Miracle-dz/UniFAR-FTUs huggingface dataset:
Variational stabilized linear forgetting in state-space models

State-space modeling of non-stationary natural signals is a notoriously difficult task. As a result of context switches, the memory depth of the model should ideally be adapted online. Stabilized linear forgetting (SLF) has been proposed as an elegant method for state-space tracking in context-switching environments. In practice, SLF leads to state and parameter estimation tasks for which no analytical solutions exist. In the literature, a few approximate solutions have been derived, making use of specific model simplifications. This paper proposes an alternative approach, in which SLF is described as an inference task on a generative probabilistic model. SLF is then executed by a variational message passing algorithm on a factor graph representation of the generative model. This approach enjoys a number of advantages relative to previous work. First, variational message passing (VMP) is an automatable procedure that adapts appropriately under changing model assumptions. This eases the search process for the best model. Secondly, VMP easily extends to estimate model parameters. Thirdly, the modular make-up of the factor graph framework allows SLF to be used as a click-on feature in a large variety of complex models. The functionality of the proposed method is verified by simulating an SLF state-space model in a context-switching data environment.
Factors Contributing to Absorbency Behaviour of Pile Fabrics

The objective of this research paper is to investigate the important factors that contribute to the absorbency characteristics of terry fabric in order to produce highly absorbent terry towels by using suitable raw materials and changing the fabric constructional parameters. Yarns produced from two varieties of cotton (100% J-34 and MCU-5) and their blends with bamboo and poly vinyl alcohol (PVA) with different counts, twist and number of plies are used to prepare terry fabric of varying loop densities, loop lengths and loop shape factors. The water absorption rate and the total amount of water absorbed are measured by a gravimetric absorbency testing system (GATS). It is found that loop density is the most important parameter for water absorption rate followed by loop length and yarn twist. For the total amount of water absorbed, loop density is again the most important parameter followed by yarn twist, loop shape factor and number of ply in the pile yarn. Furthermore, a Box-Behnken statistical design with 3 factors and 3 levels is used to determine the optimum construction parameters to obtain the desired absorbency characteristics of terry towels and also to see the interaction effect of the various factors.
Engineering the mechanical and biological properties of nanofibrous vascular grafts for in situ vascular tissue engineering

Synthetic small diameter vascular grafts have a high failure rate, and endothelialization is critical for preventing thrombosis and graft occlusion. A promising approach is in situ tissue engineering, whereby an acellular scaffold is implanted and provides stimulatory cues to guide the in situ remodeling into a functional blood vessel. An ideal scaffold should have sufficient binding sites for biomolecule immobilization and a mechanical property similar to native tissue. Here we developed a novel method to blend low molecular weight (LMW) elastic polymer during electrospinning process to increase conjugation sites and to improve the mechanical property of vascular grafts. LMW elastic polymer improved the elasticity of the scaffolds, and significantly increased the amount of heparin conjugated to the micro/nanofibrous scaffolds, which in turn increased the loading capacity of vascular endothelial growth factor (VEGF) and prolonged the release of VEGF. Vascular grafts were implanted into the carotid artery of rats to evaluate the in vivo performance. VEGF treatment significantly enhanced endothelium formation and the overall patency of vascular grafts. Heparin coating also increased cell infiltration into the electrospun grafts, thus increasing the production of collagen and elastin within the graft wall. This work demonstrates that LMW elastic polymer blending is an approach to engineer the mechanical and biological property of micro/nanofibrous vascular grafts for in situ vascular tissue engineering.
Factors Associated With the Overuse of Colorectal Cancer Screening: A Systematic Review

This systematic review examined factors associated with overuse of colorectal cancer (CRC) screening. The authors searched MEDLINE and EMBASE from January 1998 to March 2017. Studies were included if they were written in English, contained original data, involved a US population, and examined factors potentially associated with overuse of CRC screening. Paired reviewers independently screened abstracts, assessed quality, and extracted data. In 8 studies, the associations between patient factors, including age, sex, race, and number of comorbidities, were tested and were inconsistently associated with CRC screening overuse. Overuse of screening was greater in the Northeast/Mid-Atlantic regions and in urban areas and was lower in academically affiliated centers. Although the literature supports important overuse of CRC screening, it remains unclear what drives these practices. Future research should thoroughly explore these factors and test the impact of interventions to reduce overuse of screening.
The role of micro-structure changes on space charge distribution of XLPE during thermo-oxidative ageing

