Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and Characterization of a Novel Plasmodium falciparum Merozoite Apical Protein Involved in Erythrocyte Binding and Invasion

Proteins that coat Plasmodium falciparum merozoite surface and those secreted from its apical secretory organelles are considered promising candidates for the vaccine against malaria. In the present study, we have identified an asparagine rich parasite protein (PfAARP; Gene ID PFD1105w), that harbors a predicted signal sequence, a C-terminal transmembrane region and whose transcription and translation patterns are similar to some well characterized merozoite surface/apical proteins. PfAARP was localized to the apical end of the merozoites by GFP-targeting approach using an inducible, schizont-stage expression system, by immunofluorescence assays using anti-PfAARP antibodies. Immuno-electron microsopic studies showed that PfAARP is localized in the apical ends of the rhoptries in the merozoites. RBC binding assays with PfAARP expressed on COS cells surface showed that it binds to RBCs through its N-terminal region with a receptor on the RBC surface that is sensitive to trypsin and neuraminidase treatments. Sequencing of PfAARP from different P. falciparum strains as well as field isolates showed that the N-terminal region is highly conserved. Recombinant protein corresponding to the N-terminal region of PfAARP (PfAARP-N) was produced in its functional form in E. coli. PfAARP-N showed reactivity with immune sera from individuals residing in P. falciparum endemic area. The anti-PfAARP-N rabbit antibodies significantly inhibited parasite invasion in vitro. Our data on localization, functional assays and invasion inhibition, suggest a role of PfAARP in erythrocyte binding and invasion by the merozoite.
Role of leptin in the regulation of glucagon-like peptide-1 secretion.

Glucagon-like peptide-1 (GLP-1), released from intestinal endocrine L cells, is a potent insulinotropic hormone. GLP-1 secretion is diminished in obese patients. Because obesity is linked to abnormal leptin signaling, we hypothesized that leptin may modulate GLP-1 secretion. Leptin significantly stimulated GLP-1 secretion (by up to 250% of control) from fetal rat intestinal cells, a mouse L cell line (GLUTag), and a human L cell line (NCI-H716) in a dose-dependent manner (P < 0.05-0.001). The long form of the leptin receptor was shown to be expressed, and leptin induced the phosphorylation of STAT3 in the three cell types. The leptin receptor was also expressed by rodent and human intestinal L cells, and leptin (1 mg/kg i.p.) significantly stimulated GLP-1 secretion in rats and ob/ob mice. To determine the effect of leptin resistance on GLP-1 secretion, C57BL/6 mice were fed a high-fat (45%) or low-fat (10%) diet for 8 weeks. Mice on the high-fat diet became obese; developed glucose intolerance, hyperinsulinemia, and hyperleptinemia; and were leptin resistant. Mice on the high-fat diet also had twofold lower basal plasma GLP-1 and a diminished GLP-1 response to oral glucose, by 28.5 +/- 5.0% (P < 0.05). These results show for the first time that leptin stimulates GLP-1 secretion from rodent and human intestinal L cells, and they suggest that leptin resistance may account for the decreased levels of GLP-1 found in obese humans.
The evolution of galaxy star formation activity in massive haloes

