Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of the phoM gene product and its regulation in Escherichia coli K-12

Plasmids containing the chromosome region of Escherichia coli encoding phoM, whose product is a positive regulator of alkaline phosphatase expression, were isolated from the Clarke and Carbon plasmid bank. A 9.9-kilobase EcoRI fragment of plasmid pLC17-39 (subcloned into pBR322) was able to complement both phoM and thrB mutations. Restriction endonuclease analysis and in vitro mutagenesis of the hybird plasmids enabled the localization of the phoM gene locus to 3 kilobases of the cloned chromosomal fragment. The phoM gene product was identified, with maxicell techniques, as a protein with an approximate molecular weight of 55,000. A phoM-lacZ protein fusion was constructed by using a plasmid carrying the phoM gene and a derivative of phage lambda, lambda plac Mu2. Restriction endonuclease analysis of the plasmid carrying the fusion indicated that phoM is transcribed in a clockwise direction on the circular E. coli chromosome. Analysis of strains bearing the fusion on a multiple-copy plasmid or integrated at the lambda attachment site of the chromosome indicated that the synthesis of the phoM gene product was unaffected by phosphate limitation of growth. The expression of the phoM gene was studied in strains with mutations in genes encoding effectors of the pho regulon. A threefold increase in phoM expression was seen in a phoU strain in comparison with the wild-type strain.
Low Intracellular Proline: A Cause of Toxicity in Human RPE Cells?

Gyrate atrophy of the choroid and retina (GA) is an autosomal recessive disease caused by mutations in the nuclear gene coding for the mitochondrial enzyme ornithine aminotransferase (OAT; Valle & Simell, 2001). The primary symptoms for this congenital metabolic disease include night blindness, myopia, cataracts, and progressive reduction in peripheral vision culminating in blindness by the age of forty. The loss of OAT leads to high plasma levels of the amino acid ornithine and low levels of proline and creatine (Valle & Simell, 2001). Our knowledge about the pathophysiology of GA is very limited: we do not know the mechanism for toxicity or the primary toxic species. However, we do know the following: first, the initial cells affected are the retinal pigmented epithelial (RPE) cells (Wang et al., 1996); second, ornithine enters the cells primarily through the cationic amino acid transporter (CAT)-1 (Kaneko et al., 2007); third, lowering plasma levels of ornithine prevents the progression of the disease (Wang et al., 2000). Since proper CAT-1 functioning is essential for the survival of the organism, this channel cannot be systemically blocked as a treatment for GA (Kaneko et al., 2007). The most efficient treatment has been reducing the plasma ornithine level by restricting the intake of its precursor arginine (Wang et al., 2000). This treatment is not without its problems. Only about 20% of the patients are able to follow this diet (Wang et al., 2000), as it is highly restrictive and requires the patient to take many dietary supplements supplying the essential amino acids, vitamins, and minerals (Valle & Simell, 2001). Ueda et al. (1998) showed that treatment with proline prevented toxicity caused by high concentrations of ornithine in RPE cells lacking OAT. The authors suggest that low proline levels might be the primary cause of toxicity in GA. The study, however, provides inconclusive evidence to support the hypothesis. The levels of proline in the cell are not measured in the study, and toxicity to RPE cells by low levels of proline alone is not measured. The prospect that low proline levels cause GA cytotoxicity is an exciting one since dietary supplementation of proline is much easier than restriction of arginine. The cheaper and easier treatment that could result from this possibility necessitates an investigation into the role of proline in GA.
Textual Entailment as an Evaluation Framework for Metaphor Resolution: A Proposal

We aim to address two complementary deficiencies in Natural Language Processing (NLP) research: (i) Despite the importance and prevalence of metaphor across many discourse genres, and metaphor's many functions, applied NLP has mostly not addressed metaphor understanding. But, conversely, (ii) difficult issues in metaphor understanding have hindered large-scale application, extensive empirical evaluation, and the handling of the true breadth of metaphor types and interactions with other language phenomena. In this paper, abstracted from a recent grant proposal, a new avenue for addressing both deficiencies and for inspiring new basic research on metaphor is investigated: namely, placing metaphor research within the "Recognizing Textual Entailment" (RTE) task framework for evaluation of semantic processing systems.
Endophytic Fungal b-1 , 6-Glucanase Expression in the Infected Host Grass 1

