Miracle-dz/UniFAR-FTUs huggingface dataset:
Cholesterol and the Risk of Ischemic Stroke

Background and Purpose— Large epidemiological studies have not established cholesterol levels as a risk factor for ischemic stroke, but recent clinical trials have demonstrated a reduction in the ischemic stroke rate for patients taking HMG-CoA reductase inhibitors (“statins”). The goal of this study was to evaluate whether total cholesterol (TC), high-density lipoprotein (HDL), triglycerides, and the TC:HDL ratio are risk factors for ischemic stroke in apparently healthy men enrolled in the Physicians’ Health Study. Methods— We used a nested case-control study design and matched 296 ischemic stroke cases with an equal number of controls on age, tobacco use, and follow-up time. At baseline, TC, HDL, and triglyceride levels were measured. We calculated odds ratios (ORs) and their 95% confidence intervals (CIs) using conditional logistic regression, adjusting for major risk factors for ischemic stroke. Results— Compared with the reference lowest quartile, the highest quartile for TC had an adjusted OR of 1.56 (95% CI, 0.84 to 2.92), the highest quartile of HDL had an adjusted OR of 0.75 (95% CI, 0.43 to 1.30), and the highest quartile of triglycerides had an adjusted OR of 1.07 (95% CI, 0.63 to 1.82). Although the highest quartile of the TC:HDL ratio had an adjusted OR of 1.62 (95% CI, 0.93 to 2.82), the risk of ischemic stroke was not a linear relationship. Conclusions— After adjustment, TC, HDL, and triglycerides were not significantly associated with ischemic stroke risk, and for the TC:HDL ratio, a suggestion of increased risk of ischemic stroke was limited to those with the highest levels.
Tracking articulated bodies using Generalized Expectation Maximization

A generalized expectation maximization (GEM) algorithm is used to retrieve the pose of a person from a monocular video sequence shot with a moving camera. After embedding the set of possible poses in a low dimensional space using principal component analysis, the configuration that gives the best match to the input image is held as estimate for the current frame. This match is computed iterating GEM to assign edge pixels to the correct body part and to find the body pose that maximizes the likelihood of the assignments.
Comparative analysis of BLUP and GCA for parental selection in marigold (Tagetes erecta L.) for hybrid development

The area under marigold cultivation is increasing over the years and so is the demand for marigold seeds. To meet the increasing demand, hybrid varieties are preferred as they produce higher yields, for which the right parental selection is of major concern. Male sterility being the prerequisite for economical hybrid seed production of marigold, we have attempted to strategize the selection of male sterile seed parent and fertile pollen parent for yield and yield-related traits. The study was undertaken across multiple forms of male sterile lines morphologically varying in apetaloid and petaloid types, therefore use of BLUP and GCA was evaluated as a criterion to select the parents for the hybridization program. Results suggested apetaloid male sterile lines as better seed parents for days to bud initiation, while, petaloid male sterile lines can be selected for the improvement of shelf life and flower diameter. Results from BLUP and GCA were in agreement with each other for the traits studied. However, BLUP-based comparison of different lines is less tedious as it eliminates the laborious procedure of developing multiple hybrids and evaluating them to study the combining ability effects.
AMS Radiocarbon Dates on Peat Section Related with Tephra and Archaeological Sites in Carlisle Island, the Islands of Four Mountains, Alaska

ABSTRACT We obtained radiocarbon (14C) dates with accelerator mass spectrometry (AMS) of vascular plant samples and a charcoal sample collected from peat deposits near the prehistoric village site informally designated CR-03 on Carlisle Island in the Islands of Four Mountains group, Alaska, to determine the eruption age of the CR-02 tephra. A fine vitric ash erupted from Okmok caldera, Umnak Island (ca. 2 ka BP) was also discovered in the bog. The ages of the CR-02 tephra and Okmok II ash are estimated to be 1050 and 2000 cal BP, respectively. Because both tephras are distinctive and widespread, these are important chronostratigraphic markers for archaeological sites in this island group. The 14C dates obtained from this bog are 800 years younger than the dates of the charcoal fragments from cultural layers in the Unit 3 of prehistoric village site CR-02 (AMK-0003).
Supervised Collaborative Filtering Based on Ridge Alternating Least Squares and Iterative Projection Pursuit

