Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial Ecology of an Extreme Acidic Environment, the Tinto River

ABSTRACT The Tinto River (Huelva, southwestern Spain) is an extreme environment with a rather constant acidic pH along the entire river and a high concentration of heavy metals. The extreme conditions of the Tinto ecosystem are generated by the metabolic activity of chemolithotrophic microorganisms thriving in the rich complex sulfides of the Iberian Pyrite Belt. Molecular ecology techniques were used to analyze the diversity of this microbial community. The community's composition was studied by denaturing gradient gel electrophoresis (DGGE) using 16S rRNA and by 16S rRNA gene amplification. A good correlation between the two approaches was found. Comparative sequence analysis of DGGE bands showed the presence of organisms related to Leptospirillum spp. , Acidithiobacillus ferrooxidans, Acidiphilium spp. , “Ferrimicrobium acidiphilum,” Ferroplasma acidiphilum, and Thermoplasma acidophilum. The different phylogenetic groups were quantified by fluorescent in situ hybridization with a set of rRNA-targeted oligonucleotide probes. More than 80% of the cells were affiliated with the domain Bacteria, with only a minor fraction corresponding to Archaea. Members of Leptospirillum ferrooxidans, Acidithiobacillus ferrooxidans, and Acidiphilium spp. , all related to the iron cycle, accounted for most of the prokaryotic microorganisms detected. Different isolates of these microorganisms were obtained from the Tinto ecosystem, and their physiological properties were determined. Given the physicochemical characteristics of the habitat and the physiological properties and relative concentrations of the different prokaryotes found in the river, a model for the Tinto ecosystem based on the iron cycle is suggested.
Use of Modified Acute Concussion Evaluation Tools in the Emergency Department

OBJECTIVES: Accurate recognition of pediatric concussion in the emergency department (ED) is important to ensure appropriate management for safe recovery. The study objective was to determine whether the Centers for Disease Control and Prevention’s Acute Concussion Evaluation (ACE) tools, modified for ED use, improved patient follow-up and post-injury behaviors. METHODS: The original ACE tools (ACE, ACE Care Plan) were modified for ED use via Delphi methodology with an expert panel and implemented in 2 urban pediatric EDs for patients aged 5 to 21 years evaluated within 24 hours of a head injury. Pre- (February 2009 to July 2009) and post- (December 2009 to June 2010) implementation, patient phone surveys were conducted 1, 2, and 4 weeks after ED discharge. Reported rates of patient follow-up and recovery measures were analyzed. ED clinician adherence was assessed. RESULTS: During the study, 164 patients were enrolled pre-implementation and 190 post-implementation. The mean patient age was 10.6 years (SD, 3.7); 65% were males, 49% were African American, and 46% were Caucasian. Post-implementation, 58% of patients received the modified ACE diagnostic tool and 84% received the modified ACE discharge instructions. Follow-up was improved at all time points (32% vs 61% at week 4; P < .001; odds ratio, 3.4; 95% confidence interval, 2.1–5.4). Post-implementation, parental recall of discharge instructions was significantly increased, patient’s mean total post-concussion symptom score was significantly higher, and report of return to normal activity was significantly longer. CONCLUSIONS: The ACE tools, modified for ED use, were successfully implemented in the pediatric ED. Post-implementation, increased patient follow-up and improved recall of and adherence to ED discharge recommendations was demonstrated.
Quality and Sustainability in Teacher-Research

* For years now I have been advocating practitioner-research, by teachers and learners, in their own language classrooms. Increasingly, however, I have encountered an apparently irreconcilable conflict between the demands of quality and of sustainability. Practitioner-research, at its worst, seems to constitute a way of getting research done badly and making the process so demanding that it is patently unsustainable and therefore soon abandoned.
Continuous Cognitive Dynamics of the Evaluation of Trustworthiness in Williams Syndrome

