Miracle-dz/UniFAR-FTUs huggingface dataset:
A Comprehensive Analysis of Shared Loci between Systemic Lupus Erythematosus (SLE) and Sixteen Autoimmune Diseases Reveals Limited Genetic Overlap

In spite of the well-known clustering of multiple autoimmune disorders in families, analyses of specific shared genes and polymorphisms between systemic lupus erythematosus (SLE) and other autoimmune diseases (ADs) have been limited. Therefore, we comprehensively tested autoimmune variants for association with SLE, aiming to identify pleiotropic genetic associations between these diseases. We compiled a list of 446 non–Major Histocompatibility Complex (MHC) variants identified in genome-wide association studies (GWAS) of populations of European ancestry across 17 ADs. We then tested these variants in our combined Caucasian SLE cohorts of 1,500 cases and 5,706 controls. We tested a subset of these polymorphisms in an independent Caucasian replication cohort of 2,085 SLE cases and 2,854 controls, allowing the computation of a meta-analysis between all cohorts. We have uncovered novel shared SLE loci that passed multiple comparisons adjustment, including the VTCN1 (rs12046117, P = 2.02×10−06) region. We observed that the loci shared among the most ADs include IL23R, OLIG3/TNFAIP3, and IL2RA. Given the lack of a universal autoimmune risk locus outside of the MHC and variable specificities for different diseases, our data suggests partial pleiotropy among ADs. Hierarchical clustering of ADs suggested that the most genetically related ADs appear to be type 1 diabetes with rheumatoid arthritis and Crohn's disease with ulcerative colitis. These findings support a relatively distinct genetic susceptibility for SLE. For many of the shared GWAS autoimmune loci, we found no evidence for association with SLE, including IL23R. Also, several established SLE loci are apparently not associated with other ADs, including the ITGAM-ITGAX and TNFSF4 regions. This study represents the most comprehensive evaluation of shared autoimmune loci to date, supports a relatively distinct non–MHC genetic susceptibility for SLE, provides further evidence for previously and newly identified shared genes in SLE, and highlights the value of studies of potentially pleiotropic genes in autoimmune diseases.
Infant Feeding and School Attainment in Five Cohorts from Low- and Middle-Income Countries

Background Performance in intelligence tests tends to be higher among individuals breastfed as infants, but little is known about the association between breastfeeding and achieved schooling. We assessed the association of infant feeding with school achievement in five cohorts from low- and middle-income countries. Unlike high-income country settings where most previous studies come from, breastfeeding is not positively associated with socioeconomic position in our cohorts, thus reducing the likelihood of a spurious positive association. Methodology and Principal Findings Participants included 10,082 young adults from five birth cohorts (Brazil, India, Guatemala, the Philippines, and South Africa). The exposures variables were whether the subject was ever breastfed, total duration of breastfeeding, and age at introduction of complementary foods. We adjusted the estimates for age at follow up, sex, maternal age, smoking during pregnancy, birthweight and socioeconomic position at birth. The key outcome was the highest grade achieved at school. In unadjusted analyses, the association between ever breastfeeding and schooling was positive in Brazil, inverse in the Philippines, and null in South Africa; in adjusted analyses, these associations were attenuated. In Brazil, schooling was highest among individuals breastfed for 3–12 months whereas in the Philippines duration of breastfeeding was inversely associated with schooling; and null associations were observed in South Africa and Guatemala. These associations were attenuated in adjusted models. Late introduction of solid foods was associated with lower schooling achievement in Brazil and South Africa. Conclusion Measures of breastfeeding are not consistently related to schooling achievement in contemporary cohorts of young adults in lower and middle-income countries.
Estimating relative needs formulae for new forms of social care support: using an extrapolation method