This paper presents a supervised data imputation based on the class-dependent matrix factors, which are generated during matrix factorization. The proposed ridge alternating least squares imputation uses class information to create substituted values, which approximate the characteristics of their corresponding classes, for missing entries. In the training phase, the incomplete data with label information are divided into different classes based on their labels, such that basis matrices become class-dependent. Subsequently, iterative projection pursuit is proposed to perform imputation for testing data by computing the linear combination of these class-dependent basis matrices and their corresponding reconstruction weights. The class-dependent basis matrix with the minimum loss during reconstruction is regarded as the correct imputation for a testing sample, of which the substituted values are derived from the matrix factors of its class. Experiments on open data sets showed that the proposed method successfully decreased the imputation error by 40.52% on average, better than typical unsupervised collaborative filtering, while maintaining classification accuracy.
Vesicular Messages from Dental Biofilms for Neutrophils

The encounter between dental biofilm and neutrophils in periodontitis remains elusive, although it apparently plays a crucial role in the periodontal pathology and constitutes a key topic of periodontology. Dental biofilm and neutrophils were isolated from orally healthy persons and patients with periodontitis. We investigated biofilm and its particle-shedding phenomenon with electron microscopy and nanoparticle tracking analysis (NTA); biofilm shedding–neutrophil interactions were examined ex vivo with epi-fluorescence microscopy. For this purpose, we used acellular dental biofilm shedding, purified lipopolysaccharide (LPS), and phorbol 12-myristate 13-acetate (PMA) as activators, and the interleukin 8 receptor beta (CXCR2) inhibitor and the anti-interleukin 8 receptor alpha (CXCR1) antibody as modulators. The shedding of acellular dental biofilms overwhelmingly consists of bacterial extracellular vesicles (BEVs). The latter induced the moderate formation of neutrophil extracellular traps (NETs) in orally healthy subjects and a strong formation in patients with periodontitis. A CXCR2 inhibitor and an anti-CXCR1 antibody had a minor effect on NET formation. Neutrophils from patients with periodontitis exhibited NET hyper-responsiveness. BEVs were stronger inducers of NET formation than purified LPS and PMA. A plateau of neutrophil responsiveness is reached above the age of 40 years, indicating the abrupt switch of maladaptive trained immunity (TI) into the activated modus. Our results suggest that dental biofilms consist of and disseminate immense amounts of outer membrane vesicles (OMVs), which initiate NET formation via a non-canonical cytosolic LPS/caspase-4/11/Gasdermin D pathway. This modus of NET formation is independent of neutrophil elastase (NE), myeloperoxidase (MPO), peptidylarginine deiminase 4 (PAD4), and toll-like receptors (TLR). In periodontitis, the hyper-responsiveness of neutrophils to BEVs and the increased NET formation appear to be a consequence of TI.
Consistency and inconsistency in network meta-analysis: concepts and models for multi-arm studies‡

Meta‐analyses that simultaneously compare multiple treatments (usually referred to as network meta‐analyses or mixed treatment comparisons) are becoming increasingly common. An important component of a network meta‐analysis is an assessment of the extent to which different sources of evidence are compatible, both substantively and statistically. A simple indirect comparison may be confounded if the studies involving one of the treatments of interest are fundamentally different from the studies involving the other treatment of interest. Here, we discuss methods for addressing inconsistency of evidence from comparative studies of different treatments. We define and review basic concepts of heterogeneity and inconsistency, and attempt to introduce a distinction between ‘loop inconsistency’ and ‘design inconsistency’. We then propose that the notion of design‐by‐treatment interaction provides a useful general framework for investigating inconsistency. In particular, using design‐by‐treatment interactions successfully addresses complications that arise from the presence of multi‐arm trials in an evidence network. We show how the inconsistency model proposed by Lu and Ades is a restricted version of our full design‐by‐treatment interaction model and that there may be several distinct Lu–Ades models for any particular data set. We introduce novel graphical methods for depicting networks of evidence, clearly depicting multi‐arm trials and illustrating where there is potential for inconsistency to arise. We apply various inconsistency models to data from trials of different comparisons among four smoking cessation interventions and show that models seeking to address loop inconsistency alone can run into problems. Copyright © 2012 John Wiley & Sons, Ltd.
Effects of threshold choice on biological conclusions reached during analysis of gene expression by DNA microarrays.

