Miracle-dz/UniFAR-FTUs huggingface dataset:
Review of self-reported physical activity assessments for pregnancy: summary of the evidence for validity and reliability.

BACKGROUND Epidemiological studies and surveillance systems of pregnant women often rely on collection of physical activity through self-report. This systematic review identified and summarised self-reported physical activity assessments with evidence for validity and reliability among pregnant women. METHODS Peer-reviewed articles published through 2011 were included if they assessed validity and/or reliability of an interviewer- or self-administered physical activity questionnaire or diary among pregnant women. RESULTS We identified 15 studies, including 12 studies that assessed questionnaires and 4 studies that assessed diaries, conducted in Australia, Finland, Norway, the U.K., the U.S. and Vietnam. For questionnaires, 92% (11/12) assessed mode, all assessed frequency and/or duration and 58% (7/12) collected information on perceived intensity. All but one study (92%) assessed validity of the questionnaires. Questionnaires compared with objective measures (accelerometers, pedometers) ranged from slight to fair agreement, while comparison with other self-reported measures ranged from substantial to almost perfect agreement. Five studies (42%) assessed test-retest reliability of the questionnaires, ranging from substantial to almost perfect agreement. The four studies on diaries were all assessed for validity against objective measures, ranging from slight to substantial agreement. CONCLUSIONS Selection of valid and reliable physical activity measures that collect information on dose (type, frequency, duration, intensity) is recommended to increase precision and accuracy in detecting associations of physical activity with maternal and fetal outcomes.
de l ’ information Software Cost Estimation with Incomplete Data

The construction of software cost estimation models remains an active topic of research. The basic premise of cost modelling is that a historical database of software project cost data can be used to develop a quantitative model to predict the cost of future projects. One of the difficulties faced by workers in this area is that many of these historical databases contain substantial amounts of missing data. Thus far, the common practice has been to ignore observations with missing data. In principle, such a practice can lead to gross biases, and may be detrimental to the accuracy of cost estimation models. In this paper we describe an extensive simulation where we evaluate different techniques for dealing with missing data in the context of software cost modelling. Three techniques are evaluated: listwise deletion, mean imputation and eight different types of hot-deck imputation. Our results indicate that all the missing data techniques perform well, with small biases and high precision. This suggests that the simplest technique, listwise deletion, is a reasonable choice. However, this will not necessarily provide the best performance. Consistent best performance (minimal bias and highest precision) can be obtained by using hot-deck imputation with Euclidean distance and a z-score standardisation.
Effect of feeding Acacia nilotica pods to sheep on nutrient digestibility, nitrogen balance, ruminal protozoa and rumen enzymes activity

This study was conducted to evaluate the effect of supplying two levels of Acacia nilotica (A. nilotica) pods to rations of sheep on nutrient digestibility, nitrogen balance and rumen liquor parameters (pH, total protozoa count, protein concentration and enzymes activity). Twelve mature rams (50 ± 1.25 kg B.W.) were distributed into three groups, each with four rams. Animals in group one were considered as a control which fed a basal diet, consisting of concentrate mixture and Egyptian clover. The second group and the third one received the same basal diet with supplying the concentrate mixture by 1.5% and 3.0% of A. nilotica pods meal respectively. The experiment lasted for 3 weeks. It was found that supplementation of A. nilotica pods to the concentrate mixture at a rate of 1.5% and 3.0% significantly improved the total feed intake compared to the control. The digestibility of dry matter and crude fibre was significantly reduced with A. nilotica supplements, whereas the digestibility of crude protein was significantly improved. All of nitrogen intake and N-retained were significantly increased in rams fed on concentrates with 1.5% and 3.0% A. nilotica pods when compared to the control. The pH of ruminal fluid was not affected by the dietary treatments. Nevertheless, the total rumen protozoa count was significantly decreased in A. nilotica pods supplemented groups. Also, the rumen protein concentration and the ruminal enzymes activity, especially α-amylase, cellulase and protease, were lower in A. nilotica pods supplemented treatments. In conclusions, inclusion of low levels of A. nilotica pods (1.5% and 3.0%) in the concentrates can be used as a natural protein protectant in ruminants by forming tannin protein complexes in the rumen to maximize the amino acids available in the lower digestive tract. Also, these levels can increase the protein digestibility as well as the N-retained in the body .
Modeling and Estimation of Full-Chip Leakage Current Considering Within-Die Correlation

