Miracle-dz/UniFAR-FTUs huggingface dataset:
Breaking the curse of dimensionality in regression

Author(s): Zhu, Yinchu; Bradic, Jelena | Abstract: Models with many signals, high-dimensional models, often impose structures on the signal strengths. The common assumption is that only a few signals are strong and most of the signals are zero or close (collectively) to zero. However, such a requirement might not be valid in many real-life applications. In this article, we are interested in conducting large-scale inference in models that might have signals of mixed strengths. The key challenge is that the signals that are not under testing might be collectively non-negligible (although individually small) and cannot be accurately learned. This article develops a new class of tests that arise from a moment matching formulation. A virtue of these moment-matching statistics is their ability to borrow strength across features, adapt to the sparsity size and exert adjustment for testing growing number of hypothesis. GRoup-level Inference of Parameter, GRIP, test harvests effective sparsity structures with hypothesis formulation for an efficient multiple testing procedure. Simulated data showcase that GRIPs error control is far better than the alternative methods. We develop a minimax theory, demonstrating optimality of GRIP for a broad range of models, including those where the model is a mixture of a sparse and high-dimensional dense signals.
Current tools for prediction of arteriovenous fistula outcomes

It remains challenging to accurately predict whether an individual arteriovenous fistula (AVF) will mature and be useable for haemodialysis vascular access. Current best practice involves the use of routine clinical assessment and ultrasonography complemented by selective venography and magnetic resonance imaging. The purpose of this literature review is to describe current practices in relation to pre-operative assessment prior to AVF formation and highlight potential areas for future research to improve the clinical prediction of AVF outcomes.
Collaborative studies on the genetics of asthma—National Heart, Lung and Blood Institute

Information on the genetic patterns of asthma is fragmented, incomplete, and often contradictory. Genetic, molecular biological, and cell culture methods are now available to map, sequence, and define the function ofthe genes involved in the expression of asthma. Identification of these genes and their function will facilitate the development of new modes of treatment, and will lead to an understanding ofthe causal interaction between the genes and the environmental factors that are relevant in asthma. Investigators have encountered many problems in their study of the genetics of human diseases. One of the major 'lessons' that can be learned from past experience with the genetic analysis of allergy and other complex disorders is that false positive linkage results are possible, and replication of a linkage finding is extremely important. Given the major problems involved in study of the genetics of complex disorders such as asthma, a Collaborative Study on the Genetics of Asthma (CSGA) was initiated by the National Heart, Lung and Blood Institute (NHLBI) with input from the National Institute of Allergy and Infectious Diseases (NIAID). This cooperative study is to function as a unified, collaborative group and has set guidelines for the members involved. The CSGA provides the unique opportunity to replicate initial positive linkage results within this collaborative effort.
Evaluation of Early Healing Profile and Neointimal Transformation Over 24 Months Using Longitudinal Sequential Optical Coherence Tomography Assessments and 3-Year Clinical Results of the New Dual-Therapy Endothelial Progenitor Cell Capturing Sirolimus-Eluting Combo Stent: The EGO-Combo Study

Background—Current monotherapy drug-eluting stents are associated with impaired healing, neoatherosclerosis, and late stent thrombosis. The healing profile and neointimal transformation of the first dual-therapy endothelial progenitor cell–capturing sirolimus-eluting stent are unknown. Methods and Results—In this prospective, single-center study, 61 patients treated with the Combo stent had optical coherence tomography at baseline, early follow-up (4 monthly groups in a 1:2:2:1 ratio from 2 to 5 months), 9 months, and 24 months. Optical coherence tomography early strut coverage increased from 77.1% to 92.5% to 92.7% to 94.9% between 2 and 5 months. At 9 months, the major adverse cardiac event rate was 1.64%, and angiographic in-stent late loss was 0.24 mm (0.08–0.40). The 36-month major adverse cardiac event rate was 3.3%. From 9 to 24 months, neointimal regression was confirmed by optical coherence tomography: neointimal thickness (median [first quartile and third quartile]), 0.14 mm (0.08 and 0.21) versus 0.12 mm (0.07 and 0.19), P<0.001; neointimal volume, 29.9 mm3 (22.1 and 43.2) versus 26.2 mm3 (19.6 and 35.8), P=0.003; and percent neointimal volume, 17.8% (12.2 and 21.2) versus 15.7% (11.2 and 19.4), P=0.01. No definite or probable late stent thrombosis was recorded. Conclusions—With additional endothelial progenitor cell–capturing technology, the Combo stent exhibits a unique late neointimal regression (from 9 to 24 months) that has not been reported in any drug-eluting stents, translating into good 36-month clinical results with minimal restenosis and no late stent thrombosis. This is the first study testing the concept of using a longitudinal sequential optical coherence tomography protocol to continuously document early healing profile and late neointimal transformation, predicting long-term outcomes of a new novel stent platform. Clinical Trial Registration—URL: http://www.clinicaltrials. gov. Unique identifiers: NCT01274234, NCT01756807, and NCT02263313.
FOXO responses to Porphyromonas gingivalis in epithelial cells

