Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Mycoplasma hyopneumoniae in Bronchoalveolar Lavage Fluids of Pigs by PCR

ABSTRACT In the present investigation we developed a method for the detection of Mycoplasma hyopneumoniae in bronchoalveolar lavage fluid (BALF) of pigs by PCR with a primer pair flanking a DNA fragment of 853 bp specific for M. hyopneumoniae. Several methods were tested to eliminate the amplification inhibitors present in BALFs. The best results were obtained by the extraction of the DNA from the BALFs. By the PCR performed with the extracted DNA, 102 CFU of M. hyopneumoniae could be detected in 1 ml of BALF from specific-pathogen-free swine experimentally inoculated with M. hyopneumoniae. DNA from 11 other mycoplasma species and 17 cell-walled bacterial species colonizing the respiratory tracts of pigs was not amplified. In a field study BALFs from 40 pigs from farms with a history of chronic pneumonia were tested for M. hyopneumoniae by cultivation and by PCR (i) with BALFs incubated in Friis medium and (ii) with DNA extracted from the BALFs. In addition, PCR was performed with postmortem lung washings from 19 of the 40 pigs, and immunofluorescence tests were carried out with sections of lungs from 18 of the 40 pigs.M. hyopneumoniae could not be detected in 18 of the 40 pigs by any of the five methods tested. The remaining 22 pigs showed a positive reaction by the PCR with DNA extracted from the BALFs and variable positive reactions by the other tests. A complete correspondence could be observed between the immunofluorescence test result and the result of PCR with DNA. The investigation shows that the PCR with DNA extracted from BALFs is a suitable technique for the sensitive and specific in vivo detection of M. hyopneumoniae.
On the Regularity of Approximate Solutions to Conservation Laws with Piecewise Smooth Solutions

In this paper we address the questions of the convergence rate for approximate solutions to conservation laws with piecewise smooth solutions in a weighted W1,1 space. Convergence rate for the derivative of the approximate solutions is established under the assumption that a weak pointwise-error estimate is given. In other words, we are able to convert weak pointwise-error estimates to optimal error bounds in a weighted W1,1 space. For convex conservation laws, the assumption of a weak pointwise-error estimate is verified by Tadmor [ SIAM J. Numer. Anal. , 28 (1991), pp. 891--906]. Therefore, one immediate application of our W1,1- convergence theory is that for convex conservation laws we indeed have W1,1-error bounds for the approximate solutions to conservation laws. Furthermore, the $\cO(\en)$-pointwise-error estimates of Tadmor and Tang [ SIAM J. Numer. Anal. , 36 (1999), pp. 1739--1758] are recovered by the use of the W1,1-convergence result.
iMAP: discovering complex semantic matches between database schemas

Creating semantic matches between disparate data sources is fundamental to numerous data sharing efforts. Manually creating matches is extremely tedious and error-prone. Hence many recent works have focused on automating the matching process. To date, however, virtually all of these works deal only with one-to-one (1-1) matches, such as address = location. They do not consider the important class of more complex matches, such as address = concat (city, state) and room-pric = room-rate* (1 + tax-rate). We describe the iMAP system which semi-automatically discovers both 1-1 and complex matches. iMAP reformulates schema matching as a search in an often very large or infinite match space. To search effectively, it employs a set of searchers, each discovering specific types of complex matches. To further improve matching accuracy, iMAP exploits a variety of domain knowledge, including past complex matches, domain integrity constraints, and overlap data. Finally, iMAP introduces a novel feature that generates explanation of predicted matches, to provide insights into the matching process and suggest actions to converge on correct matches quickly. We apply iMAP to several real-world domains to match relational tables, and show that it discovers both 1-1 and complex matches with high accuracy.
Characterization of a spotted fever group Rickettsia from Ixodes ricinus ticks in Sweden

