Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection and Quantification of Pfiesteria piscicida by Using the Mitochondrial Cytochrome b Gene

ABSTRACT Mitochondrial cytochrome b was isolated from the dinoflagellate Pfiesteria piscicida, and the utility of the gene for species identification was examined. One of the primer sets designed was shown to be highly specific for P. piscicida. A time step PCR protocol was used to demonstrate the potential of this primer set for quantification of this species.
Structure of the subduction transition region from seismic array data in southern Peru

Data from three seismic arrays installed in southern Peru were analysed using receiver functions from P, PP and PKP wave phases, in order to image the subducted Nazca slab. The arrays cover the transition region from flat slab subduction in central Peru to normal subduction with an angle of about 30° further south. A previous study used data from the first array in the normal subduction region to image the Moho depth and slab, and showed the existence of a mid-crustal structure at 40 km depth that is suggested to be a possible underthrusting of the Brazilian shield. Here, we discuss new observations from the other two arrays that span the transition between the two subduction regimes and the flat subduction region. The results provide an image of the flattened slab from the coast to approximately 300 km inland and also across the transition region from flat to 30° subduction, which appears to be a bend rather than a tear in the slab. In the flat slab region, the slab is well defined near the coast and flattens out at 100 km depth beneath the Altiplano. The slab appears to start flattening some 400 km in advance of the subduction of the Nazca Ridge and the flattening is maintained for 1300 km after its passage. The Moho begins at a depth of around 30 km near the coast and has a maximum depth of 75 km beneath the Altiplano, consistent with the results of the other arrays. Both arrays also show a positive impedance mid-crustal structure at 40 km depth, which if explainable by underthrusting of the Brazilian shield, would add further support to the observations from the normal subduction region and show the northward and westward extent of the signal. The underthrusting hypothesis would explain the missing crust from the shortening budget needed to support the Altiplano. The Vp/Vs ratios for both arrays exhibit average values between 1.73 and 1.75 indicating a lesser likelihood that there is a high degree of partial melting or magma bodies at depth in this region. The receiver function results provide new imaging of the flat slab and transition from normal to flat slab subduction which allows for comparison of different subduction regimes.
The Study of Electoral Behavior

Scholarly studies of electoral behavior have a long and vibrant history. My aim here is to provide a selective summary of that history, focusing on developments that seem to me to have been especially important in shaping the current contours of the field. 1 Since new preoccupations and insights have usually emerged as responses to 1 Some aspects of this history are treated in greater detail elsewhere. Burdick and Brodbeck (1959) assembled a rich collection of critical assessments of voting research at an early point in its development. Converse (1987) presented a detailed history of survey research through 1960, with chapters on Columbia University's Bureau of Applied Social Research and on the University of Michigan's Survey Research Center describing the organizational history of these influential centers and sketching their scholarly contributions in a variety of fields, including the field of voting behavior. Pomper (1978) analyzed the scholarly impact of the single most important work in the field, The American Voter. Converse (2006) provided a mixture of autobiographical and critical reflections on the development of the field, while Sapiro (1998) 2 salient past successes and failures, the organization of my survey is largely (though not entirely) chronological. I have, of course, ignored many important contributions and elided many relevant details. That is inevitable, given limitations of space and of my own expertise. Fortunately, much of what is missing here is handsomely addressed in other chapters of this volume. In any event, my hope is that the range of scholarship touched upon in the following pages will provide some sense of the richness and significance of what has been accomplished by scholars of electoral behavior over the past 70 years, while also inspiring the scholars who chart the mainstream of electoral research in the future to tackle some of the many fundamental issues that remain unresolved. The modern history of academic voting research began in 1940 at Columbia University, where a team of social scientists assembled by Paul Lazarsfeld pioneered the application of survey research to the study of electoral behavior. As occasionally happens with major innovations, this pioneering effort seems even in the light of subsequent advances to have been remarkably sophisticated. Lazarsfeld and his colleagues surveyed 600 prospective voters in a single community (Erie County, Ohio) as many as seven times over the course of the 1940 presidential campaign, with a complex mixture of new and repeated questions in each …
Characterization of Tunisian Mycobacterium tuberculosis Rifampin-Resistant Clinical Isolates

