work reports results of a further MC study aiming at a better understanding of how specific properties of the microDiamond detector are influencing its output correction factor and whether this can explain at least some of the disagreements. Methods: In this study the method of a fluence‐based decomposition of the dose conversion factor was used which is considered as a useful tool to understand the response of a detector in nonreference conditions. This decomposition method yields the following three factors: (a) the stopping power ratio water to diamond, (b) a perturbation factor pint taking into account all fluence changes in the transition from a small water voxel at the point of dose determination to the bare diamond detector, and (c) a perturbation factor pext taking into account all additional fluence changes in the fully simulated diamond detector caused by the material and design details outside the sensitive volume. Results: Monte Carlo calculated output correction factors were obtained for Co‐60, 6 MV and 10 MV photon beams showing that the maximum variation with field size remained in the order of 2% for quadratic field sizes larger than about 0.3 cm. For field sizes smaller than about 0.5 cm a clear under‐response is obtained at all three radiation qualities in agreement with all known MC calculations, however, in contrast to some measured result. The shape of the output correction factor can be well explained by an opposite mode of action between under‐response expressed by the perturbation factor pint and over‐response expressed by the perturbation factor pext where the first one is mainly influenced by volume averaging, and the second one by a back scatter effect of electrons from the diamond substrate into the sensitive volume. Conclusion: The response of microDiamond detector can be well described under various measuring conditions by the dose conversion factor and the dependency of its fluence‐based subfactors on detector characteristics. Monte Carlo simulations offer an improvement in the understanding particularly of small‐field effects by relating the output correction factor to spectral fluence changes in the sensitive volume of the detector. The most significant influence factors are the finite size of the active volume and the presence of the high‐density diamond substrate causing a field size‐dependent backscattering. These perturbations are opposite in their effects. The diamond in the sensitive volume itself and in particular its density has almost no influence. Scattering of results at very small field sizes can be explained by different gradients of dose profiles around the beam axis at identical full width half maximum (FWHM) field size parameters and by possible deviations of the radius of the sensitive volume from the nominal radius. The backscattering effect also has an influence on the determination of profiles and for very small field sizes on the response at different rotation angles. [ABSTRACT FROM AUTHOR]

The mass accretion rate is a crucial parameter for the study of the evolution of accretion discs around young low-mass stellar and substellar objects (YSOs). We revisit the case of MY Lup, an object where VLT/X-shooter data suggested a negligible mass accretion rate, and show it to be accreting on a level similar to other Class II YSOs in Lupus based on Hubble Space Telescope (HST) observations. In our HST-Cosmic Origins Spectrograph (HST-COS) and -Space Telescope Imaging Spectrograph (HST-STIS) spectra, we find many emission lines, as well as substantial far-ultraviolet (FUV) continuum excess emission, which can be ascribed to active accretion. The total luminosity of the C IVλ1549 Å doublet is 4.1 × 10−4L⊙. Using scalings between accretion luminosity, Lacc, and C IV luminosity from the literature, we derive Lacc ~2 × 10−1L⊙, which is more than an order of magnitude higher than the upper limit estimated from the X-shooter observations. We discuss possible reasons for the X-shooter-HST discrepancy, the most plausible being that the low contrast between the continuum excess emission and the photospheric+chromospheric emission at optical wavelengths in MY Lup hampered detection of excess emission. The luminosity of the FUV continuum and C IV lines, strong H2 fluorescence, and a "1600 A Bump" place MY Lup in the class of accreting objects with gas-rich discs. So far, MY Lup is the only peculiar case in which a significant difference between the HST and X-shooter Ṁacc estimates exists that is not ascribable to variability. The mass accretion rate inferred from the revisited Lacc estimate is Ṁacc ~ 1(−0.5+1.5 $^{+1.5}_{-0.5}$ − 0.5 + 1.5 ) × 10−8M⊙ yr−1. This value is consistent with the typical value derived for accreting YSOs of similar mass in Lupus and points to less clearing of the inner disc than indicated by near- and mid-infrared observations. This is confirmed by Atacama Large Millimeter Array (ALMA) data, which show that the gaps and rings seen in the sub-millimetre are relatively shallow. [ABSTRACT FROM AUTHOR]