The decision to approach or avoid an unfamiliar person is based in part on one’s evaluation of facial expressions. Individuals with Williams syndrome (WS) are characterized in part by an excessive desire to approach people, but they display deficits in identifying facial emotional expressions. Likert-scale ratings are generally used to examine approachability ratings in WS, but these measures only capture an individual’s final approach/avoid decision. The present study expands on previous research by utilizing mouse-tracking methodology to visually display the nature of approachability decisions via the motor movement of a computer mouse. We recorded mouse movement trajectories while participants chose to approach or avoid computer-generated faces that varied in terms of trustworthiness. We recruited 30 individuals with WS and 30 chronological age-matched controls (mean age = 20 years). Each participant performed 80 trials (20 trials each of four face types: mildly and extremely trustworthy; mildly and extremely untrustworthy). We found that individuals with WS were significantly more likely than controls to choose to approach untrustworthy faces. In addition, WS participants considered approaching untrustworthy faces significantly more than controls, as evidenced by their larger maximum deviation, before eventually choosing to avoid the face. Both the WS and control participants were able to discriminate between mild and extreme degrees of trustworthiness and were more likely to make correct approachability decisions as they grew older. These findings increase our understanding of the cognitive processing that underlies approachability decisions in individuals with WS.
Imputation methods for a binary variable

Binary variables are common in surveys including such as employed vs unemployed, healthy vs unhealthy or poor vs non-poor. The last one is used in the examples of this paper. It is unfortunate that survey data are never complete, that is, missingness occurs, sometimes severely. In those cases missingness may violate estimates due to unit nonresponse. For this purpose, there are also sophisticated nonresponse adjustments possible to use, and these should be applied in a best way taking advantage of auxiliary variables from the individual nonrespondents as well as from the population level aggregates. In the case when the nonrespondents participate partially in the survey (item nonresponse), there exists more micro level auxiliary variables available. Such data should naturally be exploited in a best way as well. This leads to apply imputation methods. In this paper, our binary variable gives a too low poverty rate when estimating it from the completely replied respondents. So it is beneficial to improve the estimate with imputations. This is not necessarily easy since our pattern of auxiliary data is not excellent that is common in real life. Consequently, the results depend more than in a nice situation on an imputation method applied. In this case we compare several methods. The imputation process consists of the two steps, (i) imputation model and (ii) imputation task. The dependent variable of the imputation model is also binary but they are of two types: (a) the binary variable being imputed itself, or (b) the binary response indicator. The former takes advantage of the data of the respondents but the latter both from the respondents and from the nonrespondents. Since we know the true values (but so that their mechanism is not known), we can compare different methods. When using the methods with random numbers, we also can apply multiple imputation methodology. So we have both single imputation and multiple imputation methods compared in the empirical part. Our strategy is not only Bayesian for multiple imputation that is usual in software packages such as SPSS and SAS. We test their methods but concentrate on our own solutions, called non-Bayesian.
Rapid calibration method for registration and 3D tracking of ultrasound images using spatial localizer

Conventional freehand 3D ultrasound (US) is a complex process, involving calibration, scanning, processing, volume reconstruction, and visualization. Prior to calibration, a position sensor is attached to the probe for tagging each image with its position and orientation in space; then calibration process is performed to determine the spatial transformation of the scan plan with respect to the position sensor. Finding this transformation matrix is a critical, but often underrated task in US-guided surgery. The purpose of this study is to enhance previously known calibration methods by introducing a novel calibration fixture and process. The proposed phantom is inexpensive, easy to construct, easy to scan, while yielding more data points per image than previously known designs. The processing phase is semi-automated, allowing for fast processing of a massive amount of data, which in turn increases accuracy by reducing human errors.
A tree structure for web service compositions