ABSTRACT Analysis of the gene encoding the β-subunit of Mycobacterium tuberculosis RNA polymerase (rpoB) has demonstrated a small region that harbors the mutations most frequently associated with rifampin resistance. In this study, we determined the occurrence of rifampin resistance in 544 Tunisian clinical M. tuberculosis strains isolated in a university hospital between 2004 and 2006 by using the standard-proportion agar method, the INNO-LiPA Rif.TB assay, and DNA sequencing.
Biochemistry and Physiology of the β Class Carbonic Anhydrase (Cpb) from Clostridium perfringens Strain 13

ABSTRACT The carbonic anhydrase (Cpb) from Clostridium perfringens strain 13, the only carbonic anhydrase encoded in the genome, was characterized both biochemically and physiologically. Heterologously produced and purified Cpb was shown to belong to the type I subclass of the β class, the first β class enzyme investigated from a strictly anaerobic species of the domain Bacteria. Kinetic analyses revealed a two-step, ping-pong, zinc-hydroxide mechanism of catalysis with Km and kcat/Km values of 3.1 mM CO2 and 4.8 × 106 s−1 M−1, respectively. Analyses of a cpb deletion mutant of C. perfringens strain HN13 showed that Cpb is strictly required for growth when cultured in semidefined medium and an atmosphere without CO2. The growth of the mutant was the same as that of the parent wild-type strain when cultured in nutrient-rich media with or without CO2 in the atmosphere, although elimination of glucose resulted in decreased production of acetate, propionate, and butyrate. The results suggest a role for Cpb in anaplerotic CO2 fixation reactions by supplying bicarbonate to carboxylases. Potential roles in competitive fitness are discussed.
Factors affecting germination, growth, and distribution of the freshwater sponge, Spongilla fragilis Leidy (Porifera).

Gemmules of the freshwater sponge Spongilla fragilis were germinated and grown under a number of conditions in the laboratory using an artificial medium similar to stream water: germination was similar under conditions of light-dark and total dark; germination was prompted by temperatures between 6-8° C; development of the young sponge was supported by ion concentrations as low as 0.2 mg/l for Mg and Ca, 0.05 mg/l for K and Na, and 0.06 mg/l for SiO2; sponge development was inbhibted by the absence of Ca and Mg, but not Na, K, or SiO2, although no spicules were formed without SiO2.An annual survey was conducted to determine which physico-chemical parameters might limit the distribution of the species. As little difference with respect to chemical characteristics was noted among sampling stations and since sponges appear to tolerate low ion concentrations, it is suggested that distribution of sponges in the stream was affected by the interrelationship between current flow, suspended material, and substratum.
Regional Identification of the Deciduous Forests of Brazil Central Using NDVI Seasonal Variations of the Sensor MODIS and Digital Elevation Model

Paranã river basin has one of the biggest fragments of Decidual Seasonal Forest in Brazil. This kind of vegetation is widely fragmented, mostly, due to the selective wood exploitation and the growth of pasture areas. Thus, many researches have been made in order to understand its dynamics and also to maintain its diversity, most of the times endemic. Thus, the present study aimed at defining a method for regional identification of the Deciduous Forest in the Paranã river basin. Due to the characteristics vegetation, a temporal sequence of MODIS images, over a period of one year, was used for its detection. The methodology adopted can be subdivided into the following steps: (a) NDVI temporal variability examination on deciduous forest vegetation, (b) the influence analysis of rainfall parameter by spatial interpolation, (c) elaboration of the geomorphology map using the DEM and terrain attributes, (d) spectral analysis of the relationships between the NDVI time series and precipitation, and (e) comparison between classified image of NDVI series and geomorphology/geology map. NDVI multi-temporal spectra had their noises treated by the MNF method, limited by the pluviometric data. The Deciduous Forest presents spectral behaviour of NDVI multi-temporal considered typical, with higher values in the raining season and lower values in the dry season, what makes this kind of vegetation different from others. So, the methodology has proved effective for regional delimitation of Deciduous Forests considering the MODIS sensor and SRTM data. Keywords-component; deciduous forest; remote sensing; MODIS; NDVI; changing detection; rainfal; DEM.
The Giant Protein Titin: A Regulatory Node That Integrates Myocyte Signaling Pathways*

