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Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full two-dimensional (2D) image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields, and other sample-dependent properties. However, extracting this information requires complex analysis pipelines that include data wrangling, calibration, analysis, and visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open-source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail and present results from several experimental datasets. We also implement a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open-source HDF5 standard. We hope this tool will benefit the research community and help improve the standards for data and computational methods in electron microscopy, and we invite the community to contribute to this ongoing project.
Vision and hearing impairments affect 55% of people aged 60+ years and are associated with lower cognitive test performance; however, tests rely on vision, hearing, or both. We hypothesized that scores on tests that depend on vision or hearing are different among those with vision or hearing impairments, respectively, controlling for underlying cognition.
Leveraging cross-sectional data from the Baltimore Longitudinal Study of Aging (BLSA) and the Atherosclerosis Risk in Communities Neurocognitive Study (ARIC-NCS), we used item response theory to test for differential item functioning (DIF) by vision impairment (better eye presenting visual acuity worse than 20/40) and hearing impairment (better ear .5–4 kHz pure-tone average > 25 decibels).
We identified DIF by vision impairment for tests whose administrations do not rely on vision [e.g., Delayed Word Recall both in ARIC-NCS: .50 logit difference between impaired and unimpaired (p = .04) and in BLSA: .62 logits (p = .02)] and DIF by hearing impairment for tests whose administrations do not rely on hearing [Digit Symbol Substitution test in BLSA: 1.25 logits (p = .001) and Incidental Learning test in ARIC-NCS: .35 logits (p = .001)]. However, no individuals had differences between unadjusted and DIF-adjusted measures of greater than the standard error of measurement.
DIF by sensory impairment in cognitive tests was independent of administration characteristics, which could indicate that elevated cognitive load among persons with sensory impairment plays a larger role in test performance than previously acknowledged. While these results were unexpected, neither of these samples are nationally representative and each has unique selection factors; thus, replication is critical.
Older literature had repeatedly documented that physically frail male schizophrenics tended to be withdrawn with apathy, blunted affect and poor prognosis. However, in female schizophrenics, signs of virilism portend poor prognosis and severe deterioration. Three published studies of 92 male schizophrenics, from India, Iran and Japan, showed negative correlations between testosterone (T) levels and negative symptoms.
Twenty-eight (18 male and 10 female) patients, aged 25-67 (mean=34.8) years, who fulfilled DSM-IV TR criteria for schizophrenia were selected, with the approval of local ethical committee. Serum levels of T, dihydrotestosterone and DHEA were estimated by radioimmunoassay. Neuropsychological tests were administered for each patient. Pearson correlation test, linear regression analysis and independent ‘t’ test were used for statistical analysis.
Mean PANSS score for all 28 patients was 82.3; 18 patients had predominantly positive symptoms and 10 had predominantly negative symptoms. Independent ‘t’ test did not show any significant difference for any of the serum hormone levels between the groups of patients based on PANSS scores. However, when women were excluded, T levels were significantly lower in negative symptom dominant group (p=0.05). A correlation between serum T levels, but not of other hormones, and the total scores on all neuropsychological test results was also noted (p=0.017); verbal fluency showed the greatest correlation, followed by working memory. But when women were excluded, this significance disappeared.
Negative symptoms correlate negatively with T levels, but only in men. Neuropsychological findings correlate with T levels as well.
Maternal polycystic ovary syndrome (PCOS) has been proposed as a model for investigating the role of prenatal androgen exposure in the development of neuropsychiatric disorders. However, women with PCOS are at higher risk of developing psychiatric conditions and previous studies are likely confounded by genetic influences.
A Swedish nationwide register-based cohort study was conducted to disentangle the influence of prenatal androgen exposure from familial confounding in the association between maternal PCOS and offspring attention-deficit/hyperactivity disorder (ADHD), autism spectrum disorders (ASD), and Tourette's disorder and chronic tic disorders (TD/CTD). PCOS-exposed offspring (n = 21 280) were compared with unrelated PCOS-unexposed offspring (n = 200 816) and PCOS-unexposed cousins (n = 17 295). Associations were estimated with stratified Cox regression models.
PCOS-exposed offspring had increased risk of being diagnosed with ADHD, ASD, and TD/CTD compared with unrelated PCOS-unexposed offspring. Associations were stronger in girls for ADHD and ASD but not TD/CTD [ADHD: adjusted hazard ratio (aHR) = 1.61 (95% confidence interval (CI) 1.31–1.99), ASD: aHR = 2.02 (95% CI 1.45–2.82)] than boys [ADHD: aHR = 1.37 (95% CI 1.19–1.57), ASD: aHR = 1.46 (95% CI 1.21–1.76)]. For ADHD and ASD, aHRs for girls were stronger when compared with PCOS-unexposed cousins, but slightly attenuated for boys.
