Miracle-dz/UniFAR-FTUs huggingface dataset:
Metschnikowia Species Share a Pool of Diverse rRNA Genes Differing in Regions That Determine Hairpin-Loop Structures and Evolve by Reticulation

Modern taxonomy of yeasts is mainly based on phylogenetic analysis of conserved DNA and protein sequences. By far the most frequently used sequences are those of the repeats of the chromosomal rDNA array. It is generally accepted that the rDNA repeats of a genome have identical sequences due to the phenomenon of sequence homogenisation and can thus be used for identification and barcoding of species. Here we show that the rDNA arrays of the type strains of Metschnikowia andauensis and M. fructicola are not homogenised. Both have arrays consisting of diverse repeats that differ from each other in the D1/D2 domains by up to 18 and 25 substitutions. The variable sites are concentrated in two regions that correspond to back-folding stretches of hairpin loops in the predicted secondary structure of the RNA molecules. The substitutions do not alter significantly the overall hairpin-loop structure due to wobble base pairing at sites of C-T transitions and compensatory mutations in the complementary strand of the hairpin stem. The phylogenetic and network analyses of the cloned sequences revealed that the repeats had not evolved in a vertical tree-like way but reticulation might have shaped the rDNA arrays of both strains. The neighbour-net analysis of all cloned sequences of the type strains and the database sequences of different strains further showed that these species share a continuous pool of diverse repeats that appear to evolve by reticulate evolution.
Viewer's Discretion: Host Security in Mobile Code Systems

Mobile code computation is a new paradigm for structuring distributed systems. Mobile programs migrate from remote sites to a host, and interact with the resources and facilities local to that host. This new mode of distributed computation promises great opportunities for electronic commerce, mobile computing, and information harvesting. There has been a general consensus that security is the key to the success of mobile code computation. In this paper, we survey the issues surrounding the protection of a host from potentially hostile mobile programs. Decades of research in operating systems has provided signiicant experience and insight into the nature of system security. Before we propose any new security model for mobile code systems, it is wise to question why the existing protection mechanisms found in distributed operating systems do not fully address the security needs of mobile code systems. We propose three security challenges that are distinctive of the mobile code phenomenon, namely, the establishment of anonymous trust (establishing trust with programs from unfamiliar origin), layered protection (establishing ne-grained protection boundaries among mutually-distrusting parts of the same process), and implicit acquisition (coping with the implicit nature of mobile program acquisition). We also survey various approaches to protection in existing mobile code systems. We classify protection approaches into four categories: discretion, veriication, transformation , and arbitration. We evaluate each category by looking at how well they address the security needs of mobile code computation.
Measurement of Structural Deformation using Terrestrial Laser Scanners

SUMMARY Three deformation measurement experiments have been undertaken where, in each experiment, a structure was subject to controlled loading. Terrestrial laser scanners (TLSs) were used to make measurements at critical intervals during each load test. TLSs, which are a relatively recent innovation, are capable of rapidly capturing thousands of three dimensional points over the surface of an object. They are largely untried in the area of structural deformation monitoring. The purpose of these tests is to assess the sensitivity of TLSs for the measurement of vertical deformation of loaded structures and to investigate their potential for metrology tasks where remote observations (completely non-contact and targetless at distances greater than 5m) are desirable. A Riegl LMS-Z210 laser scanner was used for all three experiments and a Cyra Cyrax 2500 was available for the first. The point cloud data were represented with analytical models representing the vertical deflection of each beam. The development of these models required knowledge of the dimensions of the beam, spatial position of the load point(s) and support points. Functional models (low-order polynomials) were derived based on generalised coefficients of the analytical models. These generalised coefficients were solved as unknown parameters in a least-squares estimation process. Analysis of the accuracy of the TLSs involved computing differences between benchmark photogrammetry and laser scanner vertical deflections. In the first experiment, the RMS of differences (for eight load cases) between the Cyrax 2500 and photogrammetry was ±0.29mm and ±3.6mm for the LMS-Z210 (using 104 samples). The RMS of differences for the LMSZ210 in the second experiment was ±2.4mm for 12 load cases (using 144 samples). The RMS of differences for the final experiment, where measurements were conducted on four horizontal beams, ranged between ±4.2mm to ±9.5mm. The greatest improvement of accuracy was up to 21 times the single-point precision of the TLS. These results highlight the potential application of TLSs for precision metrology, given that their accuracy can be greatly improved by exploiting the 3D point clouds with simple modelling techniques.
A Physical Bias in Cosmological Simulations