The composition of Web services is gaining a considerable momentum as an approach to the effective integration of distributed, heterogeneous and autonomous applications to build more sophisticated and value added services. Algorithms are needed to select the best services for the individual tasks of the composition. QoS is an important criterion to select the best service for the tasks of composition. The objective of selection algorithm is to maximize the QoS of the composition based on the composite service provider's (CSP) QoS requirements. In this paper, we define the various business offers (service offers) of Web services. We classify the CSP's requirements defined on the QoS and service offers based on its structure. We propose a tree structure to represent the CSP's requirements defined on the multiple QoS properties and service offers involving AND and OR operators with varied preferences.
Change of Gene Structure and Function by Non-Homologous End-Joining, Homologous Recombination, and Transposition of DNA

An important objective in genome research is to relate genome structure to gene function. Sequence comparisons among orthologous and paralogous genes and their allelic variants can reveal sequences of functional significance. Here, we describe a 379-kb region on chromosome 1 of maize that enables us to reconstruct chromosome breakage, transposition, non-homologous end-joining, and homologous recombination events. Such a high-density composition of various mechanisms in a small chromosomal interval exemplifies the evolution of gene regulation and allelic diversity in general. It also illustrates the evolutionary pace of changes in plants, where many of the above mechanisms are of somatic origin. In contrast to animals, somatic alterations can easily be transmitted through meiosis because the germline in plants is contiguous to somatic tissue, permitting the recovery of such chromosomal rearrangements. The analyzed region contains the P1-wr allele, a variant of the genetically well-defined p1 gene, which encodes a Myb-like transcriptional activator in maize. The P1-wr allele consists of eleven nearly perfect P1-wr 12-kb repeats that are arranged in a tandem head-to-tail array. Although a technical challenge to sequence such a structure by shotgun sequencing, we overcame this problem by subcloning each repeat and ordering them based on nucleotide variations. These polymorphisms were also critical for recombination and expression analysis in presence and absence of the trans-acting epigenetic factor Ufo1. Interestingly, chimeras of the p1 and p2 genes, p2/p1 and p1/p2, are framing the P1-wr cluster. Reconstruction of sequence amplification steps at the p locus showed the evolution from a single Myb-homolog to the multi-gene P1-wr cluster. It also demonstrates how non-homologous end-joining can create novel gene fusions. Comparisons to orthologous regions in sorghum and rice also indicate a greater instability of the maize genome, probably due to diploidization following allotetraploidization.
Incremental Aggregated Proximal and Augmented Lagrangian Algorithms

We consider minimization of the sum of a large number of convex functions, and we propose an incremental aggregated version of the proximal algorithm, which bears similarity to the incremental aggregated gradient and subgradient methods that have received a lot of recent attention. Under cost function dierentiability and strong convexity assumptions, we show linear convergence for a suciently small constant stepsize. This result also applies to distributed asynchronous variants of the method, involving bounded interprocessor communication delays. We then consider dual versions of incremental proximal algorithms, which are incremental augmented Lagrangian methods for separable equality-constrained optimization problems. Contrary to the standard augmented Lagrangian method, these methods admit decomposition in the minimization of the augmented Lagrangian, and update the multipliers far more frequently. Our incremental aggregated augmented Lagrangian methods bear similarity to several known decomposition algorithms, most of which, however, are not incremental in nature: the augmented Lagrangian decomposition algorithm of Stephanopoulos and Westerberg [StW75], and the related methods of Tadjewski [Tad89] and Ruszczynski [Rus95], and the alternating direction method of multipliers (ADMM) and more recent variations. We compare these methods in terms of their properties, and highlight their potential advantages and limitations. We also address the solution of separable inequality-constrained optimization problems through the use of nonquadratic augmented Lagrangians such as the exponential, and we dually consider a corresponding incremental aggregated version of the proximal algorithm that uses nonquadratic regularization, such as an entropy function. We nally propose a closely related linearly convergent method for minimization of large dierentiable sums subject to an orthant constraint, which may be viewed as an incremental aggregated
Nitrogen fixation by sulfate-reducing bacteria indicated by nitrogen argon ratios.