Porphyromonas gingivalis is a prominent periodontal, and emerging systemic, pathogen that redirects host cell signalling pathways and modulates innate immune responses. In this study, we show that P. gingivalis infection induces the dephosphorylation and activation of forkhead box‐O (FOXO)1, 3 and 4 in gingival epithelial cells. In addition, immunofluorescence showed that FOXO1 accumulated in the nucleus of P. gingivalis‐infected cells. Quantitative reverse transcription PCR demonstrated that transcription of genes involved in protection against oxidative stress (Cat, Sod2, Prdx3), inflammatory responses (IL1β) and anti‐apoptosis (Bcl‐6) was induced by P. gingivalis, while small‐interfering RNA (siRNA)‐mediated knockdown of FOXO1 suppressed the transcriptional activation of these genes. P. gingivalis‐induced secretion of interleukin (IL)‐1β and inhibition of apoptosis were also impeded by FOXO1 knockdown. Neutralization of reactive oxygen species (ROS) by N‐acetyl‐l‐cysteine blocked the activation of FOXO1 by P. gingivalis and concomitantly suppressed the activation of oxidative stress responses, anti‐apoptosis programmes and IL‐β production. Inhibition of c‐Jun‐N‐terminal kinase (JNK) either pharmacologically or by siRNA, reduced FOXO1 activation and downstream FOXO1‐dependent gene regulation in response to P. gingivalis. The results indicate that P. gingivalis‐induced ROS activate FOXO transcription factors through JNK signalling, and that FOXO1 controls oxidative stress responses, inflammatory cytokine production and cell survival. These data position FOXO as an important signalling node in the epithelial cell–P. gingivalis interaction, with particular relevance to cell fate and dysbiotic host responses.
Sexual selection in a lekking bird: the relative opportunity for selection by female choice and male competition

Leks are classic models for studies of sexual selection due to extreme variance in male reproductive success, but the relative influence of intrasexual competition and female mate choice in creating this skew is debatable. In the lekking lance-tailed manakin (Chiroxiphia lanceolata), these selective episodes are temporally separated into intrasexual competition for alpha status and female mate choice among alpha males that rarely interact. Variance in reproductive success between status classes of adult males (alpha versus non-alpha) can therefore be attributed to male–male competition whereas that within status largely reflects female mate choice. This provides an excellent opportunity for quantifying the relative contribution of each of these mechanisms of sexual selection to the overall opportunity for sexual selection on males (Imales). To calculate variance in actual reproductive success, we assigned genetic paternity to 92.3% of 447 chicks sampled in seven years. Reproduction by non-alphas was rare and apparently reflected status misclassifications or opportunistic copulations en route to attaining alpha status rather than alternative mating strategies. On average 31% (range 7–44%, n=6 years) of the total Imales was due to variance in reproductive success between alphas and non-alphas. Similarly, in a cohort of same-aged males followed for six years, 44–58% of the total Imales was attributed to variance between males of different status. Thus, both intrasexual competition for status and female mate choice among lekking alpha males contribute substantially to the potential for sexual selection in this species.
Syndromes and phenomenological subtypes underlying acute mania: a factor analytic study of 576 manic patients.

