Miracle-dz/UniFAR-FTUs huggingface dataset:
Trace fossils associated with Burgess Shale non-biomineralized carapaces: bringing taphonomic and ecological controls into focus

The association of trace fossils and non-biomineralized carapaces has been reported from Cambrian Lagerstätten worldwide, but the abundance, ichnodiversity, taphonomy and ecological significance of such associations have yet to be fully investigated. Two main end-member hypotheses are explored based on the study of a relatively wide variety of trace fossils preserved associated to Tuzoia carapaces from the middle Cambrian Burgess Shale in British Columbia. In the ecological Tuzoia garden hypothesis, the bacterially enriched surface of carapaces provides opportunities for intricate ecologic interactions among trophic levels. In the taphonomic shielding hypothesis, the trace fossil–carapace association results from preferential preservation of traces as controlled by compaction independent of any association in life. In an attempt to better understand the role of the carapace as a medium for preservation of trace fossils and to evaluate the effects of mechanical stress related to burial, a numerical model was developed. Results indicate that the carapace can shield underlying sediment from mechanical stress for a finite time, differentially protecting trace fossils during the initial phase of burial and compaction. However, this taphonomic model alone fails to fully explain relatively high-density assemblages displaying a diversity of structures spatially confined within the perimeter of carapaces or branching patterns recording re-visitation.
TMEM266 is a functional voltage sensor regulated by extracellular Zn2+

Voltage-activated ion channels contain S1-S4 domains that sense membrane voltage and control opening of ion-selective pores, a mechanism that is crucial for electrical signaling. Related S1-S4 domains have been identified in voltage-sensitive phosphatases and voltage-activated proton channels, both of which lack associated pore domains. hTMEM266 is a protein of unknown function that is predicted to contain an S1-S4 domain, along with partially structured cytoplasmic termini. Here we show that hTMEM266 forms oligomers, undergoes both rapid (µs) and slow (ms) structural rearrangements in response to changes in voltage, and contains a Zn2+ binding site that can regulate the slow conformational transition. Our results demonstrate that the S1-S4 domain in hTMEM266 is a functional voltage sensor, motivating future studies to identify cellular processes that may be regulated by the protein. The ability of hTMEM266 to respond to voltage on the µs timescale may be advantageous for designing new genetically encoded voltage indicators.
Subjective wellbeing at different spatial scales for individuals satisfied and dissatisfied with life

Indicators that attempt to gauge wellbeing have been created and used at multiple spatial scales around the world. The most commonly used indicators are at the national level to enable international comparisons. When analyzing subjective life satisfaction (LS), an aspect of wellbeing, at multiple spatial scales in Australia, variables (drawn from environmental, social, and economic domains) that are significantly correlated to LS at smaller scales become less significant at larger sub-national scales. The reverse is seen for other variables, which become more significant at larger scales. Regression analysis over multiple scales on three groups (1) all individuals within the sample, (2) individuals with self-reported LS as dissatisfied (LS ≤ 5), and (3) individuals self-reporting LS as satisfied (LS > 5), show that variables critical for LS differ between subgroups of the sample as well as by spatial scale. Wellbeing measures need to be created at multiple scales appropriate to the purpose of the indicator. Concurrently, policies need to address the factors that are important to wellbeing at those respective scales, segments, and values of the population.
Family talk intervention in paediatric oncology: a pilot study protocol

Introduction There is evidence that families with a child diagnosed with cancer need psychosocial support throughout the illness trajectory. Unfortunately, there is little research into psychosocial interventions for such families, especially interventions where the entire family is involved. The aim of this pilot study is therefore to evaluate a psychosocial intervention, the family talk intervention (FTI), in paediatric oncology in terms of study feasibility and potential effects. Methods and analysis This pretest/post-test intervention pilot study is based on families with a child diagnosed with cancer. All families that include at least one child aged 6–19 years (ill child and/or sibling) at one of the six paediatric oncology centres in Sweden between September 2018 and September 2019 will be asked about participation. The intervention consists of six meetings with the family (part of the family or the entire family), led by two interventionists. The core elements in the intervention are to support the families in talking about the illness and related subjects, support the parents in understanding the needs of their children and how to support them and support the families in identifying their strengths and how to use them best. Mixed methods are used to evaluate the intervention (web-based questionnaires, interviews, field notes and observations). Self-reported data from all family members are collected at baseline, directly after the intervention and 6 months later. Study outcomes are family communication, knowledge about the illness, resilience, quality of life and grief. Ethics and dissemination The study has been approved by the Regional Ethical Review Board in Stockholm (Dnr 2018/250-31/2 and 2018/1852–32). Data are processed in coded form, accessible only to the research team and stored at Ersta Sköndal Bräcke University College in a secure server. Trial registration ClinicalTrials.gov Identifier NCT03650530, registered in August 2018.
A method to assess the impact of soil available water capacity uncertainty on crop models with a tipping‐bucket approach