Numerical simulations play an important role in the study of the structure formation of the universe. However, the mass resolution in current simulations is still poor. Due to technical difficulties, it is necessary to use both a greatly reduced number density of particles and a greatly raised unit particle mass. Consequently, the particle masses used in cosmological simulations are about 1070 times larger than the GeV candidates in particle physics. This is a huge physical bias that cannot be neglected when interpreting the results of the simulations. Here we discuss how such a bias affects cold dark matter (CDM) cosmological simulations. We find that the small-scale properties of the CDM particle system are changed in two aspects. (1) An upper limit is imposed on the spatial resolution of the simulation results. (2) Most importantly, an unexpected short mean free path is produced, and the corresponding two-body scattering cross section is close to the value expected in the self-interaction dark matter model. Since the mean free path of real CDM particle systems is much longer than that in the simulations, our results imply that (1) there is probably no "cusp problem" in real CDM halos and (2) a much longer time is needed to form new virialized halos in real CDM particle systems than in the simulations. The last result can help us understand the "substructure problem. " Our discussion can also explain why the massive halos in the simulations may have smaller concentration coefficients.
Conjugate and vergence oscillations during saccades and gaze shifts: implications for integrated control of binocular movement.

Saccades made between targets at optical infinity require both eyes to rotate by the same angle. Nevertheless, these saccades are consistently accompanied by transient vergence eye movements. Here we have investigated whether the dynamics of these vergence movements depend on the trajectory of the coincident conjugate movement, and whether moving the head during eye-head gaze shifts modifies vergence dynamics. In agreement with previous reports, saccades with more symmetric (i.e., "bell-shaped") conjugate velocity profiles were accompanied by stereotyped biphasic vergence transients (i.e., a divergence phase immediately followed by a convergence phase). However, we found that saccades with more asymmetric, oscillatory-like dynamics (characterized by a typical conjugate reacceleration of the eyes following the initial peak velocity) were systematically accompanied by more complex vergence movements that also exhibited oscillatory-like dynamics. These findings could be extended to conditions where the head was free to move: comparable conjugate and vergence oscillations were observed during head-restrained saccades and combined eye-head gaze shifts. The duration of the vergence oscillation increased with gaze shift amplitude, such that as many as four vergence phases (divergence-convergence-divergence-convergence) were recorded during 55 degrees gaze shifts (approximately 240 ms). To quantify these observations, we first determined whether conjugate and vergence peak velocities were systematically correlated. Conjugate peak velocity was linearly related to the peak velocity of the initial divergence phase for saccades and gaze shifts of all amplitudes, regardless of their dynamics. However, for more asymmetric saccades and gaze shifts, the subsequent convergence and divergence peak velocities were not correlated with either the initial peak conjugate velocity or the peak velocity of the conjugate reacceleration. Next, we determined that the duration of the different conjugate and vergence oscillation phases remained relatively constant across all saccades and gaze shifts, and that the conjugate and vergence profiles oscillated together at approximately 7.5-10 Hz. Using computer simulations, we show that a classic feed-forward model is unable to reproduce vergence oscillations based solely on peripheral mechanisms. Furthermore, we demonstrate that small modifications to the gain and delay of a simple feedback model for saccade generation can generate conjugate oscillations, and propose that such changes reflect the influence of lowered alertness on the tecto-reticular pathways. We conclude that peripheral mechanisms can only account for the initial divergence that accompanies all saccades, and that the conjugate and vergence oscillations observed during asymmetric movements arise centrally from an integrative binocular controller.
Relationship of Vibrio Species Infection and Elevated Temperatures to Yellow Blotch/Band Disease in Caribbean Corals

