Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging.

Neuroimaging research requires purpose-built analysis software, which is challenging to install and may produce different results across computing environments. The community-oriented, open-source Neurodesk platform ( https://www.neurodesk.org/ ) harnesses a comprehensive and growing suite of neuroimaging software containers. Neurodesk includes a browser-accessible virtual desktop, command-line interface and computational notebook compatibility, allowing for accessible, flexible, portable and fully reproducible neuroimaging analysis on personal workstations, high-performance computers and the cloud.

Neurochemical Predictors of Generalized Learning Induced by Brain Stimulation and Training.

Methods of cognitive enhancement for humans are most impactful when they generalize across tasks. However, the extent to which such "transfer" is possible via interventions is widely debated. In addition, the contribution of excitatory and inhibitory processes to such transfer is unknown. Here, in a large-scale neuroimaging individual differences study with humans (both sexes), we paired multitasking training and noninvasive brain stimulation (transcranial direct current stimulation, tDCS) over multiple days and assessed performance across a range of paradigms. In addition, we varied tDCS dosage (1.0 and 2.0 mA), electrode montage (left or right prefrontal regions), and training task (multitasking vs a control task) and assessed GABA and glutamate concentrations via ultrahigh field 7T magnetic resonance spectroscopy. Generalized benefits were observed in spatial attention, indexed by visual search performance, when multitasking training was combined with 1.0 mA stimulation targeting either the left or right prefrontal cortex (PFC). This transfer effect persisted for ∼30 d post intervention. Critically, the transferred benefits associated with right prefrontal tDCS were predicted by pretraining concentrations of glutamate in the PFC. Thus, the effects of this combined stimulation and training protocol appear to be linked predominantly to excitatory brain processes.

Warming-induced monsoon precipitation phase change intensifies glacier mass loss in the southeastern Tibetan Plateau.

Glaciers are key components of the mountain water towers of Asia and are vital for downstream domestic, agricultural, and industrial uses. The glacier mass loss rate over the southeastern Tibetan Plateau is among the highest in Asia and has accelerated in recent decades. This acceleration has been attributed to increased warming, but the mechanisms behind these glaciers' high sensitivity to warming remain unclear, while the influence of changes in precipitation over the past decades is poorly quantified. Here, we reconstruct glacier mass changes and catchment runoff since 1975 at a benchmark glacier, Parlung No. 4, to shed light on the drivers of recent mass losses for the monsoonal, spring-accumulation glaciers of the Tibetan Plateau. Our modeling demonstrates how a temperature increase (mean of 0.39 ∘C ⋅dec-1 since 1990) has accelerated mass loss rates by altering both the ablation and accumulation regimes in a complex manner. The majority of the post-2000 mass loss occurred during the monsoon months, caused by simultaneous decreases in the solid precipitation ratio (from 0.70 to 0.56) and precipitation amount (-10%), leading to reduced monsoon accumulation (-26%). Higher solid precipitation in spring (+18%) during the last two decades was increasingly important in mitigating glacier mass loss by providing mass to the glacier and protecting it from melting in the early monsoon. With bare ice exposed to warmer temperatures for longer periods, icemelt and catchment discharge have unsustainably intensified since the start of the 21st century, raising concerns for long-term water supply and hazard occurrence in the region.

Individual Differences in Decision Strategy Relate to Neurochemical Excitability and Cortical Thickness.