Estimates were similar when accounting for familial confounding (i.e. genetics and environmental factors shared by cousins) and stronger in girls for ADHD and ASD, potentially indicating a differential influence of prenatal androgen exposure v. genetic factors. These results strengthen evidence for a potential causal influence of prenatal androgen exposure on the development of male-predominant neuropsychiatric disorders in female offspring of women with PCOS.
Cognitive impairment is a core feature of psychotic disorders, but the profile of impairment across adulthood, particularly in African-American populations, remains unclear.
Using cross-sectional data from a case–control study of African-American adults with affective (n = 59) and nonaffective (n = 68) psychotic disorders, we examined cognitive functioning between early and middle adulthood (ages 20–60) on measures of general cognitive ability, language, abstract reasoning, processing speed, executive function, verbal memory, and working memory.
Both affective and nonaffective psychosis patients showed substantial and widespread cognitive impairments. However, comparison of cognitive functioning between controls and psychosis groups throughout early (ages 20–40) and middle (ages 40–60) adulthood also revealed age-associated group differences. During early adulthood, the nonaffective psychosis group showed increasing impairments with age on measures of general cognitive ability and executive function, while the affective psychosis group showed increasing impairment on a measure of language ability. Impairments on other cognitive measures remained mostly stable, although decreasing impairments on measures of processing speed, memory and working memory were also observed.
These findings suggest similarities, but also differences in the profile of cognitive dysfunction in adults with affective and nonaffective psychotic disorders. Both affective and nonaffective patients showed substantial and relatively stable impairments across adulthood. The nonaffective group also showed increasing impairments with age in general and executive functions, and the affective group showed an increasing impairment in verbal functions, possibly suggesting different underlying etiopathogenic mechanisms.
Our aim is to present a new and so far most complete catalog of optically selected young stars. The basis of this work is an extensive literature search for young stars in all the known nearby (< 2 kpc) star forming regions, included in the Handbook of Star Forming Regions [4, 5], and in 67 additional catalogs. We collected data on known young, pre-main-sequence stars detected in optical bands. The catalog contains the celestial coordinates, object names, names of the enclosing star forming region, identification methods, distances, and other information (e.g., references, binarity) for 15208 young stellar objects. It is already in use by the Gaia Photometric Science Alerts Team to identify variable young stars in the Gaia data. Our catalog was cross-correlated with the Gaia DR2 and we obtained flux and distance estimations for 86% of the stars.
The effects of fish oil (FO) supplementation on glycaemic control are unclear, and positive effects may occur only when the phospholipid content of tissue membranes exceeds 14 % as n-3 PUFA. Subjects (n 36, thirty-three completed) were paired based on metabolic parameters and allocated into a parallel double-blind randomised trial with one of each pair offered daily either 6 g of FO (3·9 g n-3 PUFA) or 6 g of maize oil (MO) for 9 months. Hyperinsulinaemic–euglycaemic–euaminoacidaemic (HIEGEAA) clamps (with [6,6 2H2 glucose]) were performed at the start and end of the intervention. Endogenous glucose production (EGP) and whole-body protein turnover (WBPT) were each measured after an overnight fast. The primary outcome involved the effect of oil type on insulin sensitivity related to glycaemic control. The secondary outcome involved the effect of oil type on WBPT. Subjects on FO (n 16) had increased erythrocyte n-3 PUFA concentrations >14 %, whereas subjects on MO (n 17) had unaltered n-3 PUFA concentrations at 9 %. Type of oil had no effect on fasting EGP, insulin sensitivity or total glucose disposal during the HIEGEAA clamp. In contrast, under insulin-stimulated conditions, total protein disposal (P=0·007) and endogenous WBPT (P=0·001) were both increased with FO. In an associated pilot study (n 4, three completed), although n-3 PUFA in erythrocyte membranes increased to >14 % with the FO supplement, the enrichment in muscle membranes remained lower (8 %; P<0·001). In conclusion, long-term supplementation with FO, at amounts near the safety limits set by regulatory authorities in Europe and the USA, did not alter glycaemic control but did have an impact on WBPT.