ABSTRACT The bacterial and temperature factors leading to yellow blotch/band disease (YBD), which affects the major reef-building Caribbean corals Montastrea spp. , have been investigated. Groups of bacteria isolated from affected corals and inoculated onto healthy corals caused disease signs similar to those of YBD. The 16S rRNA genes from these bacteria were sequenced and found to correspond to four Vibrio spp. Elevating the water temperature notably increased the rate of spread of YBD on inoculated corals and induced greater coral mortality. YBD-infected corals held at elevated water temperatures had 50% lower zooxanthella densities, 80% lower division rates, and a 75% decrease in chlorophyll a and c2 pigments compared with controls. Histological sections indicated that the algal pyrenoid was fragmented into separate segments, along with a reconfiguration and swelling of the zooxanthellae, as well as vacuolization. YBD does not appear to produce the same physiological response formerly observed in corals undergoing temperature-related bleaching. Evidence indicates that YBD affects primarily the symbiotic algae rather than coral tissue.
2′-Deoxymugineic acid promotes growth of rice (Oryza sativa L.) by orchestrating iron and nitrate uptake processes under high pH conditions

Poaceae plants release 2′-deoxymugineic acid (DMA) and related phytosiderophores to chelate iron (Fe), which often exists as insoluble Fe(III) in the rhizosphere, especially under high pH conditions. Although the molecular mechanisms behind the biosynthesis and secretion of DMA have been studied extensively, little information is known about whether DMA has biological roles other than chelating Fe in vivo. Here, we demonstrate that hydroponic cultures of rice (Oryza sativa) seedlings show almost complete restoration in shoot height and soil-plant analysis development (SPAD) values after treatment with 3–30 μm DMA at high pH (pH 8.0), compared with untreated control seedlings at normal pH (pH 5.8). These changes were accompanied by selective accumulation of Fe over other metals. While this enhanced growth was evident under high pH conditions, DMA application also enhanced seedling growth under normal pH conditions in which Fe was fairly accessible. Microarray and qRT-PCR analyses revealed that exogenous DMA application attenuated the increased expression levels of various genes related to Fe transport and accumulation. Surprisingly, despite the preferential utilization of ammonium over nitrate as a nitrogen source by rice, DMA application also increased nitrate reductase activity and the expression of genes encoding high-affinity nitrate transporters and nitrate reductases, all of which were otherwise considerably lower under high pH conditions. These data suggest that exogenous DMA not only plays an important role in facilitating the uptake of environmental Fe, but also orchestrates Fe and nitrate assimilation for optimal growth under high pH conditions.
A Purine-Sensitive Pathway Regulates Multiple Genes Involved in Axon Regeneration in Goldfish Retinal Ganglion Cells

In lower vertebrates, retinal ganglion cells (RGCs) can regenerate their axons and reestablish functional connections after optic nerve injury. We show here that in goldfish RGCs, the effects of several trophic factors converge on a purine-sensitive signaling mechanism that controls axonal outgrowth and the expression of multiple growth-associated proteins. In culture, goldfish RGCs regenerate their axons in response to two molecules secreted by optic nerve glia, axogenesis factor-1 (AF-1) and AF-2, along with ciliary neurotrophic factor. The purine analog 6-thioguanine (6-TG) blocked outgrowth induced by each of these factors. Previous studies in PC12 cells have shown that the effects of 6-TG on neurite outgrowth may be mediated via inhibition of a 47 kDa protein kinase. Growth factor-induced axogenesis in RGCs was accompanied by many of the molecular changes that characterize regenerative growth in vivo, e.g., increased expression of GAP-43 and certain cell surface glycoproteins. 6-TG inhibited all of these changes but not those associated with axotomy per se, e.g., induction of jun family transcription factors, nor did it affect cell survival. Additional studies using RGCs from transgenic zebrafish showed that expression of Tα-1 tubulin is likewise stimulated by AF-1 and blocked by 6-TG. The purine nucleoside inosine had effects opposite to those of 6-TG. Inosine stimulated outgrowth and the characteristic pattern of molecular changes in RGCs and competitively reversed the inhibitory effects of 6-TG. We conclude that axon regeneration and the underlying program of gene expression in goldfish RGCs are mediated via a common, purine-sensitive pathway.
The first 1000 cases of Italian Endovenous-laser Working Group (IEWG). Rationale, and long-term outcomes for the 1999-2003 period.