The speed-accuracy trade-off (SAT), whereby faster decisions increase the likelihood of an error, reflects a cognitive strategy humans must engage in during the performance of almost all daily tasks. To date, computational modeling has implicated the latent decision variable of response caution (thresholds), the amount of evidence required for a decision to be made, in the SAT. Previous imaging has associated frontal regions, notably the left prefrontal cortex and the presupplementary motor area (pre-SMA), with the setting of such caution levels. In addition, causal brain stimulation studies, using transcranial direct current stimulation (tDCS), have indicated that while both of these regions are involved in the SAT, their role appears to be dissociable. tDCS efficacy to impact decision-making processes has previously been linked with neurochemical concentrations and cortical thickness of stimulated regions. However, to date, it is unknown whether these neurophysiological measures predict individual differences in the SAT, and brain stimulation effects on the SAT. Using ultra-high field (7T) imaging, here we report that instruction-based adjustments in caution are associated with both neurochemical excitability (the balance between GABA+ and glutamate) and cortical thickness across a range of frontal regions in both sexes. In addition, cortical thickness, but not neurochemical concentrations, was associated with the efficacy of left prefrontal and superior medial frontal cortex (SMFC) stimulation to modulate performance. Overall, our findings elucidate key neurophysiological predictors, frontal neural excitation, of individual differences in latent psychological processes and the efficacy of stimulation to modulate these.SIGNIFICANCE STATEMENT The speed-accuracy trade-off (SAT), faster decisions increase the likelihood of an error, reflects a cognitive strategy humans must engage in during most daily tasks. The SAT is often investigated by explicitly instructing participants to prioritize speed or accuracy when responding to stimuli. Using ultra-high field (7T) magnetic resonance imaging (MRI), we found that individual differences in the extent to which participants adjust their decision strategies with instruction related to neurochemical excitability (ratio of GABA+ to glutamate) and cortical thickness in the frontal cortex. Moreover, brain stimulation to the left prefrontal cortex and the superior medial frontal cortex (SMFC) modulated performance, with the efficacy specifically related to cortical thickness. This work sheds new light on the neurophysiological basis of decision strategies and brain stimulation.

Chemical potential measurements constrain models of cholesterol-phosphatidylcholine interactions.

Bilayer membranes composed of cholesterol and phospholipids exhibit diverse forms of nonideal mixing. In particular, many previous studies document macroscopic liquid-liquid phase separation as well as nanometer-scale heterogeneity in membranes of phosphatidylcholine (PC) lipids and cholesterol. Here, we present experimental measurements of cholesterol chemical potential (µc) in binary membranes containing dioleoyl PC (DOPC), 1-palmitoyl-2-oleoyl PC (POPC), or dipalmitoyl PC (DPPC), and in ternary membranes of DOPC and DPPC, referenced to crystalline cholesterol. µc is the thermodynamic quantity that dictates the availability of cholesterol to bind other factors, and notably must be equal between coexisting phases of a phase separated mixture. It is simply related to concentration under conditions of ideal mixing, but is far from ideal for the majority of lipid mixtures investigated here. Measurements of µc can vary with phospholipid composition by 1.5 kBT at constant cholesterol mole fraction implying a more than fivefold change in its availability for binding receptors and other reactions. Experimental measurements are fit to thermodynamic models including cholesterol-DPPC complexes or pairwise interactions between lipid species to provide intuition about the magnitude of interactions. These findings reinforce that µc depends on membrane composition overall, suggesting avenues for cells to alter the availability of cholesterol without varying cholesterol concentration.

Lower hypothalamic volume with lower body mass index is associated with shorter survival in patients with amyotrophic lateral sclerosis.

BACKGROUND AND PURPOSE: Weight loss in patients with amyotrophic lateral sclerosis (ALS) is associated with faster disease progression and shorter survival. Decreased hypothalamic volume is proposed to contribute to weight loss due to loss of appetite and/or hypermetabolism. We aimed to investigate the relationship between hypothalamic volume and body mass index (BMI) in ALS and Alzheimer's disease (AD), and the associations of hypothalamic volume with weight loss, appetite, metabolism and survival in patients with ALS. METHODS: We compared hypothalamic volumes from magnetic resonance imaging scans with BMI for patients with ALS (n = 42), patients with AD (n = 167) and non-neurodegenerative disease controls (n = 527). Hypothalamic volumes from patients with ALS were correlated with measures of appetite and metabolism, and change in anthropomorphic measures and disease outcomes. RESULTS: Lower hypothalamic volume was associated with lower and higher BMI in ALS (quadratic association; probability of direction = 0.96). This was not observed in AD patients or controls. Hypothalamic volume was not associated with loss of appetite (p = 0.58) or hypermetabolism (p = 0.49). Patients with lower BMI and lower hypothalamic volume tended to lose weight (p = 0.08) and fat mass (p = 0.06) over the course of their disease, and presented with an increased risk of earlier death (hazard ratio [HR] 3.16, p = 0.03). Lower hypothalamic volume alone trended for greater risk of earlier death (HR 2.61, p = 0.07). CONCLUSION: These observations suggest that lower hypothalamic volume in ALS contributes to positive and negative energy balance, and  is not universally associated with loss of appetite or hypermetabolism. Critically, lower hypothalamic volume with lower BMI was associated with weight loss and earlier death.