Titin, the largest protein in the human body, is well known as a molecular spring in muscle cells and scaffold protein aiding myofibrillar assembly. However, recent evidence has established another important role for titin: that of a regulatory node integrating, and perhaps coordinating, diverse signaling pathways, particularly in cardiomyocytes. We review key findings within this emerging field, including those related to phosphorylation of the titin springs, and also discuss how titin participates in hypertrophic gene regulation and protein quality control.
Complications following liver resection for colorectal metastases do not impact on longterm outcome.

BACKGROUND It has been suggested that adverse postoperative outcomes may have a negative impact on longterm survival in patients with colorectal liver metastases. OBJECTIVES This study was conducted to evaluate the prognostic impact of postoperative complications in patients submitted to a potentially curative resection of colorectal liver metastases. METHODS A retrospective analysis of outcomes in 199 patients submitted to hepatic resection with curative intent for metastatic colorectal cancer during 1999-2008 was conducted. RESULTS The overall complication rate was 38% (n = 75). Of all complications, 79% were minor (Grades I or II). There were five deaths (3%). The median length of follow-up was 39 months. Rates of 5-year overall and disease-free survival were 44% and 27%, respectively. Univariate analysis demonstrated that an elevated preoperative level of carcinoembryonic antigen (CEA), intraoperative blood loss of > 300 ml, multiple metastases, large (≥ 35 mm) metastases and resection margins of < 1 mm were associated with poor overall and disease-free survival. In addition, male sex and synchronous metastases were associated with poor disease-free survival. Postoperative complications did not have an impact on either survival measure. The multivariate model did not include complications as a predictive factor. CONCLUSIONS Postoperative complications were not found to influence overall or disease-free survival in the present series. The number and size of liver metastases were confirmed as significant prognostic factors.
Three-axis digital accelerometer based wireless gait analysis with wearable System-on-Chip designs

Gait analysis is one of the ubiquitous procedures in assessing the progression of physical therapy; however, most clinical gait analyzers utilize bulk and expensive equipment and miniaturization is underway. To address this, a portable wireless gait monitoring device with a microcontroller unit was developed which can be applied at point-of-care. The system utilizes three 16G 3-axis accelerometers mounted on the leg to determine the leg's stride, angle and acceleration. Fast Fourier analysis has shown significant differences in the frequency spectrum of the different gaits. A System-On-Chip based on TSMC 0.18 um has also developed to further miniaturize the device. Such SoC consists of a low offset, and low noise analog front-end composed of chopper stabilized instrumentation amplifiers, ultra-low cut-off low pass filters, envelop/magnitude and frequency detectors.
ZuiScat: querying and visualizing information spaces on personal digital assistants

ZuiScat is a visualization concept for querying large information spaces on Personal Digital Assistants (PDA). Retrieval results are presented in a dynamic scatterplot, which is enhanced by geometric and semantic zoom techniques to provide smooth transitions from abstract visual encodings to data content. The same visualization is also used to manage bookmarks and to serve as a powerful query history tool. User feedback suggests that ZuiScat provides intuitive and efficient data access but still needs further improvement in terms of zoom usability and visual mapping.
Lesions of the dorsomedial striatum delay spatial learning and render cue-based navigation inflexible in a water maze task in mice