Most agronomic crop models use a reservoir tipping‐bucket approach to model the water budget in the soil. Soil available water capacity (AWC) is the main soil property considered in this approach. Because AWC is difficult to measure, uncertainty in AWC may be high. We developed a method using a specific kriging technique to determine the effects of uncertainty in AWC on crop model predictions. The AqYield crop model was used as an example to assess the effects of uncertainty in AWC on two agronomic output variables (grain yield and drainage). The factors considered were the climatic region, crop type and soil depth. We assessed the results using the coefficient of variation (CV) and sets of critical values for which CV exceeded 5, 10 and 15%. The experiment provided insight into the criticality of AWC uncertainty over a wide range of agropedoclimatic situations according to crop, model and output of interest. The method revealed the greater effect of AWC uncertainty on both outputs for the spring crop than for the winter crop and identified cases where AWC uncertainty was critical. There was a stronger effect of AWC uncertainty on yield for shallow soil and climatic water deficit conditions. For each situation, the AWC uncertainty levels were determined above or below which the impact becomes significant on a given output because the sensitivity was very dependent on climate–crop–soil combinations. It was also observed that uncertainty in AWC had little effect in AqYield for a wide range of situations. The method developed uses a small number of model simulations to produce accurate results to better understand the impact of this major soil input data according to the target model and specific objectives. It could help to determine the level of accuracy needed in AWC measurement, depending on the objectives.
Increased α-Linolenic Acid Intake during Pregnancy is Associated with Higher Offspring Birth Weight

Abstract Background The amount and type of fat in the maternal diet during pregnancy are important contributors to fetal growth. The importance of plant-based omega-3 fatty acid (α-linolenic acid, ALA) intake in fetal growth has not been previously examined. Objective We sought to determine the association of maternal ALA intake during pregnancy with birth weight and body composition of the offspring. Methods Mothers and their newborn infants (n = 224) were recruited from the Royal Prince Alfred Hospital, Australia. Maternal diet during pregnancy was assessed using a validated food frequency questionnaire. Plasma fatty acid composition was analyzed in a subset of mothers (n = 41). Newborn body composition was assessed using air-displacement plethysmography. All analyses were adjusted for gestational age, sex, physical activity, and total energy intake. Results Dietary fatty acid intakes were positively associated with plasma phospholipid fatty acids for total omega-3 fatty acids (β = 0.452, P = 0.003), ALA (β = 0.339, P = 0.03), linoleic acid (β = 0.353, P = 0.03), eicosapentaenoic acid (β = 0.407, P = 0.009), and docosahexaenoic acid (β = 0.388, P = 0.01). Higher maternal intake of ALA (% total fat) was associated with higher offspring birth weight [189.7-g increase per 1% higher ALA (95% CI: 14, 365 g); P = . 04], although individually neither newborn fat mass nor fat-free mass was significant. Birth weight increased across tertiles of maternal ALA intake (PANOVA = 0.05), with birth weight being 221 g (95% CI: 12, 429 g) higher in those with the highest maternal ALA intake compared with those with the lowest intake (P = 0.04). Mothers of infants born small for gestational age (n = 32) had a lower ALA intake than those born appropriate for gestational age (n = 162) or large for gestational age [(n = 21); P = 0.05]. Conclusions In otherwise healthy women giving birth at a major tertiary hospital in Australia, intake of ALA during pregnancy is associated with higher offspring birth weight. This may have implications for dietary strategies aimed at optimizing fetal growth via modification of maternal diet.
“Every Newborn-INDEPTH” (EN-INDEPTH) study protocol for a randomised comparison of household survey modules for measuring stillbirths and neonatal deaths in five Health and Demographic Surveillance sites