Mutualistic fungal endophytes infect many grass species and often confer benefits to the hosts such as reduced herbivory by insects and animals. The physiological interactions between the endophytes and their hosts have not been well characterized. Fungal-secreted proteins are likely to be important components of the interaction. In the interaction between Poa ampla and the endophyte Neotyphodium sp. , a fungal b-1,6-glucanase is secreted into the apoplast, and activity of the enzyme is detectable in endophyte-infected plants. Sequence analysis indicates the b-1,6-glucanase is homologous to enzymes secreted by the mycoparasitic fungi Trichoderma harzianum and Trichoderma virens. DNA gel-blot analysis indicated the b-1,6-glucanase was encoded by a single gene. As a secreted protein, the b-1,6-glucanase may have a nutritional role for the fungus. In culture, b-1,6-glucanase activity was induced in the presence of b-1,6-glucans. From RNA gel blots, similar b-1,6-glucanases were expressed in tall fescue (Festuca arundinacea Schreb.) and Chewings fescue (Festuca rubra L. subsp. fallax [Thuill] Nyman) infected with the endophyte species Neotyphodium coenophialum and Epichloë festucae, respectively.
A Mixture of Transformed Hidden Markov Models for Elastic Motion Estimation

Elastic motion is a nonrigid motion constrained only by some degree of smoothness and continuity. Consequently, elastic motion estimation by explicit feature matching actually contains two correlated subproblems: shape registration and motion tracking, which account for spatial smoothness and temporal continuity, respectively. If we ignore their interrelationship, solving each of them alone will be rather challenging, especially when the cluttered features are involved. To integrate them into a probabilistic model, one straightforward approach is to draw the dependence between their hidden states. With regard to their separated states, there are, however, two different explanations of motion which are still made under the individual constraint of smoothness or continuity. Each one can be error-prone, and their coupling causes error propagation. Therefore, it is highly desirable to design a probabilistic model in which a unified state is shared by the two subproblems. This paper is intended to propose such a model, i.e., a Mixture of Transformed Hidden Markov Models (MTHMM), where a unique explanation of motion is made simultaneously under the spatiotemporal constraints. As a result, the MTHMM could find a coherent global interpretation of elastic motion from local cluttered edge features, and experiments show its robustness under ambiguities, data missing, and outliers.
The telling of violence: Organizational change and atrocity tales

This paper explores the retrospective construction of atrocity narratives of organizational change in primary industries of the Latrobe Valley, located in southeast Australia. Within their narratives, participants discuss various forms of workplace violence aimed at employees by management and, in some cases, other employees. In addition, shifting narratives from violence to resignation are explored. As all participants are no longer employed in the organizations described in the narratives, causal associations between workplace violence and resignation choices are of particular interest. In this context, atrocity narratives are presented in a deliberate effort to extend the theorizing of organizational change into domains that are neither attractive nor progressive.
Melanic Coat Color Variation in Rock Pocket Mice (Chaetodius intermedius)

Coat color variation in small mammals is a classic example of phenotypic variation in response to selection in different environments (Hoekstra and Nachman, 2005); many species closely match the color of the substrate in which they live. Examples of intraspecific color variation in rodents include the canyon mouse (Peromyscus crunitus), the deer field mouse (Peromyscus maniculatus), the old-field mouse (Peromyscus polionotus), and the rock pocket mouse (Chaetodius intermedius) (Hoekstra and Nachman, 2005). The rock pocket mouse is one of the most studied models for phenotypic color variation. Many studies have found coat color variation in the rock pocket mouse in deserts of the southwestern states (Nachman, Hoekstra, and D’Agostino, 2005). Authors have showed that C. intermedius coat color matched the color of the rocks on which the mice live (Nachman, Hoekstra, and D’Agostino, 2005). Several studies have found that most light-colored mice live on light-colored rocks, but in several geographic regions, they are melanic (black or brown) and live on dark-colored basalt lava (Hoekstra and Nachman, 2003; Hoekstra, Drumm, and Nachman, 2004). Furthermore, the pocket mice on volcanic lava with dark coats do not have banded hairs, whereas mice from nearby light-colored granitic rocks have light coats that do have banded hairs. This color polymorphism is a presumed adaptation to avoid predation from avian and mammalian predators (Nachman, Hoekstra, and D’Agostino, 2005). Rock pocket mice provide a useful system for studying the genetics of adaptation. Genetics seem to play a role in that their coat color typically matches the color of the rocks on which they live. (Hoekstra and Nachman, 2003; Hoekstra, Drumm, and Nachman, 2004). The main questions that this story brings to focus are: 1) is this coat color variation a consequence of natural selection; and 2) if there is variation in more than one area or region, are these caused by the same gene of not? This paper will explore coat coloration in pocket mice based on the work of evolutionary biologist Hopi Hoekstra. It is suggested that phenotypic variation is due to natural selection and that variation in multiple regions is caused by a few interacting genes. Hoekstra received her B.A. in Integrative Biology from UC Berkeley. She then completed her Ph.D. in Zoology in 2000 as a Howard Hughes Predoctoral Fellow at the University of Washington. Hoekstra then moved to the University of Arizona as a NIH Postdoctoral Fellow where she studied the genetic basis of adaptive melanism in pocket mice. In 2003, she became an Assistant Professor at the University of California San Diego. Just recently, she moved to Harvard University, where she is the John L. Loeb Associate Professor of Biology in the Department of Organismic and Evolutionary Biology and the Curator of Mammals at the Museum of Comparative Zoology (Hoekstra home page). Pocket mice are the primary model organism for Hoesktra’s lab. Pocket mice inhabit rocky areas and desert scrub ________________________________________________
Generation of STEP AP214 Models From Discrete Event Systems for Process Planning and Control

