Miracle-dz/UniFAR-FTUs huggingface dataset:
The Reduction of Measles Transmission During School Vacations

Background: Historically, measles incidence has shown clear seasonal patterns driven by the school calendar, but since the start of mass vaccination in developed countries there are only occasional outbreaks, which may have changed the effect of school vacations on transmission. In 2013–2014, a large measles epidemic took place in a low vaccination coverage area in The Netherlands, allowing us to quantify current-day measles transmission and the effect of school vacations. Methods: We fitted a dynamic transmission model to notification and hospitalization time series data of the Dutch 2013–2014 measles epidemic. Our primary aim was to estimate the reduction in contact rate during school vacations and the number of cases averted due to the vacation. In addition, because the summer vacations were time-staggered in three regions, we could distinguish within-region from across-region effects of school vacations. Results: We estimated a 53% (95% credible interval: 45%, 60%) reduction in contact rate during school vacations, resulting in 4900 (3400–7100) averted cases (estimated outbreak size: 16,600 [12,600–23,200]). There was a shift from mainly local transmission during school term to mainly cross-regional transmission during vacations. With seroprevalence data, we derived a current-day estimate of 15 to 27 for R0 (number of secondary cases per primary case in a susceptible population). Conclusions: School vacations are associated with greatly reduced overall measles transmission. However, transmission is not eliminated, and increased long-distance travel may even promote spread to other areas. Therefore, we estimate that school closure is unlikely to prevent measles epidemics unless there are still few cases and the community is well vaccinated.
Hematopoietic stem cell transplantation : Improving alloreactive Bw 4 donor selection by genotyping codon 86 of KIR 3 DL 1 / S 1

KIR3DL1 is a Natural Killer (NK) cell receptor that recognizes the Bw4 epitope of HLA class I molecules. Following hematopoietic stem cell transplantation for patients lacking Bw4, KIR3DL1expressing NK cells from Bw4-positive donors can be alloreactive and eliminate tumour cells. However, KIR3DL1 alleles having T instead of C at nucleotide 320 (encoding leucine 86 instead of serine 86) are not expressed on the cell-surface. Thus, not all individuals testing positive for KIR3DL1 are optimal donors for Bw4-negative recipients. Therefore we developed a method for genotyping codon 86, which was validated by its perfect correlation with NK cell phenotype for 100 donors of diverse KIR3DL1/S1 genotype. We typed 600 donors and found that ~12.2% had the KIR3DL1 gene, but did not express cell-surface KIR3DL1. By contrast, high-expressing allotypes were identified when haplotypes from four families with duplicated KIR3DL1/S1 genes were characterized at high resolution. Identifying donors who have KIR3DL1 but lack cell-surface KIR3DL1 would refine donor selection. With this technique, the number of individuals identified who may not be optimal donors for Bw4 negative patients increases by three-fold, when compared with standard methods. Taken together, we propose that allele typing of KIR polymorphisms should become a standard practice when selecting donors. Corresponding author: Claudia Alicata (claudia.alicata@gmail.com). *PJN and MF contributed equally to this study. CONFLICT OF INTEREST DISCLOSURE A. Moretta is founder and shareholder of Innate Pharma (Marseille, France). The remaining authors declare no financial or commercial conflict of interest. HHS Public Access Author manuscript Eur J Immunol. Author manuscript; available in PMC 2017 June 01. Published in final edited form as: Eur J Immunol. 2016 June ; 46(6): 1511–1517. doi:10.1002/eji.201546236. A uhor M anscript
Large sensitivity in land carbon storage due to geographical and temporal variation in the thermal response of photosynthetic capacity

