Miracle-dz/UniFAR-FTUs huggingface dataset:
Refined Requirements for Protein Regions Important for Activity of the TALE AvrBs3

AvrBs3, the archetype of the family of transcription activator-like (TAL) effectors from phytopathogenic Xanthomonas bacteria, is translocated by the type III secretion system into the plant cell. AvrBs3 localizes to the plant cell nucleus and activates the transcription of target genes. Crucial for this is the central AvrBs3 region of 17.5 34-amino acid repeats that functions as a DNA-binding domain mediating recognition in a “one-repeat-to-one base pair” manner. Although AvrBs3 forms homodimers in the plant cell cytosol prior to nuclear import, it binds DNA as a monomer. Here, we show that complex formation of AvrBs3 proteins negatively affects their DNA-binding affinity in vitro. The conserved cysteine residues at position 30 of each repeat facilitate AvrBs3 complexes via disulfide bonds in vitro but are also required for the gene-inducing activity of the AvrBs3 monomer, i.e., activation of plant gene promoters. Our data suggest that the latter is due to a contribution to protein plasticity and that cysteine substitutions to alanine or serine result in a different DNA-binding mode. In addition, our studies revealed that extended parts of both the N-terminal and C-terminal regions of AvrBs3 contribute to DNA binding and, hence, gene-inducing activity in planta.
Differential control of cytokeratins and vimentin synthesis by cell- cell contact and cell spreading in cultured epithelial cells

The expression of cytokeratins and vimentin was investigated in Madin- Darby bovine epithelial cells (MDBK) in culture under conditions of varied cell spreading and cell-cell contact. When extensive cell-cell contact was achieved by seeding cells at high density in monolayer, or in suspension culture in which multicellular aggregates formed, the cells synthesized high levels of cytokeratins and low levels of vimentin. In contrast, in sparse monolayer and suspension cultures where cell-cell contact was minimal, the cells synthesized very low levels of cytokeratins. The level of vimentin synthesis was high in sparse monolayer culture and was low in both sparse and dense suspension cultures. The ratio of cytokeratin to vimentin synthesis was not affected during the cell cycle, or when cell growth was inhibited by ara C and in serum-starvation-stimulation experiments. The variations in the synthesis of cytokeratins and vimentin under the various culture conditions were also reflected at the level of mRNA activity in a cell-free in vitro translation system and as determined by RNA blot hybridization with cDNA to vimentin and cytokeratins. The results suggest that control of cytokeratin synthesis involves cell- cell contact, characteristic of epithelia in vivo, while vimentin synthesis responds to alterations in cell spreading.
Sleep and reported daytime sleepiness in normal subjects: the Sleep Heart Health Study.

STUDY OBJECTIVES To describe the distribution of nocturnal sleep characteristics and reports of daytime sleepiness in a large well-defined group of healthy adults. DESIGN The Sleep Heart Health Study is a multicenter study examining sleep and cardiopulmonary parameters through nocturnal polysomnography in adults enrolled in geographically distinct cardiovascular cohorts. SETTING Community setting. PARTICIPANTS 470 subjects enrolled in the Sleep Heart Health Study (n = 6440) were selected as a 'normative' group based on screening of health conditions and daily habits that could interfere with sleep. MEASUREMENTS AND RESULTS Home-based nocturnal polysomnography was obtained on all participants and centrally scored for sleep and respiratory parameters. Demographic and health-related data were obtained and updated at the time of the home visit. Sleep efficiency decreased by 1.6% for each 10 years of increased age. Sleep time decreased by 0.1 hours (6.0 minutes) for each 10-year age increase and was longer in women. The arousal index increased by 0.8 for each 10-year increase in age and was lower by 1.4 in women. Women had a lower mean percentage of stage 1 and stage 2 sleep. Mean percentage of slow-wave sleep was higher in women (by 6.7%). Percentage of slow-wave sleep decreased with increased age for men only (by 1.9% for each 10-year age change). CONCLUSIONS Data suggest a clear lessening in the quantity and quality of sleep with age that appears to be more rapid in males compared to females.
A Simplified, Sensitive Phagocytic Assay for Malaria Cultures Facilitated by Flow Cytometry of Differentially-Stained Cell Populations

