Software for the frontiers of quantum chemistry : An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design.This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.Peer reviewe

Measurements of muon flux in the Pyh\"asalmi underground laboratory

The cosmic-ray induced muon flux was measured at several depths in the Pyh\"asalmi mine (Finland) using a plastic scintillator telescope mounted on a trailer. The flux was determined at four different depths underground at 400 m (980 m.w.e), at 660 m (1900 m.w.e), at 990 m (2810 m.w.e) and at 1390 m (3960 m.w.e) with the trailer, and also at the ground surface. In addition, previously measured fluxes from depths of 90 m (210 m.w.e) and 210 m (420 m.w.e) are shown. A relation was obtained for the underground muon flux as a function of the depth. The measured flux follows well the general behaviour and is consistent with results determined in other underground laboratories.Comment: 8 pages, 2 figures. Submitted to Nuclear Instrum. Methods

Ontology Domain Modeling Support for Multilingual Servicies in e-commerce: MKBEEM

One of the main objectives of a truly user-friendly Information Society is to focus on advanced human language technologies enabling cost-effective interchange across language and culture and more natural interfaces to digital services. The recently launched IST-1999-10589 project MKBEEM (Multilingual Knowledge Based European Electronic Marketplace, 1st Feb. 2000 - 1st Aug. 2002) is rightly in that direction and the work will address basically, written language technologies and its use in the key sector of global business and electronic commerce. In particular MKBEEM will focus on adding multilinguality to all stages of the information cycle, including multilingual content generation and maintenance, automated translation and interpretation and enhancing the natural interactivity and usability of the service with unconstrained language input. On the Knowledge engineering side, the MKBEEM Ontologies will provide a consensual representation of the electronic commerce field in three typical Domains (Tourism, Mail order, Retailers) allowing the exchanges independently of the language of the end user, the service, or the content provider. Ontologies will be used for classifying and indexing catalogues, for filtering user’s query, for facilitating multilingual man-machine dialogues between user and software agent, and for inferring information that is relevant to the user’s request. This paper concentrates on ontology issues, while the used human language processing approaches will be presented closely in our later papers

EMMA - A New Underground Cosmic-Ray Experiment

A new type of cosmic-ray experiment is under construction in the Pyh\"asalmi mine in the underground laboratory of the University of Oulu, Finland. It aims to study the composition of cosmic rays at and above the knee region. The experiment, called EMMA, will cover approximately 150 square-metres of detector area. The array is capable of measuring the multiplicity and the lateral distribution of underground muons, and the arrival direction of the air shower. The full-size detector is expected to run by the end of 2007.Comment: Extended and updated TAUP2005 Proceedings contribution. 8 pages, 5 figures (part in colour). Preprint not submitte

Associations of age and sex with brain volumes and asymmetry in 2–5-week-old infants

Information on normal brain structure and development facilitates the recognition of abnormal developmental trajectories and thus needs to be studied in more detail. We imaged 68 healthy infants aged 2–5 weeks with high-resolution structural MRI (magnetic resonance imaging) and investigated hemispheric asymmetry as well as the associations of various total and lobar brain volumes with infant age and sex. We found similar hemispheric asymmetry in both sexes, seen as larger volumes of the right temporal lobe, and of the left parietal and occipital lobes. The degree of asymmetry did not vary with age. Regardless of controlling for gestational age, gray and white matter had different age-related growth patterns. This is a reflection of gray matter growth being greater in the first years, while white matter growth extends into early adulthood. Sex-dependent differences were seen in gray matter as larger regional absolute volumes in males and as larger regional relative volumes in females. Our results are in line with previous studies and expand our understanding of infant brain development.</p

Resting-state networks of the neonate brain identified using independent component analysis

Resting-state functional magnetic resonance imaging (rs-fMRI) has been successfully used to probe the intrinsic functional organization of the brain and to study brain development. Here, we implemented a combination of individual and group independent component analysis (ICA) of FSL on a 6-min resting-state data set acquired from 21 naturally sleeping term-born (age 26 +/- 6.7 d), healthy neonates to investigate the emerging functional resting-state networks (RSNs). In line with the previous literature, we found evidence of sensorimotor, auditory/language, visual, cerebellar, thalmic, parietal, prefrontal, anterior cingulate as well as dorsal and ventral aspects of the default-mode-network. Additionally, we identified RSNs in frontal, parietal, and temporal regions that have not been previously described in this age group and correspond to the canonical RSNs established in adults. Importantly, we found that careful ICA-based denoising of fMRI data increased the number of networks identified with group-ICA, whereas the degree of spatial smoothing did not change the number of identified networks. Our results show that the infant brain has an established set of RSNs soon after birth

Low frequency of germline E-cadherin mutations in familial and nonfamilial gastric cancer