In order to investigate the differences of the space charge distribution of XLPE aged at temperatures below and above the melting point, thermo-oxidative ageing was conducted on 110 kV cross-linked polyethylene (XLPE) cable insulation at 100 °C and much elevated temperature of 160 °C respectively. The XLPE insulation showed moderate changes on micro-structure and space charge distribution until the moment when the Oxidation Induction Time (OIT) dropped to zero. It was deduced by the results of Fourier Transform Infrared (FTIR) Spectroscopy, X-Ray Diffraction (XRD), Differential Scanning Calorimetry (DSC) and Scanning Electron Microscope (SEM) tests that thermo-oxidative ageing could lead to a significant increase in carbonyl groups and a decrease in crystallinity. At 100 °C, the thermo-oxidative ageing mainly affected the amorphous regions because of the much denser structures of crystalline regions, which might make the oxygen diffusion more difficult. At 160 °C, the thermo-oxidative ageing affected the melted spherulites and leaded to obvious impact on lamellae, resulting in a significant decrease in crystallinity and the destruction of spherulites. The space charge distribution of aged XLPE samples was studied by Pulsed Electroacustic Method (PEA) test. Hetero-charges could be found in aged XLPE samples. These hetero-charges were derived from ionization of polar groups in XLPE generated during ageing. The surface trap parameters of XLPE samples were investigated by Isothermal Surface Potential Decay (ISPD) test. It was deduced that shallow traps with the energy level of about 0.95 eV and deep traps with the energy level of about 1.05 eV on the surface of XLPE were introduced by carbonyl groups and interfaces of crystal/amorphous respectively. Thermo-oxidative ageing at 160 °C dramatically decreased the deep trap density because of the destruction of spherulites, leading to enhanced electrode injection. As a result, compared with those of unaged samples and samples aged at 100 °C, increased amount of homo-charges were found in the XLPE samples aged at 160 °C.
Automatic Analysis of Microaneurysms Turnover to Diagnose the Progression of Diabetic Retinopathy

Diabetic retinopathy (DR) is one of the most common microvascular complications and its early detection is critical for the prevention of vision loss. Recent studies have indicated that microaneurysms (MAs) are the hallmark of DR. However, the detection of MAs relies on trained clinicians and relatively expensive software. Moreover, manual errors often lower the accuracy of this detection. Therefore, an automatic analysis technique is highly demanded in the detection of DR progression. In this paper, we present a novel and complete methodology involving two different ways from the view of MAs turnover and pathological risk factors to diagnose the progression of DR. Specifically, one approach follows the traditional image analysis-based roadmap to obtain MAs turnover. The other investigates seven pathological features, related with MAs turnover, to classify the unchanged, new, and resolved MAs by means of statistical analysis and pattern classification techniques. The evaluations on Grampian diabetes database show that the proposed image analysis method could achieve a sensitivity of 94% and a specificity of 93%, while the classification model could achieve 89% sensitivity and 88% specificity, respectively. We also analyzed the potential weight of pathological risk factors leading to the MAs turnover, which could provide an alternative guidance for the progression of DR than traditional detection methods. In conclusion, this study provides a novel and noninvasive detection technique for early diagnosis of diabetic retinopathy with a competitive accuracy.
Multiple Minority Stress and LGBT Community Resilience Among Sexual Minority Men

Minority stress theory has widespread empirical support in explaining health disparities experienced by sexual and gender minorities. However, less is known about how minority stress impacts multiply marginalized groups, such as lesbian, gay, bisexual, and transgender people of color (LGBT POC). Also, although research has documented resilience in the face of minority stress at the individual level, research that examines macrolevel processes such as community resilience is needed (Meyer, 2015). In the current study, we integrate minority stress theory and intersectionality theory to examine multiple minority stress (i.e., racial–ethnic stigma in LGBT spaces and LGBT stigma in one’s neighborhood) and community resilience (i.e., connection to LGBT community) among sexual minority men of different racial–ethnic groups who use a geosocial networking application for meeting sexual partners. Results showed that Black sexual minority men reported the highest levels of racial–ethnic stigma in LGBT spaces and that White sexual minority men reported the lowest levels, with Asian and Hispanic–Latino men falling in between. Consistent with minority stress theory, racial–ethnic stigma in LGBT spaces and LGBT stigma in one’s neighborhood were associated with greater stress for sexual minority men of all racial–ethnic groups. However, connection to LGBT community played a more central role in mediating the relationship between stigma and stress for White than POC sexual minority men. Results suggest that minority stress and community resilience processes may differ for White and POC sexual minority men. Potential processes driving these differences and implications for minority stress theory are discussed.
New Insight into the Transcarbamylase Family: The Structure of Putrescine Transcarbamylase, a Key Catalyst for Fermentative Utilization of Agmatine

