AMMOS: A Software Platform to Assist in silico Screening

Three software packages based on the common platform of AMMOS (Automated Molecular Mechanics Optimization tool for in silico Screening) for assisting virtual ligand screening purposes have been recently developed. DG-AMMOS allows generation of 3D conformations of small molecules using distance geometry and molecular mechanics optimization. AMMOS_SmallMol is a package for structural refinement of compound collections that can be used prior to docking experiments. AMMOS_ProtLig is a package for energy minimization of protein-ligand complexes. It performs an automatic procedure for molecular mechanics minimization at different levels of flexibility - from rigid to fully flexible structures of both the ligand and the receptor. The packages have been tested on small molecules with a high structural diversity and proteins binding sites of completely different geometries and physicochemical properties. The platform is developed as an open source software and can be used in a broad range of in silico drug design studies

Exploring NMR ensembles of calcium binding proteins: Perspectives to design inhibitors of protein-protein interactions

<p>Abstract</p> <p>Background</p> <p>Disrupting protein-protein interactions by small organic molecules is nowadays a promising strategy employed to block protein targets involved in different pathologies. However, structural changes occurring at the binding interfaces make difficult drug discovery processes using structure-based drug design/virtual screening approaches. Here we focused on two homologous calcium binding proteins, calmodulin and human centrin 2, involved in different cellular functions via protein-protein interactions, and known to undergo important conformational changes upon ligand binding.</p> <p>Results</p> <p>In order to find suitable protein conformations of calmodulin and centrin for further structure-based drug design/virtual screening, we performed <it>in silico </it>structural/energetic analysis and molecular docking of terphenyl (a mimicking alpha-helical molecule known to inhibit protein-protein interactions of calmodulin) into X-ray and NMR ensembles of calmodulin and centrin. We employed several scoring methods in order to find the best protein conformations. Our results show that docking on NMR structures of calmodulin and centrin can be very helpful to take into account conformational changes occurring at protein-protein interfaces.</p> <p>Conclusions</p> <p>NMR structures of protein-protein complexes nowadays available could efficiently be exploited for further structure-based drug design/virtual screening processes employed to design small molecule inhibitors of protein-protein interactions.</p

Statistical Evidence for Contributions of Flares and Coronal Mass Ejections to Major Solar Energetic Particle Events

Solar energetic particle (SEP) events are related to flares and coronal mass ejections (CMEs). This work is a new investigation of statistical relationships between SEP peak intensities - deka-MeV protons and near-relativistic electrons - and characteristic quantities of the associated solar activity. We consider the speed of the CME and quantities describing the flare-related energy release: peak flux and fluence of soft X-ray (SXR) emission, fluence of microwave emission. The sample comprises 38 SEP events associated with strong SXR bursts (classes M and X) in the western solar hemisphere between 1997 and 2006, and where the flare-related particle acceleration is accompanied by radio bursts indicating electron escape to the interplanetary space. The main distinction of the present statistical analysis from earlier work is that besides the classical Pearson correlation coefficient the partial correlation coefficients are calculated in order to disentangle the effects of correlations between the solar parameters themselves. The classical correlation analysis shows the usual picture of correlations with broad scatter between SEP peak intensities and the different parameters of solar activity, and strong correlations between the solar activity parameters themselves. The partial correlation analysis shows that the only parameters that affect significantly the SEP intensity are the CME speed and the SXR fluence. The SXR peak flux and the microwave fluence have no additional contribution. We conclude that these findings bring statistical evidence that both flare acceleration and CME shock acceleration contribute to the deka-MeV proton and near-relativistic electron populations in large SEP events.Comment: The final publication is available at Springer via http://dx.doi.org/10.1007/s11207-014-0628-

