Miracle-dz/UniFAR-FTUs huggingface dataset:
Bayesian inference for the uncertainty distribution of computer model outputs

We consider a problem of inference for the output of a computationally expensive computer model. We suppose that the model is to be used in a context where the values of one or more inputs are uncertain, so that the input configuration is a random variable. We require to make inference about the induced distribution of the output. This distribution is called the uncertainty distribution, and the general problem is known to users of computer models as uncertainty analysis. To be specific, we develop Bayesian inference for the distribution and density functions of the model output. Modelling the output, as a function of its inputs, as a Gaussian process, we derive expressions for the posterior mean and variance of the distribution and density functions, based on data comprising observed outputs at a sample of input configurations. We show that direct computation of these expressions may encounter numerical difficulties. We develop an alternative approach based on simulating approximate realisations from the posterior distribution of the output function. Two examples are given to illustrate our methods. Copyright Biometrika Trust 2002, Oxford University Press.
Halftone Feature Based Classification of Commercial White Print Paper Using BP-MLP

The paper presents a machine vision approach for classification of the plain surface commercially available printing paper. In the presented method the halftone features are extracted from the images of plain surface papers that are difficult to distinguish due to flat white appearance. The extracted features have been used to train the back-propagation multi-layer perception (BP-MLP) classifier of artificial neural network (ANN). The presented method has been tested with different commercially available A4 size printing paper and found to be promising in terms of classification performance. The paper also reveals that half toning which is conventionally used for display of continuous tone images may be potentially useful for classification tasks, particularly for materials with flat surfaces.
Toward Patient-Centered Care: A Systematic Review of How to Ask Questions That Matter to Patients

AbstractClinicians rarely systematically document how their patients are feeling. Single item questions have been created to help obtain and monitor patient relevant outcomes, a requirement of patient-centered care.The objective of this review was to identify the psychometric properties for single items related to health aspects that only the patient can report (health perception, stress, pain, fatigue, depression, anxiety, and sleep quality). A secondary objective was to create a bank of valid single items in a format suitable for use in clinical practice.Data sources used were Ovid MEDLINE (1948 to May 2013), EMBASE (1960 to May 2013), and the Cumulative Index to Nursing and Allied Health Literature (1960 to May 2013). For the study appraisal, 24 articles were systematically reviewed. A critical appraisal tool was used to determine the quality of articles.Items were included if they were tested as single items, related to the construct, measured symptom severity, and referred to recent experiences.The psychometric properties of each item were extracted. Validity and reliability was observed for the items when compared with clinical interviews or well-validated measures. The items for general health perception and anxiety showed weak to moderate strength correlations (r = 0.28–0.70). The depression and stress items showed good area under the receiver operating characteristic curve of 0.85 and 0.73–0.88, respectively, with high sensitivity and specificity. The fatigue item demonstrated a strong effect size and correlations up to r = 0.80. The 2 pain items and the sleep item showed high reliability (intraclass correlation coefficient [ICC] = 0.85, &kgr; = 0.76, ICC = 0.9, respectively). The search targeted articles about psychometric properties of single items. Articles that did not have this as the primary objective may have been missed. Furthermore, not all the articles included had the complete set of psychometric properties for each item.There is sufficient evidence to warrant the use of single items in clinical practice. They are simple, easily implemented, and efficient and thus provide an alternative to multi-item questionnaires. To facilitate their use, the top performing items were combined into the visual analog health states, which provides a quick profile of how the patient is feeling. This information would be useful for regular long-term monitoring.
Mobility and Human Development

This paper argues that mobility and migration have always been an intrinsic part of human development. Migration can be considered as a fundamental capabilities-enhancing freedom itself. However, any meaningful understanding of migration needs to simultaneously analyse agency and structure. Rather than applying dichotomous classifications such as between forced and voluntary migration, it is more appropriate to conceive of a continuum running from low to high constraints under which migration occurs, in which all migrants deal with structural constraints, although to highly varying degrees. Besides being an integral part of human development, mobility also tends to affect the same structural processes of which it is part. Simplistic positive-versus-negative debates on migration and development can be overcome by integrating agency-structure dialectics in the analysis of migration impacts. This paper argues that (i) the degree to which migrants are able to affect structural change is real but limited; (ii) the nature of change in sending and receiving is not pre-determined; and (iii) that in order to enable a more focused and rigorous debate, there is a need to better distinguish and specify different levels and dimensions at which the reciprocal relationship between human mobility and development can be analysed. A critical reading of the empirical literature leads to the conclusion that it would be naive to think that despite their often considerable benefits for individuals and communities, migration and remittances alone can remove more structural development constraints. Despite their development potential, migrants and remittances can neither be blamed for a lack of development nor be expected to trigger take-off development in generally unattractive investment environments. By increasing selectivity and suffering among migrants, current immigration restrictions have a negative impact on migrants’ wellbeing as well as the poverty and inequality reducing potential of migration.
Soil disturbance by cut-to-length machinery on mid-grained soils