Global analysis of gene expression by using DNA microarrays is employed increasingly to search for differences in biological properties between normal and diseased tissue. In such studies, expression that deviates from defined thresholds commonly is used for creating genetic signatures that characterize disease vs. normality. Although it is axiomatic that the threshold parameters applied to microarray analysis will alter the contents of such genetic signatures, the extent to which threshold choice can affect the fundamental conclusions made from microarray-based studies has not been elucidated. We used GABRIEL (Genetic Analysis By Rules Incorporating Expert Logic), a platform of knowledge-based algorithms for the global analysis of gene expression, together with conventional statistical approaches, to examine the sensitivity of conclusions to threshold choice in recently published microarray-based studies. An analysis of the effects of threshold decisions in one of these studies [Ramaswamy, S. , Ross, K. N. , Lander, E. S. & Golub, T. R. (2003) Nat. Genet. 33, 49-54], which arrived at the important conclusion that the metastatic potential of primary tumors is encoded by the bulk of cells in the tumor, is the focus of this article. We discovered that support for this conclusion highly depends on the threshold used to create gene expression signatures. We also found that threshold choice dramatically affected the gene function categories represented nonrandomly in signatures. Our results suggest that the robustness of biological conclusions made by using microarray analysis should be routinely assessed by examining the validity of the conclusions by using a range of threshold parameters.
Growth Factor and Catabolic Cytokine Concentrations Are Influenced by the Cellular Composition of Platelet-Rich Plasma

Background: Previous studies of bioactive molecules in platelet-rich plasma (PRP) have documented growth factor concentrations that promote tissue healing. However, the effects of leukocytes and inflammatory molecules in PRP have not been defined. Hypothesis: The hypothesis for this study was that the concentration of growth factors and catabolic cytokines would be dependent on the cellular composition of PRP. Study Design: Controlled laboratory study. Methods: Platelet-rich plasma was made from 11 human volunteers using 2 commercial systems: Arthrex ACP (Autologous Conditioned Plasma) Double Syringe System (PRP-1), which concentrates platelets and minimizes leukocytes, and Biomet GPS III Mini Platelet Concentrate System (PRP-2), which concentrates both platelets and leukocytes. Transforming growth factor-β1 (TGF-β1), platelet-derived growth factor–AB (PDGF-AB), matrix metalloproteinase-9 (MMP-9), and interleukin-1β (IL-1β) were measured with enzyme-linked immunosorbent assay (ELISA). Results: The PRP-1 system consisted of concentrated platelets (1.99×) and diminished leukocytes (0.13×) compared with blood, while PRP-2 contained concentrated platelets (4.69×) and leukocytes (4.26×) compared with blood. Growth factors were significantly increased in PRP-2 compared with PRP-1 (TGF-β1: PRP-2 = 89 ng/mL, PRP-1 = 20 ng/mL, P < .05; PDGF-AB: PRP-2 = 22 ng/mL, PRP-1 = 6.4 ng/mL, P < .05). The PRP-1 system did not have a higher concentration of PDGF-AB compared with whole blood. Catabolic cytokines were significantly increased in PRP-2 compared with PRP-1 (MMP-9: PRP-2 = 222 ng/mL, PRP-1 = 40 ng/mL, P < .05; IL-1β: PRP-2 = 3.67 pg/mL, PRP-1 = 0.31 pg/mL, P < .05). Significant, positive correlations were found between TGF-β1 and platelets (r2 = .75, P < .001), PDGF-AB and platelets (r2 = .60, P < .001), MMP-9 and neutrophils (r2 = .37, P < .001), IL-1β and neutrophils (r2 = .73, P < .001), and IL-1β and monocytes (r2 = .75, P < .001). Conclusion: Growth factor and catabolic cytokine concentrations were influenced by the cellular composition of PRP. Platelets increased anabolic signaling and, in contrast, leukocytes increased catabolic signaling molecules. Platelet-rich plasma products should be analyzed for content of platelets and leukocytes as both can influence the biologic effects of PRP. Clinical Relevance: Depending on the clinical application, preparations of PRP should be considered based on their ability to concentrate platelets and leukocytes with sensitivity to pathologic conditions that will benefit most from increased platelet or reduced leukocyte concentration.
A Distributed Algorithm for a Reconfigurable Modular Surface