Summary Plant temperature responses vary geographically, reflecting thermally contrasting habitats and long‐term species adaptations to their climate of origin. Plants also can acclimate to fast temporal changes in temperature regime to mitigate stress. Although plant photosynthetic responses are known to acclimate to temperature, many global models used to predict future vegetation and climate–carbon interactions do not include this process. We quantify the global and regional impacts of biogeographical variability and thermal acclimation of temperature response of photosynthetic capacity on the terrestrial carbon (C) cycle between 1860 and 2100 within a coupled climate–carbon cycle model, that emulates 22 global climate models. Results indicate that inclusion of biogeographical variation in photosynthetic temperature response is most important for present‐day and future C uptake, with increasing importance of thermal acclimation under future warming. Accounting for both effects narrows the range of predictions of the simulated global land C storage in 2100 across climate projections (29% and 43% globally and in the tropics, respectively). Contrary to earlier studies, our results suggest that thermal acclimation of photosynthetic capacity makes tropical and temperate C less vulnerable to warming, but reduces the warming‐induced C uptake in the boreal region under elevated CO2.
Keep them in school: the importance of education as a protective factor against HIV infection among young South African women.

OBJECTIVE To identify risk factors for HIV infection among young women aged 15-24 years reporting one lifetime partner in South Africa. Design In 2003, we conducted a nationally representative household survey of sexual behaviour and HIV testing among 11 904 young people aged 15-24 years in South Africa. This analysis focuses on the subset of sexually experienced young women with only one reported lifetime sex partner (n = 1708). METHODS Using the proximate determinants framework and the published literature we identified factors associated with HIV in young women. The associations between these factors and HIV infection were explored in multivariable logistic regression models. RESULTS Of the young women, 15% reporting one lifetime partner were HIV positive. In multivariable analyses, young women who had not completed high school were more likely to be infected with HIV compared with those that had completed high school (AOR 3.75; 95% CI 1.34-10.46). CONCLUSIONS Young South African women in this population were at high risk of HIV infection despite reporting only having one lifetime partner. Few individual level factors were associated with HIV infection, emphasizing the importance of developing HIV prevention interventions that address structural and partner level risk factors.
[PIN+]ing down the mechanism of prion appearance

Abstract Prions are conformationally flexible proteins capable of adopting a native state and a spectrum of alternative states associated with a change in the function of the protein. These alternative states are prone to assemble into amyloid aggregates, which provide a structure for self-replication and transmission of the underlying conformer and thereby the emergence of a new phenotype. Amyloid appearance is a rare event in vivo, regulated by both the aggregation propensity of prion proteins and their cellular environment. How these forces normally intersect to suppress amyloid appearance and the ways in which these restrictions can be bypassed to create protein-only phenotypes remain poorly understood. The most widely studied and perhaps most experimentally tractable system to explore the mechanisms regulating amyloid appearance is the [PIN+] prion of Saccharomyces cerevisiae. [PIN+] is required for the appearance of the amyloid state for both native yeast proteins and for human proteins expressed in yeast. These observations suggest that [PIN+] facilitates the bypass of amyloid regulatory mechanisms by other proteins in vivo. Several models of prion appearance are compatible with current observations, highlighting the complexity of the process and the questions that must be resolved to gain greater insight into the mechanisms regulating these events.
Remote sensing of suspended sediment concentration, flow velocity, and lake recharge in the Peace‐Athabasca Delta, Canada

The transport of fine sediment, carried in suspension by water, is central to the hydrology, geomorphology, and ecological functioning of river floodplains and deltas. An extensive new field data set for the Peace‐Athabasca Delta (PAD), Canada quantifies robust positive relationships between in situ suspended sediment concentration (SSC) and remotely sensed visible/near‐infrared reflectance. These relationships are exploited using SPOT and ASTER satellite images to map suspended sediment concentrations across the PAD for four days in 2006 and 2007, revealing strong variations in water sources and flow patterns, including flow reversals in major distributaries. Near‐daily monitoring with 276 MODIS satellite images tracks hydrologic recharge of floodplain lakes, as revealed by episodic infusions of sediment‐rich water from the Athabasca River. The timing and magnitude of lake recharge are linked to springtime water level on the Athabasca River, suggesting a system sensitive to changes in river flow regime. Moreover, recharge timing differentiates lakes that are frequently and extensively recharged from those recharged more rarely. Finally, we present a first estimation of river flow velocity based on remotely sensed SSC, though saturation may occur at velocities >0.6 m/s. Viewed collectively, the different remote sensing methodologies presented here suggest strong value for visible/near‐infrared remote sensing of suspended sediment to assess hydrologic and sediment transport processes in complex flow environments. Field observations including nephelometric turbidity, specific conductivity, water temperature, Secchi disk depth, suspended sediment concentration, and water level are archived at the Oak Ridge National Laboratory Distributed Active Archive Center for Biogeochemical Dynamics (available at http://daac.ornl.gov//HYDROCLIMATOLOGY/guides/PAD.html).
Group‐level competition influences urinary steroid hormones among wild red–tailed monkeys, indicating energetic costs