Increased dietary Na intake and decreased dietary K intake are associated with higher blood pressure. It is not known whether the dietary Na:K ratio is associated with all-cause mortality or stroke incidence and whether this relationship varies according to race. Between 2003 and 2007, the REasons for Geographic And Racial Differences in Stroke (REGARDS) cohort enrolled 30 239 black and white Americans aged 45 years or older. Diet was assessed using the Block 98 FFQ and was available on 21 374 participants. The Na:K ratio was modelled in race- and sex-specific quintiles for all analyses, with the lowest quintile (Q1) as the reference group. Data on other covariates were collected using both an in-home assessment and telephone interviews. We identified 1779 deaths and 363 strokes over a mean of 4·9 years. We used Cox proportional hazards models to obtain multivariable-adjusted hazard ratios (HR). In the highest quintile (Q5), a high Na:K ratio was associated with all-cause mortality (Q5 v. Q1 for whites: HR 1·22; 95 % CI 1·00, 1·47, P for trend = 0·084; for blacks: HR 1·36; 95 % CI 1·04, 1·77, P for trend = 0·028). A high Na:K ratio was not significantly associated with stroke in whites (HR 1·29; 95 % CI 0·88, 1·90) or blacks (HR 1·39; 95 % CI 0·78, 2·48), partly because of the low number of stroke events. In the REGARDS study, a high Na:K ratio was associated with all-cause mortality and there was a suggestive association between the Na:K ratio and stroke. These data support the policies targeted at reduction of Na from the food supply and recommendations to increase K intake.
Several galaxy clusters are known to present multiple and misaligned pairs of cavities seen in X-rays, as well as twisted kiloparsec-scale jets at radio wavelengths. It suggests that the AGN precessing jets play a role in the formation of the misaligned bubbles. Also, X-ray spectra reveal that typically these systems are also able to supress cooling flows, predicted theoretically. The absence of cooling flows in galaxy clusters has been a mistery for many years since numerical simulations and analytical studies suggest that AGN jets are highly energetic, but are unable to redistribute it at all directions. We performed 3D hydrodynamical simulations of the interaction between a precessing AGN jet and the warm intracluster medium plasma, in which dynamics is coupled to a NFW dark matter gravitational potential. Radiative cooling has been taken into account and the cooling flow problem was studied. We found that precession is responsible for multiple pairs of bubbles, as observed. The misaligned bubbles rise up to scales of tens of kiloparsecs, where the thermal energy released by the jets are redistributed. After ~150 Myrs, the temperature of the gas within the cavities is kept of order of ~107 K, while the denser plasma of the intracluster medium at the central regions reaches T ~ 105 K. The existence of multiple bubbles, at diferent directions, results in an integrated temperature along the line of sight much larger than the simulations of non-precessing jets. This result is in agreement with the observations. The simulations reveal that the cooling flows cessed ~50–70 Myr after the AGN jets are started.
The seventh annual Teaching and Learning Conference (TLC) was held in Philadelphia, Pennsylvania, from February 5 to 7, 2010, with 224 attendees onsite. The theme for the meeting was “Advancing Excellence in Teaching Political Science.” Using the working-group model, the TLC track format encourages in-depth discussion and debate on research dealing with the scholarship of teaching and learning.
Two populations, one non-improved of Dactylis glomerata and one improved of Agropyron cristatum were selected in an isolated spaced plant environment (80 cm) by three selection procedures: (1) Mass honeycomb selection (MHS), (2) pedigree honeycomb selection (PHS) and (3) pedigree honeycomb selection-combined criterion (PHS-CC). The third procedure is a between-families selection based on increased family mean and reduced family coefficient of variation (CV). Response to selection assessed in sward trials in the first and second harvest year was effective for the three procedures, which ranked PHS-CC > PHS > MHS. Evaluation was based on consistent efficiency as measured by both cloned and half-sib families. The precision of assessing progeny performance under sward conditions on the basis of single plant evaluation in the isolation environment, increased with a reduction in competition among plants, the use of moving-ring selection, and the application of high selection pressures (1·6%). The efficiency of selection between unimproved families increased when families were selected concurrently for high family mean and reduced family coefficient of variation.
We have spectra, colours and morphologies from the CFHT for 240 cluster members and 80 field galaxies over a 7 × 46 arcmin field. The cluster galaxies show strong radial gradients in colour, morphology, and spectrum. The central group has only red early-type galaxies of high central concentration, which must have formed at least 5 Gy ago. The population becomes bluer and shows an increasing fraction of disk morphology and recent star-formation with clustocentric radius, and eventually blends into the field. However, the fraction of blue galaxies is significantly lower than in Butcher-Oemler clusters, and there are only two starburst galaxies (one of which is the cluster cD). Fitting of line measures with stellar population models indicates that star-formation has been truncated in the 15-20% of the cluster galaxies that have strong Hδ absorption, and that these galaxies are not all blue. There is evidence that cluster galaxies are dusty compared with the field. The morphology gradient can be fit with models of disk fading. However, there is a small fraction of interacting and merging galaxies, which must play a part in the population evolution. The cluster is accreting from the field in a non-violent way, including some distinct subgroups. This is different from what is seen at both higher and lower redshift, and if generally true, suggests a high Omega universe.
These results are being published in detail elsewhere.