OBJECTIVE There are no factor analytic studies specifically including symptoms representative of depressive inhibition among manic patients, although Kraepelin described several mixed affective states with depressive inhibition. There is controversy as to whether atypical manic features such as aggression, psychosis, and depression are likely to coexist among manic patients. The authors' goal was to examine this controversy. METHOD They used a standardized instrument to assess the presence or absence of 37 psychiatric symptoms in 576 consecutive inpatients who were diagnosed as having DSM-IV manic episode, nonmixed or mixed. RESULTS A principal-component analysis followed by varimax rotation extracted seven independent interpretable factors (depressive mood, irritable aggression, insomnia, depressive inhibition, pure manic symptoms, emotional lability/agitation, and psychosis) that were relatively stable across several patient groups. A subsequent cluster analysis identified four phenomenological subtypes underlying acute mania: pure, aggressive, psychotic, and depressive (mixed) mania. Several variables, including gender, suicidality, and outcome of treatments, significantly differentiated the subtypes. CONCLUSIONS In patients with mania, depressive inhibition may be a salient syndrome independent of depressive mood, lending some support to Kraepelin's classification of mixed manic states on the basis of the permutations of three elements-thought disorder, mood, and psychomotor activity. Depressive inhibition, together with depressive mood and emotional lability/agitation, appears to be an important phenomenological element of mixed states. Atypical manic features such as aggression, psychosis, and depression are not likely to coexist, but they are likely separately to characterize several different subtypes potentially underlying acute mania.
Laying performance and eggshell quality in laying hens fed diets supplemented with prebiotics and organic acids.

The aim of the study was to evaluate the effect of organic acids and the prebiotic fructans on egg production and eggshell quality when added to the layer diet with different levels of calcium and phos - phorus. The experiment was carried out on 168 Bovans Brown hens, allocated to 14 groups of 12 replications. Each hen (replication) was kept in an individual cage 40 cm × 40 cm in size. A 2 × 7 factorial arrangement, with two dietary levels of calcium and phosphorus (normal - 3.70% Ca, 0.65% P, and reduced - 3.25% Ca, 0.60% P) and with diets supplemented by selected additives (none, 0.75% inulin, 0.75% oligofructose, 0.50% volatile fatty acids (VFA), 0.25% medium chain fatty acid (MCFA), 0.30% VFA + 0.20% MCFA, 0.75% inulin + 0.50% VFA) was used. The experiment was carried out over 34 weeks, from the age of 26 to 70 weeks. There were no statistically confirmed effects of the factors studied in this experiment on egg performance, i.e. laying rate, egg mass, feed intake and feed conversion. Reducing the dietary levels of Ca and P significantly decreased eggshell percent, thickness, density and breaking strength. The additives used had a considerable effect on eggshell quality at 46, 58 and 70 weeks of age, and these positive effects were most pronounced in the case of inulin and MCFA. There was no significant interaction between Ca and P dietary levels and the additives used. It was thus concluded that selected feed additives which lower the pH of the diet and intestinal content can beneficially influence eggshell quality in older high-producing laying hens.
Ozone-Induced Cell Death Mediated with Oxidative and Calcium Signaling Pathways in Tobacco Bel-W3 and Bel-B Cell Suspension Cultures