Little is known about the relative contributions of genetic and environmental factors to the development of gastric cancer. Mutations in the cell adhesion molecule E-cadherin are recognized to be associated with the development of undifferentiated, diffuse and invasive gastric cancers. A recent study of two gastric cancer families has shown that germline mutations in the E-cadherin gene can be causative (Guilford P et al, Nature 1998; 26: 402–405). We have examined the E-cadherin gene for constitutive mutations in a systematic series of 106 gastric cancer patients, 10 with a family history of the disease and 96 sporadic cases. No pathogenic mutations were observed in any of the 106 patients. The results indicate that germline mutations in E-cadherin will not account for more than 3% of gastric cancers. © 1999 Cancer Research Campaig

Sex-specific association between infant caudate volumes and a polygenic risk score for major depressive disorder

Polygenic risk scores for major depressive disorder (PRS-MDD) have been identified in large genome-wide association studies, and recent findings suggest that PRS-MDD might interact with environmental risk factors to shape human limbic brain development as early as in the prenatal period. Striatal structures are crucially involved in depression; however, the association of PRS-MDD with infant striatal volumes is yet unknown. In this study, 105 Finnish mother-infant dyads (44 female, 11-54 days old) were investigated to reveal how infant PRS-MDD is associated with infant dorsal striatal volumes (caudate, putamen) and whether PRS-MDD interacts with prenatal maternal depressive symptoms (Edinburgh Postnatal Depression Scale, gestational weeks 14, 24, 34) on infant striatal volumes. A robust sex-specific main effect of PRS-MDD on bilateral infant caudate volumes was observed. PRS-MDD were more positively associated with caudate volumes in boys compared to girls. No significant interaction effects of genotype PRS-MDD with the environmental risk factor "prenatal maternal depressive symptoms" (genotype-by-environment interaction) nor significant interaction effects of genotype with prenatal maternal depressive symptoms and sex (genotype-by-environment-by-sex interaction) were found for infant dorsal striatal volumes. Our study showed that a higher PRS-MDD irrespective of prenatal exposure to maternal depressive symptoms is associated with smaller bilateral caudate volumes, an indicator of greater susceptibility to major depressive disorder, in female compared to male infants. This sex-specific polygenic effect might lay the ground for the higher prevalence of depression in women compared to men

Health service use in indigenous Sami and non-indigenous youth in North Norway: A population based survey

<p>Abstract</p> <p>Background</p> <p>This is the first population based study exploring health service use and ethno-cultural factors in indigenous Sami and non-Sami youth in North Norway. The first aim of the present study was to compare the frequency of health service use between Sami adolescents and their non-indigenous peers. The second aim was to explore the relationships between health service use and ethno-cultural factors, such as ethnic context, Sami self-identification, perceived discrimination and Sami language competence. Finally, we wanted to explore the relationship between use of health services and emotional and behavioural problems.</p> <p>Method</p> <p>The Norwegian Arctic Adolescent Health Study was conducted among 10th graders (15-16 years old) in junior high schools in North Norway. The sample consisted of 4,449 adolescents, of whom 450 (10.1%) were indigenous Sami and 3,999 (89.9%) were non-Sami.</p> <p>Results</p> <p>Sami and non-Sami youth used all health services with equal frequency. However, several ethno-cultural factors were found to influence health service use. Sami youth in more assimilated ethnic contexts used general practitioners more than non-Sami youth. Youth with Sami self-identification had a higher probability of using the school health service compared with other youth. Ethnic barriers to health service use were also identified. Sami speaking youth with a high degree of perceived discrimination had lower probability of using school health services than non-Sami speaking youth. Sami youth with conduct problems were less likely than non-Sami to use psychologist/psychiatrist. The present study demonstrated a relationship between health need and actual health service use.</p> <p>Conclusion</p> <p>Culture-specific factors influenced the help-seeking process in indigenous youth; some factors acted as barriers against health service use and other factors increased the probability of health service use.</p

Partial Support for an Interaction Between a Polygenic Risk Score for Major Depressive Disorder and Prenatal Maternal Depressive Symptoms on Infant Right Amygdalar Volumes

Psychiatric disease susceptibility partly originates prenatally and is shaped by an interplay of genetic and environmental risk factors. A recent study has provided preliminary evidence that an offspring polygenic risk score for major depressive disorder (PRS-MDD), based on European ancestry, interacts with prenatal maternal depressive symptoms (GxE) on neonatal right amygdalar (US and Asian cohort) and hippocampal volumes (Asian cohort). However, to date, this GxE interplay has only been addressed by one study and is yet unknown for a European ancestry sample. We investigated in 105 Finnish mother-infant dyads (44 female, 11-54 days old) how offspring PRS-MDD interacts with prenatal maternal depressive symptoms (Edinburgh Postnatal Depression Scale, gestational weeks 14, 24, 34) on infant amygdalar and hippocampal volumes. We found a GxE effect on right amygdalar volumes, significant in the main analysis, but nonsignificant after multiple comparison correction and some of the control analyses, whose direction paralleled the US cohort findings. Additional exploratory analyses suggested a sex-specific GxE effect on right hippocampal volumes. Our study is the first to provide support, though statistically weak, for an interplay of offspring PRS-MDD and prenatal maternal depressive symptoms on infant limbic brain volumes in a cohort matched to the PRS-MDD discovery sample