A spotted fever group rickettsia isolated from the common tick, Ixodes ricinus, was genetically characterized by PCR and genomic sequencing. This study was performed with nymphal and adult ticks collected in southern and central Sweden. I. ricinus is the only North European tick species of medical importance which is regularly collected from humans. No species of the genus Rickettsia has previously been found in Scandinavian ticks, nor has any case of domestic rickettsial infection in humans or animals been reported. According to the nucleotide sequencing, the present Rickettsia sp. belongs to the spotted fever group of rickettsiae. Ticks are the most common arthropod reservoirs and vectors of the rickettsiae of this group. Among 748 ticks investigated, 13 (1.7%) were positive for a Rickettsia sp. Borrelia burgdorferi was detected in 52 (7%) of the ticks, a prevalence similar to or somewhat lower than that previously been recorded in other Swedish studies. There was no evidence of ehrlichial or chlamydial DNA in these ticks. The Rickettsia sp. was further characterized by 16S ribosomal DNA (rDNA) sequencing and restriction fragment length polymorphism (RFLP). The 16S rDNA sequencing resulted in a sequence identical to that described for Rickettsia helvetica, but the pattern obtained with RFLP of the citrate synthetase gene diverged from previously known patterns. The rickettsial agent of one tick which was positive by PCR was confirmed by transmission electron microscopy. The morphology of this rickettsia was similar to that of the spotted fever and typhus group rickettsiae. This represents the first documented isolate of a Rickettsia sp. from Swedish ticks.
The Green Potential of RFID Projects: A Case-Based Analysis

RFID has been a popular technology in the areas of supply-chain management, asset tracking, and manufacturing. In general, research related to RFID's potential contributions fall under technological, applications-related, or policy and security issues. However, there's little discussion in the extant literature on the environmentally responsible management of RFID. Traditionally, information and communications technologies (ICT) have been viewed as having a negative impact on the environment, and RFID, as part of ICT, has earned a similar reputation. RFID is also one of the main technologies of pervasive computing, which consumes enough energy to negatively impact the environment. Furthermore, some experience has suggested that we need to take precautionary measures to prevent the likely negative results from the final disposal of RFID labels. Currently, RFID tags are neither biodegradable nor recyclable. Nonetheless, RFID could indeed be a part of green IT, not only by adding economic value to organizations but also by improving environmentally responsible practices related to IT-for example, by accurately tracking a perishable item and preventing its spoilage, RFID can save energy in operations ranging from growing and harvesting to packaging and refrigeration. To explore RFID's potential in green IT, we reviewed 13 case studies, evaluating RFID's contribution to green objectives.
Automatic Interpretation and Coding of Face Images Using Flexible Models

Face images are difficult to interpret because they are highly variable. Sources of variability include individual appearance, 3D pose, facial expression, and lighting. We describe a compact parametrized model of facial appearance which takes into account all these sources of variability. The model represents both shape and gray-level appearance, and is created by performing a statistical analysis over a training set of face images. A robust multiresolution search algorithm is used to fit the model to faces in new images. This allows the main facial features to be located, and a set of shape, and gray-level appearance parameters to be recovered. A good approximation to a given face can be reconstructed using less than 100 of these parameters. This representation can be used for tasks such as image coding, person identification, 3D pose recovery, gender recognition, and expression recognition. Experimental results are presented for a database of 690 face images obtained under widely varying conditions of 3D pose, lighting, and facial expression. The system performs well on all the tasks listed above.
Functional Analysis of a 450–Amino Acid N-Terminal Fragment of Phytochrome B in Arabidopsis

Phytochrome, a major photoreceptor in plants, consists of two domains: the N-terminal photosensory domain and the C-terminal domain. Recently, the 651–amino acid photosensory domain of phytochrome B (phyB) has been shown to act as a functional photoreceptor in the nucleus. The phytochrome (PHY) domain, which is located at the C-terminal end of the photosensory domain, is required for the spectral integrity of phytochrome; however, little is known about the signal transduction activity of this domain. Here, we have established transgenic Arabidopsis thaliana lines expressing an N-terminal 450–amino acid fragment of phyB (N450) lacking the PHY domain on a phyB-deficient background. Analysis of these plants revealed that N450 can act as an active photoreceptor when attached to a short nuclear localization signal and β-glucuronidase. In vitro spectral analysis of reconstituted chromopeptides further indicated that the stability of the N450 Pfr form, an active form of phytochrome, is markedly reduced in comparison with the Pfr form of full-length phyB. Consistent with this, plants expressing N450 failed to respond to intermittent light applied at long intervals, indicating that N450 Pfr is short-lived in vivo. Taken together, our findings show that the PHY domain is dispensable for phyB signal transduction but is required for stabilizing the Pfr form of phyB.
Swash Zone Morphodynamics on a Steep, High Energy Beach

Abstract : LONG-TERM GOALS. The long-term goal of this program is to understand the processes that determine the erosion/accretion rates and patterns on a steep, porous beach face for a wide range of incident wave conditions. OBJECTIVES. The objective of this project is to relate incident wave conditions and the resulting foreshore morphology response at Waimea Bay, a steep pocket beach on the north shore of Oahu, Hawaii. The run-up variability, characterized using Argus video imagery, will be compared to offshore and breaking wave heights. The resulting picture of incident wave forcing will be related to three-dimensional morphology changes determined using high resolution RTK-GPS (Real-Time Kinematic GPS) surveys. The results from this high energy, reflective beach will then be compared with observations from more dissipative beaches. We seek to determine whether characteristic beach parameters are useful for categorizing and understanding swash zone morphodynamics for high energy environments.
THE STRENGTH OF WEAK TIES YOU CAN TRUST : THE MEDIATING ROLE OF TRUST IN EFFECTIVE KNOWLEDGE TRANSFER

Recent research suggests that people obtain useful knowledge from others with whom they work closely and frequently (i.e., strong ties). Yet there has been limited empirical work examining why this is so. Moreover, other research suggests that weak ties provide useful knowledge. To help integrate these multiple findings, we propose and test a model of two-party (dyadic) knowledge exchange, with strong support in each of the three companies surveyed. First, the link between strong ties and receipt of useful knowledge (as reported by the knowledge seeker) was mediated by competenceand benevolence-based trust. Second, once we controlled for these two trust dimensions, the structural benefit of weak ties became visible. This latter finding is consistent with prior research suggesting that weak ties provide access to non-redundant information. Third, we found that competence-based trust was especially important for the receipt of tacit knowledge. We discuss implications for theory and practice.
Malate Dehydrogenase and NAD Malic Enzyme in the Oxidation of Malate by Sweet Potato Mitochondria.

Over a range of concentrations from less than 0.1 mm to more than 70 mm, sweet potato root mitochondria display a bimodal substrate saturation isotherm for malate. The high affinity portion of the isotherm has an apparent Km for malate of 0.85 mm and fits a rectangular hyperbolic function. The low affinity portion of the isotherm is sigmoid in character and gives an apparent S(0.5) of 40.6 mm and a Hill number of 3.7. Extracts of sweet potato mitochondria contain both malate dehydrogenase and NAD malic enzyme. The malate dehydrogenase, assayed in the forward direction at pH 7.2, shows typical Michaelis-Menten kinetics with a Km for malate of 0.38 mm. The NAD malic enzyme shows pronounced sigmoidicity in response to malate with a Hill number of 3.5 and an S(0.5) of 41.6 mm.On the basis of the normal kinetics, the Km, and the fact that oxaloacetate production from malate by mitochondria appears most active at low malate concentrations, the high affinity portion of the malate isotherm with mitochondria is attributed to malate dehydrogenase. The low affinity portion of the malate isotherm with mitochondria is thought, on the basis of the similarity of S(0.5) values, the Hill numbers, and the greater production of pyruvate from malate at high malate concentrations, to represent the activity of the NAD malic enzyme.
Quadratic Program-Based Modularity Maximization for Fuzzy Community Detection in Social Networks

One of the most important elements of social network analysis is community detection, i.e., finding groups of similar people based on their traits. In this paper, we present the fuzzy modularity maximization (FMM) approach for community detection, which finds overlapping - that is, fuzzy - communities (where appropriate) by maximizing a generalized form of Newman's modularity. The first proposed FMM solution uses a tree-based structure to find a globally optimal solution, while the second proposed solution uses alternating optimization to efficiently search for a locally optimal solution. Both of these approaches are based on a proposed algorithm called one-step modularity maximization (OSMM), which computes the optimal cluster memberships for one person in the social network. We prove that OSMM can be formulated as a simplified quadratic knapsack optimization problem, which is O(n) time complexity. We then propose a tree-based algorithm, called FMM/Find Best Leaf Node (FMM/FBLN), which represents sequences of OSMM steps in a tree-based structure. It is proved that FMM/FBLN finds globally optimal solutions for FMM; however, the time complexity of FMM/FBLN is O(nd), d ≥ 2; thus, it is impractical for most real-world networks. To combat this inefficiency, we propose five heuristic-based alternating optimization schemes, i.e., FMM/H1-H5, which are all shown to be O(n2) time complexity. We compare the results of the FMM/H solutions with those of state-of-the-art community detection algorithms, MULTICUT spectral FCM (MSFCM) and GALS, and with those of two fuzzy community detection algorithms called GA and vertex-similarity based gradient-descent method (VSGD) on ten real-world datasets. We conclude that one of the five heuristic algorithms (FMM/H2) is very competitive with GALS and much more effective than MSFCM, GA, and VSGD. Furthermore, all of the FMM/H schemes are at least two orders of magnitude faster than GALS in run time. Finally, FMM/H, unlike GALS (which only produces crisp partitions) and MSFCM (which always finds fuzzy partitions), is the only fuzzy community detection algorithm to date that can find the max-modularity partition, fuzzy or crisp.
A Survey of Accuracy Evaluation Metrics of Recommendation Tasks

Recommender systems are now popular both commercially and in the research community, where many algorithms have been suggested for providing recommendations. These algorithms typically perform differently in various domains and tasks. Therefore, it is important from the research perspective, as well as from a practical view, to be able to decide on an algorithm that matches the domain and the task of interest. The standard way to make such decisions is by comparing a number of algorithms offline using some evaluation metric. Indeed, many evaluation metrics have been suggested for comparing recommendation algorithms. The decision on the proper evaluation metric is often critical, as each metric may favor a different algorithm. In this paper we review the proper construction of offline experiments for deciding on the most appropriate algorithm. We discuss three important tasks of recommender systems, and classify a set of appropriate well known evaluation metrics for each task. We demonstrate how using an improper evaluation metric can lead to the selection of an improper algorithm for the task of interest. We also discuss other important considerations when designing offline experiments.
Differences in the Time or Frequency of Meals, Alcohol and Caffeine Ingestion, and Smoking Found between ‘Morning’ and ‘Evening’ Types

The present study investigated some differences between ‘morning’ and ‘evening’ types in life habits, particularly concerning meals, ingestion of caffeine and alcohol, and smoking. The Life Habits Inventory and the Japanese version of Home and Östberg Morningness-Eveningness Questionnaire were administered to approximately 1500 students, and data on life habits of the morning types were compared with those of the evening types. Significant differences between these types were found in frequency of night meals, smoking, and ingestion of caffeine and alcohol. Although significant differences were not found for mealtimes, 34.8% of the evening types typically did not eat breakfast. These differences were discussed from viewpoint of chronopharmacology and personality.
Beyond Mouse and Keyboard: Expanding Design Considerations for Information Visualization Interactions

The importance of interaction to Information Visualization (InfoVis) and, in particular, of the interplay between interactivity and cognition is widely recognized [12, 15, 32, 55, 70]. This interplay, combined with the demands from increasingly large and complex datasets, is driving the increased significance of interaction in InfoVis. In parallel, there have been rapid advances in many facets of interaction technologies. However, InfoVis interactions have yet to take full advantage of these new possibilities in interaction technologies, as they largely still employ the traditional desktop, mouse, and keyboard setup of WIMP (Windows, Icons, Menus, and a Pointer) interfaces. In this paper, we reflect more broadly about the role of more “natural” interactions for InfoVis and provide opportunities for future research. We discuss and relate general HCI interaction models to existing InfoVis interaction classifications by looking at interactions from a novel angle, taking into account the entire spectrum of interactions. Our discussion of InfoVis-specific interaction design considerations helps us identify a series of underexplored attributes of interaction that can lead to new, more “natural,” interaction techniques for InfoVis.
Occupation as marker of self: Occupation in relation to self among people with advanced cancer

Abstract Background: Living with advanced cancer can have a profound impact on the person’s self. A person’s self is influenced by various aspects of daily life, including engagement in occupation. From an occupational perspective, little research has been done to explore how the self of people with advanced cancer is formed through their engagement in occupation. Aim: The purpose of this study was to explore how people with advanced cancer experience that their sense of self is formed through engagement in occupation. Methods: A total of 28 interviews were conducted with 22 people with advanced cancer. Grounded theory guided the collection and analysis of data. Results: ‘Occupation as marker of self’ was identified as the core category. Occupations served as markers of the participants’ self (1) by mirroring their abilities and positioning of their self in the illness trajectory; and (2) as means of expressing their self. The core category provided explanations about how the participants’ experiences of occupation influenced their self-perceptions, as explained in the sub-categories ‘defining the self through occupation’ and ‘reassessing self and accepting limitations’. Conclusions: For people with advanced cancer, engagement in occupation influences their self as current abilities become apparent and positions of their self can be created and expressed.
Prognostic significance of hypoxia inducible factor-1α and vascular endothelial growth factor expression in patients with diffuse large B-cell lymphoma treated with rituximab

Abstract We evaluated hypoxia inducible factor-1α (HIF-1α) and vascular endothelial growth factor (VEGF) expression and their prognostic significance in diffuse large B-cell lymphoma (DLBCL). Expression of HIF-1α and VEGF was studied in 78 patients and results correlated with clinicopathological and prognostic data. HIF-1α and VEGF were expressed in 67% and 84% of patients, respectively, and a significant correlation was demonstrated between them (p < 0.001). Outcome was analyzed according to treatment. HIF-1α positive patients given rituximab demonstrated improved outcome, with 5-year overall survival of 72% for those receiving rituximab versus 65% for those not receiving rituximab, and 5-year progression-free survival (PFS) 76% versus 57%. No correlation was demonstrated between HIF-1α and other prognostic biomarkers including BCL6, CD10 and MUM-1. We demonstrated significantly improved PFS (p = 0.003) in patients receiving rituximab and showing BCL6 overexpression. The results confirm the significant association between HIF-1α and VEGF expression and suggest that HIF-1α expression is a favorable prognostic factor in patients with DLBCL treated with rituximab.
A concomitant loss of dormant origins and FANCC exacerbates genome instability by impairing DNA replication fork progression

Abstract Accumulating evidence suggests that dormant DNA replication origins play an important role in the recovery of stalled forks. However, their functional interactions with other fork recovery mechanisms have not been tested. We previously reported intrinsic activation of the Fanconi anemia (FA) pathway in a tumor-prone mouse model (Mcm4chaos3) with a 60% loss of dormant origins. To understand this further, we introduced a null allele of Fancc (Fancc−), encoding a member of the FA core complex, into the Mcm4chaos3 background. Primary embryonic fibroblasts double homozygous for Mcm4chaos3 and Fancc− (Mcm4chaos3/chaos3;Fancc−/−) showed significantly increased levels of markers of stalled/collapsed forks compared to either single homozygote. Interestingly, a loss of dormant origins also increased the number of sites in which replication was delayed until prophase, regardless of FA pathway activation. These replication defects coincided with substantially elevated levels of genome instability in Mcm4chaos3/chaos3;Fancc−/− cells, resulting in a high rate of perinatal lethality of Mcm4chaos3/chaos3;Fancc−/− mice and the accelerated tumorigenesis of surviving mice. Together, these findings uncover a specialized role of dormant origins in replication completion while also identifying important functional overlaps between dormant origins and the FA pathway in maintaining fork progression, genome stability, normal development and tumor suppression.