We present an efficient technique for finding the mean and variance of the full-chip leakage of a candidate design, while considering logic-structures and both die-to-die and within-die process variations, and taking into account the spatial correlation due to within-die variations. Our model uses a "random gate" concept to capture high-level characteristics of a candidate chip design, which are sufficient to determine its leakage. We show empirically that, for large gate count, the set of all chip designs that share the same high level characteristics have approximately the same leakage, with very small error. Therefore, our model can be used as either an early or a late estimator of leakage, with high accuracy. In its simplest form, we show that full-chip leakage estimation reduces to finding the area under a scaled version of the within-die channel length auto-correlation function, which can be done in constant time.
Value of dobutamine stress myocardial contrast perfusion echocardiography in patients with advanced liver disease

Although dobutamine stress echocardiography has been used for the preoperative evaluation of patients with advanced liver disease (ALD), no data exist regarding the value of myocardial perfusion imaging (MPI) with real‐time myocardial contrast echocardiography (RTMCE) in this patient population. We sought to determine the value of MPI during dobutamine stress RTMCE for predicting prognosis in patients with ALD. We examined both wall motion and MPI in 230 patients with ALD who underwent dobutamine stress RTMCE using intravenous commercially available contrast agents (Optison, GE‐Amersham, Princeton, NJ; or Definity, Bristol‐Myers Squibb Medical Imaging, North Billerica, MA). The prognostic value of clinical variables, including the Model for End‐Stage Liver Disease (MELD) score, and echocardiographic data were examined using a Cox Hazard model. The primary endpoint was mortality of all causes. Among the 85 patients who underwent orthotopic liver transplantation, 4 had abnormal MPI and 81 had normal perfusion. The hospital mortality rate was 50% (2/4) in patients with abnormal MPI and 2% (2/81) in patients with normal MPI (P = 0.01). Among patients with abnormal MPI, 1 died from myocardial infarction in the first postoperative day and the second 1 from hemorrhagic shock. During a median follow‐up of 15 months, 53 (23%) patients died. The independent predictors of death were an age of ≥65 yr (RR = 2.2; 95% confidence interval (CI) = 1.1–4.4; P = 0.03), MELD score of ≥25 (RR = 3.2; 95% CI = 1.8–5.5; P < 0.0001), and abnormal MPI (RR = 2.4; 95% CI = 1.1–5.2; P = 0.02). The 2‐yr mortality was 24% for patients with normal MPI and 45% for those with inducible MPI abnormalities (P = 0.003). In conclusion, MPI obtained by RTMCE appears to be a useful tool in predicting mortality in patients with ALD. Further studies are required to verify its independent value. Liver Transpl 12:592–599, 2006. © 2006 AASLD.
Osteogenic cell differentiation on H-terminated and O-terminated nanocrystalline diamond films

Nanocrystalline diamond (NCD) films are promising materials for bone implant coatings because of their biocompatibility, chemical resistance, and mechanical hardness. Moreover, NCD wettability can be tailored by grafting specific atoms. The NCD films used in this study were grown on silicon substrates by microwave plasma-enhanced chemical vapor deposition and grafted by hydrogen atoms (H-termination) or oxygen atoms (O-termination). Human osteoblast-like Saos-2 cells were used for biological studies on H-terminated and O-terminated NCD films. The adhesion, growth, and subsequent differentiation of the osteoblasts on NCD films were examined, and the extracellular matrix production and composition were quantified. The osteoblasts that had been cultivated on the O-terminated NCD films exhibited a higher growth rate than those grown on the H-terminated NCD films. The mature collagen fibers were detected in Saos-2 cells on both the H-terminated and O-terminated NCD films; however, the quantity of total collagen in the extracellular matrix was higher on the O-terminated NCD films, as were the amounts of calcium deposition and alkaline phosphatase activity. Nevertheless, the expression of genes for osteogenic markers – type I collagen, alkaline phosphatase, and osteocalcin – was either comparable on the H-terminated and O-terminated films or even lower on the O-terminated films. In conclusion, the higher wettability of the O-terminated NCD films is promising for adhesion and growth of osteoblasts. In addition, the O-terminated surface also seems to support the deposition of extracellular matrix proteins and extracellular matrix mineralization, and this is promising for better osteoconductivity of potential bone implant coatings.
Mitochondrial DNA Diversity in the Polish Roma