Background Under-five and maternal mortality were halved in the Millennium Development Goals (MDG) era, with slower reductions for 2.6 million neonatal deaths and 2.6 million stillbirths. The Every Newborn Action Plan aims to accelerate progress towards national targets, and includes an ambitious Measurement Improvement Roadmap. Population-based household surveys, notably Demographic and Health Surveys (DHS) and Multiple Indicator Cluster Surveys, are major sources of population-level data on child mortality in countries with weaker civil registration and vital statistics systems, where over two-thirds of global child deaths occur. To estimate neonatal/child mortality and pregnancy outcomes (stillbirths, miscarriages, birthweight, gestational age) the most common direct methods are: (1) the standard DHS-7 with Full Birth History with additional questions on pregnancy losses in the past 5 years (FBH+) or (2) a Full Pregnancy History (FPH). No direct comparison of these two methods has been undertaken, although descriptive analyses suggest that the FBH+ may underestimate mortality rates particularly for stillbirths. Methods This is the protocol paper for the Every Newborn-INDEPTH study (INDEPTH Network, International Network for the Demographic Evaluation of Populations and their Health Every Newborn, Every Newborn Action Plan), aiming to undertake a randomised comparison of FBH+ and FPH to measure pregnancy outcomes in a household survey in five selected INDEPTH Network sites in Africa and South Asia (Bandim in urban and rural Guinea-Bissau; Dabat in Ethiopia; IgangaMayuge in Uganda; Kintampo in Ghana; Matlab in Bangladesh). The survey will reach >68 000 pregnancies to assess if there is ≥15% difference in stillbirth rates. Additional questions will capture birthweight, gestational age, birth/death certification, termination of pregnancy and fertility intentions. The World Bank’s Survey Solutions platform will be tailored for data collection, including recording paradata to evaluate timing. A mixed methods assessment of barriers and enablers to reporting of pregnancy and adverse pregnancy outcomes will be undertaken. Conclusions This large-scale study is the first randomised comparison of these two methods to capture pregnancy outcomes. Results are expected to inform the evidence base for survey methodology, especially in DHS, regarding capture of stillbirths and other outcomes, notably neonatal deaths, abortions (spontaneous and induced), birthweight and gestational age. In addition, this study will inform strategies to improve health and demographic surveillance capture of neonatal/child mortality and pregnancy outcomes.
Gesture-based registration correction using a mobile augmented reality image-guided neurosurgery system

In image-guided neurosurgery, a registration between the patient and their pre-operative images and the tracking of surgical tools enables GPS-like guidance to the surgeon. However, factors such as brainshift, image distortion, and registration error cause the patient-to-image alignment accuracy to degrade throughout the surgical procedure no longer providing accurate guidance. The authors present a gesture-based method for manual registration correction to extend the usage of augmented reality (AR) neuronavigation systems. The authors’ method, which makes use of the touchscreen capabilities of a tablet on which the AR navigation view is presented, enables surgeons to compensate for the effects of brainshift, misregistration, or tracking errors. They tested their system in a laboratory user study with ten subjects and found that they were able to achieve a median registration RMS error of 3.51 mm on landmarks around the craniotomy of interest. This is comparable to the level of accuracy attainable with previously proposed methods and currently available commercial systems while being simpler and quicker to use. The method could enable surgeons to quickly and easily compensate for most of the observed shift. Further advantages of their method include its ease of use, its small impact on the surgical workflow and its small-time requirement.
Laparoscopic Microwave Ablation of Hepatocellular Carcinoma at Liver Surface: Technique Effectiveness and Long-Term Outcomes

Background and Aims: To evaluate long-term outcomes and prognostic factors of laparoscopic microwave ablation as a first-line treatment for hepatocellular carcinoma located at the liver surface not feasible for percutaneous ablation. Methods: 51 consecutive patients receiving laparoscopic microwave ablation in our center between January 11, 2012, and July 31, 2014, were enrolled. Technique effectiveness (complete ablation or incomplete ablation) was evaluated 1 month postprocedure. Procedure-related complications were recorded. The influences of patients’ baseline characteristics on recurrence-free survival and overall survival were analyzed after a median follow-up of 34.0 (ranging 19.0-49.0) months. Results: Complete ablation was gained in 47 (92.2%) of the 51 patients. No patients died within 30 days of microwave ablation procedure. A total of 3 (5.9%) cases of complications were observed. Tumor progression/recurrence were observed in 40 patients (78.4%). The median recurrence-free survival and median overall survival of the total cohort was 11.0 months (95% confidence interval: 7.573-14.427) and 34.0 months (95% confidence interval: 27.244-40.756), respectively. Multivariate analysis identified alanine transaminase level and tumor number as independent significant prognosticators of recurrence-free survival whereas α-fetoprotein level as significant prognosticators of overall survival. Conclusions: As a first-line treatment, laparoscopic microwave ablation provides high technique effectiveness rate and is well tolerated in patients with hepatocellular carcinoma located at liver surface. Alanine transaminase and tumor number were significant predictors of recurrence-free survival, whereas α-fetoprotein level was significant predictor of overall survival. Laparoscopic microwave ablation might serve as a rational treatment option for patients with hepatocellular carcinoma with tumors at the liver surface, which merits validation in future perspective studies.
Predicting queue wait time probabilities for multi-scale computing