Technical Papers Recovery from Radiation Injury: L. 0. Jacobson et al. 510 Nitrogen Fixation by Sulfate-reducing Bacteria Indicated by Nitrogen/Argon Ratios: Frederick D. Sisler and Claude E. ZoBell . 511 Chemical Constitution and Biological Activity in Reversed Carboxyl (RC) Analogues of Acetylcholine: F. W. Schueler, H. H. Keasling, and R. M. Featherstone . -. 512 A New Versatile Respirator: Curtis Marshall . 514 Louisiana and Gulf Coast Oysters: Gordon Gunter . 516 Organic Origin of Soimie Calcareous Sediments from the Red Sea: Bushdi Said . 517 Synergistic Action of 2,4-D and of Coconut Milk:
Children's Moral Motive Strength and Temperamental Inhibition Reduce Their Immoral Behavior in Real Moral Conflicts

This study is concerned with the prediction of interindividual differences in children's immoral behavior in real moral conflicts by moral motive strength (appropriate attribution of moral emotions to story characters), temperamental inhibition, and ego control. Children were tempted to cheat at age 6 when they felt unobserved, or to contend for a scarce resource in peer triads at age 7. Moral motive strength and inhibition, but not ego control, predicted low cheating and low nonverbal rivalry to a similar extent. Extreme group analyses of children low or high in both traits showed that cheating/noncheating could be predicted with a hit rate above 90%. Nonverbal rivalry in a group increased exponentially with the number of low-moral uninhibited children in the group, a finding replicated within the same sample. Discussion focuses on the influence of moral motive strength, temperamental inhibition, ego control, and their interaction on the reduction of immoral behavior.
Parenthetical Classification for Information Extraction

The article focuses on a rather unexplored topic in NLP: parenthetical classification. Parentheticals are defined as any text sequence between parentheses. They have been approached from isolated perspectives, like translation pairs extraction, but a full account of their syntactic and semantic properties is lacking. This article proposes a new comprehensive scheme drawn from corpus-based linguistic studies on French news. This research is part of a project investigating the structural aspects of punctuation signs and their usefulness for Information Extraction. Parenthetical classification is approached as a relation extraction problem split into three correlated subtasks: syntactic and semantic classification and head recognition. Corpus-based studies singled out 11 syntactic and 18 semantic relation subtypes. The article addresses automatic classification, using a combination of CRF and SVM. This baseline system reports 0.674 (head recognition), 0.908 (syntax), 0.734 (semantics), and 0.518 (end-to-end) of F1.
Condition monitoring of electrical equipment using thermal image processing

Excessive temperature rise leads to majority of failures in electrical equipment. Therefore, the thermal monitoring always plays a significant role for identifying incipient faults. Now a days cost effective, reliable and non contact type infrared thermographic inspection system is being widely utilized for monitoring and fault diagnosis. In this paper, thermal images of some electrical equipment have been taken and converted to HSI color model for further processing. Unlike other techniques, instead of gray scale images, in the proposed method hue region has been taken into consideration. Then different gradient based edge detection like Prewitt, Roberts and Sobel are used to identify hot region of the thermal image. Based on some image metrics like Mean Squared Error (MSE) and Peak Signal-to-Noise Ratio (PSNR), the best method is chosen for processing of the thermal image. Lastly, Clustering based Otsu image segmentation method is introduced taking hue region. These methods are tested on 27 numbers of standard thermal images. The proposed technique gives better segmentation results for all images than the standard grey scale approaches. Hence the proposed model may produce better features for thermal monitoring of electrical equipment in future.
Type I and Type II Neuron Models Are Selectively Driven by Differential Stimulus Features

Neurons in the nervous system exhibit an outstanding variety of morphological and physiological properties. However, close to threshold, this remarkable richness may be grouped succinctly into two basic types of excitability, often referred to as type I and type II. The dynamical traits of these two neuron types have been extensively characterized. It would be interesting, however, to understand the information-processing consequences of their dynamical properties. To that end, here we determine the differences between the stimulus features inducing firing in type I and type II neurons. We work with both realistic conductance-based models and minimal normal forms. We conclude that type I neurons fire in response to scale-free depolarizing stimuli. Type II neurons, instead, are most efficiently driven by input stimuli containing both depolarizing and hyperpolarizing phases, with significant power in the frequency band corresponding to the intrinsic frequencies of the cell.
Endoderm‐specific deletion of Tbx1 reveals an FGF‐independent role for Tbx1 in pharyngeal apparatus morphogenesis