Acknowledgement This report is independent research commissioned and funded by the Department of Health Policy Research Programme (Study to Review and Update RNF Allocation Formulae for Adult Social Care, 056/0018). The views expressed in this publication are those of the author(s) and not necessarily those of the Department of Health. We would like to thank Olena Nizalova, Jose-Luis Fernandez and Jane Dennett for their support with this report. Furthermore, we are very grateful for the comments and suggestions from Sarah Horne, Jonathon White and other colleagues in DH, DCLG and DWP. We also like to thank the local authorities that took part in the research and provided data, and members of the advisory panel for their invaluable comments. Executive Summary Introduction 1. Local authorities in England have responsibility for securing adult social care for their local populations. Historically, social care support has included: services such as home care and residential care; personal budgets and direct payments; equipment; and also some professional support like social work. The majority of public social care funding, however, comes from central Government, and is distributed to local authorities in the form of both open-ended grants (the majority) and some ring-fenced grants. 2. Following the Layfield enquiry in 1976 (Cmnd 6453 1976) central Government grants have been allocated to local authorities using a formula to help account for differences in local funding requirements (Bebbington and Davies 1980). The latest incarnation – in operation since 2006/7 – is the relative need formula (RNF) (Darton, Forder et al. 2010). 3. The fundamental principle underpinning the use of allocation formulas is to ensure equal opportunity of access to 'support' for equal need. The conventional way to interpret this principle is that each council should have, after their allocation, sufficient net funding so that they can provide an equivalent level of support (services or otherwise) to all people in their local population who would satisfy national standard eligibility conditions (Gravelle, Sutton et al. 2003; Smith 2007). 4. The number of people satisfying eligibility tests for public support for social are, and the amount of that support, will vary between local authorities according to a range of 'need-related' and wealth/income factors. These factors can be largely regarded as being 'exogenous', beyond the (reasonable) control of the local council, and therefore funding allocations should be adjusted to compensate local authorities accordingly. 5. Following implementation of the Care Act 2014 local authorities will …
Modeling Within-Host Effects of Drugs on Plasmodium falciparum Transmission and Prospects for Malaria Elimination

Achieving a theoretical foundation for malaria elimination will require a detailed understanding of the quantitative relationships between patient treatment-seeking behavior, treatment coverage, and the effects of curative therapies that also block Plasmodium parasite transmission to mosquito vectors. Here, we report a mechanistic, within-host mathematical model that uses pharmacokinetic (PK) and pharmacodynamic (PD) data to simulate the effects of artemisinin-based combination therapies (ACTs) on Plasmodium falciparum transmission. To contextualize this model, we created a set of global maps of the fold reductions that would be necessary to reduce the malaria RC (i.e. its basic reproductive number under control) to below 1 and thus interrupt transmission. This modeling was applied to low-transmission settings, defined as having a R0<10 based on 2010 data. Our modeling predicts that treating 93–98% of symptomatic infections with an ACT within five days of fever onset would interrupt malaria transmission for ∼91% of the at-risk population of Southeast Asia and ∼74% of the global at-risk population, and lead these populations towards malaria elimination. This level of treatment coverage corresponds to an estimated 81–85% of all infected individuals in these settings. At this coverage level with ACTs, the addition of the gametocytocidal agent primaquine affords no major gains in transmission reduction. Indeed, we estimate that it would require switching ∼180 people from ACTs to ACTs plus primaquine to achieve the same transmission reduction as switching a single individual from untreated to treated with ACTs. Our model thus predicts that the addition of gametocytocidal drugs to treatment regimens provides very small population-wide benefits and that the focus of control efforts in Southeast Asia should be on increasing prompt ACT coverage. Prospects for elimination in much of Sub-Saharan Africa appear far less favorable currently, due to high rates of infection and less frequent and less rapid treatment.
Biotechnological uses of enzymes from psychrophiles

The bulk of the Earth's biosphere is cold (e.g. 90% of the ocean's waters are ≤ 5°C), sustaining a broad diversity of microbial life. The permanently cold environments vary from the deep ocean to alpine reaches and to polar regions. Commensurate with the extent and diversity of the ecosystems that harbour psychrophilic life, the functional capacity of the microorganisms that inhabitat the cold biosphere are equally diverse. As a result, indigenous psychrophilic microorganisms provide an enormous natural resource of enzymes that function effectively in the cold, and these cold‐adapted enzymes have been targeted for their biotechnological potential. In this review we describe the main properties of enzymes from psychrophiles and describe some of their known biotechnological applications and ways to potentially improve their value for biotechnology. The review also covers the use of metagenomics for enzyme screening, the development of psychrophilic gene expression systems and the use of enzymes for cleaning.
A mystery solved: the mass ratio of the dwarf nova EM Cygni