The dorsal striatum is involved in cue-based navigation strategies and in the development of habits. It has been proposed that striatum-dependent cued navigation competes with hippocampus-dependent spatial navigation in some circumstances. We have previously shown that large lesions of the dorsal striatum, as well as impairment of corticostriatal synaptic plasticity in transgenic mice, can enhance spatial learning in a water maze task, presumably by the disruption of competitive interference. However, the dorsal striatum is not a homogeneous structure; both anatomical considerations and experimental studies in various paradigms show that dorsomedial and dorsolateral striatum are functionally distinct, although there is no precise anatomical or neurochemical boundary between them. Here we investigated the effect of restricted excitotoxic lesions of dorsomedial striatum (DMS) on cued and spatial water maze learning. We find that dorsomedial striatal lesions delay spatial learning but permit cued learning. After cued learning, lesioned animals showed inflexible search, resulting in repeated visits to the escape platform-associated cue. These results support a role for the DMS in behavioral flexibility rather than in cue-based navigation.
The Potentiality of Authenticity in Becoming a Teacher

This paper arises out of the transition from a PhD thesis on Heidegger's phenomenology to my attempts to come to terms with ‘becoming a teacher’. The paper will provide a phenomenological interpretation of being a teacher in relation to the question of an ‘authentic’ interpretation of teaching/learning and the possibility of an authentic interpretative praxis. I will argue that being a teacher is a phenomenon of human existence which can be interpreted as a possible way of being with authentic and inauthentic potentialities. This way of being is intrinsically linked to that of learning; of becoming human or becoming the authentic possibilities of being‐human. As such, the problem of being a teacher is primarily an ethical question (or a question of ɛτηοσ—dwelling); of who we are as humans and of how being a teacher engages with the in‐formation of the becoming of students as authentic human beings. This then leads to the problem of how a phenomenological interpretation of education can be applied or lived; of authenticity in teaching/learning and the possibilities of authentic learning environments (educational dwelling).
Systemic hyperoxia decreases vascular endothelial growth factor gene expression in ischemic primate retina.

OBJECTIVES To determine whether systemic hyperoxia can reverse retinal hypoxia and decrease vascular endothelial growth factor (VEGF) gene expression in ischemic nonhuman primate retina. METHODS Six eyes of 3 cynomolgus monkeys were studied. Retinal ischemia was induced via laser vein occlusion and confirmed with fluorescein angiography. Animals were randomly assigned to treatment with either 21% or 100% inhaled oxygen. Arterial PO2 was monitored while systemic acid-base status was maintained. An oxygen microelectrode on a micromanipulator was used to measure preretinal oxygen concentrations in ischemic and nonischemic retina in situ. RNA was isolated from fresh whole retinas, and VEGF messenger RNA levels were quantified with Northern blotting. RESULTS The preretinal PO2 in ischemic retina was less than the PO2 in nonischemic retina in animals breathing 21% oxygen (intervascular zone PO2, 14.3+/-0.53 vs 21.8+/-0.55 mm Hg; P=.002). After 8 hours of systemic hyperoxia (arterial PO2, 512+/-18 mm Hg), the preretinal PO2 in ischemic retina increased to 166.2+/-15.6 mm Hg (21.8% oxygen) and retinal VEGF messenger RNA levels were reduced by an average of 55%. CONCLUSIONS These data demonstrate that systemic hyperoxia can lower retinal VEGF gene expression and reoxygenate ischemic adult primate retina.
Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model