Estimating the localization spread function of static single-molecule localization microscopy images.

Single-molecule localization microscopy (SMLM) permits the visualization of cellular structures an order of magnitude smaller than the diffraction limit of visible light, and an accurate, objective evaluation of the resolution of an SMLM data set is an essential aspect of the image processing and analysis pipeline. Here, we present a simple method to estimate the localization spread function (LSF) of a static SMLM data set directly from acquired localizations, exploiting the correlated dynamics of individual emitters and properties of the pair autocorrelation function evaluated in both time and space. The method is demonstrated on simulated localizations, DNA origami rulers, and cellular structures labeled by dye-conjugated antibodies, DNA-PAINT, or fluorescent fusion proteins. We show that experimentally obtained images have LSFs that are broader than expected from the localization precision alone, due to additional uncertainty accrued when localizing molecules imaged over time.

Critical Phenomena in Plasma Membrane Organization and Function.

Lateral organization in the plane of the plasma membrane is an important driver of biological processes. The past dozen years have seen increasing experimental support for the notion that lipid organization plays an important role in modulating this heterogeneity. Various biophysical mechanisms rooted in the concept of liquid-liquid phase separation have been proposed to explain diverse experimental observations of heterogeneity in model and cell membranes with distinct but overlapping applicability. In this review, we focus on the evidence for and the consequences of the hypothesis that the plasma membrane is poised near an equilibrium miscibility critical point. Critical phenomena explain certain features of the heterogeneity observed in cells and model systems but also go beyond heterogeneity to predict other interesting phenomena, including responses to perturbations in membrane composition.

Structural determinants of tailored behavioral health services for sexual and gender minorities in the United States, 2010 to 2020: a panel analysis.

BACKGROUND: Research indicates that tailored programming for sexual and gender minority (SGM; e.g., lesbian, gay, bisexual, transgender, queer) people, compared to non-tailored programming, is effective for reducing the disproportionate health burden SGM people experience relative to the general population. However, the availability of SGM-tailored programming is often over-reported and inconsistent across behavioral health (i.e., substance use and mental health) facilities in the United States (U.S.). METHODS: Using panel analysis, the National Survey of Substance Abuse Treatment Services (N-SSATS), and the National Mental Health Services Survey (N-MHSS), this study examines structural stigma and government funding as two structural determinants affecting the availability of SGM-tailored programming in the U.S. RESULTS: Results indicated that from 2010 to 2020, reductions in structural stigma (i.e., increases in state-level supportive SGM policies) were positively associated with increases in the proportion of substance use treatment facilities offering SGM-tailored programming. This effect was significant after controlling for over-reporting of SGM-tailored programming and time- and state-specific heterogeneity. On average, the effect of reduced structural stigma resulted in approximately two new SGM-tailored programs in the short term and about 31 new SGM-tailored programs in the long term across U.S. substance use treatment facilities. Structural stigma did not predict the availability of SGM-tailored programming in mental health treatment facilities. Government funding was not significant in either data set. However, without correcting for over-reporting, government funding became a significant predictor of the availability of SGM-tailored programming at substance use treatment facilities. CONCLUSIONS: Because SGM-tailored programming facilitates access to healthcare and the current study found longitudinal associations between structural stigma and the availability of SGM-tailored programming in substance use treatment facilities, our findings support claims that reducing structural stigma increases access to behavioral health treatment specifically and healthcare generally among SGM people. This study's findings also indicate the importance of correcting for over-reporting of SGM-tailored programming, raising concerns about how respondents perceive the N-SSATS and N-MHSS questions about SGM-tailored programming. Implications for future research using the N-SSATS and N-MHSS data and for public health policy are discussed.