AIM The innovations for disease management need to be thoroughly evaluated so that their benefits and potential downsides can be compared with the already existing approaches. Endovascular laser (EVL) treatment for varicose veins offers today several advantages over surgical standard stripping. The Italian Endovenous-laser Working Group (IEWG) is a homogeneous group of surgeons and phlebologists who have been using EVL since 1999 and has undertaken to examine EVL in a multicenter study starting from a well defined rationale, with the benefit of a single protocol to use. METHODS In a cooperative, multicenter, clinical study, 1076 limbs in 1050 patients, mean age of 54.5 years, 241 males and 809 females affected by chronic venous insufficiency (CVI) were considered eligible for surgery and stratified by CEAP classification in a four-year period (January 1999 December 2003). Inclusion criteria were insufficiency of the great and/or small saphenous vein at various levels, beyond those accessory saphenous trunks with incompetence in the saphenofemoral junction. In all cases truncular reflux apparead up on duplex scan examination, with or without associated varicosities. All the patients underwent a surgery on the basis of the clinical assessment. All the centres involved performed treatment in conformity with the Food and Drug Administration (FDA) validated procedure, using an endo-laser venous system kit with a 810-980 nm diode. Duplex scan was performed in all patients after 36 months with very few lost to follow-up cases. RESULTS In the immediate postoperative period the results have been impressive, with a very effective closure of incompetent great saphenous vein and the other treated varicose veins (the early occlusion rate has been 99%). Major complications have not been detected: in particular, no deep venous thrombosis (DVT) evaluated duplex ultrasound. The patients' acceptability and satisfaction regarding the procedure, have been measured by means of a questionnaire on the quality of life, and the result was 96.7%. After 36 months, the total occusion rate of saphenous trunks has been 97%. CONCLUSIONS The first important Italian experience with EVL based on preoperative, perioperative and postoperative duplex control and which is also based on the patients' satisfaction at mid/long-term has indicated some advantages over the standard treatment with the stripping method. In terms of reduced postoperative pain, shorter sick leave, a faster resumption of the normal activities, and, in particular, the total absence of DVT, we can conclude that EVL is a good solution for all patients with anatomic and hemodinamic patterns for saphenous vein surgery.
Molecular Characterization of Multidrug-Resistant Mycobacterium tuberculosis Isolated in Nepal

ABSTRACT Despite the fact that Nepal is one of the first countries globally to introduce multidrug-resistant tuberculosis (MDR-TB) case management, the number of MDR-TB cases is continuing to rise in Nepal. Rapid molecular tests applicable in this setting to identify resistant organisms would be an effective tool in reversing this trend. To develop such tools, information about the frequency and distribution of mutations that are associated with phenotypic drug resistance in Mycobacterium tuberculosis is required. In the present study, we investigated the prevalence of mutations in rpoB and katG genes and the inhA promoter region in 158 M. tuberculosis isolates (109 phenotypically MDR and 49 non-MDR isolates collected in Nepal) by DNA sequencing. Mutations affecting the 81-bp rifampin (RIF) resistance-determining region (RRDR) of rpoB were identified in 106 of 109 (97.3%) RIF-resistant isolates. Codons 531, 526, and 516 were the most commonly affected, at percentages of 58.7, 15.6, and 15.6%, respectively. Of 113 isoniazid (INH)-resistant isolates, 99 (87.6%) had mutations in the katG gene, with Ser315Thr being the most prevalent (81.4%) substitution. Mutations in the inhA promoter region were detected in 14 (12.4%) INH-resistant isolates. The results from this study provide an overview of the current situation of RIF and INH resistance in M. tuberculosis in Nepal and can serve as a basis for developing or improving rapid molecular tests to monitor drug-resistant strains in this country.
The reduction of retinal autofluorescence caused by light exposure.