Context. There is now a large consensus that the current epoch of the cosmic star formation history (CSFH) is dominated by low mass galaxies while the most active phase, between redshifts 1 and 2, is dominated by more massive galaxies, which evolve more quickly. Aims. Massive galaxies tend to inhabit very massive haloes, such as galaxy groups and clusters. We aim to understand whether the observed “galaxy downsizing” could be interpreted as a “halo downsizing”, whereas the most massive haloes, and their galaxy populations, evolve more rapidly than the haloes with lower mass. Methods. We studied the contribution to the CSFH of galaxies inhabiting group-sized haloes. This is done through the study of the evolution of the infra-red (IR) luminosity function of group galaxies from redshift 0 to redshift ~1.6. We used a sample of 39 X-ray-selected groups in the Extended Chandra Deep Field South (ECDFS), the Chandra Deep Field North (CDFN), and the COSMOS field, where the deepest available mid- and far-IR surveys have been conducted with Spitzer MIPS and with the Photodetector Array Camera and Spectrometer (PACS) on board the Herschel satellite. Results. Groups at low redshift lack the brightest, rarest, and most star forming IR-emitting galaxies observed in the field. Their IR-emitting galaxies contribute ≤10% of the comoving volume density of the whole IR galaxy population in the local Universe. At redshift ≳1, the most IR-luminous galaxies (LIRGs and ULIRGs) are mainly located in groups, and this is consistent with a reversal of the star formation rate (SFR) vs. density anti-correlation observed in the nearby Universe. At these redshifts, group galaxies contribute 60–80% of the CSFH, i.e. much more than at lower redshifts. Below z ~ 1, the comoving number and SFR densities of IR-emitting galaxies in groups decline significantly faster than those of all IR-emitting galaxies. Conclusions. Our results are consistent with a “halo downsizing” scenario and highlight the significant role of “environment” quenching in shaping the CSFH.
Diversity and fruiting patterns of ectomycorrhizal and saprobic fungi in an old-growth Mediterranean forest dominated by Quercus ilex L.

We collected and mapped epigeous fruitbodies of both ectomycorrhizal (ECM) and saprobic fungi in an old- growth Quercus ilex L. Mediterranean forest within a permanent transect of 6400 m 2 over three consecutive fruiting seasons. Out of 5382 fruitbodies, a total of 234 species were found, including 166 and 68 ECM and saprobic taxa, re- spectively. Both communities were mainly composed of rare species. Two genera, Russula and Cortinarius, accounted for 34.4% of ECM fruitbodies and 50% of species diversity. The three most abundant ECM species were Laccaria laccata (Scop.: Fr.) Berk. & Broome, Inocybe tigrina R. Heim, and Lactarius chrysorrheus Fr. The fruiting ECM com- munity encompassed a few Mediterranean species and numerous broad host range temperate species. We also analysed the fruiting patterns in relation to forest structure, host composition, and natural canopy gaps. The results showed (i )a significant correlation of species richness to tree density, (ii) a richness decrease as the number of vegetation layers in- creases, and (iii) a preferential fruiting of some species near Q. ilex or Arbutus unedo L. Another noteworthy feature was that richness and production were greatly enhanced in canopy gaps. Selective fruiting was also observed among species. These results highlight the importance of forest structure and large woody debris for fungal conservation.
Topic modeling for analyzing open-ended survey responses

ABSTRACT Open-ended responses are widely used in market research studies. Processing of such responses requires labour-intensive human coding. This paper focuses on unsupervised topic models and tests their ability to automate the analysis of open-ended responses. Since state-of-the-art topic models struggle with the shortness of open-ended responses, the paper considers three novel short text topic models: Latent Feature Latent Dirichlet Allocation, Biterm Topic Model and Word Network Topic Model. The models are fitted and evaluated on a set of real-world open-ended responses provided by a market research company. Multiple components such as topic coherence and document classification are quantitatively and qualitatively evaluated to appraise whether topic models can replace human coding. The results suggest that topic models are a viable alternative for open-ended response coding. However, their usefulness is limited when a correct one-to-one mapping of responses and topics or the exact topic distribution is needed.
Women and Education in Saudi Arabia: Challenges and Achievements.

The historical socio-economic and political conditions of Saudi Arabia are an essential aspect of understanding a woman’s position in Saudi society. The persistence of women’s exclusion from public life in contemporary Saudi Arabia is one of the most heated debates not only among Muslims but also worldwide, as Saudi society comes under more and more scrutiny internationally. In 1980, there were more female graduates in the humanities than male. University women could study most of the same subjects as their male counterparts except those, which might lead to their mixing with men. This paper explores some of the restraints and achievements of women in the field of education in Saudi Arabia today.
Developing a Test of Scientific Literacy Skills (TOSLS): Measuring Undergraduates’ Evaluation of Scientific Information and Arguments