Background: The T‐box transcription factor Tbx1, is essential for the normal development of multiple organ systems in the embryo. One of the most striking phenotypes in Tbx1−/− embryos is the failure of the caudal pharyngeal pouches to evaginate from the foregut endoderm. Despite considerable interest in the role of Tbx1 in development, the mechanisms whereby Tbx1 controls caudal pouch formation have remained elusive. In particular, the question as to how Tbx1 expression in the pharyngeal endoderm regulates pharyngeal pouch morphogenesis in the mouse embryo is not known. Results: To address this question, we produced mouse embryos in which Tbx1 was specifically deleted from the pharyngeal endoderm and, as expected, embryos failed to form caudal pharyngeal pouches. To determine the molecular mechanism, we examined expression of Fgf3 and Fgf8 ligands and downstream effectors. Although Fgf8 expression is greatly reduced in Tbx1‐deficient endoderm, FGF signaling levels are unaffected. Furthermore, pouch morphogenesis is only partially perturbed by the loss of both Fgf3 and Fgf8 from the endoderm, indicating that neither are required for pouch formation. Conclusions: Tbx1 deletion from the pharyngeal endoderm is sufficient to cause caudal pharyngeal arch segmentation defects by FGF‐independent effectors that remain to be identified. Developmental Dynamics 243:1143–1151, 2014. © 2014 Wiley Periodicals, Inc.
Multidecadal streamflow regimes in the interior western United States: Implications for the vulnerability of water resources

In the interior western United States, increased demand for water coupled with the uncertain nature of anthropogenic and natural hydroclimatic variations add challenges to the task of assessing the adequacy of the existing regional water resources systems. Current availability of relatively short instrumental streamflow records further limits the diagnosis of multidecadal and longer time variations. Here we develop a long‐term perspective of streamflow variations using a 285‐year long tree‐ring reconstruction at Middle Boulder Creek, Colorado. Analysis of the reconstructed streamflow provides useful insights for assessing vulnerability: (a) a wider range of hydrologic variations on multidecadal time scales, not seen in the instrumental record, (b) wet/dry regimes show disparate fluctuations across various flow thresholds, and (c) temporal changes in the flow probabilities have varied “flavors” corresponding to wet and dry regimes and their spatial extent. Based on these results, we discuss implications for the climate‐related vulnerability of regional water resources.
The junction tree algorithm

In the previous scribes, we introduced general objects used in graphical models as well message passing schemes such as the sum-product algorithm and the max-sum algorithm for efficient computation of local marginals over subsets of the graph as well as the most probable state of the graph. For graphs which are trees, we noted that the algorithms are exact. In this article, we discuss a more flexible tool known as the junction tree algorithm which is used to compute local marginals of subsets of arbitrary graphs and yet still retains the property of being exact. The article draws largely from the exposition contained in Bishop[2], Lauritzen[4], Barber[1], and Wainwright and Jordan[5].
A multiresolution segmentation method for tree crown image using wavelets

Tree crown image segmentation is a major step of many applications, such as crown transparency estimation, virtual plant, and so on. Varying image characteristics caused by differing levels of foliation and fluctuating lighting conditions present a unique challenge for tree segmentation. For example, small leaves surrounded by bright sky, small openings among dense canopy, and mixed pixels. This paper proposes a new segmentation method, based on wavelets and Markov random field model, and considering color information (green band). The morphological wavelet transform provides a powerful transform domain for modeling singularity-rich structure images. The Markov random field model provides a good tool for distinguishing between different textures. The new method provides both lower classification error rates and better visual results, especially where crown objects may have complex backgrounds.