Transcarbamylases reversibly transfer a carbamyl group from carbamylphosphate (CP) to an amine. Although aspartate transcarbamylase and ornithine transcarbamylase (OTC) are well characterized, little was known about putrescine transcarbamylase (PTC), the enzyme that generates CP for ATP production in the fermentative catabolism of agmatine. We demonstrate that PTC (from Enterococcus faecalis), in addition to using putrescine, can utilize L-ornithine as a poor substrate. Crystal structures at 2.5 Å and 2.0 Å resolutions of PTC bound to its respective bisubstrate analog inhibitors for putrescine and ornithine use, N-(phosphonoacetyl)-putrescine and δ-N-(phosphonoacetyl)-L-ornithine, shed light on PTC preference for putrescine. Except for a highly prominent C-terminal helix that projects away and embraces an adjacent subunit, PTC closely resembles OTCs, suggesting recent divergence of the two enzymes. Since differences between the respective 230 and SMG loops of PTC and OTC appeared to account for the differential preference of these enzymes for putrescine and ornithine, we engineered the 230-loop of PTC to make it to resemble the SMG loop of OTCs, increasing the activity with ornithine and greatly decreasing the activity with putrescine. We also examined the role of the C-terminal helix that appears a constant and exclusive PTC trait. The enzyme lacking this helix remained active but the PTC trimer stability appeared decreased, since some of the enzyme eluted as monomers from a gel filtration column. In addition, truncated PTC tended to aggregate to hexamers, as shown both chromatographically and by X-ray crystallography. Therefore, the extra C-terminal helix plays a dual role: it stabilizes the PTC trimer and, by shielding helix 1 of an adjacent subunit, it prevents the supratrimeric oligomerizations of obscure significance observed with some OTCs. Guided by the structural data we identify signature traits that permit easy and unambiguous annotation of PTC sequences.
Ocean biogeochemistry modeled with emergent trait-based genomics

Functional ocean biogeography Marine ecosystems are well represented in metagenomic and transcriptomic data. These data are not routinely used to test ecosystem models that explore ocean biogeography or biogeochemistry. Coles et al. built a model in which genes for a range of functions were assigned to different suites of simulated microbes (see the Perspective by Rynearson). Communities emerged from the model with realistic biogeographical and biogeochemical profiles when compared to microbial data collected from the Amazon River plume. However, functional composition trumped the details of taxonomy, and different, coevolving community compositions emerged that provided similar biogeochemical outcomes. Science, this issue p. 1149; see also p. 1129 Results of genomic-based microbe community modeling resemble real-world observations from the Amazon River plume. Marine ecosystem models have advanced to incorporate metabolic pathways discovered with genomic sequencing, but direct comparisons between models and “omics” data are lacking. We developed a model that directly simulates metagenomes and metatranscriptomes for comparison with observations. Model microbes were randomly assigned genes for specialized functions, and communities of 68 species were simulated in the Atlantic Ocean. Unfit organisms were replaced, and the model self-organized to develop community genomes and transcriptomes. Emergent communities from simulations that were initialized with different cohorts of randomly generated microbes all produced realistic vertical and horizontal ocean nutrient, genome, and transcriptome gradients. Thus, the library of gene functions available to the community, rather than the distribution of functions among specific organisms, drove community assembly and biogeochemical gradients in the model ocean.
Probability of k-Hop Connection under Random Connection Model

Consider a wireless sensor network with Ltd. sensors following a homogeneous Poisson distribution in a given area A in ℜ<sup>2</sup>. A sensor located at x<sub>2</sub> ∈ A is directly connected to a sensor located at x<sub>1</sub> ∈ A with probability g (x<sub>2</sub> - x<sub>1</sub>), independent of any other distinct pair of sensors. In this letter, we provide a recursive formula for computing Pr (k|x), the probability that a node x ∈ A apart from another node is connected to that node at exactly k hops, for a generic random connection function g : ℜ<sup>2</sup> → . The recursive formula is accurate for k = 1, 2 and provides an approximation for Pr (k|x) for k > 2. The exact and approximate analytical results are validated by simulations. The knowledge of Pr (k|x) can be used in a number of areas in sensor networks.
In Vitro Site Selection of a Consensus Binding Site for the Drosophila melanogaster Tbx20 Homolog Midline

We employed in vitro site selection to identify a consensus binding sequence for the Drosophila melanogaster Tbx20 T-box transcription factor homolog Midline. We purified a bacterially expressed T-box DNA binding domain of Midline, and used it in four rounds of precipitation and polymerase-chain-reaction based amplification. We cloned and sequenced 54 random oligonucleotides selected by Midline. Electromobility shift-assays confirmed that 27 of these could bind the Midline T-box. Sequence alignment of these 27 clones suggests that Midline binds as a monomer to a consensus sequence that contains an AGGTGT core. Thus, the Midline consensus binding site we define in this study is similar to that defined for vertebrate Tbx20, but differs from a previously reported Midline binding sequence derived through site selection.
Guided Tissue Regeneration in Mucogingival Surgery.