Various theories emphasize that intergroup competition should affect intragroup cooperation and social relationships, especially if the cost of intergroup competition outweighs that of intragroup competition. This cost of intergroup competition may be quantified by changes in physiological status, such as in the steroid hormones cortisol (C) and testosterone (T), which rise or are depressed during periods of energetic stress, respectively. Here we tested for changes in urinary C and T after intergroup encounters (IGEs) among wild red‐tailed monkeys (Cercopithecus ascanius), a species that experiences frequent intergroup feeding competition, at the Ngogo station in Kibale National Park, Uganda. We assayed 108 urine samples, of which 36 were collected after IGEs, from 23 individuals in four social groups. Bayesian multilevel models controlling for various confounds revealed that IGEs increased C and decreased T relative to baseline, consistent with an energetic cost to IGEs. The C change was more apparent in samples collected early after IGEs, suggesting an anticipatory increase, whereas the T change was stronger in later samples, suggesting sustained energetic trade‐offs. Hormone responses were not affected by the IGE outcome. This cost to intergroup competition, together with little evidence for intragroup competition in redtails and other guenons, establishes an interesting test case for theories emphasizing the effect of intergroup competition on intragroup cooperation.
Stable carbon isotopes as indicators for environmental change in palsa peats

Abstract. Palsa peats are unique northern ecosystems formed under an arctic climate and characterized by a high biodiversity and sensitive ecology. The stability of the palsas are seriously threatened by climate warming which will change the permafrost dynamic and induce a degradation of the mires. We used stable carbon isotope depth profiles in two palsa mires of Northern Sweden to track environmental change during the formation of the mires. Soils dominated by aerobic degradation can be expected to have a clear increase of carbon isotopes (δ13C) with depth, due to preferential release of 12C during aerobic mineralization. In soils with suppressed degradation due to anoxic conditions, stable carbon isotope depth profiles are either more or less uniform indicating no or very low degradation or depth profiles turn to lighter values due to an enrichment of recalcitrant organic substances during anaerobic mineralisation which are depleted in 13C. The isotope depth profile of the peat in the water saturated depressions (hollows) at the yet undisturbed mire Storflaket indicated very low to no degradation but increased rates of anaerobic degradation at the Stordalen site. The latter might be induced by degradation of the permafrost cores in the uplifted areas (hummocks) and subsequent breaking and submerging of the hummock peat into the hollows due to climate warming. Carbon isotope depth profiles of hummocks indicated a turn from aerobic mineralisation to anaerobic degradation at a peat depth between 4 and 25 cm. The age of these turning points was 14C dated between 150 and 670 yr and could thus not be caused by anthropogenically induced climate change. We found the uplifting of the hummocks due to permafrost heave the most likely explanation for our findings. We thus concluded that differences in carbon isotope profiles of the hollows might point to the disturbance of the mires due to climate warming or due to differences in hydrology. The characteristic profiles of the hummocks are indicators for micro-geomorphic change during permafrost up heaving.
Properties of Oriented Strand Boards with External Layers made of Non-Strand Chips

This study evaluated the possibility of producing oriented strand boards (OSB) from non-strand chips. Properties of the produced boards were compared with commercially available OSB/3. Research has shown that replacing the strand chips of external layers with smaller chips allowed for the manufacturing of OSB/3 using chips up to four times shorter than standard strand chips. Oriented strand board manufacturers should consider preparing a new standard and introducing the market to a new type of OSB with very good mechanical properties and made of selected strand chips comprising one of the fractions obtained during screening.
Unobserved components in corporate defaults and bond prices