Ozone (O3)-induced cell death in two suspension-cultured cell lines of tobacco (Nicotiana tabacum L.) derived from Bel-W3 (hyper-sensitive to O3) and Bel-B (highly tolerant to O3) varieties were studied. By exposing the newly prepared cell lines to the pulse of ozonized air, we could reproduce the conditions demonstrating the difference in O3 sensitivity as observed in their original plants, depending on the exposure time. Since O3-induced acute cell death was observed in the dark, the requirement for photochemical reactions could be eliminated. Addition of several ROS scavengers and chelators inhibited the cell death induced by O3, indicating that singlet oxygen (1O2), hydrogen peroxide (H2O2), hydroxyl radical and redox-active metals such as Fe2+ play central roles in O3-induced acute damages to the cells. As expected, we observed the generation of 1O2 and H2O2 in the O3-treated cells using chemiluminescent probes. On the other hand, an NADPH oxidase inhibitor, superoxide dismutase (SOD), and some SOD mimics showed no inhibitory effect. Thiols added as antioxidants unexpectedly behaved as prooxidants drastically enhancing the O3-induced cell death. It is noteworthy that some ROS scavengers effectively rescued the cells from dying even treated after the pulse of O3 exposure, confirming the post-ozone progress of ROS-dependent cell death mechanism. Since one of the key differences between Bel-B and Bel-W3 was suggested to be the capacity for ROS detoxification by catalase, the endogenous catalase activities were compared in vivo in two cell lines. As expected, catalase activity in Bel-B cells was ca. 7-fold greater than that in Bel-W3 cells. Interestingly, Ca2+ chelators added prior to (not after) the pulse of O3 effectively inhibited the induction of cell death. In addition, increases in cytosolic Ca2+ concentration sensitive to Ca2+ chelators, ion channel blockers, and ROS scavengers were observed in the transgenic Bel-W3 cells expressing aequorin, suggesting the action of Ca2+ as a secondary messenger initiating the oxidative cell death. The O3-induced calcium response in Bel-W3 cells was much greater than Bel-B cells. Based on the results, possible pathways for O3-dependent generation of the lethal level of ROS and corresponding signaling mechanism for induction of cell death were discussed.
International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society classification predicts occult lymph node metastasis in clinically mediastinal node-negative lung adenocarcinoma.

OBJECTIVES We investigated the role of the 2011 International Association for the Study of Lung Cancer, American Thoracic Society, and European Respiratory Society (IASLC/ATS/ERS) classification in predicting occult lymph node metastasis in clinically mediastinal node-negative lung adenocarcinoma. METHODS We reviewed lung adenocarcinoma patients who had clinically N2-negative status, were evaluated by preoperative positron emission tomography combined with computed tomography (PET/CT) and had undergone lobectomy or pneumonectomy at Memorial Sloan Kettering Cancer Center (n = 297). Tumours were classified according to the 2011 IASLC/ATS/ERS classification. The associations between occult lymph node metastasis and clinicopathological variables were analysed using Fisher's exact test and logistic regression analysis. RESULTS Thirty-two (11%) cN0-1 patients had occult mediastinal lymph node metastasis (pN2) whereas 25% of cN1 patients had pN2 disease. Increased micropapillary pattern was associated with increased risk of pN2 disease (P = 0.001). On univariate analysis, high maximum standard uptake value of the primary tumour on PET/CT (P = 0.019) and the presence of micropapillary (P = 0.014) and solid pattern (P = 0.014) were associated with occult pN2 disease. On multivariable analysis, micropapillary pattern was positively associated with risk of pN2 disease (odds ratio = 3.41; 95% confidence intervals = 1.42-8.19; P = 0.006). CONCLUSIONS The presence of micropapillary pattern is an independent predictor of occult mediastinal lymph node metastasis. Our observations have potential therapeutic implications for management of early-stage lung adenocarcinoma.
Engineering properties of geopolymer concrete

Abstract: This chapter deals with fly ash-based geopolymer concrete. The mixture design, production, and curing of geopolymer concrete are briefly given. The behaviour and the short-term properties in compression and tension are then described. The chapter also includes an account of the drying shrinkage and creep properties of geopolymer concrete. Excellent resistance offered by the fly ash-based geopolymer concrete to sulfate and acid attacks is also demonstrated.
Translating knowledge to practice: an occupational therapy perspective.

BACKGROUND/AIM Translating knowledge to practice, also called 'knowledge translation', is increasingly recognised as a driving force to strengthen and improve the healthcare system. How knowledge translation fits with occupational therapy practice deserves examination. METHODS This paper will explore how an action process model, the Knowledge-To-Action Process, may advance knowledge translation in occupational therapy. Occupational therapists typically view knowledge in a broad sense, encompassing research, tacit knowledge, expert opinion and client evidence. The Knowledge-To-Action Process facilitates application of client, therapist and research knowledge to occupational therapy practice. RESULTS Examination of knowledge translation through the lens of the Knowledge-To-Action Process creates awareness of the value of client, therapist and research knowledge. It also highlights opportunities as practitioners to implement knowledge translation. CONCLUSIONS Models able to flexibly reflect an occupational therapy perspective of knowledge have a potentially vital role in successful knowledge translation. Furthermore, these models allow therapists and other stakeholders to analyse complex situations and identify targeted knowledge translation strategies.
Competitive Randomized Nonlinear Prediction Under Additive Noise