Mitochondrial DNA variability in the Polish Roma population has been studied by means of hypervariable segment I and II (HVS I and II) sequencing and restriction fragment‐length polymorphism analysis of the mtDNA coding region. The mtDNA haplotypes detected in the Polish Roma fall into the common Eurasian mitochondrial haplogroups (H, U3, K, J1, X, I, W, and M*). The results of complete mtDNA sequencing clearly indicate that the Romani M*‐lineage belongs to the Indian‐specific haplogroup M5, which is characterized by three transitions in the coding region, at sites 12477, 3921 and 709. Molecular variance analysis inferred from mtDNA data reveals that genetic distances between the Roma groups are considerably larger than those between the surrounding European populations. Also, there are significant differences between the Bulgarian Roma (Balkan and Vlax groups) and West European Roma (Polish, Lithuanian and Spanish groups). Comparative analysis of mtDNA haplotypes in the Roma populations shows that different haplotypes appear to demonstrate impressive founder effects: M5 and H (16261–16304) in all Romani groups; U3, I and J1 in some Romani groups. Interestingly, haplogroup K (with HVS I motif 16224‐16234‐16311) found in the Polish Roma sample seems to be specific for Ashkenazi Jewish populations.
Evolutionary bursts in Euphorbia (Euphorbiaceae) are linked with photosynthetic pathway

The mid‐Cenozoic decline of atmospheric CO2 levels that promoted global climate change was critical to shaping contemporary arid ecosystems. Within angiosperms, two CO2‐concentrating mechanisms (CCMs)—crassulacean acid metabolism (CAM) and C4—evolved from the C3 photosynthetic pathway, enabling more efficient whole‐plant function in such environments. Many angiosperm clades with CCMs are thought to have diversified rapidly due to Miocene aridification, but links between this climate change, CCM evolution, and increased net diversification rates (r) remain to be further understood. Euphorbia (∼2000 species) includes a diversity of CAM‐using stem succulents, plus a single species‐rich C4 subclade. We used ancestral state reconstructions with a dated molecular phylogeny to reveal that CCMs independently evolved 17–22 times in Euphorbia, principally from the Miocene onwards. Analyses assessing among‐lineage variation in r identified eight Euphorbia subclades with significantly increased r, six of which have a close temporal relationship with a lineage‐corresponding CCM origin. Our trait‐dependent diversification analysis indicated that r of Euphorbia CCM lineages is approximately threefold greater than C3 lineages. Overall, these results suggest that CCM evolution in Euphorbia was likely an adaptive strategy that enabled the occupation of increased arid niche space accompanying Miocene expansion of arid ecosystems. These opportunities evidently facilitated recent, replicated bursts of diversification in Euphorbia.
Veins Improve Fracture Toughness of Insect Wings