We have discovered that the spectrum of the well-known dwarf nova EM Cyg is contaminated by light from a K2–5V star (in addition to the K-type mass donor star). The K2–5V star contributes approximately 16 per cent of the light from the system and if not taken into account has a considerable effect upon radial velocity measurements of the mass donor star. We obtain a new radial velocity amplitude for the mass donor star of K2 = 202 ± 3kms −1 , which compares with the value of K2 = 135 ± 3kms −1 obtained in Stover, Robinson & Nather’s classic 1981 study of EM Cyg. The revised value of the amplitude combined with a measurement of rotational broadening of the mass donor v sini = 140 ± 6kms −1 , leads to a new mass ratio of q = M2/M1 = 0.88 ± 0.05. This solves a long standing problem with EM Cyg because Stover et al.’s measurements indicated a mass ratio q > 1, a value which should have led to dynamically unstable mass transfer for the secondary mass deduced by Stover et al. The revised value of the mass ratio combined with the orbital inclination i = 67±2 ◦ leads to masses of 0.99±0.12M⊙ and 1.12±0.08M⊙ for the mass donor and white dwarf respectively. The mass donor is evolved, since it has a later spectral type (K3) than its mass would imply. We discuss whether the K star could be physically associated with EM Cyg or not, and present the results of the spectroscopic study.
Wind turbine-energy storage control system for delivering constant demand power shared by DFIGs through droop characteristics

This paper investigates embedding Energy Storage (ES) with multiple wind turbines in order to deliver to the grid a smooth and constant power as demanded by the system operator. The demand power is shared by DFIGs proportional to their ratings utilizing classical voltage and frequency droop characteristics. The paper addresses the system control methodologies for delivering constant power to the grid whilst also ensuring good system stability and good utilization of the inherent inertial energy storage capacity of the turbine. A wind farm consisting of DFIG generators feeding an HVDC link is chosen for illustration, but the methods can be applied to many technologies. The simulations, which are done by PSCAD/EMTDC, demonstrate that the total power delivered by the wind farm is constant and equal to the total demand power while each DFIG-ES delivers a constant power proportional to its rating determined by droop characteristics. The calculation of the size of ES (power and energy) for a deterministic wind statistics is beyond the scope of this paper and will be explained in a future paper.
Alternative Splicing in CaV2.2 Regulates Neuronal Trafficking via Adaptor Protein Complex-1 Adaptor Protein Motifs

N-type voltage-gated calcium (CaV2.2) channels are expressed in neurons and targeted to the plasma membrane of presynaptic terminals, facilitating neurotransmitter release. Here, we find that the adaptor protein complex-1 (AP-1) mediates trafficking of CaV2.2 from the trans-Golgi network to the cell surface. Examination of splice variants of CaV2.2, containing either exon 37a (selectively expressed in nociceptors) or 37b in the proximal C terminus, reveal that canonical AP-1 binding motifs, YxxΦ and [DE]xxxL[LI], present only in exon 37a, enhance intracellular trafficking of exon 37a-containing CaV2.2 to the axons and plasma membrane of rat DRG neurons. Finally, we identify differential effects of dopamine-2 receptor (D2R) and its agonist-induced activation on trafficking of CaV2.2 isoforms. D2R slowed the endocytosis of CaV2.2 containing exon 37b, but not exon 37a, and activation by the agonist quinpirole reversed the effect of the D2R. Our work thus reveals key mechanisms involved in the trafficking of N-type calcium channels. SIGNIFICANCE STATEMENT CaV2.2 channels are important for neurotransmitter release, but how they are trafficked is still poorly understood. Here, we describe a novel mechanism for trafficking of CaV2.2 from the trans-Golgi network to the cell surface which is mediated by the adaptor protein AP-1. Alternative splicing of exon 37 produces CaV2.2-exon 37a, selectively expressed in nociceptors, or CaV2.2-exon 37b, which is the major splice isoform. Our study reveals that canonical AP-1 binding motifs (YxxΦ and [DE]xxxL[LI]), present in exon 37a, but not 37b, enhance intracellular trafficking of exon 37a-containing CaV2.2 to axons and plasma membrane of DRG neurons. Interaction of APs with CaV2.2 channels may also be key underlying mechanisms for differential effects of the dopamine D2 receptor on trafficking of CaV2.2 splice variants.
An adaptive steganography algorithm based on block sensitivity vectors using HVS features