The aim of this paper is to show how the international standard STEP-AP214 can be used for communication and storing of process specifications. Even though there are several software tools available for the generation of both product and resource information systems, there is still a lack of tools related to the STEP standard for producing process information, e.g., sequence of operations and system capabilities for resource allocation. Therefore, such a tool is suggested, which makes use of a high-level language for discrete-event systems based on process algebra and Petri nets. This language, called process algebra Petri net), has been developed in accordance with the process relations defined in STEP-AP214. More specifically, it is shown how process specifications created with the PPN tool can be mapped to the STEP AP-214 format. Note to Practioners-Rapidly changing market needs is making demands on flexibility and ability to shorten lead times. Standards for exchanging information, as well as formal methods for automatic development of programmable controller code have been important research topics for many years. There are a lot of software tools available for the generation of both product- and resource information, but there is still a lack of tools for producing process information. Moreover, the connection between information exchange standards and such tools is absent, which makes the development of programmable controller code an isolated activity. This activity is often time consuming and performed in an ad hoc manner resulting in unnecessary production delay. The aim of this paper is to show how the international standard STEP-AP214 (a standard for exchange of product-, process-, and resource related information) can be used for communicating and storing process specifications. In order to achieve this, a tool which makes use of a formal high-level language is suggested. This tool can be used for automatic control generation and has been developed in accordance with the process relations defined in STEP-AP214. A further aim is to shown how the mentioned tool can be used to specify complex systems in a compact, yet highly readable manner, which is a crucial incentive for industry to use formal methods. The presented method will guarantee that expected information is delivered quickly and without errors caused by the human factor, something that is very important in our ambition to achieve shortened lead times. The quick information exchange also makes it possible to perform simulation, supervisor synthesis, and verification early in the development phase. This is a first attempt at using a formal language for creating a tool that can automatically generate specifications in accordance with the international STEP-standard.
The Reliability and Concurrent Validity of the Spanish Translation of the Behavior Problem Checklist

The reliability and concurrent validity of the Spanish translation of the Behavior Problem Checklist were studied. Subscale means and SD's, alpha reliabilities, and intercorrelations were obtained for a sample of 86 Cuban American adolescents referred for family therapy because of drug abuse. Relationships between parent ratings on two of the subscales and teacher nominations for aggressive and withdrawn behavior were examined in a sample of 40 Cuban American males attending two secondary schools.
Estimating the Benefits of Early Warning Systems in Reducing Urban Flood Risk to People: A Spatially Explicit Bayesian Model

Flood risk assessment usually focuses on damages to material objects (indirect tangible costs) and downplays the broader socio-economic aspects of flood-prone systems. Such aspects are crucial for an accurate assessment of risk to human receptors and of the benefits of non-structural measures. For example, an early warning system (EWS) that reduces the amount of direct tangible costs only partially could: (i) save lives (direct intangible costs); (ii) help avoid long-lasting trauma (indirect intangible costs); (iii) prevent post-disaster evacuation costs (indirect tangible costs). We present a methodology to assess flood risk to people, which integrates people’s vulnerability and ability to cushion hazards by coping and adapting. The study area covers the lower part of the Sihl valley (Switzerland) including the city of Zurich. Flood risk to people is modelled using a spatially explicit Bayesian network model calibrated on expert opinions (25 experts were involved). Risk to people is assessed in terms of: (1) likelihood of non-fatal physical injury; (2) likelihood of post-traumatic stress disorder; (3) likelihood of death. The model is used to estimate the benefits of improving an existing EWS, taking into account reliability, lead-time and scope. The proposed approach can: (1) improve flood cost estimation by extending its scope beyond direct and tangible damages; (2) complement quantitative and semi-quantitative data with subjective and local knowledge, improving the use of commonly available information; and (3) produce estimates of model uncertainty by providing probability distributions for all its outputs.
Does small-sided games training improve physical fitness and team-sport-specific skills? A systematic review and meta-analysis.