Frog: a FRee Online druG 3D conformation generator

In silico screening methods based on the 3D structures of the ligands or of the proteins have become an essential tool to facilitate the drug discovery process. To achieve such process, the 3D structures of the small chemical compounds have to be generated. In addition, for ligand-based screening computations or hierarchical structure-based screening projects involving a rigid-body docking step, it is necessary to generate multi-conformer 3D models for each input ligand to increase the efficiency of the search. However, most academic or commercial compound collections are delivered in 1D SMILES (simplified molecular input line entry system) format or in 2D SDF (structure data file), highlighting the need for free 1D/2D to 3D structure generators. Frog is an on-line service aimed at generating 3D conformations for drug-like compounds starting from their 1D or 2D descriptions. Given the atomic constitution of the molecules and connectivity information, Frog can identify the different unambiguous isomers corresponding to each compound, and generate single or multiple low-to-medium energy 3D conformations, using an assembly process that does not presently consider ring flexibility. Tests show that Frog is able to generate bioactive conformations close to those observed in crystallographic complexes. Frog can be accessed at http://bioserv.rpbs.jussieu.fr/Frog.html

Neural Networks for Hyperspectral Imaging of Historical Paintings: A Practical Review

Hyperspectral imaging (HSI) has become widely used in cultural heritage (CH). This very efficient method for artwork analysis is connected with the generation of large amounts of spectral data. The effective processing of such heavy spectral datasets remains an active research area. Along with the firmly established statistical and multivariate analysis methods, neural networks (NNs) represent a promising alternative in the field of CH. Over the last five years, the application of NNs for pigment identification and classification based on HSI datasets has drastically expanded due to the flexibility of the types of data they can process, and their superior ability to extract structures contained in the raw spectral data. This review provides an exhaustive analysis of the literature related to NNs applied for HSI data in the CH field. We outline the existing data processing workflows and propose a comprehensive comparison of the applications and limitations of the various input dataset preparation methods and NN architectures. By leveraging NN strategies in CH, the paper contributes to a wider and more systematic application of this novel data analysis method

Comparison of 30 THz impulsive burst time development to microwaves, H-alpha, EUV, and GOES soft X-rays

The recent discovery of impulsive solar burst emission in the 30 THz band is raising new interpretation challenges. One event associated with a GOES M2 class flare has been observed simultaneously in microwaves, H-alpha, EUV, and soft X-ray bands. Although these new observations confirm some features found in the two prior known events, they exhibit time profile structure discrepancies between 30 THz, microwaves, and hard X-rays (as inferred from the Neupert effect). These results suggest a more complex relationship between 30 THz emission and radiation produced at other wavelength ranges. The multiple frequency emissions in the impulsive phase are likely to be produced at a common flaring site lower in the chromosphere. The 30 THz burst emission may be either part of a nonthermal radiation mechanism or due to the rapid thermal response to a beam of high-energy particles bombarding the dense solar atmosphere.Comment: accepted to Astronomy and Astrophysic

Impact of language proficiency on mental health service use, treatment and outcomes: "Lost in Translation"

Background Mastery of a language is bound to place of origin; low language proficiency is thus related to migration and cultural differences, all of which influence access to mental health care, treatment and outcomes. Switzerland, being multilingual, allows the disentangling of language proficiency from migration and, to some extent, culture. This study uses propensity score matching to explore how language proficiency relates to help-seeking behaviour, service use, treatment and outcomes in patients with mental health disorders. Methods We used the first admission of patients admitted to and discharged from an academic psychiatric hospital in Switzerland between January 1st, 2013 and December 31st, 2019, with an observation period of one-year post-discharge (until December 31st, 2020). We paired 2101 patients with low language proficiency to 2101 language proficient patients, balancing baseline sociodemographic and clinical characteristics using propensity score matching. Results Patients with low language proficiency had a higher probability of compulsory admission (OR: 1.79, 99%CI: 1.60–2.02); which remained after adjustment for confounders (OR: 1.51; 99%CI: 1.21–1.89). Whilst in treatment, they had higher rates of compulsory medication (OR: 1.73, 99%CI: 1.16–2.59) and seclusion/restraint (OR: 1.87, 99%CI: 1.25–2.79). Furthermore, patients initially admitted voluntarily had a higher probability of being compulsorily retained (OR: 1.74, 99%CI: 1.24–2.46). Both groups showed similar clinical improvement rates and service use parameters. Conclusions Our results demonstrate that low language proficiency constitutes a risk factor for coercive measures throughout hospitalisation. The results demonstrate the need for an increase in language sensitivity in psychiatric care

