Miracle-dz/UniFAR-FTUs huggingface dataset:
pCal, a highly unusual Ty1/copia retrotransposon from the pathogenic yeast Candida albicans

Retrotransposons are mobile genetic elements. They can transpose via the reverse transcription of mRNA into double-stranded DNA (dsDNA) followed by the insertion of this dsDNA into new sites within the host genome. The unintegrated, linear, dsDNA form of retrotransposons is usually very rare. We report here the isolation of a retrotransposon from Candida albicans which is unusual in this respect. This element, which we have named pCal, was first identified as a distinct band when uncut C. albicans DNA was examined on an agarose gel. Sequence analysis of the cloned element revealed that it is a retrotransposon belonging to the Ty1/copia group. It is estimated that pCal produces 50 to 100 free, linear, dsDNA copies of itself per cell. This is a much higher level of expression than even that of the system in which Ty1 is expressed behind the highly active GAL1 promoter on a high-copy-number plasmid (about 10 copies per cell). Another unusual feature of pCal is that its Pol enzymes are likely to be expressed via the pseudoknot-assisted suppression of an upstream, in-phase stop codon, as has been shown for Moloney murine leukemia virus.
Postoperative Changes in Pelvic Parameters and Sagittal Balance in Adult Isthmic Spondylolisthesis

BACKGROUND: Correction of deformity in adult isthmic spondylolisthesis can affect the pelvic parameters and sagittal balance. OBJECTIVE: To evaluate the correlation with the amount of deformity correction and the subsequent change in pelvic parameters after surgical correction of adult isthmic spondylolisthesis and to determine which deformity parameter most affects the postoperative restoration of spinopelvic sagittal alignment. METHODS: Fifty-eight patients with 1-level isthmic spondylolisthesis were included. Their average age was 55 years (range, 24-76 years). All patients underwent operation by posterior lumbar interbody fusion and posterior instrumentation. The pre- and postoperative sacral slope, pelvic tilt, lumbar lordosis (LL), and sagittal balance were measured, and then the correlation between these parameters and deformity parameters such as slip degree, slip angle, and height of the intervertebral disc (HOD) was evaluated. RESULTS: The slip degree, slip angle, and HOD were significantly recovered after surgery. Pelvic parameters and sagittal balance changed subsequently. Sacral slope was increased by 4.4 degrees, and pelvic tilt was decreased by 4.4 degrees. LL was increased by 5.2 degrees and sagittal balance was displaced 5.6 mm posteriorly. Only the restoration of the HOD showed a significant correlation with the change in LL (r = 0.305, P = .02) and sagittal balance (r = 0.377, P = .004). CONCLUSION: Surgical correction of adult isthmic spondylolisthesis with posterior lumbar interbody fusion and posterior instrumentation resulted in improvement of sacral slope, pelvic tilt, LL, and sagittal balance. Only restoration of the HOD was significantly correlated with improvement of LL and sagittal balance. Therefore we presume it is important to restore the HOD in surgical correction of adult isthmic spondylolisthesis.
Randomized study of the effect of antenatal dexamethasone on growth and development of premature children at the corrected age of 2 years

The objective of the series was to study the effect of prenatal dexamethasone therapy on the growth and neurological development of preterm children until the age of 2 years. Eighty‐two children with a mean gestational age of 30 (24–33) weeks and a mean weight of 1291 (530–2360) g at birth, treated antenatally with either dexamethasone (n= 50) or placebo (n= 32), were examined at the adjusted age of 24 months by a paediatric neurologist, a neuropsychologist and a speech therapist. Neurological development was defined as normal if all scores of neuropaediatric, neuropsychological and verbal tests were within the normal range. Normal neurological development was found in 52% of the dexamethasone‐treated and in 34% of the placebo‐treated children. The incidence of cerebral palsy was 10% in the dexamethasone group and 22% in the placebo group. Minor developmental delay was found in 42% of dexamethasone‐treated and in 53% of placebo‐treated children. Our follow‐up results indicate that the beneficial effect of prenatal glucocorticoid treatment on cerebral complications I intraventricular haemorrhage or periventricular leucomalacia) demonstrated during the neonatal period may be followed by a lower incidence of cerebral palsy in surviving premature children.
HYPERMEDIA RESEARCH: PRESENT AND FUTURE