If there is an unobserved component in corporate default intensities, then part of the fluctuation in corporate bond prices can be attributed to the variation in beliefs about this latent factor over time. Using sequential Markov Chain Monte Carlo techniques, we show evidence of a latent frailty process in the default intensities in U.S. corporate defaults. The factor is robust to the inclusion of both macro and firm specific variables. We use the sequentially estimated changes in conditional expectations of the frailty level, persistence and volatility to proxy for changes in agents’ beliefs about the unobserved default intensities. We find that changes in frailty related variables help to explain the variation in U.S. corporate credit spreads and increase explanatory power by 10%–22%.
Comparative Study of Heavy Metals in different Parts of Domestic and Broiler Chickens

This study was designed to evaluate the heavy metals like Zn, Mn, Ag, Pb, Cu, Fe, and Ni in different body parts of broiler and domestic chickens. Broiler (Cock & Hen) and domestic chicken (Cock & Hen) were selected from Bannu to comprise different heavy metals present in different parts of their body. Samples of muscle, liver, gizzard, kidney and heart of both chickens were analyzed to determine the contents of heavy metals in these parts. Cu, Zn, Mn and Fe were found in large quantity and Ag, Pb and Cd were present in small concentration in domestic chicken. Similarly Zn, Pb, and Cu were found in higher concentration in broiler. Liver, kidney and gizzard samples of domestic chickens showed higher accumulation of Zn, Mn, Cu and Fe than broiler and Ag was the only heavy metal that showed higher concentration in broiler than domestic birds.
YOLOv3: An Incremental Improvement

We present some updates to YOLO! We made a bunch of little design changes to make it better. We also trained this new network that's pretty swell. It's a little bigger than last time but more accurate. It's still fast though, don't worry. At 320x320 YOLOv3 runs in 22 ms at 28.2 mAP, as accurate as SSD but three times faster. When we look at the old . 5 IOU mAP detection metric YOLOv3 is quite good. It achieves 57.9 mAP@50 in 51 ms on a Titan X, compared to 57.5 mAP@50 in 198 ms by RetinaNet, similar performance but 3.8x faster. As always, all the code is online at this https URL
P 300-based brain-computer interface ( BCI ) event-related potentials ( ERPs ) : People with amyotrophic lateral sclerosis ( ALS ) vs . age-matched controls

Objective: Brain-computer interfaces (BCIs) aimed at restoring communication to people with severe neuromuscular disabilities often use event-related potentials (ERPs) in scalp-recorded EEG activity. Up to the present, most research and development in this area has been done in the laboratory with young healthy control subjects. In order to facilitate the development of BCI most useful to people with disabilities, the present study set out to: (1) determine whether people with amyotrophic lateral sclerosis (ALS) and healthy, age-matched volunteers (HVs) differ in the speed and accuracy of their ERP-based BCI use; (2) compare the ERP characteristics of these two groups; and (3) identify ERP-related factors that might enable improvement in BCI performance for people with disabilities. Methods: Sixteen EEG channels were recorded while people with ALS or healthy age-matched volunteers (HVs) used a P300-based BCI. The subjects with ALS had little or no remaining useful motor control (mean ALS Functional Rating Scale-Revised 9.4 (±9.5SD) (range 0–25)). Each subject attended to a target item as the items in a 6 6 visual matrix flashed. The BCI used a stepwise linear discriminant function (SWLDA) to determine the item the user wished to select (i.e., the target item). Offline analyses assessed the latencies, amplitudes, and locations of ERPs to the target and non-target items for people with ALS and agematched control subjects. Results: BCI accuracy and communication rate did not differ significantly between ALS users and HVs. Although ERP morphology was similar for the two groups, their target ERPs differed significantly in the location and amplitude of the late positivity (P300), the amplitude of the early negativity (N200), and the latency of the late negativity (LN). Conclusions: The differences in target ERP components between people with ALS and age-matched HVs are consistent with the growing recognition that ALS may affect cortical function. The development of BCIs for use by this population may begin with studies in HVs but also needs to include studies in people with ALS. Their differences in ERP components may affect the selection of electrode montages, and might
ORGaNICs: A Theory of Working Memory in Brains and Machines