PURPOSE A prior study showed that long exposure to 568-nm light at levels below the maximum permissible exposure safety limit produces retinal damage preceded by a transient reduction in the autofluorescence of retinal pigment epithelial (RPE) cells in vivo. The present study shows how the effects of exposure power and duration combine to produce this autofluorescence reduction and find the minimum exposure causing a detectable autofluorescence reduction. METHODS Macaque retinas were imaged using a fluorescence adaptive optics scanning laser ophthalmoscope to resolve individual RPE cells in vivo. The retina was exposed to 568-nm light over a square subtending 0.5 degrees with energies ranging from 1 to 788 J/cm(2), where power and duration were independently varied. RESULTS In vivo exposures of 5 J/cm(2) and higher caused an immediate decrease in autofluorescence followed by either full autofluorescence recovery (exposures <or= 210 J/cm(2)) or permanent RPE cell damage (exposures >or= 247 J/cm(2)). No significant autofluorescence reduction was observed for exposures of 2 J/cm(2) and lower. Reciprocity of exposure power and duration held for the exposures tested, implying that the total energy delivered to the retina, rather than its distribution in time, determines the amount of autofluorescence reduction. CONCLUSIONS That reciprocity held is consistent with a photochemical origin, which may or may not cause retinal degeneration. The implementation of safe methods for delivering light to the retina requires a better understanding of the mechanism causing autofluorescence reduction. Finally, RPE imaging was demonstrated using light levels that do not cause a detectable reduction in autofluorescence.
Defining the Role of the Instructional Technologist in Higher Education.

Many colleges and universities have begun to hire Instructional Technologists. The role, qualifications, and responsibilities of the Instructional Technologist are often illdefined. This paper describes the various roles the Instructional Technologist can play in higher education and describes the typical activities and qualifications of each role. The paper includes a description of ten recent Instructional Technologist position announcements from colleges around the country. The paper also includes a discussion of the key questions colleges should ask themselves before hiring an Instructional Technologist. A series of recommendations for developing a position description are included. "PERMISSION TO REPRODUCE THIS MATERIAL HAS BEEN GRANTED BY Lucinda T. Lea TO THE EDUCATIONAL RESOURCES INFORMATION CENTER (ERIC). " Running Head: Defining the Role of the Instructional Technologist 2 BEST COPY AVA0 LADLE 304 Defining the Role of the Instructional Technologist Defining the Role of the Instructional Technologist in Higher Education Overview An impressive variety of changes in society, technology, and the economy have been exerting pressure on higher education for decades. Direct government subsidies for higher education, never in great supply, have begun to shrink at a rapid pace. Fewer, less experienced, faculty are having to teach an increasingly large number of students. Students are getting older, with many students working at least part time and unable to attend classes full time. In spite of these, and a litany of other changes, the traditionalist in higher education has argued that, in the end, the structure and organization of the university were hallowed and timeless and would endure in spite of any external influences, regardless how powerful. While the traditionalist view of higher education is still prevalent, many observers, inside and out of academe, have gradually come to see the need for reform. A recent review of higher education in U.S. News & World Report (1994) effectively and bluntly described the situation: Like it or not, colleges and universities are, in fact, labor intensive enterprises that operate in high cost environments and produce a human product that promises to remain in heavy oversupply for the foreseeable future Given the fundamentals, no amount of downsizing, restructuring or tinkering with the economic edges will alter the disheartening outlook. That disheartening outlook has forced even the most optimistic supporter of higher education to begin to consider alternatives to the present situation. Almost every college