Significance During initiation of DNA replication in eukaryotes, the origin recognition complex, with Cdc6 and Cdt1, assembles an inactive Mcm2-7 double hexamer on the dsDNA. Later, the double hexamer recruits Cdc45 and GINS to form two active and separate DNA helicases. The active Cdc45–Mcm2-7–GINS helicase encircles the leading strand while excluding the lagging strand. One of the fundamental unanswered questions is how each Mcm2-7 hexamer converts from binding dsDNA to binding one of the single strands. The structure of the double hexamer on dsDNA reveals how DNA interacts with key elements inside the central channel, leading us to propose a lagging-strand extrusion mechanism. This work advances our understanding of eukaryotic replication initiation. During replication initiation, the core component of the helicase—the Mcm2-7 hexamer—is loaded on origin DNA as a double hexamer (DH). The two ring-shaped hexamers are staggered, leading to a kinked axial channel. How the origin DNA interacts with the axial channel is not understood, but the interaction could provide key insights into Mcm2-7 function and regulation. Here, we report the cryo-EM structure of the Mcm2-7 DH on dsDNA and show that the DNA is zigzagged inside the central channel. Several of the Mcm subunit DNA-binding loops, such as the oligosaccharide–oligonucleotide loops, helix 2 insertion loops, and presensor 1 (PS1) loops, are well defined, and many of them interact extensively with the DNA. The PS1 loops of Mcm 3, 4, 6, and 7, but not 2 and 5, engage the lagging strand with an approximate step size of one base per subunit. Staggered coupling of the two opposing hexamers positions the DNA right in front of the two Mcm2–Mcm5 gates, with each strand being pressed against one gate. The architecture suggests that lagging-strand extrusion initiates in the middle of the DH that is composed of the zinc finger domains of both hexamers. To convert the Mcm2-7 DH structure into the Mcm2-7 hexamer structure found in the active helicase, the N-tier ring of the Mcm2-7 hexamer in the DH-dsDNA needs to tilt and shift laterally. We suggest that these N-tier ring movements cause the DNA strand separation and lagging-strand extrusion.
Latent Structure of Reflective Learning at the Higher Educational Institution: Mixed Methods Research Results

The article presents results of the research, conducted using mixed methods research strategy: the reflective learning model as a prerequisite for curriculum development and improvement in university studies. The qualitative study was implemented using unstructured reflections, written by 65 prospective special educators studying at the university. The phenomenological hermeneutical method of data analysis enabled to disclose students’ experiences as preconditions for reflective learning, continuing studies at the university, and reveal impact on changes in personal conceptions, based on reflection of experienced situations. The quantitative study, which was attended by 389 students, aimed to disclose general trends of students’ reflective learning in theoretical and practical studies. Primary and secondary factor analyses enabled to disclose the latent structure of the investigated phenomenon – reflective learning. The constructed reflective learning model, based on prospective special educators’ example, can be described by 7 key dimensions, which can be treated as main trends, seeking improvement of the curriculum, implementing reflective learning at the higher education institution, and development of students’ reflection competency during studies.
XcpX Controls Biogenesis of the Pseudomonas aeruginosa XcpT-containing Pseudopilus*

Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen equipped with multiple secretion systems. The type II secretion machinery (Xcp secreton) is involved in the release of toxins and enzymes. The Xcp secreton is a multiprotein complex, and most of its components share homology with proteins involved in type IV pili biogenesis. Among them, the XcpT-X pseudopilins possess characteristics of the major constituent of the type IV pili, the pilin PilA. We have shown previously that XcpT can be assembled in a multifibrillar structure that was called the pseudopilus. By using two different microscopic approaches, we show here that the pseudopili are preferentially isolated fibers rather than tight bundles. Moreover, none of the other four pseudopilins are able to form a pseudopilus, suggesting that the assembly of such a structure is a unique property of XcpT. Moreover, we show that 5 of the 12 Xcp proteins are not required for pseudopilus biogenesis, whereas they are for type II secretion. Most interestingly, we showed that one pseudopilin, XcpX, controls the assembly of XcpT into a pseudopilus. Indeed, when the number of XcpX subunits increases, the length of the pseudopilus decreases. Conversely, in the absence of XcpX, the pseudopilus length is abnormally long. Our results indicate that XcpT and XcpX directly interact with each other. Furthermore, this interaction induces a clear destabilization of XcpT. The interaction between XcpT and XcpX could be part of the molecular mechanism underlying the dynamic control of pseudopilus elongation, which could be crucial for type II-dependent protein secretion.