ABSTIRACT Hypermedia learning systems have been gaining much attention over the past two decades. Although several theorists have indicated that hypermedia structures can be structured to reflect the human minds cognitive structure, it has yet to be determined whether hypertext systems can simulate different types of learning environments so as to facilitate the achievement of different typ s of learning objectives. The purpose of this study was to review literature related to how students learning within hypermedia leaming environments and to identify current perccived problems related to hypermedia research which is limiting its use and generalizability. Identified problems include: (1) irrelevant assessment of outcome variables, (2) weal, methodological design in conducting experimental research, (3) lack of theoretical foundations in designing hypertext systems (4) lack of specification of precise learning outcomes and (5) lack of of learner's prior knowledge in the content area. Furthermore, suggestions are made to reform the future hypermedia research agenda. The suggestions include: (1) future research should focus on assessing relevant student's leaming outcomes (knowledge acquisition, knowledge integration, knowledge generation) (2) researchers should develop reliable and valid instruments and methodology of experimental design ( reporting reliability of criterion measures), (3) hypermedia design should reflect hypotheses derived from established leaming and instructional design theory, and (4) future studies should consider leamers' prior knowledge and varied leaming styles. The ultimate goal of this article was to examine the research base in hypermedia on learning in order to identify existing limitation inherent in existing research and to provide a research agenda the results of which would assist instructional designers in producing appropriate instructional materials to facilitate student achievement of the varied levels of performance outcomes.
Asymmetric Michael Addition Organocatalyzed by α,β-Dipeptides under Solvent-Free Reaction Conditions

The application of six novel α,β-dipeptides as chiral organocatalysts in the asymmetric Michael addition reaction between enolizable aldehydes and N-arylmaleimides or nitroolefins is described. With N-arylmaleimides as substrates, the best results were achieved with dipeptide 2 as a catalyst in the presence of aq. NaOH. Whereas dipeptides 4 and 6 in conjunction with 4-dimethylaminopyridine (DMAP) and thiourea as a hydrogen bond donor proved to be highly efficient organocatalytic systems in the enantioselective reaction between isobutyraldehyde and various nitroolefins.
An Accurate Range Model Based on the Fourth-Order Doppler Parameters for Geosynchronous SAR

This letter presents an accurate range model, named as Doppler parameter range model (DRM), to perform signal processing for geosynchronous synthetic aperture radar (Geo-SAR). Besides that a credible approach, defined as accurate coordinate numeric model (ACNM), is proposed to simulate the raw echo signals. To improve the accuracy of DRM and ACNM, the rotating Earth is modeled as an ellipsoid and the eccentricity of the satellite's orbit is analyzed. The superiority of DRM that it is more precise than hyperbolic range equation (HRE) and advanced hyperbolic range equation (AHRE), presented before, is illuminated. The point target 2-D frequency spectrum of DRM is derived. Finally, the simulation results validate that DRM and ACNM has a good effect on an L-Band Geo-SAR system with an azimuth resolution around 5 m.
Culture and Characterization of Epithelial Cells from Bovine Choroid Plexus

Abstract Epithelial cells were isolated from choroid plexus, which plays a major role in cerebrospinal fluid production and regulation. Incubation of bovine choroid plexuses with pronase released cells which attached to plastic dishes with a plating efficiency of 5%. The cells were predominantly polygonal as judged by phase‐contrast microscopy. These polygonal cells undergo limited cell division and survive for 1 – 2 weeks in culture before being overgrown by fibroblasts. The fibroblastic cells could be selectively removed from the cultures by the addition of 100 μg/ml cis‐hydroxyproline to the medium for several days. The specific activities of three membrane‐bound enzymes, γ‐glutamyl transpeptidase, alkaline phosphatase, and leucine aminopeptidase were compared in selective cultures of polygonal cells and fibroblasts. Polygonal cells were found to have 4–5 times the γ‐glutamyl transpeptidase of fibroblasts, whereas fibroblasts have 2–3 times the alkaline phosphatase of polygonal cells. Leucine aminopeptidase levels in the two cultures were roughly equivalent. The polygonal cells rapidly lost γ‐glutamyl transpeptidase activity over a 4‐day period in culture but acquired increased levels of leucine aminopeptidase. Alkaline phosphatase remained roughly constant. Under similar conditions fibroblasts showed a 3‐ to 4‐fold increase in the specific activities of all three enzymes; these changes coincided with a substantial increase in cell density. Based on morphology, resistance to cis‐hydroxyproline, absence of antihemophilic factor antigen, and enzymatic characteristics, we believe the polygonal cells to be of epithelial origin.
Results of resections for hepatocellular carcinoma in a new hepatobiliary unit