Factors affecting soil disturbance caused by harvester and forwarder were studied on mid-grained soils in Finland. Sample plots were harvested using a one-grip harvester. The harvester operator processed the trees outside the strip roads, and the remaining residues were removed to exclude the covering effect of residues. Thereafter, a loaded forwarder made up to 5 passes over the sample plots. The average rut depth after four machine passes was positively correlated to the volumetric water content at a depth of 0â10 cm in mineral soil, as well as the thickness of the organic layer and the harvester rut depth, and negatively correlated with penetration resistance at depths of both 0â20 cm and 5â40 cm. We present 5 models to predict forwarder rut depth. Four include the cumulative mass driven over a measurement point and combinations of penetration resistance, water content and the depth of organic layer. The fifth model includes harvester rut depth and the cumulative overpassed mass and provided the best fit. Changes in the penetration resistance (PR) were highest at depths of 20â40 cm. Increase in BD and VWC decreased PR, which increased with total overdriven mass. After four to five machine passes PR values started to stabilize.
Developmental Progression in the Coral Acropora digitifera Is Controlled by Differential Expression of Distinct Regulatory Gene Networks

Corals belong to the most basal class of the Phylum Cnidaria, which is considered the sister group of bilaterian animals, and thus have become an emerging model to study the evolution of developmental mechanisms. Although cell renewal, differentiation, and maintenance of pluripotency are cellular events shared by multicellular animals, the cellular basis of these fundamental biological processes are still poorly understood. To understand how changes in gene expression regulate morphogenetic transitions at the base of the eumetazoa, we performed quantitative RNA-seq analysis during Acropora digitifera’s development. We collected embryonic, larval, and adult samples to characterize stage-specific transcription profiles, as well as broad expression patterns. Transcription profiles reconstructed development revealing two main expression clusters. The first cluster grouped blastula and gastrula and the second grouped subsequent developmental time points. Consistently, we observed clear differences in gene expression between early and late developmental transitions, with higher numbers of differentially expressed genes and fold changes around gastrulation. Furthermore, we identified three coexpression clusters that represented discrete gene expression patterns. During early transitions, transcriptional networks seemed to regulate cellular fate and morphogenesis of the larval body. In late transitions, these networks seemed to play important roles preparing planulae for switch in lifestyle and regulation of adult processes. Although developmental progression in A. digitifera is regulated to some extent by differential coexpression of well-defined gene networks, stage-specific transcription profiles appear to be independent entities. While negative regulation of transcription is predominant in early development, cell differentiation was upregulated in larval and adult stages.
Porphyromonas gingivalis and Treponema denticola Exhibit Metabolic Symbioses

Porphyromonas gingivalis and Treponema denticola are strongly associated with chronic periodontitis. These bacteria have been co-localized in subgingival plaque and demonstrated to exhibit symbiosis in growth in vitro and synergistic virulence upon co-infection in animal models of disease. Here we show that during continuous co-culture a P. gingivalis:T. denticola cell ratio of 6∶1 was maintained with a respective increase of 54% and 30% in cell numbers when compared with mono-culture. Co-culture caused significant changes in global gene expression in both species with altered expression of 184 T. denticola and 134 P. gingivalis genes. P. gingivalis genes encoding a predicted thiamine biosynthesis pathway were up-regulated whilst genes involved in fatty acid biosynthesis were down-regulated. T. denticola genes encoding virulence factors including dentilisin and glycine catabolic pathways were significantly up-regulated during co-culture. Metabolic labeling using 13C-glycine showed that T. denticola rapidly metabolized this amino acid resulting in the production of acetate and lactate. P. gingivalis may be an important source of free glycine for T. denticola as mono-cultures of P. gingivalis and T. denticola were found to produce and consume free glycine, respectively; free glycine production by P. gingivalis was stimulated by T. denticola conditioned medium and glycine supplementation of T. denticola medium increased final cell density 1.7-fold. Collectively these data show P. gingivalis and T. denticola respond metabolically to the presence of each other with T. denticola displaying responses that help explain enhanced virulence of co-infections.
Connecting the Smudges : How Analytic Info-Murals May Be of Help in Dealing With Social Messes