The lipidation of peptide drugs is one strategy to obtain extended half‐lives, enabling once‐daily or even less frequent injections for patients. The half‐life extension results from a combination of self‐association and association with human serum albumin (albumin). The self‐association and association with albumin of two insulin analogues, insulin detemir and insulin degludec, were investigated by small‐angle X‐ray scattering (SAXS) and dynamic light scattering (DLS) in phenolic buffers. Detemir shows concentration‐dependent self‐association, with an equilibrium between hexamer, dihexamer, trihexamer and larger species, while degludec appears as a dihexamer independent of concentration. The solution structure of the detemir trihexamer has a bent shape. The stoichiometry of the association with albumin was studied using DLS. For albumin–detemir the molar stoichiometry was determined to be 1:6 (albumin:detemir ratio) and for albumin–degludec it was between 1:6 and 1:12 (albumin:degludec ratio). Batch SAXS measurements of a 1:6 albumin:detemir concentration series revealed a concentration dependence of complex formation. The data allowed the modelling of a complex between albumin and a detemir hexamer and a complex consisting of two albumins binding to opposite ends of a detemir dihexamer. Measurements of size‐exclusion chromatography coupled to SAXS revealed a complex between a degludec dihexamer and albumin. Based on the results, equilibria for the albumin–detemir and albumin–degludec mixtures are proposed. Solution structures of complexes between human serum albumin and the two lipidated insulin analogues detemir and degludec are presented and models for the equilibria are suggested. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations of diglyceride monolayers at the air–water interface have been performed to study the dynamical behavior of these Langmuir layers at surface densities varying from 36.2 to 40.5 Å2/molecule. The monolayers are treated in full atomic detail, with the exception of methyl and methylene groups that are considered to be ‘‘anisotropic united atoms.’’ The presence of phase transitions are explored and correlated to the changes in the microstructure of the layer. Good agreement is found between the surface pressure–surface area (π-A) isotherms calculated in the simulations and determined in monolayer technique experiments. The diglyceride film shows a complex dynamical behavior during expansion. On expansion from a closely packed, highly ordered state, the film undergoes two phase transitions. The first transition, which occurs at 38.3 Å2/molecule, involves a ‘‘seesaw’’ mechanism of the sn-1 and sn-2 carboxyester groups. The latter forms the backbone of the diglyceride molecule at high surface pressure. This mechanism is governed by hydrophobic/hydrophilic forces. It is stabilized by a balance between inter- and intramolecular interactions. On expansion, the intermolecular interaction decreases, and at the first transition, the intramolecular interaction between the two chains are strong enough to cause an increase of the cross sectional area of the molecules. This swelling of the molecules is accompanied with an increase of intermolecular contributions. The second transition, which occurs at 39.8 Å2/molecule, is caused by tilting over nearest neighbors. [ABSTRACT FROM AUTHOR]

Monte Carlo simulations of mixtures of charged and multipolar hard spheres with equivalent diameters are presented. A solution with dipolar solvent at a state point considered earlier, with greatly different results, by Chan et al. [Mol. Phys. 66, 299 (1989)] and by Caillol et al. [Mol. Phys. 69, 199 (1990)] is re-examined. Structural, thermodynamic, and dielectric properties are determined and particle number dependence in these averages is examined. The rate of convergence is shown to be satisfactory for correlation functions, other than that of repulsive ion pairs, and for thermodynamic properties. These are in good agreement with hypernetted chain theory. The reliability of the Metropolis Monte Carlo technique for the evaluation of thermodynamic properties in conveniently small systems of this solution model is established. We also consider a solution in which the solvent has both dipolar and linear quadrupolar symmetry. Two smaller systems give structural and thermodynamic properties in good agreement with hypernetted chain theory. In a larger system ionic clustering occurs to produce very different solution structure. [ABSTRACT FROM AUTHOR]