Background: Hepatocellular carcinoma (HCC) is the fourth commonest cancer in Singapore. Surgical resection offers the only chance of ‘cure’. Resection tends to be difficult in HCC because of late presentation and concomitant liver cirrhosis. Specialized units with higher volume of operations are known to produce better results. The present review aims to evaluate early results with HCC resection and discuss the correlation between various tumour prognostic factors and the outcome.
Limitations of routine spiral computerized tomography in the evaluation of blunt renal trauma.

PURPOSE We have observed that injury to the renal collecting system may be missed during routine abdominal spiral computerized tomography (CT) for trauma. A definitive protocol for spiral CT has been established to identify all cases of renal collecting system injury. MATERIALS AND METHODS A retrospective review of 35 consecutive cases of blunt renal trauma evaluated with spiral CT between 1994 and 1997 at our Level I trauma center was performed. Each patient received 100 cc intravenous contrast at 2 cc per second. There was a 60-second delay after the start of contrast infusion before scanning was initiated. RESULTS Of the 35 cases 3 (8.6%) injuries to the renal collecting system were detected on delayed scans obtained after the initial CT failed to demonstrate contrast extravasation. Therefore, at our institution we have modified the protocol for spiral CT for abdominal trauma by repeating scans of the kidneys after the initial scans are completed. CONCLUSIONS Injury to the renal collecting system may be missed during routine spiral CT, thereby incorrectly under staging renal trauma. In all cases of suspected blunt renal trauma evaluated with spiral CT repeat scans of the kidneys should be performed.
Presynaptic Induction and Expression of Homosynaptic Depression at Aplysia Sensorimotor Neuron Synapses

The cellular mechanisms underlying the induction and expression of homosynaptic depression at the glutamatergic synapse betweenAplysia sensory and motor neurons were studied in dissociated cell culture. Intracellular microelectrodes were used to stimulate action potentials in the presynaptic sensory neuron and record the depolarizing EPSP from the motor neuron. Homosynaptic depression (HSD) was induced by repeatedly stimulating the sensory neuron at rates as low as one action potential per minute. Activation of postsynaptic Glu receptors was neither sufficient nor necessary to induce HSD. Thus, repeated applications of exogenous Glu did not depress the synaptically evoked EPSP. Moreover, normal HSD was observed when the sensory neuron was stimulated during a period when the Glu receptors were blocked with the antagonist DNQX. The induction of HSD is thus likely to occur within the presynaptic terminal. We explored the role of presynaptic calcium in the induction of HSD by injecting the sensory neuron with EGTA, a relatively slow calcium chelator that does not alter rapid release but effectively buffers the slow residual calcium transient thought to be important for plasticity. EGTA had little effect on HSD, indicating that residual Caiis not involved. HSD does not appear to involve a decrease in presynaptic calcium influx, because there was no change in the presynaptic calcium transient, measured by calcium indicator dyes, during HSD. We conclude that HSD is induced and expressed in the presynaptic terminal, possibly by a mechanism directly coupled to the release process.
Mining a Written Values Affirmation Intervention to Identify the Unique Linguistic Features of Stigmatized Groups