During the lifetime of a flying insect, its wings are subjected to mechanical forces and deformations for millions of cycles. Defects in the micrometre thin membranes or veins may reduce the insect’s flight performance. How do insects prevent crack related material failure in their wings and what role does the characteristic vein pattern play? Fracture toughness is a parameter, which characterises a material’s resistance to crack propagation. Our results show that, compared to other body parts, the hind wing membrane of the migratory locust S. gregaria itself is not exceptionally tough (1.04±0.25 MPa√m). However, the cross veins increase the wing’s toughness by 50% by acting as barriers to crack propagation. Using fracture mechanics, we show that the morphological spacing of most wing veins matches the critical crack length of the material (1132 µm). This finding directly demonstrates how the biomechanical properties and the morphology of locust wings are functionally correlated in locusts, providing a mechanically ‘optimal’ solution with high toughness and low weight. The vein pattern found in insect wings thus might inspire the design of more durable and lightweight artificial ‘venous’ wings for micro-air-vehicles. Using the vein spacing as indicator, our approach might also provide a basis to estimate the wing properties of endangered or extinct insect species.
High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals

Background: The intestinal microbiota is associated with human health and diseases. The luminal microbiota (LM) and the mucosal-associated microbiota (MAM) are 2 distinct ecosystems with different metabolic and immunological functions. Aim: To characterize the intestinal LM and MAM in humans using high throughput sequencing of the 16S rRNA gene. Methods: Fresh fecal samples and distal colonic mucosal biopsies collected from 24 healthy subjects before (fecal) and during (mucosa) a flexible sigmoidoscopy of an un-prepared bowel. High throughput sequencing of the 16S rRNA gene was used to characterize bacterial communities. Sequences were processed using the QIIME pipeline. Results: LM and MAM populations were significantly different (ANOSIM: R = 0.49, P = 0.001). The LM displayed tighter clustering compared to the MAM (average weighted UniFrac distances 0.27 ± 0.05 vs. 0.43 ± 0.09, P < 0.001, respectively), and showed higher diversity (Shannon diversity index: 4.96 ± 0.37 vs 4.14 ± 0.56, respectively, P < 0.001). The dominant phyla in the LM and MAM were significantly different: Firmicutes (41.4% vs. 29.1%, FDR < 0.0001, respectively), Bacteroidetes (20.2% vs. 26.3%, FDR < 0.05, respectively), Actinobacteria (22% vs. 12.6%, FDR < 0.0001, respectively) and Proteobacteria (9.3% vs. 19.3%, FDR < 0.0001, respectively). The abundance of 56 genera differed significantly (FDR < 0.1) between the 2 niches. All of the genera in the fecal microbiota were present in the MAM while 10 genera were found to be unique to the MAM. Conclusion: The LM and MAM are distinct microbial ecosystems that differ significantly from each other in microbial diversity and composition. These two microbial niches should be investigated independently to better understand the role of the intestinal microbiota in health and disease.
DNA Double-Strand Breaks

The activation-induced cytidine deaminase (AID) is required for somatic hypermutation (SHM) and class-switch recombination (CSR) of immunoglobulin (Ig) genes, both of which are associated with DNA double-strand breaks (DSBs). As AID is capable of deaminating deoxy-cytidine (dC) to deoxy-uracil (dU), it might induce nicks (single strand DNA breaks) and also DNA DSBs via a U-DNA glycosylase-mediated base excision repair pathway (‘DNA-substrate model’). Alternatively, AID functions like its closest homologue Apobec1 as a catalytic subunit of a RNA editing holoenzyme (‘RNA-substrate model’). Although rearranged Vλ genes are preferred targets of SHM we found that germinal center (GC) B cells of AID-proficient and -deficient Vλ1-expressing GC B cells display a similar frequency, distribution, and sequence preference of DSBs in rearranged and also in germline Vλ1 genes. The possible roles of DSBs in relation to AID function and SHM are discussed.
Design Study Methodology: Reflections from the Trenches and the Stacks