Helmholtz free energies, internal energies, and pressures of mixtures of charged and dipolar hard spheres are obtained from Monte Carlo computer simulation. Ionic and solvent contributions to these properties of this electrolyte solution model are reported for a large number of states, with variations in total density, ionic concentration, and the ratio of ionic charge to solvent polarity. From this data we show that, in contrast to solution theories based on replacement of the solvent by a continuum with dielectric constant ε0, there is a correspondence in properties of states at fixed κ02=κ2ε0, where κ is the inverse Debye length. [ABSTRACT FROM AUTHOR]

Purpose: The dose conversion factor plays an important role in the dosimetry by enabling the absorbed dose in the sensitive volume of a detector to be converted into the absorbed dose in the surrounding medium (in most cases water). The purpose of this paper is to demonstrate that a specific fluence‐based approach for the decomposition of the dose conversion factor is in particular useful for the interpretation of the influences of detector properties on measurements under nonreference conditions. Methods: Data for the dose conversion factor and secondary fluence spectra were obtained by the Monte Carlo method. The calculation of the secondary charged particle fluence (electrons and positrons) in the sensitive detector volume was imbedded into the code for the calculation of absorbed dose in the detector. The decomposition method into subfactors is based on the use of these fluence data applied to a stepwise transition from the dose at the point of measurement next to a pure water detector and finally to the fully simulated detector geometry. Each subfactor is obtained as a ratio, at which the stopping power only is different in the numerator and the denominator or at which the fluence only is different in the numerator and the denominator. This method was applied at photon dose profiles obtained in water at different radiation qualities and with various detectors of cylindrical type. Results: The resulting subfactors can be well identified as a stopping power ratio and as perturbation factors each reflecting particular detector properties. Two of them ( f 1 and f4) are equivalent with perturbation factors which have already been introduced by other authors previously. These are the volume perturbation factor and the extracameral perturbation factor. Subfactor f 2 denoted as medium perturbation factor was found to resemble the density perturbation factor. Results obtained for the volume perturbation factor applied to dose profiles measured with cylindrical detectors confirm that the volume effect can be well described by a convolution of the true profile in water with a Gaussian kernel. It was found that the sigma parameter depends on the cylinder radius only and amounts almost exactly to half of its value. The medium perturbation factor strongly depends on the density of the detector medium. For an air‐filled detector, the influence of the air again can be described by a Gauss convolution, however, with a less good agreement. For detectors with a density of the cavity medium larger than that of water, for instance, for a diamond detector, it was found that there is a tendency of compensation between the volume averaging effect and the medium effect. Conclusion: The fluence‐based decomposition of the dose conversion factor leads to a fluence‐based formulation of perturbation factors, referred to as volume, medium, and extracameral perturbation factor. These factors offer useful explanations for the behavior of detectors in nonreference conditions. An example was given for cylindrical detectors at dose profile measurements. [ABSTRACT FROM AUTHOR]

Disk warps around classical T Tauri stars (CTTSs) can periodically obscure the central star for some viewing geometries. For these so- called AA Tau-like variables, the obscuring material is located in the inner disk and absorption spectroscopy allows one to characterize its dust and gas content. Since the observed emission from CTTSs consists of several components (photospheric, accretion, jet, and disk emission), which can all vary with time, it is generally challenging to disentangling disk features from emission variability. Multi- epoch, flux-calibrated, broadband spectra provide us with the necessary information to cleanly separate absorption from emission variability. We applied this method to three epochs of VLT/X-shooter spectra of the CTTS V 354 Mon (CSI Mon-660) located in NGC 2264 and find that: (a) the accretion emission remains virtually unchanged between the three epochs; (b) the broadband flux evolution is best described by disk material obscuring part of the star, and (c) the Na and K gas absorption lines show only a minor increase in equivalent width during phases of high dust extinction. The limits on the absorbing gas column densities indicate a low gas-to-dust ratio in the inner disk, less than a tenth of the ISM value. We speculate that the evolutionary state of V 354 Mon, rather old with a low accretion rate, is responsible for the dust excess through an evolution toward a dust dominated disk or through the fragmentation of larger bodies that drifted inward from larger radii in a still gas dominated disk. [ABSTRACT FROM AUTHOR]