A distributed algorithm is proposed in order to control block motion of a reconfigurable micro-electro-mechanical modular surface. The modular surface is designed to convey fragile and tiny micro-parts. The distributed algorithm solves a discrete trajectory optimization problem. In particular, the algorithm computes the shortest path between two points of the modular surface using a strategy based on minimum hop count. The proposed method based on distributed asynchronous iterative elections is scalable.
Use of Total Cerebral Blood Flow as an Imaging Biomarker of Known Cardiovascular Risks

Background and Purpose— This study examined whether overall cerebral blood flow was associated with known vascular risk factors, including cardiometabolic risk factors that comprise the metabolic syndrome, carotid artery intima-media thickness, and the Framingham risk score. Methods— Three separate samples were available for analysis. Two comparable samples were combined to form a primary sample of middle-aged participants (n=576; 30–55 years of age) that completed both a risk factor assessment and a resting brain scan. Samples were recruited via mailings and advertisements within an urban area. Quantitative measures of cerebral blood flow were derived from arterial spin–labeled MRI in this sample and in a validation/generalization sample (n=76; 30–55 years). Results— Cerebral blood flow was inversely associated with cardiometabolic risk indices, that is, associated with lower waist circumference, systolic blood pressure, glucose, and triglyceride and high-density lipoprotein. Moreover, cerebral blood flow was also related to Framingham risk and carotid intima-media thickness. In the validation sample, which used a slightly different brain imaging technique, significant relationships were replicated for cardiometabolic risk, but not for Framingham risk. Conclusions— Reduced cerebral blood flow seems to be a correlate of vascular disease risk factors associated with cardiometabolic dysregulation. Cerebral blood flow may provide a valid imaging biomarker for cardiovascular risk.
Language support for lightweight transactions

Concurrent programming is notoriously difficult. Current abstractions are intricate and make it hard to design computer systems that are reliable and scalable. We argue that these problems can be addressed by moving to a declarative style of concurrency control in which programmers directly indicate the safety properties that they require. In our scheme the programmer demarks sections of code which execute within lightweight software-based transactions that commit atomically and exactly once. These transactions can update shared data, instantiate objects, invoke library features and so on. They can also block, waiting for arbitrary boolean conditions to become true. Transactions which do not access the same shared memory locations can commit concurrently. Furthermore, in general, no performance penalty is incurred for memory accesses outside transactions.We present a detailed design of this proposal along with an implementation and evaluation. We argue that the resulting system (i) is easier for mainstream programmers to use, (ii) prevents lock-based priority-inversion and deadlock problems and (iii) can offer performance advantages.
Number of conspecifics and reproduction in the invasive plant Eschscholzia californica (Papaveraceae): is there a pollinator-mediated Allee effect?