Steganography is the technique to hide secret data in certain media, digital image for example, without leaving any obvious evidence. As a branch of steganography, HVS feature for years has been one of the issues researchers focus on. In this paper, we introduce an improved adaptive steganography algorithm-SVBA algorithm, which fully analyzes the area statistical properties and adopts HVS features. SVBA algorithm first divides the image into 8∗8 blocks and analyzes the mean, variance and entropy value of gray by block, then sets a sensitivity vector for each block with considering HVS features and adjusts the steganography schema dynamically according to the block sensitivity vectors. Simulation experiment results on Matlab7.0 show this algorithm has a balanced performance on efficiency, capacity, imperceptibility and robustness.
Live Texturing of Augmented Reality Characters from Colored Drawings

Coloring books capture the imagination of children and provide them with one of their earliest opportunities for creative expression. However, given the proliferation and popularity of digital devices, real-world activities like coloring can seem unexciting, and children become less engaged in them. Augmented reality holds unique potential to impact this situation by providing a bridge between real-world activities and digital enhancements. In this paper, we present an augmented reality coloring book App in which children color characters in a printed coloring book and inspect their work using a mobile device. The drawing is detected and tracked, and the video stream is augmented with an animated 3-D version of the character that is textured according to the child's coloring. This is possible thanks to several novel technical contributions. We present a texturing process that applies the captured texture from a 2-D colored drawing to both the visible and occluded regions of a 3-D character in real time. We develop a deformable surface tracking method designed for colored drawings that uses a new outlier rejection algorithm for real-time tracking and surface deformation recovery. We present a content creation pipeline to efficiently create the 2-D and 3-D content. And, finally, we validate our work with two user studies that examine the quality of our texturing algorithm and the overall App experience.
Hasselt UIMS: a tool for describing multimodal interactions with composite events

Implementing multimodal interactive systems with event-driven tools requires splitting the code across multiple event handlers, which greatly complicate programmers' work. To alleviate this complexity we propose to extend the capabilities of existing event-driven tools so that instead of detecting user events as if they were independent, they are able to detect sequences of semantically related events defined by programmers. Such extended capability can only be possible with notations for (1) defining event patterns, and for (2) binding these patterns with one or multiple event handlers, and (3) specifying human-machine dialogs. This paper presents Hasselt UIMS, a tool that supports the creation of multimodal interfaces with these notations.
Interplay Between Phospholipids and Digalactosyldiacylglycerol in Phosphate Limited Oats