New visualization methods can help deal with social messes (also known as " ill-structured " or " wicked " problems). Social messes are more than complicated problems. They are very complex and ambiguous. They require visualization techniques that, we might say, are composed of smudges. Our project at Stanford University been developing new forms of " information murals " to help task forces address such smudgy social messes. Some of the problems addressed are: severe limitations of ordinary prose documents to communicate complex subject matter; the necessity to help groups create common mental models; and the need to show context and multiple views for strategy discussions and decisions. These info-murals provide the scaffolding for thinking bigger thoughts. They facilitate seeing the big picture as well as needed detail. They reveal new and novel patterns. They sometimes even enable us to connect the smudges. Our visualization research addresses such challenges as how to: show large processes or larger contexts that form the background of public policy issues; represent serious and complex debates; portray different cultures; represent multiple strategies; understand ideologies; get a more comprehensive picture of unknowns; represent mindsets and worldviews, including one's own. Examples of progress on developing different visualization scaffoldings will be presented and discussed. We all live in the midst of social messes – also known as " ill-structured " or " wicked " problems. Russell Ackoff defines messes as follows: " We have also come to realize that no problem ever exists in complete isolation. Every problem interacts with other problems and is therefore part of a set of interrelated problems, a system of problems. For example, the race problem, the poverty problem, the urban problem, and the crime problem, to mention but a few, are clearly interrelated. Furthermore, solutions to most problems produce other problems; for example, buying a car may solve a transportation problem but it may also create a need for a garage, a financial problem, a maintenance problem, and conflict among family members for its use. English does not contain a suitable word for " system of problems. " Therefore, I have had to coin one. I choose to call such a system a mess. " (Ackoff 1974) Social messes are far more than complicated problems. They are very complex; ambiguous; highly constrained; tightly interconnected, economically, socially, and politically ; seen differently from different points of views and worldviews; and contain many value …
Acoustic data transmission by extension on the time domain approach

The main goal of acoustic data transmission is to deliver data by overcoming acoustic channel distortion. This paper presents a data transmission method that modifies the amplitude of the time domain audio signal imperceptibly. The main advantage of the proposed method is that the synchronization process can be conducted simultaneously while data is being extracted at the receiver side. The evaluation results show that the proposed method successfully overcomes indoor acoustic channel distortion and delivers data.
Prevalence and Genotypic Characterization of Extended-Spectrum Beta-Lactamases Produced by Gram Negative Bacilli at a Tertiary Care Hospital in Rural South Western Uganda

Aim To determine the prevalence and genotypic characterisation of extended spectrum beta-lactamases produced by gram negative bacilli isolated at Mbarara Regional Referral Hospital (MRRH). Samples Gram negative clinical isolates. Study Design Laboratory-based descriptive cross-sectional study. Place and Duration of the Study MRRH, June and August 2012. Methods Gram negative clinical isolates were sub cultured, and identified using biochemical tests. They were screened for ESBL by using oxyimino-cephalosporins and confirmed by double disc synergy Genotyping was performed using the PCR for TEM, SHV and CTX-M. Susceptibility pattern for the extended spectrum beta-lactamases, (ESBL) - positive isolates to other antibiotic classes was performed by the Kirby Bauer Technique. Results A total of 484 isolates were included in the study. The commonest ESBL producers were Escherichia coli (34%), followed by unidentified coliforms (19.3%) and Klebsiella spp. (12.7%). Phenotypically, 88/484 were ESBL producers while genotypically 213/ 484 possessed ESBL genes. The ESBL genes were blaCTX-M (146; 70%), blaSHV (72; 34%) and blaTEM (100; 47%). 87of 213 isolates expressed more than one ESBL gene. Of these 36 (7.4%) produced blaCTX-M/blaSHV, 28 (5.8%) blaCTX-M /blaTEM, 4 (0.8%) blaSHV/ blaTEM and 19 (3.9%) blaCTX-M/blaSHV/blaTEM. Sixty two (16%) were phenotypically and genotypically positive, 12 (3%) of the isolates were phenotypically positive but genotypically negative and 140 (37%) isolates were phenotypically negative but genotypically positive. The ESBL producers were highly susceptible to imipenem (95%), nitrofurantoin (66%) but less susceptible to ampicillin (4%) and ticarcillin (7%). Conclusion ESBL production among the Gram-negative clinical isolates at MRRH is very high with several isolates possessing multiple genes. The ESBL producers are highly susceptible to imipenem, but very resistant to ciprofloxacin.
Functional Dissection of Trigger Factor and DnaK: Interactions with Nascent Polypeptides and Thermally Denatured Proteins

Abstract In Escherichia coli, the ribosomeassociated Trigger Factor (TF) cooperates with the DnaK system in the folding of newly synthesized cytosolic polypeptides. Here we investigated the functional relationship of TF and DnaK by comparing various functional properties of both chaperones. First, we analyzed the ability of TF and DnaK to associate with nascent polypeptides and fulllength proteins released from the ribosome. Toward this end, we established an E. coli based transcription/translation system containing physiological ratios of TF, DnaK and ribosomes. In this system, TF can be crosslinked to nascent polypeptides of σ32. No TF crosslink was found to fulllength σ32, which is known to be a DnaK substrate. In contrast, DnaK crosslinked to both nascent and fulllength σ32. DnaK crosslinks critically depended on the type of chemical crosslinker. Crosslinks represent specific substratechaperone interactions since they relied on the association of the nascent polypeptides with the substrate binding pocket of DnaK. While DnaK is known to be the major chaperone to prevent protein aggregation under heat shock conditions, we found that TF did not prevent aggregation of thermally unfolded proteins in vitro and was not able to complement the heatsensitive phenotype of a δnaK52 mutant in vivo. These data indicate that TF and DnaK show strong differences in their ability to prevent aggregation of denatured proteins and to associate with native like substrates, but share the ability to associate with nascent polypeptides.
Recent Advances in T Cell Signaling in Aging