Life sciences faculty agree that developing scientific literacy is an integral part of undergraduate education and report that they teach these skills. However, few measures of scientific literacy are available to assess students’ proficiency in using scientific literacy skills to solve scenarios in and beyond the undergraduate biology classroom. In this paper, we describe the development, validation, and testing of the Test of Scientific Literacy Skills (TOSLS) in five general education biology classes at three undergraduate institutions. The test measures skills related to major aspects of scientific literacy: recognizing and analyzing the use of methods of inquiry that lead to scientific knowledge and the ability to organize, analyze, and interpret quantitative data and scientific information. Measures of validity included correspondence between items and scientific literacy goals of the National Research Council and Project 2061, findings from a survey of biology faculty, expert biology educator reviews, student interviews, and statistical analyses. Classroom testing contexts varied both in terms of student demographics and pedagogical approaches. We propose that biology instructors can use the TOSLS to evaluate their students’ proficiencies in using scientific literacy skills and to document the impacts of curricular reform on students’ scientific literacy.
Inflammatory and hemostatic biomarkers associated with early recurrent ischemic lesions in acute ischemic stroke.

BACKGROUND AND PURPOSE Early recurrent ischemic lesions (ERILs) on diffusion-weighted imaging after acute ischemic stroke have been suggested as a potential marker of early recurrent stroke. We hypothesized that biomarkers of inflammation or coagulation may be associated with the pathogenesis of ERILs and sought to investigate whether these biomarkers provide prognostic information on the risk of development of ERILs independently of clinical and imaging variables. METHODS This prospective study enrolled 153 consecutive patients with acute ischemic stroke who underwent diffusion-weighted imaging within 24 hours and subsequently at 5 days after onset and whose plasma or serum for biomarkers (C-reactive protein, fibrinogen, d-dimer, tissue plasminogen activator, and plasminogen activator inhibitor-1) were collected within 24 hours of onset. Those receiving thrombolysis or interventional therapy were excluded. ERILs were defined as new ischemic lesions on 5-day diffusion-weighted imaging separate from the index stroke lesions, which were not accompanied by subsequent recanalization. RESULTS ERILs were observed in 37 patients (24.2%). In univariate analysis, shorter time from onset to initial MRI (P=0.013), initial acute multiple infarcts (P<0.001), initial larger infarct volume (P=0.005), stroke subtype (P<0.001), elevated d-dimer (P=0.028), and anticoagulation after admission (P=0.001) were associated with ERILs. In multivariate analysis, initial acute multiple infarcts (OR, 16.60; 95% CI, 5.73 to 48.08), large artery atherosclerosis (OR, 4.62; 95% CI, 1.51 to 14.11), and log d-dimer (OR, 3.20; 95% CI, 1.14 to 9.00) remained independent predictors of ERILs. CONCLUSIONS These data suggest that elevated d-dimer level reflecting increase of thrombin generation and fibrin turnover may be an independent factor predicting ERILs.
Time to Measure the Pi

The Raspberry Pi platform is increasingly being used for network measurement due to its low cost, ease of deployment, and ability to run Linux. Timestamps are a critical part of measurement data, yet the suitability of the Pi for timing has not been established. We use reference hardware to characterize the Pi's STC hardware counter, and to evaluate its performance when paired with a low cost yet powerful GPS 'hat'. We find that the platform can support timing adequate for most measurement purposes, but with some caveats.
The cross-correlation between galaxies and groups: probing the galaxy distribution in and around dark matter haloes

We determine cross-correlation function between galaxies and galaxy groups, using both the Two-Degree Field Galaxy Redshift Survey (2dFGRS) and the Sloan Digital Sky Survey (SDSS). Groups are identified using the halo-based group finder developed by Yang et al., which is optimized to associate to a group those galaxies which belong to the same dark matter halo. Our galaxy-group cross-correlation function is therefore a surrogate for the galaxy-halo cross-correlation function. We study the cross-correlation as a function of group mass, and as a function of the luminosity, stellar mass, colour, spectral type and specific star formation rate of the galaxies. All these cross-correlation functions show a clear transition from the 'one-halo' to the 'two-halo' regimes on a scale comparable to the virial radius of the groups under consideration. On scales larger than the virial radius, all cross-correlation functions are roughly parallel, consistent with the linear bias model. In particular, the large-scale correlation amplitudes are higher for more massive groups, and for brighter and redder galaxies. In the 'one-halo' regime, the cross-correlation function depends strongly on the definition of the group centre. We consider both a luminosity-weighted centre (LW centre) and a centre defined by the location of the brightest group galaxy (BG centre). With the first definition, the bright early-type galaxies in massive groups are found to be more centrally concentrated than the fainter, late-type galaxies. Using the BG centre, and excluding the brightest galaxy from the cross-correlation analysis, we only find significant segregation in massive groups (M greater than or similar to 10(13)h(-1) M-circle dot) for galaxies of different spectral types (or colours or specific star formation rates). In haloes with masses less than or similar to 10(13)h(-1) M-circle dot, there is a significant deficit of bright satellite galaxies. Comparing the results from the 2dFGRS with those obtained from realistic mock samples, we find that the distribution of galaxies in groups is much less concentrated than dark matter haloes predicted by the current Lambda CDM model.
Human OATP1B1, OATP1B3 and OATP1A2 can mediate the in vivo uptake and clearance of docetaxel