Background Phagocytosis of infected and uninfected erythrocytes is an important feature of malaria infections. Flow cytometry is a useful tool for studying phagocytic uptake of malaria-infected erythrocytes in vitro. However, current approaches are limited by the inability to discriminate between infected and uninfected erythrocytes and a failure to stain the early developmental ring stages of infected erythrocytes. The majority of infected erythrocytes in circulation are of the ring stage and these are therefore important targets to study. Methodology/Principal Findings In vitro P. falciparum cultures comprising infected and uninfected erythrocytes were labeled and exposed to cells derived from the human monocytic THP-1 cell line. Phagocytosis was assayed by flow cytometry. Dual labeling of Plasmodium DNA and erythrocyte cytoplasm with dihydroethidium and CellTrace™ Violet respectively allowed, for the first time, the detection and enumeration of phagocytes with ingested erythrocytes from both early ring- and late schizont-stage P, falciparum cultures. The sensitivity of the method was tested using varying conditions including phagocyte type (monocytes versus macrophages), parasite stage (rings versus schizonts), and negative (incubation with cytochalasin D) and positive (incubation with immune sera) effectors of phagocytosis. The current assay clearly demonstrated uptake of infected and uninfected erythrocytes exposed to phagocytes; the extent of which was dependent on the conditions mentioned. Conclusions We describe a simple, sensitive and rapid method for quantifying phagocytosis of P. falciparum-infected erythrocytes, by flow cytometry. This approach can be applied for studying parasite-phagocyte interactions under a variety of conditions. The investigation of phagocytosis of P. falciparum-infected erythrocytes can extend from looking solely at late-staged infected erythrocytes to include early-staged ones as well. It does away with the need to purify infected cells, allowing the study of effects on neighboring uninfected cells. This method may also be translated for use with different types of phagocytes.
Visual category recognition for the improved storage and retrieval performance of the CCTV camera system

In this paper, we propose a category level object recognition system for the efficient use of CCTV cameras in terms of storage and retrieval. We investigate the performance of the proposed approach by using four different classifiers. More specifically, we considered image sequences with cars, bikes and pedestrian as our three targeted object categories for classification and ultimately efficient storage and retrieval with reference to our CCTV cameras system. We utilized Linear Discriminant Analysis (LDA), Support Vector Machine (SVM), K-Nearest Neighbors (KNN) and Cartesian Genetic Programming (CGP) algorithms for the considered object categories classification. The Linear Discriminant Analysis (LDA), KNN and Support Vector Machine (SVM) are Statistical algorithms while Cartesian Genetic Programming (CGP) is Evolutionary Algorithm. More specifically, we utilized the standard “Caltech 101” dataset for investigating the performance of our proposed classifiers. Scale Invariant Feature Transform (SIFT) has been used to extract the scale, orientation and translational invariant features from the considered images which are input to the classifiers. Our empirical results show that in most of the cases, the results of LDA and SVM are relatively the same. To be specific, LDA gives an average accuracy of 85.3% and SVM 83.6%. Similarly, KNN gives an average accuracy of 74.6% while CGP outperforming the three gives accuracy rate of 89%.
Response of Soil CO2 Emission and Summer Maize Yield to Plant Density and Straw Mulching in the North China Plain

Demand for food security and the current global warming situation make high and strict demands on the North China Plain for both food production and the inhibition of agricultural carbon emissions. To explore the most effective way to decrease soil CO2 emissions and maintain high grain yield, studies were conducted during the 2012 and 2013 summer maize growing seasons to assess the effects of wheat straw mulching on the soil CO2 emissions and grain yield of summer maize by adding 0 and 0.6 kg m−2 to fields with plant densities of 100 000, 75 000, and 55 000 plants ha−1. The study indicated that straw mulching had some positive effects on summer maize grain yield by improving the 1000-kernel weight. Meanwhile, straw mulching effectively controlled the soil respiration rate and cumulative CO2 emission flux, particularly in fields planted at a density of 75 000 plants ha−1, which achieved maximum grain yield and minimum carbon emission per unit yield. In addition, soil microbial biomass and microbial activity were significantly higher in mulching treatments than in nonmulching treatments. Consequently, summer maize with straw mulching at 75 000 plants ha−1 is an environmentally friendly option in the North China Plain.
Beginning of exocytosis captured by rapid-freezing of Limulus amebocytes