Photonic integrated circuit based compressive sensing radio frequency receiver using waveguide speckle.

A photonic integrated circuit (PIC) comprised of an 11 cm long multimode speckle waveguide, a 1 × 32 splitter, and a linear grating coupler array is fabricated and utilized to receive 2 GHz of radio-frequency (RF) signal bandwidth from 2.5 to 4.5 GHz using compressive sensing (CS). Incoming RF signals are modulated onto chirped optical pulses which are input to the multimode waveguide. The multimode waveguide produces the random projections needed for CS via optical speckle. The time-varying phase and amplitude of two test RF signals between 2.5 and 4.5 GHz are successfully recovered using the standard penalized l1-norm method. The PIC reduces the speckle mixer footprint compared with the previously demonstrated fiber system. Two new PIC structures, the "waveguide bus trombone flare" and the "matched 90 degree bus bend" are developed to support precise analog signal routing. The use of a passive PIC serves as an initial critical step towards the miniaturization of a compressive sensing RF receiver.

"MoCl3(dme)" Revisited: Improved Synthesis, Characterization, and X-ray and Electronic Structures.

"MoCl3(dme)" (dme = 1,2-dimethoxyethane) is an important precursor for midvalent molybdenum chemistry, particularly for triply Mo-Mo bonded compounds of the type Mo2X6 (X = bulky anionic ligand). However, its exact structural identity has been obscure for more than 50 years. In search of a convenient, large-scale synthesis, we have found that trans-MoCl4(Et2O)2 dissolved in dme can be cleanly reduced with dimethylphenylsilane, Me2PhSiH, to provide khaki Mo2Cl6(dme)2 in ∼90% yield. If the reduction is performed on a small scale, single crystals suitable for X-ray crystallography can be obtained. Two different crystal morphologies were identified, each belonging to the P21/n space group, but with slightly different unit cell constants. The refined structure of each form is an edge-shared bioctahedron with overall Ci symmetry and metal-metal separations on the order of 2.8 Å. The bulk material is diamagnetic as determined by both the Gouy method and SQUID magnetometry. Density functional theory calculations suggest a σ2π2δ*2 ground state for the dimer with the diamagnetism arising from a singlet diradical "broken symmetry" electronic configuration. In addition to a definitive structural assignment for "MoCl3(dme)", this work highlights the utility of organosilanes as easy to handle, alternative reductants for inorganic synthesis.

Ce-Si Mixed Oxide: A High Sulfur Resistant Catalyst in the NH3-SCR Reaction through the Mechanism-Enhanced Process.

Investigating catalytic reaction mechanisms could help guide the design of catalysts. Here, aimed at improving both the catalytic performance and SO2 resistance ability of catalysts in the selective reduction of NO by NH3 (NH3-SCR), an innovative CeO2-SiO2 mixed oxide catalyst (CeSi2) was developed based on our understanding of both the sulfur poisoning and reaction mechanisms, which exhibited excellent SO2/H2O resistance ability even in the harsh working conditions (containing 500 ppm of SO2 and 5% H2O). The strong interaction between Ce and Si (Ce-O-Si) and the abundant surface hydroxyl groups on CeSi2 not only provided fruitful surface acid sites but also significantly inhibited SO2 adsorption. The NH3-SCR performance of CeSi2 was promoted by an enhanced Eley-Rideal (E-R) mechanism in which more active acid sites were preserved under the reaction conditions and gaseous NO could directly react with adsorbed NH3. This mechanism-enhanced process was even further promoted on sulfated CeSi2. This work provides a reaction mechanism-enhanced strategy to develop an environmentally friendly NH3-SCR catalyst with superior SO2 resistance.