INTRODUCTION This paper aimed to systematically review the training effects of small-sided games (SSG) on physical fitness and specific skills related to team sport according to the level of play and the period of the season. EVIDENCE ACQUISITION The search covered the following electronic databases (PubMed, Google Scholar, and ScienceDirect). The publications' search period ranged from 2000 to 2016. The terms (small-sided game, training, skill-based game, aerobic fitness, sprint, agility, jump and team sports) were used either singularly or combined in a systematic sequence. Appraisal of 16 articles (15 were analyzed) was performed after the application of exclusion criteria and quality assurance processes and the standardized mean effects were measured using random effects. EVIDENCE SYNTHESIS The results revealed that SSG training had a large beneficial effect on maximal oxygen uptake V̇O2max (effect size 1.94; 95% CI: 0.15, 3.74; I2=94%), agility (-1.49; 95% CI: -2.27, -0.71; I2=80%), and repeated sprint ability (-1.19; 95% CI: -2.17, -0.21; I2= 53%). There was a moderate beneficial effect on 10- and 20-m sprint performance (-0.89; 95% CI: -1.7, -0.07; I2=88%), jump height (0.68; 95% CI: 0.03, 1.33; I2= 79%), and intermittent endurance (0.61; 95% CI: 0.17, 1.05; I2= 0%). The results also showed greater positive effects on specific skills (specific endurance and agility tests and techniques) after SSG when compared with generic or agility training. CONCLUSIONS Small-sided games may represent an effective strategy of multicomponent training that can induce greater positive effects on specific skills tasks when compared with interval or agility training and moderate to large improvements in team sport-related physical fitness.
Methoxylated fatty acids reported in Rhizobium isolates arise from chemical alterations of common fatty acids upon acid-catalyzed transesterification procedures

We obtained from a phospholipid extract of wild-type Rhizobium leguminosarum bv. trifolii ANU843 methoxylated fatty acids that had been previously reported as constitutive unusual Rhizobium fatty acids. The use of deuterated reagents and subsequent gas-liquid chromatography-mass spectrometry analyses showed that these methoxylated fatty acid derivatives are the products of chemical alterations of common cyclopropane-containing and unsaturated fatty acids occurring during various acid-catalyzed transesterification treatments aimed at producing the methyl ester derivatives. Similar results were obtained from a phospholipid extract of Escherichia coli K-12. In contrast, these chemical alterations were not induced by an alkaline methanolysis method of transesterification. If an acidic treatment is needed to release the fatty acids from the source molecule, the finding of unusual methoxylated fatty acids should be carefully confirmed with deuterated reagents.
Structural Equation Modeling of Spatial Presence: The Influence of Cognitive Processes and Traits

This article examines the formation process of spatial presence, which is conceived as a two-step process involving the construction of a mental model of the mediated environment, followed by the emergence of spatial presence. During both stages, cognitive processes and user traits are in effect. We present data derived from a pooled set of data of three studies using the same virtual environment. Structural equation modeling is used to confirm the proposed theoretical model. The results show that attention and the trait of visual spatial imagery are positive predictors of the mental model of the mediated environment. In the second step, the formation of spatial presence is governed by involvement, the suspension of disbelief, and the domain-specific interest, together with the mental model.
Critical Paths Selection for Delay Faults

Extended Abstract Right timing of complex digital circuits and systems in nanotechnology need careful design steps and testing. Incorrect timing can be caused during design or manufacturing processes. Incorrect timing is manifested as delay faults. The delay faults in digital circuit testing are more and more important due to huge number of gates and lines integrated on a chip specifically in nanotechnologies. Some test vectors have to be prepared for delay faults testing depending on fault models. Various fault models exist for test vectors generation from which the gate delay fault model, the transition fault model and the path delay fault model are basic models for time specification testing. The paths delay faults are crucial for nanotechnologies based on their tiny geometries in digital integrated circuits. These faults are tested only via selected critical paths in a tested digital circuit because huge number of paths exists in its structure. Nowadays, the critical paths are specified e.g. by static timing analysis (STA), dynamic timing analysis (DTA) and others. During last decade new aspects have been recognized in critical paths selection. Many factors such as multiple input switching, power supply noise, type of propagated signal edge (rising, falling) and others affecting the signal delay propagation and thus they can increase path criticality (Wu et al., 2010). The impact of each parameter to the path delay faults has been solved and published in some papers by (Dobai et al., 2010), (Wu et al., 2008) and (Metzler et al., 2013) but their joint effects should be also investigated. The paper presents a new method and a new formula for evaluation of paths criticality. The method contributes to higher delay fault coverage in digital circuits. Experiments over benchmark circuits have proved effectiveness of the method and its implementation to an automatic system for critical paths selection based on multiple parameters effects. A new general method for critical path selection has been developed and implemented based on influence on multiple parameters, STA, DFT and new defined formula. The main idea is sort a list of critical paths founded by STA using the new defined requirement – path criticality for increasing path delay fault coverage. Path criticality cp based on multiple parameters is expressed by formula: