Miracle-dz/UniFAR-FTUs huggingface dataset:
Genotypic and Phenotypic Characterization of “Streptococcus milleri” Group Isolates from a Veterans Administration Hospital Population

ABSTRACT Because identification of the species within the “Streptococcus milleri” group is difficult for the clinical laboratory as the species share overlapping phenotypic characteristics, we wished to confirm biochemical identification with identification by 16S rRNA gene sequence analysis. Ninety-four clinical isolates previously identified as the “Streptococcus milleri” group were reclassified as S. anginosus, S. constellatus, or S. intermedius with the API 20 Strep system (bioMerieux Vikek, Hazelton, Mo.) and the Fluo-card (Key Scientific, Round Rock, Tex.). In addition, we determined the Lancefield group, hemolysis, colony size, colony texture, repetitive extragenic palindromic PCR (rep-PCR) pattern, and cellular fatty acid (CFA) profile (MIDI, Newark, Del.). 16S rRNA gene sequence analysis with 40 selected representative strains showed three distinct groups, with S. constellatus andS. intermedius found to be more closely related to each other than to S. anginosus, and further distinguished a biochemically distinct group of urogenital isolates within the S. anginosus group of isolates. Except for strains unreactive with the Fluo-card (8%), all S. anginosus and S. intermedius strains identified by sequencing were similarly identified by biochemical testing. However, 23% of the selectedS. constellatus isolates identified by sequencing (9% of all S. constellatus isolates) would have been identified asS. anginosus or S. intermedius by biochemical tests. Although most S. anginosus strains formed one unique cluster by CFA analysis and most S. constellatus strains showed similar rep-PCR patterns, neither method was sufficiently dependable for identification. Whereas Lancefield group or lactose fermentation did not correspond to sequence or biochemical type,S. constellatus was most likely to be beta-hemolytic andS. intermedius was most likely to have a dry colony type. The most frequent isolate in our population was S. constellatus, followed by S. anginosus. There was an association of S. anginosus with a gastrointestinal or urogenital source, and there was an association of S. constellatus and S. intermedius with both the respiratory tract and upper-body abscesses.
Evidence for phenotypic bistability resulting from transcriptional interference of bvgAS in Bordetella bronchiseptica

Bordetella species cause respiratory infections in mammals. Their master regulatory system BvgAS controls expression of at least three distinct phenotypic phases in response to environmental cues. The Bvg+ phase is necessary and sufficient for respiratory infection while the Bvg− phase is required for survival ex vivo. We obtained large colony variants (LCVs) from the lungs of mice infected with B. bronchiseptica strain RBX9, which contains an in‐frame deletion mutation in fhaB, encoding filamentous haemagglutinin. RBX9 also yielded LCVs when switched from Bvg− phase conditions to Bvg+ phase conditions in vitro. We determined that LCVs are composed of both Bvg+ and Bvg− phase bacteria and that they result from defective bvgAS positive autoregulation. The LCV phenotype was linked to the presence of a divergent promoter 5′ to bvgAS, suggesting a previously undescribed mechanism of transcriptional interference that, in this case, leads to feedback‐based bistability (FBM). Our results also indicate that a small proportion of RBX9 bacteria modulates to the Bvg− phase in vivo. In addition to providing insight into transcriptional interference and FBM, our data provide an example of an in‐frame deletion mutation exerting a ‘polar’ effect on nearby genes.
Neurotube® for facial nerve repair

Facial nerve reconstruction for lesions with nerve gaps frequently require autologous or tubulized grafts of biological or synthetic origin. Neurotube®, a bioabsorbable polyglycolic acid tube, represents a valid solution for this kind of defect in emergency and planned surgery. Seven posttraumatic lesions of terminal branches of the facial nerve were repaired by means of Neurotube® from September 1999–September 2001. The nerve gap size ranged between 1–3 cm. Nerve regeneration was evaluated at 7–12 months of follow‐up when muscle recovery function was examined. Muscle function was very good in 1 case, good in 4, and fair in 2 (71% positive results). No intolerance or discomfort was reported or observed. Neurotube® is useful for the reconstruction of facial nerve lesions with a small nerve gap (less then 3 cm) when a direct anastomosis of the two stumps is not possible, or when the suture appears to be in tension. It is a valid alternative to autologous and biological tubulized grafts. The limits of this method are: 1) it can only be used with gaps of less than 3 cm; 2) it is quite costly; 3) there are reports of possible intolerance; and 4) it is not suitable for lesions of the proximal part of the facial nerve. © 2005 Wiley‐Liss, Inc. Microsurgery 25:268–271, 2005.
Horse Riding in Protected Areas: A Critical Review and Implications for Research and Management

Horse riding is a popular, high-impact recreational activity that occurs worldwide. The United States and Australia have a long history of recreational horse riding in protected areas and controversy accompanies this activity in both countries. This review describes and critiques research to date, and then draws out the implications for future research and management. Previous research has been experimental (using trampling lanes to determine impacts away from trails) and quasi-experimental (based on existing use of trails and describing impacts). The off-trail experimental research clearly demonstrates that horses can cause considerable damage. The trail-based quasi-experimental research also showed degradation from horses; however, critiques of this methodology make it more difficult to draw robust conclusions. In addition to biophysical impacts, social research based on surveying users has identified a number of issues associated with horse riding (e.g. conflict with other users) as well as exploring horse riders’ preferences for management actions. A major gap in current research is evaluating the effectiveness of management actions, such as trail construction and codes of conduct. Recommendations for future research include more attention to experimental design, research across and into new ecosystems to improve the generalisation of findings, and attention to researching management effectiveness.
Evolving microbial cooperation and specialisation in the prisoner ’ s dilemma by Klaas Schuijtemaker Supervised

Faculty of Sciences Artificial Intelligence Department MSc Artificial Intelligence by Klaas Schuijtemaker This thesis describes experiments performed on simulated microbes in the prisoner’s dilemma. The microbes evolve a decision making strategy in the one-shot prisoner’s dilemma, using an evolutionary algorithm. In the experiments, we test the effects of a genetic similarity measure and cell differentiation on the microbe’s decision making behaviour. The microbes ability to cooperate and specialise are analysed. The results show that cooperation emerges between microbes that are genetically similar. The results also show that, in some cases, specialisation among microbes emerged when unicellular microbes with the ability of cell differentiation can base decisions on genetic similarity.
Arterial embolization hyperthermia in porcine renal tissue.

BACKGROUND Arterial embolization hyperthermia (AEH) consists of arterially embolizing tumors with ferromagnetic particles that generate hysteretic heating on exposure to an alternating magnetic field. It was the objective of this study to evaluate AEH using the kidney of a large animal as a tumor model. METHODS Between 50 and 400 mg of ferromagnetic microspheres (32 microm in diameter) was arterially infused into the kidneys of three pigs. Temperature probes were inserted into renal tissue, skin, and subcutaneous fat. Each subject was then exposed to an alternating magnetic field for 5 min, while under a general anesthetic. A femoral artery catheter was used to monitor the cardiac pulse. Three days after treatment the renal tissue was chemically analyzed for iron content, which was then correlated with tissue heating rates. RESULTS There was a linear relationship between heating rate and iron concentration (N = 18, correlation = 0.72, P < 0.001) that suggested tissue iron concentrations in the range of 1.55 to 4.05 mg/g would yield tissue heating rates of 0.5 to 1.0 degrees C/min. No temperature increases were detected in control renal tissue (N = 6). The median increase in skin temperature after 5 min of heating was 0.8 degrees C (N = 6, min = 0.7 degrees C, max = 1.3 degrees C), and that in subcutaneous fat was 1.1 degrees C (N = 6, min = 0.8 degrees C, max = 1.2 degrees C). There was no detectable stimulation of cardiac or skeletal muscle or peripheral nerves during treatment. All subjects had uneventful 3-day posttreatment survivals. CONCLUSION This study has shown that AEH can target deep-seated, vascularized tissue in a large animal with therapeutic temperatures (> 42 degrees C), and that the treatment is safe and well tolerated. Further assessment of treatment schedules should allow for a human trial in the near future.
Title Tests of Homoscedasticity , Normality , and Missing Completely at Random for Incomplete Multivariate Data Permalink

Test of homogeneity of covariances (or homoscedasticity) among several groups has many applications in statistical analysis. In the context of incomplete data analysis, tests of homoscedasticity among groups of cases with identical missing data patterns have been proposed to test whether data are missing completely at random (MCAR). These tests of MCAR require large sample sizes n and/or large group sample sizes ni, and they usually fail when applied to non-normal data. Hawkins (1981) proposed a test of multivariate normality and homoscedasticity that is an exact test for complete data when ni are small. This paper proposes a modification of this test for complete data to improve its performance, and extends its application to test of homoscedasticity and MCAR when data are multivariate normal and incomplete. Moreover, it is shown that the statistic used in the Hawkins test in conjunction with a nonparametric k-sample test can be used to obtain a nonparametric test of homoscedasticity that works well for both normal and non-normal data. It is explained how a combination of the proposed normal-theory Hawkins test and the nonparametric test can be employed to test for homoscedasticity, MCAR, and multivariate normality. Simulation studies show that the newly proposed tests generally outperform their existing competitors in terms of type I error rejection rates. Also, a power study of the proposed tests indicates good power. The proposed methods use appropriate missing data imputations to impute missing data. Methods of multiple imputation are described and one of the methods is employed to confirm the result of our single imputation methods. Examples are provided where multiple imputation enables one to identify group or groups whose covariance matrices differ from the majority of other groups.
Pho85 kinase, a yeast cyclin‐dependent kinase, regulates the expression of UGP1 encoding UDP‐glucose pyrophosphorylase

The PHO85 gene is a negative regulator of the PHO system in the yeast Saccharomyces cerevisiae and encodes a protein kinase (Pho85) highly homologous to the Cdc28 kinase (Cdc28). Ten cyclin‐like proteins are known to interact with Pho85, and combination with different cyclins is believed to be responsible for distinct Pho85 functions, including phosphate metabolism, carbon source utilization and cell cycle regulation. However, only a limited number of substrates of Pho85 kinase, including Pho4, Gsy2 and Sicl, have so far been identified. To search for more targets of Pho85 and to clarify the genetic control mechanisms by Pho85 kinase in these cellular functions, we carried out a genome‐wide analysis of the effect of a pho85Δ mutation on gene expression. We found that expression of various genes involved in carbon metabolism are affected by the mutation and that among them, UGP1 promoter activity was increased in the absence of Pho85 kinase. This increase in the promoter activity was not observed in a pho4Δ mutant or with a mutant UGP1 promoter that is devoid of putative Pho4 and Bas2 binding sites, suggesting that UGP1 expression is modulated by Pho85 through Pho4. We also found that expression of several Pho85–cyclin genes were altered by the carbon source, the growth phase and Pho85 kinase itself. Copyright © 2000 John Wiley & Sons, Ltd.
Design of Mutually Coupled Switched Reluctance Motors (MCSRMs) for Extended Speed Applications Using 3-Phase Standard Inverters

Design of a mutually coupled switched reluctance motor (MCSRM) competitive to the third generation interior permanent magnet synchronous motor (IPMSM) of Toyota Prius 2010 is presented. Compared with conventional SRM (CSRM), the proposed machine utilizes the standard six-switch voltage source inverter, which can facilitate the adoption of reluctance machines for traction applications. The structure of the MCSRM has been optimized for 60 kW output power over wide speed range of operation (2768-13500 r/min). Design details to improve machine torque density and to achieve the wide constant power speed range are presented. Performance evaluation under the targeted benchmark shows that the designed MCSRM can attain competitive performance metrics as that of the third generation IPMSM.
A New Improved Genetic Algorithms and its Property Analysis

In order to deal with constraints in the optimization problems, there are a few improved Genetic Algorithms (namely GAs). These GAs have lots of advantages and their applications respectively. But disadvantages in common are that they are strongly dependent on the optimization problem and have narrow applications. Studied based on existing methods, a new improved Genetic Algorithms based on Converting Infeasible individuals into Feasible ones (hereinafter shorted as the CIFGA) is proposed in this paper. The main principle of the CIFGA is that every infeasible individual must be converted compulsively into feasible one in every generation and the population size keep unchanged. The CIFGA, with either binary coding or real coding, is also proved to converge to global optimum solution. The on-line and off-line performances show that compare with other GAs, the CIFGA has a great advantage on convergence property and has good ability of solving constrained optimization in general purpose.
A preliminary study of space charge distribution measurements at nanometer spatial resolution

The continuous reduction in size of devices, such as integrated circuits or micro-electro-mechanical systems (MEMS), results in the need to control with better and better resolution the materials involved, and in particular the electrical properties of the insulating and semiconducting parts. In this paper we propose an approach applicable to space charge measurement methods for improving the resolution to the nanometer range by using femtosecond laser pulses. It is shown that a resolution of about 60 nm in SiO2 can be achieved with thermal and pressure wave propagation methods. Concerning the pulsed electro-acoustic method, the interfacial displacement as small as 100 fm can be measured at THz rate
Integration of Circular Polarized Array and LNA in LTCC as a 60-GHz Active Receiving Antenna

A compact 60-GHz active receiving antenna array is designed and fabricated using low temperature co-fired ceramic (LTCC) technology. It integrates a 4 × 4 circularly polarized (CP) patch array and a 21-dB low noise amplifier (LNA) into the same package substrate. By applying a stripline sequential rotation feeding scheme the CP array exhibits a wide impedance bandwidth (SWR <; 2) and 3-dB axial ratio bandwidth, both over 8 GHz, as well as a beam-shaped pattern with a 3-dB beam width of 20° and a peak gain of 16.8 dBi. By applying a bond wire compensation scheme and low-loss transition optimization, the LNA is successfully integrated into the package. The final fabricated prototype measures only 13 × 20 × 1.4 mm3, demonstrates the good integration performance as well as the CP polarization characteristics in measurement, and is estimated to have a peak overall gain of at least 35 dBi.
Strategies for fast and low-dose laboratory-based phase contrast tomography for microstructural scaffold analysis in tissue engineering

The application of x-ray phase contrast computed tomography (PCT) to the field of tissue engineering is dis- cussed. Specific focus is on the edge illumination PCT method, which can be adapted to weakly coherent x-ray sources, permitting PCT imaging in standard (non-synchrotron) laboratory environments. The method was applied to a prominent research topic in tissue engineering, namely the development of effective and reliable decellularization protocols to derive scaffolds from native tissue. Results show that edge illumination PCT provides sufficient image quality to evaluate the microstructural integrity of scaffolds and, thus, to assess the performance of the used decellularization technique. In order to highlight that edge illumination PCT can ultimately comply with demands on a high specimen throughput and low doses of radiation, recently developed strategies for scan time and dose reduction are discussed.
QUINT: A tool to detect qualitative treatment–subgroup interactions in randomized controlled trials

Abstract Objective: The detection of subgroups involved in qualitative treatment–subgroup interactions (i.e., for one subgroup of clients treatment A outperforms treatment B, whereas for another the reverse holds true) is crucial for personalized health. In typical Randomized Controlled Trials (RCTs), the combination of a lack of a priori hypotheses and a large number of possible moderators leaves current methods insufficient to detect subgroups involved in such interactions. A recently developed method, QUalitative INteraction Trees (QUINT), offers a solution. However, the paper in which QUINT has been introduced is not easily accessible for non-methodologists. In this paper, we want to review the conceptual basis of QUINT in a nontechnical way, and illustrate its relevance for psychological applications. Method: We present a concise introduction into QUINT along with a summary of available evidence on its performance. Subsequently, we subject RCT data on the effect of motivational interviewing in a treatment for substance abuse disorders to a reanalysis with QUINT. As outcome variables, we focus on measures of retention and substance use. Results: A qualitative treatment–subgroup interaction is found for retention. By contrast, no qualitative interaction is detected for substance use. Conclusions: QUINT may lead to insightful and well-interpretable results with straightforward implications for personalized treatment assignment.
Crowd Mobility Analysis using WiFi Sniffers