The immune system of mammalian organisms undergoes alterations that may account for an increased susceptibility to certain infections, autoimmune diseases, or malignancies. Well characterized are age-related defect in T cell functions and cell-mediated immunity. Although it is well established that the functional properties of T cells decrease with age, its biochemical and molecular nature is poorly understood. The available data suggest that changes in the signal transduction machinery are responsible for the impairment of T cell function during aging. T cell activation is initiated when an antigenic peptide is recognized by the antigen receptor of T cells. This recognition event promotes sequential activation of a network of signaling molecules such as phospholipases, kinases, phosphatases, and adaptor proteins that couple the stimulatory signal received from T cell receptor (TCR) to intracellular signaling pathways. The coordinate activation of these signaling molecules is sufficient to stimulate the activation of transcription factors and the expression of the immediate-early genes that are crucial in regulation of T cell function. Iran. Biomed. J. 3 (1 & 2): 1-13 1999
Job engagement in higher education

Employees’ job engagement is a key driver for organizational success and competitive advantage. Based on Kahn’s engagement theory and social exchange theory, the purpose of this paper is to examine the relationships between job engagement, transformational leadership, high-performance human resource (HR) practices, climate for innovation, and contextual performance. ,A questionnaire survey, conducted at two different points in time, was employed to collect data from 394 pairs of Vietnamese university academics and their leaders. Data were analyzed by structural equation modeling (SEM) and multilevel SEM using the Statistical Package for Social Science Version 24 and Mplus Version 7.4. ,The findings indicated that transformational leadership and high-performance HR practices were key drivers of employees’ job engagement. A climate for innovation contributed effectively to mediate the effect of transformational leadership on employees’ job engagement. Further, employees’ job engagement was positively and significantly related to contextual performance. ,The short time lag between the two data collection phases might limit the ability to reach definite causal conclusions. Future research using a longitudinal design is needed to provide stronger validation for the underlying model. ,This study is a rare attempt that investigates the process from which employees’ job engagement is generated and contributes to improve contextual performance in the higher education sector.
Poultry rearing and slaughtering practices in rural Egypt: an exploration of risk factors for H5N1 virus human transmission

Please cite this paper as: Lohiniva et al. (2012) Poultry rearing and slaughtering practices in rural Egypt: an exploration of risk factors for H5N1 virus human transmission. Influenza and Other Respiratory Viruses DOI: 10.1111/irv.12023.
Food Restriction Enhances the Central Rewarding Effect of Abused Drugs

Chronic food restriction increases the systemic self-administration and locomotor-stimulating effect of abused drugs. However, it is not clear whether these behavioral changes reflect enhanced rewarding potency or a CNS-based modulatory process. The purpose of this study was to determine whether food restriction specifically increases the rewarding potency of drugs, as indexed by their threshold-lowering effect on lateral hypothalamic self-stimulation, and whether any such effect can be attributed to an enhanced central response rather than changes in drug disposition. When drugs were administered systemically, food restriction potentiated the threshold-lowering effect of amphetamine (0.125, 0.25, and 0.5 mg/kg, i.p.), phencyclidine (1.0, 2.0, and 3.0 mg/kg, i.p.), and dizocilpine (MK-801) (0.0125, 0.05, and 0.1 mg/kg, i.p.) but not nicotine (0.15, 0.3, 0.45 mg/kg, s.c.). When amphetamine (25.0, 50.0, and 100.0 μg) and MK-801 (5.0, 10.0, and 20.0 μg) were administered via the intracerebroventricular route, food restriction again potentiated the threshold-lowering effects and increased the locomotor-stimulating effects of both drugs. These results indicate that food restriction increases the sensitivity of neural substrates for rewarding and stimulant effects of drugs. In light of work that attributes rewarding effects of MK-801 to blockade of NMDA receptors on medium spiny neurons in nucleus accumbens, the elements affected by food restriction may lie downstream from the mesoaccumbens dopamine neurons whose terminals are the site of amphetamine-rewarding action. Possible metabolic–endocrine triggers of this effect are discussed, as is the likelihood that mechanisms mediating the modulatory effect of food restriction differ from those mediating sensitization by intermittent drug exposure.