Organic anion transporting polypeptides (human: OATPs and mouse: Oatps) are uptake transporters with important roles in drug pharmacokinetics and toxicity. We aimed to study the in vivo impact of mouse and human OATP1A/1B transporters on docetaxel plasma clearance and liver and intestinal uptake. Docetaxel was administered to Oatp1a/1b knockout and liver‐specific humanized OATP1B1, OATP1B3 and OATP1A2 transgenic mice. Experiments were conducted with a low polysorbate 80 (2.8%) formulation, as 8% polysorbate somewhat inhibited docetaxel plasma clearance after intravenous administration. After intravenous administration (10 mg/kg), Oatp1a/1b knockout mice had an approximately threefold higher plasma area under the curve (AUC). Impaired liver uptake was evident from the significantly reduced (approximately threefold) liver‐to‐plasma AUC ratios. Absence of mouse Oatp1a/1b transporters did not affect the intestinal absorption of orally administered docetaxel (10 mg/kg), while the systemic exposure of docetaxel was again substantially increased owing to impaired liver uptake. Most importantly, liver‐specific expression of each of the human OATP1B1, OATP1B3 and OATP1A2 transporters provided a nearly complete rescue of the increased plasma levels of docetaxel in Oatp1a/1b‐null mice after intravenous administration. Our data show that one or more of the mouse Oatp1a/1b transporters and each of the human OATP1A/1B transporters can mediate docetaxel uptake in vivo. This might be clinically relevant for OATP1A/1B‐mediated tumor uptake of docetaxel and for docetaxel clearance in patients in whom the transport activity of OATP1A/1B transporters is reduced owing to genetic variation or pharmacological inhibition, leading to potentially altered toxicity and therapeutic efficacy of this drug.
Modulation of Ether-à-Go-Go Related Gene (ERG) Current Governs Intrinsic Persistent Activity in Rodent Neocortical Pyramidal Cells

While cholinergic receptor activation has long been known to dramatically enhance the excitability of cortical neurons, the cellular mechanisms responsible for this effect are not well understood. We used intracellular recordings in rat (both sexes) neocortical brain slices to assess the ionic mechanisms supporting persistent firing modes triggered by depolarizing stimuli following cholinergic receptor activation. We found multiple lines of evidence suggesting that a component of the underlying hyperexcitability associated with persistent firing reflects a reduction in the standing (leak) K+ current mediated by Ether-a-go-go-Related Gene (ERG) channels. Three chemically diverse ERG channel blockers (terfenadine, ErgToxin-1, and E-4031) abolished persistent firing and the underlying increase in input resistance in deep pyramidal cells in temporal and prefrontal association neocortex. Calcium accumulation during triggering stimuli appears to attenuate ERG currents, leading to membrane potential depolarization and increased input resistance, two critical elements generating persistent firing. Our results also suggest that ERG current normally governs cortical neuron responses to depolarizing stimuli by opposing prolonged discharges and by enhancing the poststimulus repolarization. The broad expression of ERG channels and the ability of ERG blocks to abolish persistent firing evoked by both synaptic and intracellular step stimuli suggest that modulation of ERG channels may underlie many forms of persistent activity observed in vivo. SIGNIFICANCE STATEMENT Persistent activity, where spiking continues beyond the triggering stimulus, is a common phenomenon observed in many types of neurons. Identifying the mechanism underlying this elementary process of memory is a step forward in understanding higher cognitive function including short-term memory. Our results suggest that a reduction in the currents normally mediated by Ether-a-go-go-Related Gene (ERG) K+ channels contributes to persistent firing in neocortical pyramidal cells. ERG currents have been previously studied primarily in the heart; relatively little is known about ERG function in the brain, although mutations in ERG channels have recently been linked to schizophrenia. The present study is among the first to describe its role in neocortex in relation to biophysical correlates of memory function.
Regulation of USP28 Deubiquitinating Activity by SUMO Conjugation*

