Cue polarization and representation in mouse home base behaviors.

The nature of the representation guiding spatial navigation has been investigated extensively; however, most of this work has used behavioral tasks that involved learning the location of food reward or an escape platform. In contrast, relatively few studies have focused on the spatial representation of a home base, a ubiquitous feature of open-field behavior, and its ability to be encoded relative to environmental cues. The current set of experiments investigated acquisition and retention of the location of home base establishment. In general, proximal cues anchored the position of the home base during acquisition sessions across all four experiments. Although mice established a home base during retention sessions, previous experience did not influence its position during retention sessions. These observations demonstrate that stimulus control of home base position depends on access to proximal cues. Further work is needed to determine the extent that home base establishment may provide a framework to encode goal-directed spatial behaviors.

Direct calculation of the temperature dependence of 2D-IR spectra: Urea in water.

A method for directly calculating the temperature derivative of two-dimensional infrared (2D-IR) spectra from simulations at a single temperature is presented. The approach is demonstrated by application to the OD stretching spectrum of isotopically dilute aqueous (HOD in H2O) solutions of urea as a function of concentration. Urea is an important osmolyte because of its ability to denature proteins, which has motivated significant interest in its effect on the structure and dynamics of water. The present results show that the temperature dependence of both the linear IR and 2D-IR spectra, which report on the underlying energetic driving forces, is more sensitive to urea concentration than the spectra themselves. Additional physical insight is provided by calculation of the contributions to the temperature derivative from different interactions, e.g., water-water, water-urea, and urea-urea, present in the system. Finally, it is demonstrated how 2D-IR spectra at other temperatures can be obtained from only room temperature simulations.

Artificial intelligence (AI)-assisted exome reanalysis greatly aids in the identification of new positive cases and reduces analysis time in a clinical diagnostic laboratory.

PURPOSE: Artificial intelligence (AI) and variant prioritization tools for genomic variant analysis are being rapidly developed for use in clinical diagnostic testing. However, their clinical utility and reliability are currently limited. Therefore, we performed a validation of a commercial AI tool (Moon) and a comprehensive reanalysis of previously collected clinical exome sequencing cases using an open-source variant prioritization tool (Exomiser) and the now-validated AI tool to test their feasibility in clinical diagnostics. METHODS: A validation study of Moon was performed with 29 positive cases determined by previous manual analysis. After validation, reanalysis was performed on 80 previously manually analyzed nondiagnostic exome cases using Moon. Finally, a comparison between Moon and Exomiser was completed regarding their ability to identify previously completed positive cases and to identify new positive cases. RESULTS: Moon correctly selected the causal variant(s) in 97% of manually analyzed positive cases and identified 7 new positive cases. Exomiser correctly identified the causal gene in 85% of positive cases and agreed with Moon by ranking the new gene in its top 10 list 43% of the time. CONCLUSION: The use of AI in diagnostic laboratories greatly enhances exome sequencing analysis by reducing analysis time and increasing the diagnostic rate.

Polar metals by geometric design.

Gauss's law dictates that the net electric field inside a conductor in electrostatic equilibrium is zero by effective charge screening; free carriers within a metal eliminate internal dipoles that may arise owing to asymmetric charge distributions. Quantum physics supports this view, demonstrating that delocalized electrons make a static macroscopic polarization, an ill-defined quantity in metals--it is exceedingly unusual to find a polar metal that exhibits long-range ordered dipoles owing to cooperative atomic displacements aligned from dipolar interactions as in insulating phases. Here we describe the quantum mechanical design and experimental realization of room-temperature polar metals in thin-film ANiO3 perovskite nickelates using a strategy based on atomic-scale control of inversion-preserving (centric) displacements. We predict with ab initio calculations that cooperative polar A cation displacements are geometrically stabilized with a non-equilibrium amplitude and tilt pattern of the corner-connected NiO6 octahedral--the structural signatures of perovskites--owing to geometric constraints imposed by the underlying substrate. Heteroepitaxial thin-films grown on LaAlO3 (111) substrates fulfil the design principles. We achieve both a conducting polar monoclinic oxide that is inaccessible in compositionally identical films grown on (001) substrates, and observe a hidden, previously unreported, non-equilibrium structure in thin-film geometries. We expect that the geometric stabilization approach will provide novel avenues for realizing new multifunctional materials with unusual coexisting properties.

Anisotropic spin-orbit torque generation in epitaxial SrIrO3 by symmetry design.

Spin-orbit coupling (SOC), the interaction between the electron spin and the orbital angular momentum, can unlock rich phenomena at interfaces, in particular interconverting spin and charge currents. Conventional heavy metals have been extensively explored due to their strong SOC of conduction electrons. However, spin-orbit effects in classes of materials such as epitaxial 5d-electron transition-metal complex oxides, which also host strong SOC, remain largely unreported. In addition to strong SOC, these complex oxides can also provide the additional tuning knob of epitaxy to control the electronic structure and the engineering of spin-to-charge conversion by crystalline symmetry. Here, we demonstrate room-temperature generation of spin-orbit torque on a ferromagnet with extremely high efficiency via the spin-Hall effect in epitaxial metastable perovskite SrIrO3 We first predict a large intrinsic spin-Hall conductivity in orthorhombic bulk SrIrO3 arising from the Berry curvature in the electronic band structure. By manipulating the intricate interplay between SOC and crystalline symmetry, we control the spin-Hall torque ratio by engineering the tilt of the corner-sharing oxygen octahedra in perovskite SrIrO3 through epitaxial strain. This allows the presence of an anisotropic spin-Hall effect due to a characteristic structural anisotropy in SrIrO3 with orthorhombic symmetry. Our experimental findings demonstrate the heteroepitaxial symmetry design approach to engineer spin-orbit effects. We therefore anticipate that these epitaxial 5d transition-metal oxide thin films can be an ideal building block for low-power spintronics.

Direct observation of a two-dimensional hole gas at oxide interfaces.

The discovery of a two-dimensional electron gas (2DEG) at the LaAlO3/SrTiO3 interface 1 has resulted in the observation of many properties2-5 not present in conventional semiconductor heterostructures, and so become a focal point for device applications6-8. Its counterpart, the two-dimensional hole gas (2DHG), is expected to complement the 2DEG. However, although the 2DEG has been widely observed 9 , the 2DHG has proved elusive. Herein we demonstrate a highly mobile 2DHG in epitaxially grown SrTiO3/LaAlO3/SrTiO3 heterostructures. Using electrical transport measurements and in-line electron holography, we provide direct evidence of a 2DHG that coexists with a 2DEG at complementary heterointerfaces in the same structure. First-principles calculations, coherent Bragg rod analysis and depth-resolved cathodoluminescence spectroscopy consistently support our finding that to eliminate ionic point defects is key to realizing a 2DHG. The coexistence of a 2DEG and a 2DHG in a single oxide heterostructure provides a platform for the exciting physics of confined electron-hole systems and for developing applications.

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

BACKGROUND: Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes. RESULTS: The Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal. CONCLUSIONS: PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download.

Mining for pairs: shared clinic visit dates identify steady HIV-positive partnerships.

OBJECTIVES: Here we examined the hypothesis that some stable HIV-infected partnerships can be found in cohort studies, as the patients frequently attend the clinic visits together. METHODS: Using mathematical approximations and shuffling to derive the probabilities of sharing a given number of visits by chance, we identified and validated couples that may represent either transmission pairs or serosorting couples in a stable relationship. RESULTS: We analysed 434 432 visits for 16 139 Swiss HIV Cohort Study patients from 1990 to 2014. For 89 pairs, the number of shared visits exceeded the number expected. Of these, 33 transmission pairs were confirmed on the basis of three criteria: an extensive phylogenetic tree, a self-reported steady HIV-positive partnership, and risk group affiliation. Notably, 12 of the validated transmission pairs (36%; 12 of 33) were of a mixed ethnicity with a large median age gap [17.5 years; interquartile range (IQR) 11.8-22 years] and these patients harboured HIV-1 of predominantly non-B subtypes, suggesting imported infections. CONCLUSIONS: In the context of the surge in research interest in HIV transmission pairs, this simple method widens the horizons of research on within-pair quasi-species exchange, transmitted drug resistance and viral recombination at the biological level and targeted prevention at the public health level.

General practice performance in referral for suspected cancer: influence of number of cases and case-mix on publicly reported data.

BACKGROUND: Publicly available data show variation in GPs' use of urgent suspected cancer (USC) referral pathways. We investigated whether this could be due to small numbers of cancer cases and random case-mix, rather than due to true variation in performance. METHODS: We analysed individual GP practice USC referral detection rates (proportion of the practice's cancer cases that are detected via USC) and conversion rates (proportion of the practice's USC referrals that prove to be cancer) in routinely collected data from GP practices in all of England (over 4 years) and northeast Scotland (over 7 years). We explored the effect of pooling data. We then modelled the effects of adding random case-mix to practice variation. RESULTS: Correlations between practice detection rate and conversion rate became less positive when data were aggregated over several years. Adding random case-mix to between-practice variation indicated that the median proportion of poorly performing practices correctly identified after 25 cancer cases were examined was 20% (IQR 17 to 24) and after 100 cases was 44% (IQR 40 to 47). CONCLUSIONS: Much apparent variation in GPs' use of suspected cancer referral pathways can be attributed to random case-mix. The methods currently used to assess the quality of GP-suspected cancer referral performance, and to compare individual practices, are misleading. These should no longer be used, and more appropriate and robust methods should be developed.

Virological failure after 1 year of first-line ART is not associated with HIV minority drug resistance in rural Cameroon .

OBJECTIVES: The aim of this study was to describe clinical and virological outcomes in therapy-naive HIV-1-positive patients treated in a routine ART programme in rural Cameroon. METHODS: In a prospective cohort, 300 consecutive patients starting first-line ART were enrolled and followed for 12 months. Among 238 patients with available viral load data at Month 12, logistic regression was used to analyse risk factors for virological failure (≥1000 HIV RNA copies/mL) including clinical, immunological and virological parameters, as well as data on drug adherence. Population sequencing was performed to detect the presence of drug-resistance mutations in patients with virological failure at Month 12; minority drug-resistance mutations at baseline were analysed using next-generation sequencing in these patients and matched controls. RESULTS: At Month 12, 38/238 (16%) patients experienced virological failure (≥1000 HIV RNA copies/mL). Patients with virological failure were younger, had lower CD4 cell counts and were more often WHO stage 3 or 4 at baseline. Sixty-three percent of patients with virological failure developed at least one drug-resistance mutation. The M184V (n = 18) and K103N (n = 10) mutations were most common. At baseline, 6/30 patients (20%) experiencing virological failure and 6/35 (17%) matched controls had evidence of minority drug-resistance mutations using next-generation sequencing (P = 0.77). Lower CD4 count at baseline (OR per 100 cells/mm(3) lower 1.41, 95% CI 1.02-1.96, P = 0.04) and poorer adherence (OR per 1% lower 1.05, 95% CI 1.02-1.08, P < 0.001) were associated with a higher risk of virological failure. Unavailability of ART at the treatment centre was the single most common cause for incomplete adherence. CONCLUSIONS: Virological failure after 1 year of ART was not associated with minority drug resistance at baseline but with incomplete adherence. Strategies to assure adherence and uninterrupted drug supplies are pivotal factors for therapy success.

Role of Organics in Regulating ClNO2 Production at the Air-Sea Interface.

We report measurements of the product yield for nitryl chloride (ClNO2) production following the reactive uptake of dinitrogen pentoxide (N2O5) to a wide variety of ambient seawater samples as well as seawater mimics. The ClNO2 yield, as measured for ambient seawater collected from both coastal and open ocean waters, was found to be both insensitive to chlorophyll-a, a marker for biological activity, and significantly lower (0.16-0.30) than that expected for equivalent salt-containing solutions (0.82 ± 0.05). Suppression in the ClNO2 yield can be induced by the addition of aromatic organic compounds (e.g., phenol and humic acid) to synthetic seawater matrices. In the case of phenol, surface tension measurements reveal that the surface phenol:chloride ratio can be enhanced by more than a factor of 100 as compared to bulk ratios for subtle changes in surface tension (<1.5 mN m(-1)), providing a mechanism to suppress ClNO2 production at low bulk phenol concentrations. We interpret measurements of the dependence of the ClNO2 yield on phenol using a kinetic model, where we confine the surface enhancement in phenol to the top 1 nm of the interface. Our results are most consistent with a model where N2O5 is ionized within the first three water monolayers (<1 nm), where the product nitronium ions react rapidly with interfacial phenol molecules. These results suggest that ClNO2 may not be formed at the air-sea interface at the yield expected for NaCl, and that the reactive uptake of N2O5 and the subsequent product yield of ClNO2 may serve as a unique probe for the composition of the interfacial region of the sea surface microlayer.

Time from first presentation in primary care to treatment of symptomatic colorectal cancer: effect on disease stage and survival.