Phosphate is an essential nutrient. In most soils it is limiting, which has resulted in that phosphate is supplied as fertilizer to increase crop yield. Through evolution, plants have adapted several mechanisms to increase phosphate uptake from the soil and to household with acquired phosphate. A recent discovered house-holding mechanism is that plants utilize the phosphate bound in the headgroups of phospholipids: under phosphate-limiting conditions, phospholipids can be replaced by the non-phosphate containing lipid digalactosyldiacylglycerol (DGDG), previously assumed to reside in plastid membranes. The extra-plastidial phospholipid-to-DGDG replacement occurs in plasma membrane, tonoplast and mitochondria and has led to discoveries of new enzymes and metabolic pathways in plants. This thesis reports that phosphate limitation-induced biochemical and lipid compositional changes in oat root plasma membranes occur prior to any morphological changes in the oat. The phospholipase kinetics suggests that the plasma membrane is continuously supplied with phospholipids and that the products of plasma membrane lipase activities, phosphatidic acid and diacylglycerol, both are removed from the membrane. Furthermore, the phospholipid-to-DGDG replacement is reversible and when phosphate is resupplied the proportion of phospholipids increases and DGDG decreases in the oat root plasma membrane. Membrane lipids are more than a two dimensional liquid where membrane proteins reside. The specific lipid composition and distribution enables the membrane to function as a barrier to solutes and the interactions between lipids and proteins are important for the correct function. The lateral and transversal lipid distribution in oat root plasma membranes shows that DGDG does not replace phospholipids molecule for molecule; whereas phospholipids occur in both leaflets of the plasma membrane, DGDG is almost exclusively localized in the cytosolic leaflet. Model membrane studies suggests that one of the reasons that DGDG is absent in the apoplastic leaflet is its incompatibility to properly interact with the high sterol content of this leaflet. The oat seed contains enough phosphate to complete an entire generation without any exogenously supplied phosphate. The overall seed yield is much lower in phosphate-limited oat compared to fully fertilized oat, but the seed quality (starch, �-glucan, lipid, soluble protein) is very similar, including that the phospholipids-to-DGDG replacement is absent from the mature oat seeds, here membrane lipid composition is conserved. Oat thus produce a few seeds of acceptable quality rather than more seeds of poor quality.
A random walk on the rook placements on a Ferrers board

Let $B$ be a Ferrers board, i.e., the board obtained by removing the Ferrers diagram of a partition from the top right corner of an $n\times n$ chessboard. We consider a Markov chain on the set $R$ of rook placements on $B$ in which you can move from one placement to any other legal placement obtained by switching the columns in which two rooks sit. We give sharp estimates for the rate of convergence of this Markov chain using spectral methods. As part of this analysis we give a complete combinatorial description of the eigenvalues of the transition matrix for this chain. We show that two extremes cases of this Markov chain correspond to random walks on groups which are analyzed in the literature. Our estimates for rates of convergence interpolate between those two results.
Human object estimation via backscattered radio frequency signal

In this paper, we propose a system called R# to estimate the number of human objects using passive RFID tags but without attaching anything to human objects. The idea is based on our observation that the more human objects are present, the higher the variance in the RSS values of the tag backscattered RF signal. Thus, based on the received RF signal, the reader can estimate the number of human objects. R# includes an RFID reader and some (say 20) passive tags, which are deployed in the region that we want to monitor the number of human objects, such as the region in front of a painting. The RFID reader periodically emits RF signal to identify all tags and the tags simply respond with their IDs via C1G2 standard protocols. We implemented R# using commercial Impinj H47 passive RFID tags and Impinj reader model R420. We conducted experiments in a simulated picking aisle area of the supermarket environment. The experimental results show that R# can achieve high estimation accuracy (more than 90%).
Fault Diagnosis of Rolling Element Bearing Based on Improved Ensemble Empirical Mode Decomposition

The fault signal of rolling bearing has the characteristic of non-stationary, nonlinear and so on, the mode mixing phenomenon may occur in the process of empirical mode de-composition. Ensemble empirical mode decomposition (EEMD) algorithm is introduce random Gaussian white noise sequence in the original signal to change the local time of the signal span, Which can inhibit the mode mixing phenomenon in the process of the conventional empirical mode decomposition. On the basis of the principles of the EEMD, This paper introduced the Amplitude standard deviation criterion to select the EEMD parameters. And for each intrinsic mode function (IMF) components decomposed by correlation coefficient method to extract the effect intrinsic mode component, then through threshold and reconstructing each effective intrinsic mode function. Finally the envelop spectrum of the signal was analyzed, extracted the fault characteristics of the rolling bearings. Simulation and fault signals experimental results show that, EEMD method can be effectively applied to fault diagnosis of rolling bearings.