Comparison of three methods for routine detection of staphylococcus aureus isolated from bovine mastitis

The present study aimed to compare three identification methods that are routinely used for the detection of Staphylococcus aureus as bovine mastitis agent. The evaluated methods were as followed: conventional biochemical method, commercial identification system BioLog (Gen III MicroPlate) and amplification of species-specific gene (nuc) by polymerase chain reaction (PCR). A total of 73 staphylococcal isolates were collected from 453 individual milk samples from dairy cows with subclinical and clinical mastitis from different farms in Bulgaria. This isolates were determined as 60 coagulase-positive, 3 catalase-negative and 10 coagulase-negative by conventional methods. BioLog system identified 72 isolates as S. аureus subsp. aureus and one coagulase-positive isolate as S. schleiferi subsp. coagulans. PCR amplification of nuc gene further confirmed S. аureus subsp. aureus isolates identified by the BioLog system. The primary identification of S. aureus on the basis of coagulase level led to erroneous determination of 14 (19.2%) of the isolates. Based on the findings, BioLog system and PCR appear to be more reliable detection systems for S. aureus from milk. In conclusion, the present study showed that a routine approach using a combination of phenotypic and molecular detection systems could improve S. aureus detection in milk

Relationship Between Time of Admission, Help-Seeking Behavior, and Psychiatric Outcomes: “From Dusk Till Dawn”

Introduction: Day and time of admission influence treatment outcomes and prognosis in several medical specialties; this seems related to resources' ability. It is largely unknown whether this also applies to mental health services. We investigate the relationship between time of admission, patients' demographic and clinical profile, and treatment outcomes. Methods: Demographic and clinical profiles of admitted and discharged patients to a general psychiatric ward between January 1st, 2013 and December 31st, 2020, were analyzed. In addition, we used the last year (i.e., 2020) to monitor rehospitalization. Time of admission was defined as weekdays (working day, weekend) and dayshifts (daytime, dusk, and dawn). Results: During the study period, 12,449 patient admissions occurred. The mean age of the sample was 48.05 ± 20.90 years, with 49.32% (n = 6,140) females. Most admissions (n = 10,542, 84%) occurred on working days. Two-fifths of admissions (39.7%, n = 4,950) were compulsory, with a higher rate outside daytime hours. Patients had slight differences in the clinical profile, resulting from evaluating the different items of the Health of Nation Outcome Scale (HoNOS). Patients admitted on night shifts, weekends, and holidays showed a shorter length of stay; patients compulsorily admitted during daytime (disregarding the day of the week) had a longer length of stay. All patient groups achieved a robust clinical improvement (i.e., an HoNOS score reduction of around 50%), with similar readmission rates. Discussion: The main finding of our study is the relationship between "daytime hours" and fewer compulsory admissions, a result of the interplay between demographics, clinical characteristics, and out-of-clinic service availability (such as ambulatory psychiatric- psychological praxis; day-clinic; home-treatment). The differing clinical profile, in turn, determines differences in treatment selection, with patients admitted after office hours experiencing a higher rate of coercive measures. The shorter length of stay for out-of-office admissions might result from the hospitalization as an intervention. These results should encourage the implementation of outpatient crisis-intervention services, available from dusk till dawn. Keywords: coercive measures; day and time of admission; help-seeking behavior; psychiatric outcomes; service use

Ultrafast temporal evolution of interatomic Coulombic decay in NeKr dimers

We investigate interatomic Coulombic decay in NeKr dimers after neon inner-valence photoionization [Ne+(2s-1)] using a synchrotron light source. We measure with high energy resolution the two singly charged ions of the Coulomb-exploding dimer dication and the photoelectron in coincidence. By carefully tracing the post-collision interaction between the photoelectron and the emitted ICD electron we are able to probe the temporal evolution of the state as it decays. Although the ionizing light pulses are 80 picoseconds long, we determine the lifetime of the intermediate dimer cation state and visualize the contraction of the nuclear structure on the femtosecond time scale