We consider sequential nonlinear prediction of a bounded, real-valued and deterministic signal from its noise-corrupted past samples in a competitive algorithm framework. We introduce a randomized algorithm based on context-trees . The introduced algorithm asymptotically achieves the performance of the best piecewise affine model that can both select the best partition of the past observations space (from a doubly exponential number of possible partitions) and the affine model parameters based on the desired clean signal in hindsight. Although the performance measure including the loss function is defined with respect to the noise-free clean signal, the clean signal, its past samples or prediction errors are not available for training or constructing predictions. We demonstrate the performance of the introduced algorithm when applied to certain chaotic signals.
Eclogites and eclogites: Oxygen isotope evidence of a shared subduction origin for Franciscan eclogites and Moses Rock eclogite xenoliths

Eclogites can be found in two distinct tectonic settings in the western USA: in the Franciscan Complex as tectonic blocks in a fossil accretionary wedge, and in the Navajo Volcanic Field as xenoliths in diatremes. Intra-crystal oxygen isotope analyses of garnets from these two settings provide important information on the source, composition and timing of fluid interactions in both eclogite settings. Because of the well-documented relationship between Franciscan subduction and the volcanism in the Navajo Volcanic Field, the samples in this study can be directly compared to determine if they share a common origin. The Navajo eclogites in this study have the first intra-garnet oxygen isotope zoning found in any mantle xenoliths. Xenolith garnets record core δO values of 7.8 to 10.3‰ consistent with altered upper oceanic crust. Rim values are lower in δO with values of 5.8 to 6.9‰, consistent with late garnet growth in equilibrium with slab-contaminated mantle fluids. Three garnets homogenous in δO were found. Atoll textures present in one sample record altered upper oceanic crust values in the atoll, with replacement cores and rims consistent with a mantle-dominated fluid. The presence of garnets homogenous in δO within a few mm of garnets zoned in δO suggests textural control, both intraand inter-garnet, on oxygen zoning. In particular, a relationship between the extent of healed fracturing and oxygen zoning is observed across all the Navajo eclogite samples. Garnets homogenous in δO still record cation zoning, which is inconsistent with homogenization by diffusion. The presence of zoning in both cations and oxygen in these samples suggests a short residence time in the mantle, and a Mesozoic-Cenozoic origin. Franciscan eclogite garnets record altered upper oceanic crust core δO values of 9.3 to 13.3‰. Rim values in these samples range from 6.7 to 9.5‰. Low-δO rims record interaction with mantle or serpentinization fluids. High-δO rims suggest protection from these fluids due to location and/or channelized fluid flow. Oscillation in δO values between cores and rims suggests exposure to changing fluid environments or some movement of these samples within the subduction channel before exhumation. No definitive genetic link was found between the Franciscan and Moses Rock eclogites, however time constraints placed upon the Moses Rock xenoliths suggest that the two may have originated within the same subduction zone.
Crime and the Labor Market in a Search Model with Pairwise-Efficient Separations

This paper extends the Pissarides (2000) model of the labor market to include crime and punishment A la Becker (1968). All workers, irrespective of their labor force status can commit crimes and the employment contract is determined optimally. The model is used to study, analytically and quantitatively, the effects of various labor market and crime policies. For instance, a more generous unemployment insurance system reduces the crime rate of the unemployed but its effect on the crime rate of the employed depends on job duration and jail sentences. When the model is calibrated to U.S. data, the overall effect on crime is positive but quantitatively small. Wage subsidies reduce unemployment and crime rates of employed and unemployed workers, and improve society's welfare. Hiring subsidies reduce unemployment but they can raise the crime rate of employed workers. Crime policies (police technology and jail sentences) affect crime rates significantly but have only negligible effects on the labor market.