The component Allee effect has been defined as 'a positive relationship between any measure of individual fitness and the number or density of conspecifics'. Larger plant populations or large patches have shown a higher pollinator visitation rate, which may give rise to an Allee effect in reproduction of the plants. We experimentally tested the effect of number of conspecifics on reproduction and pollinator visitation in Eschscholzia californica Cham. , an invasive plant in Chile. We then built patches with two, eight and 16 flowering individuals of E. californica (11 replicates per treatment) in an area characterised by dominance of the study species. We found that E. californica exhibits a component Allee effect, as the number of individuals of this species has a positive effect on individual seed set. However, individual fruit production was not affected by the number of plants examined. Pollinator visitation rate was also independent of the number of plants, so this factor would not explain the Allee effect. This rate was positively correlated with the total number of flowers in the patches. We also found that the number of plants did not affect the seed mass or proportion of germinated seeds in the patches. Higher pollen availability in patches with 16 plants and pollination by wind could explain the Allee effect. The component Allee effect identified could lead to a weak demographic Allee effect that might reduce the rate of spread of E. californica. Knowledge of this would be useful for management of this invasive plant in Chile.
Tidal Marsh Record of Nutrient Loadings in Barnegat Bay, New Jersey

ABSTRACT Velinsky, D.J.; Paudel, B. ; Belton, T.J., and Sommerfield, C.K. , 2017. Tidal marsh record of nutrient loadings in Barnegat Bay, New Jersey. In: Buchanan, G.A. ; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay-Little Egg Harbor, New Jersey. Sediment and nutrient burial in tidal marshes of Barnegat Bay was investigated using age-dated sediment cores collected along a north-to-south transect. Measurements of radionuclides (210Pb and 137Cs) and stable isotopes (13C and 15N) were accompanied by nutrient and organic matter concentrations. Sediment accumulation rates, measured using 210Pb and 137Cs chronology, ranged from 48 to 81 mg cm2 y−1, whereas corresponding accretion rates ranged from 0.16 to 0.30 cm y−1. Sediment nitrogen (N) accumulation rates increased twofold at an upper bay site, starting in the mid-1950s, whereas at other locations, only small to no increases were seen with time. Phosphorus (P) accumulation was minimal with time. N and P accumulation rates were higher between the 1940s to 1950s at stations BB-1 and BB-3, while higher accumulation rate in the down-bay (BB-4) was identified in the early 1990s. Results indicate that bay marshes can sequester approximately 79 ± 11% of N and 54 ± 34% of P entering the Bay from upland sources; thus, these marshes perform an important ecosystem service in the form of nutrient sequestration. Marsh accretion rates at the coring sites fall at, to just below, rates of relative sea-level rise recorded by nearby tide gauges. These relatively low rates of accretion render the marsh vulnerable to inundation should the rate of sea-level rise accelerate in the future.
Social search and personalization through demographic filtering

Most existing personalized search systems do not consider group profiling. Group profiling can be an efficient retrieval mechanism, where a user profile is inferred from the profile of the social groups to which the user belongs. The authors propose an XML search system called DemoFilter which employs the concept of group profiling. DemoFilter simplifies the personalization process by pre-defining various categories of social groups and then identifying their preferences. Social groups are characterized based on demographic, ethnic, cultural, religious, age, or other characteristics. DemoFilter can be used for various practical applications, such as Internet or other businesses that market preference-driven products. In the ontology, the preferences of a social group are identified from published studies about the social group. They experimentally evaluate the search effectiveness of DemoFilter and compare it to an existing search engine.
Mass transport by large and very-large amplitude mode-2 internal solitary waves: experimental observations

The present experiments provide the first quantitative measurements of the mass transport by mode-2 internal solitary waves (ISW) propagating on a thin pycnocline. The ISW were generated by the release of fluid from an initially mixed volume. It was found that the amplitude and amount of mass transported, by the leading and second following ISW, was proportional to the level of forcing and was attenuated at an approximately uniform rate as the ISW propagated downstream. At the highest level of ISW forcing over 40% of the mixed fluid was transported within the leading ISW. Excellent agreement was found with the numerical simulations of Salloum et al. (2012) that were designed to replicate the present experimental configuration. In addition, a new ISW regime was identified, termed very large-amplitude ISW, where the ISW bulge wavelength and extent of mass transported increased with amplitude at a rate greater than the lesser amplitude ISW. In recent years the frequent occurrence of large amplitude ISW in the coastal ocean has been observed. The present experiments and the associated numerical simulations can provide insight into the effects of ISW transport on coastal mixing and biological material distribution.