Miracle-dz/UniFAR-FTUs huggingface dataset:
A combined rheometry and imaging study of viscosity reduction in bacterial suspensions

Significance A pot of paint is more viscous than water due to many “bits and pieces” suspended in paint, such as pigment particles. Amazingly, the viscosity of a dilute suspension of swimming bacteria has been found to be lower than that of water. A number of theories claim to explain this effect. We test a crucial prediction of one of these theories, viz., that viscosity reduction should be strongly dependent on the system size in which the measurements are made. Such strong size dependence was not observed. Instead, we find direct evidence that when the viscosity of the bacterial suspension is reduced to near zero, the swimming microbes begin to “swarm” in a way reminiscent of flocking in birds or fish. Suspending self-propelled “pushers” in a liquid lowers its viscosity. We study how this phenomenon depends on system size in bacterial suspensions using bulk rheometry and particle-tracking rheoimaging. Above the critical bacterial volume fraction needed to decrease the viscosity to zero, ϕc≈0.75%, large-scale collective motion emerges in the quiescent state, and the flow becomes nonlinear. We confirm a theoretical prediction that such instability should be suppressed by confinement. Our results also show that a recent application of active liquid-crystal theory to such systems is untenable.
Single cell analysis reveals human cytomegalovirus drives latently infected cells towards an anergic-like monocyte state

Human cytomegalovirus (HCMV) causes a lifelong infection through establishment of latency. Although reactivation from latency can cause life-threatening disease, our molecular understanding of HCMV latency is incomplete. Here we use single cell RNA-seq analysis to characterize latency in monocytes and hematopoietic stem and progenitor cells (HSPCs). In monocytes, we identify host cell surface markers that enable enrichment of latent cells harboring higher viral transcript levels, which can reactivate more efficiently, and are characterized by reduced intrinsic immune response that is important for viral gene expression. Significantly, in latent HSPCs, viral transcripts could be detected only in monocyte progenitors and were also associated with reduced immune-response. Overall, our work indicates that regardless of the developmental stage in which HCMV infects, HCMV drives hematopoietic cells towards a weaker immune-responsive monocyte state and that this anergic-like state is crucial for the virus ability to express its transcripts and to eventually reactivate.
Discontinuous Galerkin method for computing gravitational waveforms from extreme mass ratio binaries

Gravitational wave emission from extreme mass ratio binaries (EMRBs) should be detectable by the joint NASA–ESA LISA project, spurring interest in analytical and numerical methods for investigating EMRBs. We describe a discontinuous Galerkin (dG) method for solving the distributionally forced 1+1 wave equations which arise when modeling EMRBs via the perturbation theory of Schwarzschild black holes. Despite the presence of jump discontinuities in the relevant polar and axial gravitational ‘master functions’, our dG method achieves global spectral accuracy, provided that we know the instantaneous position, velocity and acceleration of the small particle. Here these variables are known, since we assume that the particle follows a timelike geodesic of the Schwarzschild geometry. We document the results of several numerical experiments testing our method, and in our concluding section discuss the possible inclusion of gravitational self-force effects.
Utility of primary cells to examine NPC1 receptor expression in Mops condylurus, a potential Ebola virus reservoir

The significance of the integral membrane protein Niemann-Pick C1 (NPC1) in the ebolavirus entry process has been determined using various cell lines derived from humans, non-human primates and fruit bats. Fruit bats have long been purported as the potential reservoir host for ebolaviruses, however several studies provide evidence that Mops condylurus, an insectivorous microbat, is also an ebolavirus reservoir. NPC1 receptor expression in the context of ebolavirus replication in microbat cells remains unstudied. In order to study Ebola virus (EBOV) cellular entry and replication in M. condylurus, we derived primary and immortalized cell cultures from 12 different organs. The NPC1 receptor expression was characterized by confocal microscopy and flow cytometry comparing the expression levels of M. condylurus primary and immortalized cells, HeLa cells, human embryonic kidney cells and cells from a European microbat species. EBOV replication kinetics was studied for four representative cell cultures using qRT-PCR. The aim was to elucidate the suitability of primary and immortalized cells from different tissues for studying NPC1 receptor expression levels and their potential influence on EBOV replication. The NPC1 receptor expression level in M. condylurus primary cells differed depending on the organ they were derived from and was for most cell types significantly lower than in human cell lines. Immortalized cells showed for most cell types higher expression levels than their corresponding primary cells. Concluding from our infection experiments with EBOV we suggest a potential correlation between NPC1 receptor expression level and virus replication rate in vitro.
Acrosin is essential for sperm penetration through the zona pellucida in hamsters

Significance Mammalian oocytes are surrounded by the zona pellucida, a glycoprotein coat that protects the oocyte and embryo from mechanical damage during their preimplantation development within the oviduct. Fertilizing spermatozoa must penetrate the zona, but we do not know the exact mechanisms underlying this process. Sperm proteases were thought to work as zona lysins, but gene-knockout studies in mice did not support this assumption. In this study, we generated hamsters without acrosin, the major acrosomal protease, to examine its role in both in vivo and in vitro fertilization. Surprisingly, mutant male hamsters were completely infertile because their spermatozoa were unable to penetrate the zona. We thus demonstrated that, at least in hamsters, acrosin is essential for sperm penetration through the zona. During natural fertilization, mammalian spermatozoa must pass through the zona pellucida before reaching the plasma membrane of the oocyte. It is assumed that this step involves partial lysis of the zona by sperm acrosomal enzymes, but there has been no unequivocal evidence to support this view. Here we present evidence that acrosin, an acrosomal serine protease, plays an essential role in sperm penetration of the zona. We generated acrosin-knockout (KO) hamsters, using an in vivo transfection CRISPR/Cas9 system. Homozygous mutant males were completely sterile. Acrosin-KO spermatozoa ascended the female genital tract and reached ovulated oocytes in the oviduct ampulla, but never fertilized them. In vitro fertilization (IVF) experiments revealed that mutant spermatozoa attached to the zona, but failed to penetrate it. When the zona pellucida was removed before IVF, all oocytes were fertilized. This indicates that in hamsters, acrosin plays an indispensable role in allowing fertilizing spermatozoa to penetrate the zona. This study also suggests that the KO hamster system would be a useful model for identifying new gene functions or analyzing human and animal disorders because of its technical facility and reproducibility.
The ‘indisciplinarity’ of stylistics

Abstract This paper aims at showing why the stylistician can be construed as a prolific “impostor” in a most positive sense: pledged to no specific linguistic prophet, she can opt for different theoretical linguistic tools (in the sphere of pragmatics, critical discourse analysis, cognitive grammar, etc.) depending on her object of study and what her research question is. The liberty claimed by the stylistician explains why stylistics is the “undisciplined” child of linguistics, shirking any clear definition of its boundaries. It will be argued that stylistics can only exist as a cross-disciplinary field given its conception of language as fundamentally contextualized. If it was a discipline determined by clear-cut pre-established boundaries, stylistics would be far more “disciplined” but would run the risk of serving only itself. The broad goal of this paper is thus to evince that the “indisciplinarity” of stylistics constitutes its very defining essence. With this aim in mind, it will demonstrate what stylistics owes to other disciplines, what it shares with similar language-based disciplines and what it can offer to other fields or practices of knowledge.
Testing ecological interactions between Gnomoniopsis castaneae and 14

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Navigating Through Time: A Spatial Navigation Perspective on How the Brain May Encode Time.

Interval timing, which operates on timescales of seconds to minutes, is distributed across multiple brain regions and may use distinct circuit mechanisms as compared to millisecond timing and circadian rhythms. However, its study has proven difficult, as timing on this scale is deeply entangled with other behaviors. Several circuit and cellular mechanisms could generate sequential or ramping activity patterns that carry timing information. Here we propose that a productive approach is to draw parallels between interval timing and spatial navigation, where direct analogies can be made between the variables of interest and the mathematical operations necessitated. Along with designing experiments that isolate or disambiguate timing behavior from other variables, new techniques will facilitate studies that directly address the neural mechanisms that are responsible for interval timing. Expected final online publication date for the Annual Review of Neuroscience, Volume 43 is July 8, 2020. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.
Widespread remodeling of proteome solubility in response to different protein homeostasis stresses

Significance The protein homeostasis system prevents proteins from misfolding and aggregation. It is unclear, however, how this system is organized to fulfil this role under different insults. To investigate this problem, we examined how six different stresses affected proteome solubility in a mouse neuroblastoma cell line. We found that, although different stresses substantially changed the solubility of many proteins, no proteins substantially aggregated in common. Instead, each stress distinctly remodeled protein–ligand networks involved in key cellular processes, notably SG formation and metabolism. We conclude that cells are endowed with a wide range of regulatory responses, which are tailored for distinct stresses and buffer against widespread protein aggregation. The accumulation of protein deposits in neurodegenerative diseases has been hypothesized to depend on a metastable subproteome vulnerable to aggregation. To investigate this phenomenon and the mechanisms that regulate it, we measured the solubility of the proteome in the mouse Neuro2a cell line under six different protein homeostasis stresses: 1) Huntington’s disease proteotoxicity, 2) Hsp70, 3) Hsp90, 4) proteasome, 5) endoplasmic reticulum (ER)-mediated folding inhibition, and 6) oxidative stress. Overall, we found that about one-fifth of the proteome changed solubility with almost all of the increases in insolubility were counteracted by increases in solubility of other proteins. Each stress directed a highly specific pattern of change, which reflected the remodeling of protein complexes involved in adaptation to perturbation, most notably, stress granule (SG) proteins, which responded differently to different stresses. These results indicate that the protein homeostasis system is organized in a modular manner and aggregation patterns were not correlated with protein folding stability (ΔG). Instead, distinct cellular mechanisms regulate assembly patterns of multiple classes of protein complexes under different stress conditions.
Novel Intranasal Drug Delivery: Geraniol Charged Polymeric Mixed Micelles for Targeting Cerebral Insult as a Result of Ischaemia/Reperfusion