Wi-fi enabled devices such as today’s smart-phones are regularly in-search for connectivity. They continuously send management frames called Probe Requests searching for previ-ously accessed networks. These frames contain the sender’s MAC addresses in clear text, which can be used as an identifier for that sender. Being able to sniff that MAC address at several locations allows us to understand the mobility behavior of that device. In this paper, we present a solar-powered, beagle-bone based standalone system that continuously sniffs the air for probes and extract their MAC addresses. We deployed the system in the world’s largest gathering (The Hajj) and tested it at scale. Our objective was to build an infrastructure for non-invasive mass crowd analysis. Our deployment had a total of 8 sniffers covering a population of 185,000 people. We detected 37.5% of the population, analysed their arrival and departure behaviours, identified their smartphone manufacturers and extracted their transition patterns from one sub-location to another. By pre-senting valuable insights on the mobility of our target crowd, we validated the potential of our platform for crowd mobility analysis.
Rescue of Prothrombin-deficiency by Transgene Expression in Mice

Summary Prothrombin has diverse biological functions in addition to its well established role in blood coagulation. In order to study these functions in more detail mouse model systems are needed. Since deficiency of prothrombin in mice results in partial embryonic lethality and neonatal death, alternative approaches are required to study the biology of prothrombin in the adult mouse. The liver is the major site of synthesis of prothrombin and therefore liver-specific promoters were used to express prothrombin in transgenic mice. Mice generated from crosses with these transgenic mice and mice hemizygous for the knock-out allele were used to test whether liver-specific expression is sufficient to correct the phenotype of null mice and whether liver-specific expression is sufficient for the development and survival of mice to adulthood. The mouse albumin promoter/enhancer was used initially for transgene expression without success in obtaining transgene positive, endogenous prothrombin null mice. Two lines of transgene positive, endogenous prothrombin deficient mice were obtained using the mouse transthyretin (TTR) promoter/enhancer driving expression of a human prothrombin cDNA. One line was able to rescue both the embryonic and the neonatal lethality while the other line was only able to correct the embryonic lethality. Expression of prothrombin was restricted to the liver and stomach in one line and to the liver, pancreas, stomach and kidney in the other line of mice. Thrombin activity for one line was determined to be at 5-10% of wildtype levels. These mice developed normally and did not have spontaneous bleeding events unless traumatized. Therefore, transgenic expression of human prothrombin is sufficient for the rescue of the lethality found for prothrombin deficiency in mice.
Real-Time Estimation of Camera Orientation by Tracking Orthogonal Vanishing Points in Videos

In man-made urban environments, vanishing points are pertinent visual cues for navigation task. But estimating the orientation of an embedded camera relies on the ability to find a reliable triplet of orthogonal vanishing points in real-time. Based on previous works, we propose a pipeline to achieve an accurate estimation of the camera orientation while preserving a short processing time. Our algorithm pipeline relies on two contributions: a novel sampling strategy among finite and infinite vanishing points extracted with a RANSAC-based line clustering and a tracking along a video sequence to enforce the accuracy and the robustness by extracting the three most pertinent orthogonal directions. Experiments on real images and video sequences show that the proposed strategy for selecting the triplet of vanishing points is pertinent as our algorithm gives better results than the recently published RNS optimal method (Mirzaei, 2011), in particular for the yaw angle, which is actually essential for navigation task.
Complete Genome Sequence of Weissella koreensis KACC 15510, Isolated from Kimchi

ABSTRACT Weissella koreensis KACC 15510 was isolated from kimchi, a representative traditional Korean fermented food. Here, we announce the complete genome sequence of W. koreensis KACC 15510, consisting of a 1,422,478-bp chromosome and one 18,992-bp plasmid, and provide a description of their annotation.