Social identity threat refers to the process through which an individual underperforms in some domain due to their concern with confirming a negative stereotype held about their group. Psychological research has identified this as one contributor to the underperformance and underrepresentation of women, Blacks, and Latinos in STEM fields. Over the last decade, a brief writing intervention known as a values affirmation, has been demonstrated to reduce these performance deficits. Presenting a novel dataset of affirmation essays, we address two questions. First, what linguistic features discriminate gender and race? Second, can topic models highlight distinguishing patterns of interest between these groups? Our data suggest that participants who have different identities tend to write about some values (e.g., social groups) in fundamentally different ways. These results hold promise for future investigations addressing the linguistic mechanism responsible for the effectiveness of values affirmation interventions.
Basal Body Structures Differentially Affect Transcription of RpoN- and FliA-Dependent Flagellar Genes in Helicobacter pylori

ABSTRACT Flagellar biogenesis in Helicobacter pylori is regulated by a transcriptional hierarchy governed by three sigma factors, RpoD (σ80), RpoN (σ54), and FliA (σ28), that temporally coordinates gene expression with the assembly of the flagellum. Previous studies showed that loss of flagellar protein export apparatus components inhibits transcription of flagellar genes. The FlgS/FlgR two-component system activates transcription of RpoN-dependent genes though an unknown mechanism. To understand better the extent to which flagellar gene regulation is coupled to flagellar assembly, we disrupted flagellar biogenesis at various points and determined how these mutations affected transcription of RpoN-dependent (flaB and flgE) and FliA-dependent (flaA) genes. The MS ring (encoded by fliF) is one of the earliest flagellar structures assembled. Deletion of fliF resulted in the elimination of RpoN-dependent transcripts and an ∼4-fold decrease in flaA transcript levels. FliH is a cytoplasmic protein that functions with the C ring protein FliN to shuttle substrates to the export apparatus. Deletions of fliH and genes encoding C ring components (fliM and fliY) decreased transcript levels of flaB and flgE but had little or no effect on transcript levels of flaA. Transcript levels of flaB and flgE were elevated in mutants where genes encoding rod proteins (fliE and flgBC) were deleted, while transcript levels of flaA was reduced ∼2-fold in both mutants. We propose that FlgS responds to an assembly checkpoint associated with the export apparatus and that FliH and one or more C ring component assist FlgS in engaging this flagellar structure. IMPORTANCE The mechanisms used by bacteria to couple transcription of flagellar genes with assembly of the flagellum are poorly understood. The results from this study identified components of the H. pylori flagellar basal body that either positively or negatively affect expression of RpoN-dependent flagellar genes. Some of these basal body proteins may interact directly with regulatory proteins that control transcription of the H. pylori RpoN regulon, a hypothesis that can be tested by examining protein-protein interactions in vitro.
TWO-STEP SANDWICH ENZYME IMMUNOASSAY USING MONOCLONAL ANTIBODIES FOR DETECTION OF SOLUBLE AND MEMBRANE- ASSOCIATED HUMAN MEMBRANE TYPE 1-MATRIX METALLOPROTEINASE

ABSTRACT A two-step sandwich enzyme immunoassay (EIA) system for the detection of human membrane Type 1-matrix metalloproteinase (MT1-MMP) was established by using two monoclonal antibodies against recombinant MT1-MMP. MT1-MMP in which samples were reacted with solid-phase antibody and then detected with peroxidase-labeled second antibody. At least 1.25 ng/mL was detected by the EIA system, and linearity was obtained between 1.25 and 160 ng/mL. This EIA system is specific for MT1-MMP and did not show cross-reactivity against several other MMP's examined. Shedding of soluble MT1-MMP into the medium by some cancer cell lines was also detected by this system. However, soluble MT1-MMP in serum from normal and cancer patients was under the detection limit. Membrane-associated MT1-MMP of cancer cell lines was also detected after solubilization of the membranes with extraction buffer containing detergent. Additionally, MT1-MMP in clinical samples was examined. Elevated levels of MT1-MMP were detected in homogenate of cancer tissue compared with the levels for normal tissue and the level of MT1-MMP in tumors correlated with the rate of metastasis to the regional lymph nodes. Thus, we demonstrated that this EIA system is the first to measure MT1-MMP in clinical specimens, thus suggesting its useful for diagnosis of cancer or prediction of malignancy.
Clustering large data sets based on data compression technique and weighted quality measures