Structural changes underlying exocytosis evoked by the application of endotoxin to Limulus amebocytes were studied at the level of detail afforded by freeze-fracture and freeze-substitution techniques combined with the time resolution of direct rapid-freezing. The results with amebocytes prepared in this manner differed from those with other secretory cells prepared by conventional means. Exocytosis begins within seconds of endotoxin treatment when the plasmalemma invaginates to form pedestallike appositions with peripheral secretory granules. The juxtaposed membranes at these pedestal appositions form several punctate pentalaminar contacts, but examination of freeze-fractured pedestals failed to reveal any corresponding changes in the intramembrane particle distribution. Small secretory granule openings or pores, which are very infrequent, appear within the first 5 s after endotoxin treatment. These pores rapidly widen and this widening is immediately followed by the sequential dissolution of the granule contents, which then move into the surrounding extracellular space. Cytoplasmic filaments connecting the plasmalemma with the granule membrane are suitably deployed to be responsible for the plasmalemma invaginations. How pores begin is not certain, but the appearance of clear spaces between the granule core and the granule membrane at this point in exocytosis supports the possibility of a role of osmotic forces.
Parkin (PARK 2) Mutations Are Rare in Czech Patients with Early-Onset Parkinson's Disease

Objective The aim of the study is to determine the frequency of parkin allelic variants in Czech early-onset Parkinson's disease patients and healthy controls. Methods A total of 70 early-onset Parkinson's disease patients (age at onset ≤40 years) and 75 controls were screened for the sequence variants and exon rearrangements in the parkin gene. Results Parkin mutations were identified in five patients (7.1%): the p.R334C point mutation was present in one patient, four patients had exon deletions. The detected mutations were observed in the heterozygous state except one homozygous deletion of the exon 4. No mutations were obtained in control subjects. A novel sequence variant p.V380I (c.1138G>A) was identified in one control. Non-pathogenic polymorphisms p.S167N and p.D394N were seen in similar percentage in patients and controls, polymorphism p.V380L was almost twice as frequent in controls as in patients. Conclusions Our study contributes to the growing body of evidence on the low frequency of the parkin mutations in the early-onset Parkinson's disease suggesting the potential role of other genes in the pathogenesis of the disease.
Essays on international capital flows

This thesis examines the impact of international capital flows on small open economies from a theoretical and empirical perspective. The �first chapter shows that where maturity mismatch is widespread, as in emerging markets, greater capital flow volatility negatively affects investment, output, and aggregate productivity. I build a model of a small open economy in which �financial frictions force �firms to engage in maturity mismatch, funding long-term projects with short-term debt. Greater uncertainty regarding the future availability of foreign borrowing causes �firms to cut long-term investment, depressing aggregate investment and generating an endogenous drop in aggregate productivity. The second chapter examines the relationship between capital flow volatility and economic performance using unique monthly frequency data set on international capital flows. I show that it is specifically the volatility of portfolio debt flows that negatively affects investment. Using �financial development as a proxy for the extent of maturity mismatch in the economy, I �find that the negative impact of debt flows is smaller where financial markets are more developed. Finally, I use industry-level data to show capital flow volatility depresses investment more in industries with longer average time-to-build. These �findings are consistent with a role for maturity mismatch in transmitting volatility shocks. The third chapter studies episodes of large capital in flows. These events are typically followed by an economic downturn and a reallocation of labor and capital into the nontradables sector. The extent of labor reallocation is significantly related to the depth and length of the post-episode downturn. We interpret our results using a model of a two sector economy, showing that capital in flows episodes generated by a fall in international interest rates or a rise in future productivity will push labor into the notradables sector. In flows caused by a productivity increase that has already occurred shift labor into tradables production. Allocation of labor therefore provides information on the underlying shock driving the capital inflows.
APOBEC3A Is a Specific Inhibitor of the Early Phases of HIV-1 Infection in Myeloid Cells