The use of expanded polytetrafluoroethylene (ePTFE) membranes in the treatment of mucogingival problems such as gingival recession, has been recently described. The major issues raised dealt with creating and maintaining space under the membrane and designing a flap that could be coronally positioned and at the same time capable of maintaining a good blood supply. The authors proposed the use of a trapezoidal flap and some technical space-making solutions, such as the use of a suturing technique and different metal structures to support the membranes. J Periodontol 1993; 64:1184-1191.
Disclosure Control in Business Data-Experiences with Multiply Imputed Synthetic Datasets for the German IAB Establishment Survey

Generating synthetic datasets based on the ideas of multiple imputation is an innovative method for statistical disclosure control. The basic idea is to replace the values for some confidential variables X with several draws from the posterior predictive distribution of X given some non confidential variables Y. Since the synthetic values are based on models for the joint distribution of the data, many dependencies between the variables are preserved in the released data. Furthermore, the method can be applied to discrete and continuous variables and constraints like non negativity can be incorporated directly at the modeling stage. Especially for business surveys, where usual disclosure control methods like swapping or microaggregation would have to be applied on a very high level because of the skewness of the data, the approach yields very promising results. The German Institute for Employment Research (IAB) is developing synthetic datasets for one of its establishment surveys, the IAB Establishment Panel. An actual release of a scientific use file based on synthetic datasets for the last wave of the Panel is planned for 2009. In this paper we discuss the challenges of implementing this approach for a large survey and give preliminary results on the applicability of these ideas for real world datasets.
Effect of human milk formula with bovine colostrum supplementation on bone mineral density in infant cynomolgus macaques

Insulin-like growth factor 1 (IGF1) is a regulator of human growth during infancy and childhood, known to promote bone and muscle growth as well as lipid accumulation. This study aimed to investigate the effects of formula milk with or without IGF1 supplementation (in the form of pure IGF1 or bovine colostrum) on growth and body composition in infant cynomolgus macaques during the first 6 months of life. Three groups of infants were nursery-reared and received formula milk with or without IGF1 or bovine colostrum supplementation for 4 months, and a fourth group consisting of breast-fed infants was included for comparison (n=6 for each group). Ranked-based analysis of covariance was used to detect differences between adjusted means for sex. No differences in weight, height, fat mass, and fat-free mass could be detected between groups. However, bone mineral density (BMD) was significantly different between groups at the end of formula feeding. Infants that received bovine colostrum supplementation displayed higher mean BMD than infants of all other groups, with no differences between the latter three groups. In conclusion, our results suggest that supplementation with bovine colostrum can enhance BMD in formula-fed infants, an effect that apparently does not depend on IGF1. Bovine colostrum supplementation could be beneficial for long-term bone health in infants with suboptimal bone growth.
A Mathematical Model of Comprehensive Test-and-Treat Services and HIV Incidence among Men Who Have Sex with Men in the United States

Background Early diagnosis and treatment of HIV infection and suppression of viral load are potentially powerful interventions for reducing HIV incidence. A test-and-treat strategy may have long-term effects on the epidemic among urban men who have sex with men (MSM) in the United States and may achieve the 5-year goals of the 2010 National AIDS Strategy that include: 1) lowering to 25% the annual number of new infections, 2) reducing by 30% the HIV transmission rate, 3) increasing to 90% the proportion of persons living with HIV infection who know their HIV status, 4) increasing to 85% the proportion of newly diagnosed patients linked to clinical care, and 5) increasing by 20% the proportion of HIV-infected MSM with an undetectable HIV RNA viral load. Methods and Findings We constructed a dynamic compartmental model among MSM in an urban population (based on New York City) that projects new HIV infections over time. We compared the cumulative number of HIV infections in 20 years, assuming current annual testing rate and treatment practices, with new infections after improvements in the annual HIV testing rate, notification of test results, linkage to care, initiation of antiretroviral therapy (ART) and viral load suppression. We also assessed whether five of the national HIV prevention goals could be met by the year 2015. Over a 20-year period, improvements in test-and-treat practice decreased the cumulative number of new infections by a predicted 39.3% to 69.1% in the urban population based on New York City. Institution of intermediate improvements in services would be predicted to meet at least four of the five goals of the National HIV/AIDS Strategy by the 2015 target. Conclusions Improving the five components of a test-and-treat strategy could substantially reduce HIV incidence among urban MSM, and meet most of the five goals of the National HIV/AIDS Strategy.