Various algorithms have been proposed for clustering large data sets for the hard and fuzzy case, not as much work has been done for automatic clustering approaches in which the number of clusters is unknown for the user. These approaches need some measures, called validity function to evaluate the clustering result and to give to the user the optimal number of clusters. In order to obtain this number, three conditions are necessary: (1) a good compression technique for data reduction with limited memory allocated, (b) good measures for the evaluation of the goodness of clusters for varying number of clusters, and (c) a good cluster algorithm that can automatically produce the number of clusters and takes into account the used compression technique. In this paper, we propose new clustering approaches which deals with new compression technique based on quality measures.
Journal of Complementary and Integrative Medicine Influence of Benefits , Barriers and Cues to Action for Complementary and Alternative Medicine Use among University Students

The purpose of the study was to explore the influence of perceived benefits, barriers, and cues to action on Complementary and Alternative Medicine (CAM) use among university students. This was a prospective, cross sectional questionnaire-based study conducted at a large urban university in Houston, Texas. Of the 400 students surveyed, 143 (35.8%) were current CAM users (used CAM in the past 12 months). Biologically based medications such as herbs, vitamins, supplements and natural products were found to be most profoundly used among students (42%). Perceived benefits (OR 9.14, 95% CI 4.64-18), barriers to CAM use (OR 0.49, 95% CI 0.27-0.89) and cues to action (OR 5.21, 95% CI 1.02-26.51) were significant determinants of CAM use among students. Perceived ability of CAM to improve body defenses was found to be the major perceived benefit for CAM use while lack of sufficient scientific testing was found to be the major barrier. Recommendation by health care provider and CAM use by parents and grandparents significantly (p < 0.0001) influenced current CAM use among students. Thus, perceived benefits and cues to action for CAM use significantly promoted CAM usage while perceived barriers were found to hinder CAM use among students.
Fine scale mapping of genomic introgressions within the Drosophila yakuba clade

The process of speciation involves populations diverging over time until they are genetically and reproductively isolated. Hybridization between nascent species was long thought to directly oppose speciation. However, the amount of interspecific genetic exchange (introgression) mediated by hybridization remains largely unknown, although recent progress in genome sequencing has made measuring introgression more tractable. A natural place to look for individuals with admixed ancestry (indicative of introgression) is in regions where species co-occur. In west Africa, D. santomea and D. yakuba hybridize on the island of São Tomé, while D. yakuba and D. teissieri hybridize on the nearby island of Bioko. In this report, we quantify the genomic extent of introgression between the three species of the Drosophila yakuba clade (D. yakuba, D. santomea), D. teissieri). We sequenced the genomes of 86 individuals from all three species. We also developed and applied a new statistical framework, using a hidden Markov approach, to identify introgression. We found that introgression has occurred between both species pairs but most introgressed segments are small (on the order of a few kilobases). After ruling out the retention of ancestral polymorphism as an explanation for these similar regions, we find that the sizes of introgressed haplotypes indicate that genetic exchange is not recent (>1,000 generations ago). We additionally show that in both cases, introgression was rarer on X chromosomes than on autosomes which is consistent with sex chromosomes playing a large role in reproductive isolation. Even though the two species pairs have stable contemporary hybrid zones, providing the opportunity for ongoing gene flow, our results indicate that genetic exchange between these species is currently rare. AUTHOR SUMMARY Even though hybridization is thought to be pervasive among animal species, the frequency of introgression, the transfer of genetic material between species, remains largely unknown. In this report we quantify the magnitude and genomic distribution of introgression among three species of Drosophila that encompass the two known stable hybrid zones in this genetic model genus. We obtained whole genome sequences for individuals of the three species across their geographic range (including their hybrid zones) and developed a hidden Markov model-based method to identify patterns of genomic introgression between species. We found that nuclear introgression is rare between both species pairs, suggesting hybrids in nature rarely successfully backcross with parental species. Nevertheless, some D. santomea alleles introgressed into D. yakuba have spread from São Tomé to other islands in the Gulf of Guinea where D. santomea is not found. Our results indicate that in spite of contemporary hybridization between species that produces fertile hybrids, the rates of gene exchange between species are low.