We describe a method for queue wait time prediction in supercomputing clusters. It was designed for use as a part of multi-criteria brokering mechanisms for resource selection in a multi-site High Performance Computing environment. The aim is to incorporate the time jobs stay queued in the scheduling system into the selection criteria. Our method can also be used by the end users to estimate the time to completion of their computing jobs. It uses historical data about the particular system to make predictions. It returns a list of probability estimates of the form (ti, pi), where pi is the probability that the job will start before time ti. Times ti can be chosen more or less freely when deploying the system. Compared to regression methods that only return a single number as a queue wait time estimate (usually without error bars) our prediction system provides more useful information. The probability estimates are calculated using the Bayes theorem with the naive assumption that the attributes describing the jobs are independent. They are further calibrated to make sure they are as accurate as possible, given available data. We describe our service and its REST API and the underlying methods in detail and provide empirical evidence in support of the method's efficacy. This article is part of the theme issue ‘Multiscale modelling, simulation and computing: from the desktop to the exascale’.
Widespread introgression in Chinese indigenous chicken breeds from commercial broiler

Chinese indigenous chickens (CICs) constitute world‐renowned genetic resources due to their excellent traits, including early puberty, good meat quality and strong resistance to disease. Unfortunately, the introduction of a large number of commercial chickens in the past two decades has had an adverse effect on CICs. Using the chicken 60 K single nucleotide polymorphism chip, we assessed the genetic diversity and population structure of 1,187 chickens, representing eight Chinese indigenous chicken breeds, two hybrid chicken breeds, two ancestral chicken breeds, two commercial populations and additional red jungle fowl. By investigating haplotype similarity, we found extensive gene introgression from commercial broiler to almost all CICs. Approximately 15% of the genome, on average, of CICs was introgressed, ranging from 0.64% for Tibetan chicken to 21.52% for Huiyang Bearded chicken. Further analysis revealed signals consistent with positive selection in the introgression loci. For the first time, we systematically mapped and quantified introgression from commercial broiler to CICs at the whole genome level. Our data provided a usable resource for chicken genetic diversity, and our findings indicated a dire need for protecting the genetic resources of CICs.
Implementing and measuring the impact of a clinical and translational research mentor recognition program

Abstract Introduction Research shows incentives can motivate faculty to increase their engagement in mentoring, despite a myriad of institutional barriers. One such incentive may be the implementation of a university-wide mentor award program to promote a culture of mentorship. Methods A new mentorship award was created at a research-intensive university and faculty recipients were surveyed to assess their perceptions of the award’s impact on their mentoring practices and career. Results Sixty-two percent of awardees (n=21) completed the survey and felt the recognition incentivized them to engage in further mentoring and participate in formal mentorship training. Most awardees referenced the award in their CVs, performance evaluations, and grant proposals. Additionally, they felt the award effectively promoted mentoring among the broader faculty community. Conclusion Growth of clinical and translational research depends in part on the mentorship received by early career faculty. Therefore, other research universities may benefit from implementing such awards.
Pollen morphology of the African Sclerosperma (Arecaceae)

Abstract Three currently accepted Sclerosperma species appear to produce four different pollen morphologies. Sclerosperma mannii and S. walkeri pollen share the same distinct reticulate sculpture, but S. profizianum produces three different pollen types (microreticulate, fossulate, and perforate). The pollen morphology suggests that S. mannii and S. walkeri are sister taxa of the same intrageneric lineage. The pollen diversity observed in S. profizianum suggests (a) this taxon is unique regarding its pollen diversity despite being a non-heterostylous plant or (b) that circumscription of S. profizianum as a species may well be in the need of redefinition.
Beyond Motor Noise: Considering Other Causes of Impaired Reinforcement Learning in Cerebellar Patients

Motor and reinforcement learning have been classically linked to functionally independent brain networks centered on the cerebellum and the basal ganglia, respectively. In a recent study published in eNeuro , Therrien et al. (2018) showed that increasing motor noise in healthy subjects disrupts reinforcement learning. However, this impairment remained well below that detected in cerebellar patients even when motor noise in healthy subjects was adjusted to match that observed in the patients. This suggests that impaired reinforcement learning following cerebellar damage cannot be solely accounted for by altered motor noise in these patients. Based on recent anatomic and functional evidence, we argue that the cerebellum may directly contribute to reinforcement learning, consistent with its tight connections with the basal ganglia. The ability to adapt to changes occurring in the environment is a fundamental feature of human behavior, which relies on both sensory and reward feedbacks. On the one hand, the role of sensory feedback has been largely considered by studying how motor commands adapt to visual perturbations (e.g., a visuomotor rotation), a process called error-based learning (Shadmehr et al., 2010; Wolpert et al., 2011; Kim et al., 2018; Roemmich and Bastian, 2018). This type of motor learning involves the computation of sensory prediction errors (SPEs), namely, the difference between predicted and actual sensory outcome (Tseng et al., 2007; Schlerf and Ivry, 2012; Shadmehr, 2017, 2018). On the other hand, the role of reward feedback has been mostly investigated in tasks that require learning what action to select or not, by updating reward predictions based on previous experience, a process named reinforcement learning (Lee et al., 2012; Derosiere et al., 2017a,b; Gershman and Daw, 2017; O’Doherty et al., 2017). A central …