BACKGROUND: British 5-year survival from colorectal cancer (CRC) is below the European average, but the reasons are unclear. This study explored if longer provider delays (time from presentation to treatment) were associated with more advanced stage disease at diagnosis and poorer survival. METHODS: Data on 958 people with CRC were linked with the Scottish Cancer Registry, the Scottish Death Registry and the acute hospital discharge (SMR01) dataset. Time from first presentation in primary care to first treatment, disease stage at diagnosis and survival time from date of first presentation in primary care were determined. Logistic regression and Cox survival analyses, both with a restricted cubic spline, were used to model stage and survival, respectively, following sequential adjustment of patient and tumour factors. RESULTS: On univariate analysis, those with <4 weeks from first presentation in primary care to treatment had more advanced disease at diagnosis and the poorest prognosis. Treatment delays between 4 and 34 weeks were associated with earlier stage (with the lowest odds ratio occurring at 20 weeks) and better survival (with the lowest hazard ratio occurring at 16 weeks). Provider delays beyond 34 weeks were associated with more advanced disease at diagnosis, but not increased mortality. Following adjustment for patient, tumour factors, emergency admissions and symptoms and signs, no significant relationship between provider delay and stage at diagnosis or survival from CRC was found. CONCLUSIONS: Although allowing for a nonlinear relationship and important confounders, moderately long provider delays did not impact adversely on cancer outcomes. Delays are undesirable because they cause anxiety; this may be fuelled by government targets and health campaigns stressing the importance of very prompt cancer diagnosis. Our findings should reassure patients. They suggest that a health service's primary emphasis should be on quality and outcomes rather than on time to treatment.

De novo mutation in the dopamine transporter gene associates dopamine dysfunction with autism spectrum disorder.

De novo genetic variation is an important class of risk factors for autism spectrum disorder (ASD). Recently, whole-exome sequencing of ASD families has identified a novel de novo missense mutation in the human dopamine (DA) transporter (hDAT) gene, which results in a Thr to Met substitution at site 356 (hDAT T356M). The dopamine transporter (DAT) is a presynaptic membrane protein that regulates dopaminergic tone in the central nervous system by mediating the high-affinity reuptake of synaptically released DA, making it a crucial regulator of DA homeostasis. Here, we report the first functional, structural and behavioral characterization of an ASD-associated de novo mutation in the hDAT. We demonstrate that the hDAT T356M displays anomalous function, characterized as a persistent reverse transport of DA (substrate efflux). Importantly, in the bacterial homolog leucine transporter, substitution of A289 (the homologous site to T356) with a Met promotes an outward-facing conformation upon substrate binding. In the substrate-bound state, an outward-facing transporter conformation is required for substrate efflux. In Drosophila melanogaster, the expression of hDAT T356M in DA neurons-lacking Drosophila DAT leads to hyperlocomotion, a trait associated with DA dysfunction and ASD. Taken together, our findings demonstrate that alterations in DA homeostasis, mediated by aberrant DAT function, may confer risk for ASD and related neuropsychiatric conditions.

Evaluation of a non-adherent, povidone-iodine dressing in a case series of chronic wounds.

Here we report a product evaluation for a non-adherent, povidone-iodine (PVP-I) dressing, determining the clinical need for the product, performing a literature review, clinical evaluation and cost-analysis, and developing a recommendation. This evaluation included 20 patients who experienced dressing pain with the previous antimicrobial dressing. Two patients discontinued the evaluation and four ulcers were non-healing; the remaining wounds closed with the PVP-I dressing. Patients indicated a preference for the PVP-I dressing, primarily due to lack of dressing pain. The PVP-I dressing was also the most cost-efficient.

Proliferation of elongate fishes in the deep sea.

It was hypothesized that energetically efficient anguilliform swimming and axial elongation in fishes is favoured in the deep sea and predicted that the degree of elongation of the body form of fishes would increase with depth. An index of fish shape was derived from the relationship between length and mass. This was combined with data on abundance of c. 266 fish species from 389 research trawl tows made at depths of between 300 and 2030 m in the north-east Atlantic Ocean. The degree of elongation of the fish increased with depth to c. 1250 m before levelling off. The strength of this phenomenon varied between higher level taxa, being most apparent in the Gadiformes and Osmeriformes, and weak or absent in the Perciformes and Selachimorpha. The advantage of efficient elongate body forms may explain why certain taxa such as the grenadiers (Macrouridae) have dominated the deep sea, some have restricted depth ranges, e.g. the sharks, skates and rays, and others are almost entirely absent, e.g. the flatfishes (Pleuronectiformes).

Firearm injuries to children in Cape Town, South Africa: impact of the 2004 Firearms Control Act.