Myeloid cells play numerous roles in HIV-1 pathogenesis serving as a vehicle for viral spread and as a viral reservoir. Yet, cells of this lineage generally resist HIV-1 infection when compared to cells of other lineages, a phenomenon particularly acute during the early phases of infection. Here, we explore the role of APOBEC3A on these steps. APOBEC3A is a member of the APOBEC3 family that is highly expressed in myeloid cells, but so far lacks a known antiviral effect against retroviruses. Using ectopic expression of APOBEC3A in established cell lines and specific silencing in primary macrophages and dendritic cells, we demonstrate that the pool of APOBEC3A in target cells inhibits the early phases of HIV-1 infection and the spread of replication-competent R5-tropic HIV-1, specifically in cells of myeloid origins. In these cells, APOBEC3A affects the amount of vDNA synthesized over the course of infection. The susceptibility to the antiviral effect of APOBEC3A is conserved among primate lentiviruses, although the viral protein Vpx coded by members of the SIVSM/HIV-2 lineage provides partial protection from APOBEC3A during infection. Our results indicate that APOBEC3A is a previously unrecognized antiviral factor that targets primate lentiviruses specifically in myeloid cells and that acts during the early phases of infection directly in target cells. The findings presented here open up new venues on the role of APOBEC3A during HIV infection and pathogenesis, on the role of the cellular context in the regulation of the antiviral activities of members of the APOBEC3 family and more generally on the natural functions of APOBEC3A.
A six year satellite-based assessment of the regional variations in aerosol indirect effects

Abstract. Aerosols act as cloud condensation nuclei (CCN) for cloud water droplets, and changes in aerosol concentrations have significant microphysical impacts on the corresponding cloud properties. Moderate Resolution Imaging Spectroradiometer (MODIS) aerosol and cloud properties are combined with NCEP Reanalysis data for six different regions around the globe between March 2000 and December 2005 to study the effects of different aerosol, cloud, and atmospheric conditions on the aerosol indirect effect (AIE). Emphasis is placed in examining the relative importance of aerosol concentration, type, and atmospheric conditions (mainly vertical motion) to AIE from region to region. Results show that in most regions, AIE has a distinct seasonal cycle, though the cycle varies in significance and period from region to region. In the Arabian Sea (AS), the six-year mean anthropogenic + dust AIE is −0.27 Wm−2 and is greatest during the summer months (
The Chemical Compositions of the Type II Cepheids—The BL Herculis and W Virginis Variables

Abundance analyses from high-resolution optical spectra are presented for 19 type II Cepheids in the Galactic field. The sample includes both short-period (BL Her) and long-period (W Vir) stars. This is the first extensive abundance analysis of these variables. The C, N, and O abundances with similar spreads for the BL Her and W Vir show evidence for an atmosphere contaminated with 3α process and CN-cycling products. A notable anomaly of the BL Her stars is an overabundance of Na by a factor of about 5 relative to their presumed initial abundances. This overabundance is not seen in the W Vir stars. The abundance anomalies running from mild to extreme in W Vir stars but not seen in the BL Her stars are attributed to dust-gas separation that provides an atmosphere deficient in elements of high condensation temperature, notably, Al, Ca, Sc, Ti, and s-process elements. Such anomalies have previously been seen among RV Tau stars which represent a long-period extension of the variability enjoyed by the type II Cepheids. Comments are offered on how the contrasting abundance anomalies of BL Her and W Vir stars may be explained in terms of the stars' evolution from the blue horizontal branch.
Co-transplantation of olfactory ensheathing glia and mesenchymal stromal cells does not have synergistic effects after spinal cord injury in the rat.