Design studies are an increasingly popular form of problem-driven visualization research, yet there is little guidance available about how to do them effectively. In this paper we reflect on our combined experience of conducting twenty-one design studies, as well as reading and reviewing many more, and on an extensive literature review of other field work methods and methodologies. Based on this foundation we provide definitions, propose a methodological framework, and provide practical guidance for conducting design studies. We define a design study as a project in which visualization researchers analyze a specific real-world problem faced by domain experts, design a visualization system that supports solving this problem, validate the design, and reflect about lessons learned in order to refine visualization design guidelines. We characterize two axes - a task clarity axis from fuzzy to crisp and an information location axis from the domain expert's head to the computer - and use these axes to reason about design study contributions, their suitability, and uniqueness from other approaches. The proposed methodological framework consists of 9 stages: learn, winnow, cast, discover, design, implement, deploy, reflect, and write. For each stage we provide practical guidance and outline potential pitfalls. We also conducted an extensive literature survey of related methodological approaches that involve a significant amount of qualitative field work, and compare design study methodology to that of ethnography, grounded theory, and action research.
Poisson Naive Bayes for Text Classification with Feature Weighting

In this paper, we investigate the use of multivariate Poisson model and feature weighting to learn naive Bayes text classifier. Our new naive Bayes text classification model assumes that a document is generated by a multivariate Poisson model while the previous works consider a document as a vector of binary term features based on the presence or absence of each term. We also explore the use of feature weighting for the naive Bayes text classification rather than feature selection, which is a quite costly process when a small number of the new training documents are continuously provided.Experimental results on the two test collections indicate that our new model with the proposed parameter estimation and the feature weighting technique leads to substantial improvements compared to the unigram language model classifiers that are known to outperform the original pure naive Bayes text classifiers.
RIN ZF, a Novel Zinc Finger Gene, Encodes Proteins That Bind to the CACC Element of the Gastrin Promoter*

Expression of gastrin, a gut hormone and growth factor, has tissue-specific transcriptional regulation and can be induced in some tumors. Previous studies have shown that a CACCcis-regulatory element is important for transcriptional activation in pancreatic insulinoma cells. To identify CACC-binding proteins, a λ phage cDNA library derived from a rat insulinoma cell line, RIN 38A, was screened by a Southwestern method. A novel member of the Cys2-His2 zinc finger gene family was cloned and designated RIN ZF, having a cDNA sequence of 3.8 kilobases. One full-length and a shorter splice variant were sequenced and had predicted protein masses of 91.6 and 88.7 kDa. Expression of both splice forms were ubiquitous in fetal and adult rat tissues. Recombinant RIN ZF protein exhibited sequence-specific binding to the gastrin CACC element in a gel mobility shift assay. In transient transfections, both splice variants appeared to have only weak activating effects on gastrin-luciferase reporter gene transcription. Furthermore, RIN ZF coexpression with Sp1 appeared to block the strongly activating effects of Sp1 mediated through the CACC element. These findings suggest that a novel set of zinc finger proteins may help regulate gastrin gene expression by interfering with Sp1 transactivation.
Network histograms and universality of blockmodel approximation

Significance Representing and understanding large networks remains a major challenge across the sciences, with a strong focus on communities: groups of network nodes whose connectivity properties are similar. Here we argue that, independently of the presence or absence of actual communities in the data, this notion leads to something stronger: a histogram representation, in which blocks of network edges that result from community groupings can be interpreted as two-dimensional histogram bins. We provide an automatic procedure to determine bin widths for any given network and illustrate our methodology using two publicly available network datasets. In this paper we introduce the network histogram, a statistical summary of network interactions to be used as a tool for exploratory data analysis. A network histogram is obtained by fitting a stochastic blockmodel to a single observation of a network dataset. Blocks of edges play the role of histogram bins and community sizes that of histogram bandwidths or bin sizes. Just as standard histograms allow for varying bandwidths, different blockmodel estimates can all be considered valid representations of an underlying probability model, subject to bandwidth constraints. Here we provide methods for automatic bandwidth selection, by which the network histogram approximates the generating mechanism that gives rise to exchangeable random graphs. This makes the blockmodel a universal network representation for unlabeled graphs. With this insight, we discuss the interpretation of network communities in light of the fact that many different community assignments can all give an equally valid representation of such a network. To demonstrate the fidelity-versus-interpretability tradeoff inherent in considering different numbers and sizes of communities, we analyze two publicly available networks—political weblogs and student friendships—and discuss how to interpret the network histogram when additional information related to node and edge labeling is present.