Longitudinal Automatic Segmentation of Hippocampal Subfields (LASHiS) using multi-contrast MRI.

The volumetric and morphometric examination of hippocampus formation subfields in a longitudinal manner using in vivo MRI could lead to more sensitive biomarkers for neuropsychiatric disorders and diseases including Alzheimer's disease, as the anatomical subregions are functionally specialised. Longitudinal processing allows for increased sensitivity due to reduced confounds of inter-subject variability and higher effect-sensitivity than cross-sectional designs. We examined the performance of a new longitudinal pipeline (Longitudinal Automatic Segmentation of Hippocampus Subfields [LASHiS]) against three freely available, published approaches. LASHiS automatically segments hippocampus formation subfields by propagating labels from cross-sectionally labelled time point scans using joint-label fusion to a non-linearly realigned 'single subject template', where image segmentation occurs free of bias to any individual time point. Our pipeline measures tissue characteristics available in in vivo high-resolution MRI scans, at both clinical (3 â€‹T) and ultra-high field strength (7 â€‹T) and differs from previous longitudinal segmentation pipelines in that it leverages multi-contrast information in the segmentation process. LASHiS produces robust and reliable automatic multi-contrast segmentations of hippocampus formation subfields, as measured by higher volume similarity coefficients and Dice coefficients for test-retest reliability and robust longitudinal Bayesian Linear Mixed Effects results at 7 â€‹T, while showing sound results at 3 â€‹T. All code for this project including the automatic pipeline is available at https://github.com/CAIsr/LASHiS.

The efficacy of transcranial direct current stimulation to prefrontal areas is related to underlying cortical morphology.

Applying a weak electrical current to the cortex can have effects on a range of behaviours. Techniques such as transcranial direct current stimulation (tDCS) have been widely used in both research and clinical settings. However, there is significant variability across individuals in terms of their responsiveness to stimulation, which poses practical challenges to the application of tDCS, but also provides a unique opportunity to study the link between the brain and behaviour. Here, we assessed the role of individual differences in cortical morphology - specifically in prefrontal cortical regions of interest - for determining the influence of tDCS on decision-making performance. Specifically, we employed magnetic resonance imaging (MRI) and a previously replicated paradigm in which we modulated learning in a simple decision-making task by applying tDCS to the left prefrontal cortex in human subjects of both sexes. Cortical thickness of the left (but not right) prefrontal cortex accounted for almost 35% of the variance in stimulation efficacy across subjects. This is the first demonstration that variations in cortical architecture are associated with reliable differences in the effects of tDCS on cognition. Our findings have important implications for predicting the likely efficacy of different non-invasive brain stimulation treatments on a case by case basis.

Non-linear realignment improves hippocampus subfield segmentation reliability.

Participant movement can deleteriously affect MR image quality. Further, for the visualization and segmentation of small anatomical structures, there is a need to improve image quality, specifically signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR), by acquiring multiple anatomical scans consecutively. We aimed to ameliorate movement artefacts and increase SNR in a high-resolution turbo spin-echo (TSE) sequence acquired thrice using non-linear realignment in order to improve segmentation consistency of the hippocampus subfields. We assessed the method in 29 young healthy participants, 11 Motor Neuron Disease patients, and 11 age matched controls at 7T, and 24 healthy adolescents at 3T. Results show improved image segmentation of the hippocampus subfields when comparing template-based segmentations with individual segmentations with Dice overlaps N = 75; ps < 0.001 (Friedman's test) and higher sharpness ps < 0.001 in non-linearly realigned scans as compared to linearly, and arithmetically averaged scans.

A Combined Mechanochemical and Calcination Route to Mixed Cobalt Oxides for the Selective Catalytic Reduction of Nitrophenols.