BACKGROUND: Before the introduction of the Firearms Control Act in 2004, the epidemiology of childhood firearm injuries from 1991 to 2001 in Cape Town, South Africa, was reported. This study analyses current data as a comparator to assess the impact of the Act. METHODS: Firearm injuries seen at Red Cross War Memorial Children's Hospital, Cape Town, from 2001 to 2010 were respectively reviewed. Data recorded included the patients' folder numbers, gender, date of birth, age, date of presentation, date discharged and inpatient stay, firearm type, number of shots, circumstances, injury sites, injury type, treatment, resulting morbidities and survival. These data were compared with the 1991 - 2001 data. RESULTS: One hundred and sixty-three children presented with firearm injuries during this period. The results showed a decrease in incidence from 2001 to 2010. Older children and males had a higher incidence than younger children and females. Most injuries were to an extremity and were unintentional. Mortality had reduced significantly from the previous study (6% to 2.6%), as did the total number of inpatient days (1 063 to 617). CONCLUSIONS: Compared with the earlier study, this study showed a significant reduction in the number of children presenting with a firearm-related injury. Mortality and inpatient stay were also significantly reduced. The study shows the impact that the Firearms Control Act has had in terms of paediatric firearm-related injury and provides evidence that the medical profession can play an important role in reducing violence.

VAEs with structured image covariance applied to compressed sensing MRI.

Objective.This paper investigates how generative models, trained on ground-truth images, can be used as priors for inverse problems, penalizing reconstructions far from images the generator can produce. The aim is that learned regularization will provide complex data-driven priors to inverse problems while still retaining the control and insight of a variational regularization method. Moreover, unsupervised learning, without paired training data, allows the learned regularizer to remain flexible to changes in the forward problem such as noise level, sampling pattern or coil sensitivities in MRI.Approach.We utilize variational autoencoders that generate not only an image but also a covariance uncertainty matrix for each image. The covariance can model changing uncertainty dependencies caused by structure in the image, such as edges or objects, and provides a new distance metric from the manifold of learned images.Main results.We evaluate these novel generative regularizers on retrospectively sub-sampled real-valued MRI measurements from the fastMRI dataset. We compare our proposed learned regularization against other unlearned regularization approaches and unsupervised and supervised deep learning methods.Significance.Our results show that the proposed method is competitive with other state-of-the-art methods and behaves consistently with changing sampling patterns and noise levels.

The influence of motivation in recruitment and retention of rural and remote allied health professionals: a literature review.

INTRODUCTION: Recruitment and retention of allied health professionals (AHPs) to remote and rural Australia is challenging and correlates with poorer health status of remote and rural residents. While much has been written about the recruitment and retention problem, this study took a new approach by reviewing the literature describing the motivation of AHPs to work in remote and rural areas and then analyzing the findings from the perspective of motivation theory using Herzberg's extrinsic and intrinsic classification. Intrinsic motivation incentives are known to contribute to job satisfaction and come from within the individual, for example the pleasure derived from autonomy or challenge at work. In contrast, extrinsic motivation incentives are provided by the job and include such factors as salary and professional development provisions. Extrinsic incentives are important because they prevent job dissatisfaction. Job satisfaction has been shown to be linked with increased retention. METHOD: Thirty-five articles, including 26 from Australia, met the inclusion criteria. The key findings related to motivation from each article are outlined and the results classified into the extrinsic-intrinsic framework. The incentives are then further analyzed as having a positive or a negative influence. RESULTS: In total, 38 different incentives were described a total of 246 times. Of the total, almost half (n=115) comprised extrinsic incentives with a negative influence, with poor access to professional development, professional isolation and insufficient supervision the most frequently reported. Rural lifestyle and diverse caseloads were the most frequently mentioned positive extrinsic incentives, while autonomy and community connectedness were the most cited positive intrinsic incentives. Negative intrinsic incentives were mentioned least frequently (n=18); however, of these, feeling overwhelmed and that your work was not valued by the community were the most commonly reported. CONCLUSIONS: The results demonstrate the significant burden of extrinsic incentives with a negative influence that are perceived by AHPs in remote and rural areas. The high turnover rate of AHPs in remote and rural areas is likely to be, in part, due to the job dissatisfaction from these disincentives. More positive intrinsic incentives were reported than negative. This suggests the potential for intrinsic incentives, known to contribute to job satisfaction, to be mediating the extrinsic disincentives. The policy implications of this work include the importance of addressing extrinsic disincentives. Simultaneously, the existing intrinsic incentives need to be nurtured and developed. Organizations that implement strategies to enhance both extrinsic and intrinsic motivation incentives are more likely to successfully address their AHP workforce shortage.