Working memory is a cognitive process that is responsible for temporarily holding and manipulating information. Most of the empirical neuroscience research on working memory has focused on measuring sustained activity in prefrontal cortex (PFC) and/or parietal cortex during simple delayed-response tasks, and most of the models of working memory have been based on neural integrators. But working memory means much more than just holding a piece of information online. We describe a new theory of working memory, based on a recurrent neural circuit that we call ORGaNICs (Oscillatory Recurrent GAted Neural Integrator Circuits). ORGaNICs are a variety of Long Short Term Memory units (LSTMs), imported from machine learning and artificial intelligence. ORGaNICs can be used to explain the complex dynamics of delay-period activity in prefrontal cortex (PFC) during a working memory task. The theory is analytically tractable so that we can characterize the dynamics, and the theory provides a means for reading out information from the dynamically varying responses at any point in time, in spite of the complex dynamics. ORGaNICs can be implemented with a biophysical (electrical circuit) model of pyramidal cells, combined with shunting inhibition via a thalamocortical loop. Although introduced as a computational theory of working memory, ORGaNICs are also applicable to models of sensory processing, motor preparation and motor control. ORGaNICs offer computational advantages compared to other varieties of LSTMs that are commonly used in AI applications. Consequently, ORGaNICs are a framework for canonical computation in brains and machines.
CORONARY DISEASE AND METABOLIC SYNDROME

Data from the Framingham Offspring Study indicate that the risk of coronary heart disease (CHD) in men and women, who were followed for 16 years, was directly related to the number of coronary heart disease risk factors (high cholesterol, low HDL-cholesterol, high body mass index, high systolic blood pressure, high triglyceride levels, and high blood glucose). Each of these risk factors also is associated with obesity (Wilson et al. 1999). Data from the Framingham Offspring Study also demonstrate that small changes in body weight are associated with significant changes in the sum of CHD risk factors. A gain in weight of 2.25 kg or more over 16 years significantly increased the sum of risk factors for CHD by 20% in men and 37% in women. Conversely, a reduction in weight by 2.25 kg or more significantly decreased the risk factor sum by 48% in men and 40% in women.
Soleus H‐reflex operant conditioning changes the H‐reflex recruitment curve

Introduction: Operant conditioning can gradually change the human soleus H‐reflex. The protocol conditions the reflex near M‐wave threshold. In this study we examine its impact on the reflexes at other stimulus strengths. Methods: H‐reflex recruitment curves were obtained before and after a 24‐session exposure to an up‐conditioning (HRup) or a down‐conditioning (HRdown) protocol and were compared. Results: In both HRup and HRdown subjects, conditioning affected the entire H‐reflex recruitment curve. In 5 of 6 HRup and 3 of 6 HRdown subjects, conditioning elevated (HRup) or depressed (HRdown), respectively, the entire curve. In the other HRup subject or the other 3 HRdown subjects, the curve was shifted to the left or to the right, respectively. Conclusions: H‐reflex conditioning does not simply change the H‐reflex to a stimulus of particular strength; it also changes the H‐reflexes to stimuli of different strengths. Thus, it is likely to affect many actions in which this pathway participates. Muscle Nerve 47: [? show $1534v]–[? show $1535v], 2013
First UK case report of kidney transplantation from an HIV-infected deceased donor to two HIV-infected recipients

Abstract Kidney transplantation is now considered the treatment of choice for many human immunodeficiency virus (HIV)-infected patients with end-stage renal disease (ESRD). Graft survival rates using HIV-negative donors and carefully selected HIV-positive ESRD patients are similar to those observed in HIV-uninfected kidney transplant recipients. To address the relative shortfall in donated organs it has been proposed that organs from HIV-infected deceased donors might be allocated to HIV-infected patients on the transplant waiting list. Preliminary experience in South Africa reports promising short-term outcomes in a small number of HIV-infected recipients of kidney transplants from HIV-infected donors. We sought to replicate this experience in the UK by accepting kidney offers from HIV infected deceased donors for patients with HIV-infection on the kidney transplant waiting list. Here we report the UK’s first cases of kidney transplantation between HIV-positive donors and recipients.