Para-, or 4-nitrophenol, and related nitroaromatics are broadly used compounds in industrial processes and as a result are among the most common anthropogenic pollutants in aqueous industrial effluent; this requires development of practical remediation strategies. Their catalytic reduction to the less toxic and synthetically desirable aminophenols is one strategy. However, to date, the majority of work focuses on catalysts based on precisely tailored, and often noble metal-based nanoparticles. The cost of such systems hampers practical, larger scale application. We report a facile route to bulk cobalt oxide-based materials, via a combined mechanochemical and calcination approach. Vibratory ball milling of CoCl2(H2O)6 with KOH, and subsequent calcination afforded three cobalt oxide-based materials with different combinations of CoO(OH), Co(OH)2, and Co3O4 with different crystallite domains/sizes and surface areas; Co@100, Co@350 and Co@600 (Co@###; # = calcination temp). All three prove active for the catalytic reduction of 4-nitrophenol and related aminonitrophenols. In the case of 4-nitrophenol, Co@350 proved to be the most active catalyst, therein its retention of activity over prolonged exposure to air, moisture, and reducing environments, and applicability in flow processes is demonstrated.

More highly myelinated white matter tracts are associated with faster processing speed in healthy adults.

The objective of this study was to investigate whether the estimated myelin content of white matter tracts is predictive of cognitive processing speed and whether such associations are modulated by age. Associations between estimated myelin content and processing speed were assessed in 570 community-living individuals (277 middle-age, 293 older-age). Myelin content was estimated in-vivo using the mean T1w/T2w magnetic resonance ratio, in six white matter tracts (anterior corona radiata, superior corona radiata, pontine crossing tract, anterior limb of the internal capsule, genu of the corpus callosum, and splenium of the corpus callosum). Processing speed was estimated by extracting a principal component from 5 separate tests of processing speed. It was found that estimated myelin content of the bilateral anterior limb of the internal capsule and left splenium of the corpus callosum were significant predictors of processing speed, even after controlling for socio-demographic, health and genetic variables and correcting for multiple comparisons. One SD higher in the estimated myelin content of the anterior limb of the internal capsule was associated with 2.53% faster processing speed and within the left splenium of the corpus callosum with 2.20% faster processing speed. In addition, significant differences in estimated myelin content between middle-age and older participants were found in all six white matter tracts. The present results indicate that myelin content, estimated in vivo using a neuroimaging approach in healthy older adults, is sufficiently precise to predict variability in processing speed in behavioural measures.

The Use of Recovery Strategies Among Participants of the BUPA Great North Run: A Cross-Sectional Survey.

OBJECTIVE: To investigate half-marathon runners' frequency of use of recovery strategies, perceptions regarding the most beneficial recovery strategy, and reasons for using recovery strategies. DESIGN: Cross-sectional survey. PARTICIPANTS: 186 participants of the 13.1 mile BUPA Great North Run 2013. METHODS: A questionnaire was developed which required participants to indicate how frequently they used 12 different recovery strategies, identify which recovery strategy they believed to be most beneficial, and rank 6 reasons for using recovery strategies in order of importance. Data were analyzed using a Friedman nonparametric ANOVA and additional nonparametric tests. RESULTS: All participants used recovery strategies. Stretching was the most commonly used recovery strategy (P < .001), whereas the use of nutritional supplements was the most commonly selected most beneficial recovery strategy. More than 50% of respondents indicated that they never used strategies such as kinesio tape (80%), hydrotherapy (78%), or ice baths (71%). A significant difference was observed between reasons for using recovery strategy (χ2 (5) = 292.29, P < .001). Reducing muscle tightness (rank 4.87) and reducing injury (rank 4.35) were the most frequently chosen most important reasons for using recovery strategies. Minor sex and age differences in the responses were identified. CONCLUSION: Recovery strategy usage appears to be widespread among half-marathon runners; however, disparities exist between the frequency of use and perceived effectiveness of different recovery strategies. Further research in this area is needed to facilitate the development of recovery strategy guidelines which are both evidence-based and practically relevant.