Background: USP28 is a deubiquitinating enzyme implicated in the DNA damage response, Myc stabilization, and cancer progression. Results: USP28 activity is regulated by SUMO conjugation on the N-terminal region. Conclusion: The N-terminal ubiquitin-binding domains of USP28 are not required for polyubiquitin processing. Significance: Cross-talk exists between SUMO and ubiquitin in the regulation of USP28 enzymatic activity. USP28 (ubiquitin-specific protease 28) is a deubiquitinating enzyme that has been implicated in the DNA damage response, the regulation of Myc signaling, and cancer progression. The half-life stability of major regulators of critical cellular pathways depends on the activities of specific ubiquitin E3 ligases that target them for proteosomal degradation and deubiquitinating enzymes that promote their stabilization. One function of the post-translational small ubiquitin modifier (SUMO) is the regulation of enzymatic activity of protein targets. In this work, we demonstrate that the SUMO modification of the N-terminal domain of USP28 negatively regulates its deubiquitinating activity, revealing a role for the N-terminal region as a regulatory module in the control of USP28 activity. Despite the presence of ubiquitin-binding domains in the N-terminal domain, its truncation does not impair deubiquitinating activity on diubiquitin or polyubiquitin chain substrates. In contrast to other characterized USP deubiquitinases, our results indicate that USP28 has a chain preference activity for Lys11, Lys48, and Lys63 diubiquitin linkages.
Grasping force control of multi-fingered robot hand based on slip detection using tactile sensor

To achieve a human like grasping with a multi- fingered robot hand, the grasping force should be controlled without using information from the grasped object such as its weight and friction coefficient. In this study, we propose a method for detecting the slip of a grasped object using the force output of Center of Pressure (CoP) tactile sensors. CoP sensors can measure the center position of a distributed load and the total load applied on the surface of the sensor, within 1 ms. These sensors are arranged on the fingers of the robot hand, and their effectiveness as slip detecting sensors is confirmed in tests of slip detection during grasping. Finally, we propose a method for controlling grasping force to resist tangential force applied to the grasped object using a feedback control system with the CoP sensor force output.
Effects of external airway obstruction on work capacity and pulmonary gas exchange.

The effects of artificial airway obstruction on the respiratory responses to exercise are of interest for several reasons. First, such obstruc­ tion provides a first approximation model of clinical obstructive disease in which the quantita­ tive effects of the obstruction can be studied independent of the ·physical training status of the subject. This permits the measurement of any changes in oxygen consumption (Vo2) in the presence and absence of a specific degree of obstruction to delineate any potential limita­ tions of aerobic capacity. Second, this approach permits the study of the separate effects of expiratory or inspiratory obstruction and their combination. Differences associated with the site of obstruction might be anticipated because inspiration is the active phase of respiration and because Hanson and associates (1) have reported a reduction in pulmonary compliance in the presence of external expiratory respiratory obstruction Third, the effects of the changes in transpulmonary pressures associated with the obstruction might produce changes in intra­ pulmonary gas exchange mechanisms. Such effects are well recognized with sustained Mueller and Valsalva maneuvers (2) and modification of intrapulmonary gas exchange mechanisms has been reported in the presence of external expira­ tory obstruction (3). The use of external obstruc­ tion permits the study of the effects of these changes in intrathoracic pressure in the absence of lung disease. This study was designed to define the effects of the three types of external obstruction on intrapulmonary gas exchange mechanisms and Vo2 during exercise up to workloads approaching maximal oxygen consumption.