BACKGROUND AIMS Olfactory ensheathing glia (OEG) and mesenchymal stromal cells (MSC) are suitable candidates for transplantation therapy of spinal cord injury (SCI). Both facilitate functional improvement after SCI by producing trophic factors and cytokines. In this study, the co-transplantation of both types of cells was studied to clarify their additive and/ or synergistic effects on SCI. METHODS A balloon-induced compression lesion was used to produce SCI in rats. OEG, MSC or both OEG and MSC (3 x 10(5) cells of each cell type) were implanted by intraspinal injection 1 week after SCI. The effect of transplantation was assessed using behavioral, electrophysiologic and histologic methods. RESULTS Hindlimb function was examined with Basso, Beattie and Bresnahan (BBB) and Plantar tests. Improvement was found in all three groups of transplanted rats with different time-courses, but there was no significant difference among the groups at the end of the experiment. Motor-evoked potentials after SCI decreased in amplitude from 7 mV to 10 microV. Linear regression analysis showed a modest recovery in amplitude following transplantation, but no change in the control rats. Histologic findings showed that the white and gray matter were significantly spared by transplantation after SCI. CONCLUSIONS Functional improvement was achieved with transplantation of OEG and/or MSC, but the co-transplantation of OEG and MSC did not show synergistic effects. The poor migration of OEG and MSC might prevent their concerted action. Pre-treatment with a Rho antagonist and a combination of intraspinal and intravenous injection of the cells might be beneficial for SCI therapy.
Expertise, attention, and memory in sensorimotor skill execution: Impact of novel task constraints on dual-task performance and episodic memory

Two experiments explored the attention and memory processes governing sensorimotor skill. Experiment 1 compared novice and experienced golf putting performance in single-task (putting in isolation) and dual-task conditions (putting while performing an auditory word search task). At specific intervals, participants also produced episodic descriptions of specific putts. Experiment 2 assessed novice performance following training on the same putting task. In Experiment 1, experienced golfers did not differ in putting accuracy from single- to dual-task conditions and, compared to novices, had higher recognition memory for words heard while putting but diminished episodic memories of specific putts. However, when using an s-shaped arbitrarily weighted “funny putter” designed to disrupt the mechanics of skill execution, experienced golfers produced extensive episodic memories of specific putts but showed decreased dual-task putting accuracy and recognition memory for secondary task words. Trained novices produced results intermediate between the untrained novices and experienced golfers. As predicted by current theories of practice-based automaticity, expertise leads to proceduralized control that does not require constant attention. Resources are free to devote to secondary task demands, yet episodic memory for primary task performance is impoverished. Novel task constraints (e.g., a funny putter) increase attention to execution, compromising secondary task performance but enhancing memory for skill execution.
The effect of overnourishing singleton-bearing adult ewes on nutrient partitioning to the gravid uterus

Overnourishing the singleton-bearing adolescent sheep throughout pregnancy promotes maternal tissue synthesis at the expense of the nutrient requirements of the gravid uterus. Consequently, the growth of the placenta is impaired and results in the premature delivery of low-birth-weight lambs relative to moderately fed adolescents of equivalent age. To establish if this phenomenon is unique to the growing animal, singleton pregnancies to a single sire were established by embryo transfer into primiparous adult ewes who had attained the normal mature body size for their genotype. Thereafter ewes were offered a maintenance or a high level of a complete diet throughout gestation. High maternal intakes resulted in elevated maternal insulin, no significant change in growth hormone or glucose, and attenuated progesterone and NEFA concentrations. Live weight gain during the first 93 d of gestation was 48 and 244 g/d, and adiposity score at term was 2·4 and 3·7 in the maintenance and high groups, respectively (P<0·001). In spite of achieving levels of adiposity similar to overnourished adolescents, placental (477 (sem 30) v. 518 (sem 41) g) and fetal (5190 (sem 320) v. 5420 (sem 250) g) weights were equivalent in maintenance and high groups. Gestation length was shorter (P<0·01) and colostrum yield at parturition lower (P<0·05) in high v. maintenance dams. Thus, adult sheep appear to be relatively insensitive to the oversupply of nutrients during pregnancy and have the ability to meet the nutrient requirements for normal conceptus growth in spite of their increased adiposity.