Brain damage caused by cerebral ischaemia/reperfusion (I/R) can lead to handicapping. So, the present study aims to evaluate the prophylactic and therapeutic effects of geraniol in the form of intranasal polymeric mixed micelle (PMM) on the central nervous system in cerebral ischaemia/reperfusion (I/R) injury. A 32 factorial design was used to prepare and optimize geraniol PMM to investigate polymer and stabilizer different concentrations on particle size (PS) and percent entrapment efficiency (%EE). F3 possessing the highest desirability value (0.96), with a PS value of 32.46 ± 0.64 nm, EE of 97.85 ± 1.90%, and release efficiency of 59.66 ± 0.64%, was selected for further pharmacological and histopathological studies. In the prophylactic study, animals were classified into a sham-operated group, a positive control group for which I/R was done without treatment, and treated groups that received vehicle (plain micelles), geraniol oil, and geraniol micelles intranasally before and after I/R. In the therapeutic study, treated rats received geraniol oil and micelles after I/R. Evaluation of the effect of geraniol on behavior was done by activity cage and rotarod and the analgesic effect tested by hot plate. Anti-inflammatory activity was assessed by measuring interleukin β6, cyclooxygenase-2, hydrogen peroxide, and inducible nitric oxide synthase. Histopathogical examination of cerebral cortices was also done to confirm the results of a biochemical assay. Geraniol nanostructured polymeric mixed micelles showed an enhanced neuro-protective effect compared to geraniol oil, confirming that PMM via intranasal route could be an efficient approach for delivering geraniol directly to the brain through crossing the blood–brain barrier.
Evaluation of Crocins in Cheeses Made with Saffron by UHPLC

Saffron is a widespread consumed spice with potential health promoting compounds. In dairy technologies it is often used to enhance color and flavor of cheeses, so it would be recommended to know the content of saffron functional compounds in cheese made with this spice, as they could still have potential bioactivity. For this purpose, an UHPLC (ultra high performance liquid chromatography) method was developed, with the aim of reducing analysis time and solvent consumption. A methanol:water solution (80:20 v/v) was used to extract saffron compounds from cheese with stirring for 1 h in the dark at room temperature, then the samples were centrifuged at 3500 rpm, for 5 min at 4 °C and the residues were extracted twice. A linear gradient elution of acetonitrile in water allowed to simultaneously determine picrocrocin and crocins in saffron in a short time (16 min), and allowed a quantitative determination of crocins in commercial cheeses.
Antibiotic Exposure and Risk for Hospital-Associated Clostridioides difficile Infection

Clostridioides difficile infection (CDI) is a health care-associated infection associated with significant morbidity and cost, with highly varied risk across populations. More effective, risk-based prevention strategies are needed. Here, we investigate risk factors for hospital-associated CDI in a large integrated health system. In a retrospective cohort of all adult admissions to 21 Intermountain Healthcare hospitals from 2006 to 2012, we identified all symptomatic (i) hospital-onset and (ii) health care-facility-associated, community-onset CDI. ABSTRACT Clostridioides difficile infection (CDI) is a health care-associated infection associated with significant morbidity and cost, with highly varied risk across populations. More effective, risk-based prevention strategies are needed. Here, we investigate risk factors for hospital-associated CDI in a large integrated health system. In a retrospective cohort of all adult admissions to 21 Intermountain Healthcare hospitals from 2006 to 2012, we identified all symptomatic (i) hospital-onset and (ii) health care-facility-associated, community-onset CDI. We then evaluated the risk associated with antibiotic exposure, including that of specific agents, using multivariable logistic regression. A total of 2,356 cases of CDI among 506,068 admissions were identified (incidence, 46.6 per 10,000). Prior antibiotic use was the dominant risk factor, where for every antibiotic day of therapy prior to the index admission, the odds of subsequent CDI increased by 12.8% (95% confidence interval [CI], 12.2 to 13.4%; P < 0.0001). This was a much stronger association than was inpatient antibiotic exposure (odds ratio [OR], 1.007 [95% CI, 1.005 to 1.009]; P < 0.0001). The highest-risk antibiotics included second-generation and later cephalosporins (especially oral), carbapenems, fluoroquinolones, and clindamycin, while doxycycline and daptomycin were associated with a lower CDI risk. We concluded that cumulative antibiotic exposure prior to admission is the greatest contributor to the risk of subsequent CDI. Most classes of antibiotics carry some risk, which varies by drug and route. This information may be useful for antimicrobial stewardship efforts.
The Suffering Minds: Cognitive Stylistic Approach to Characterization in "The Child- Who-Was-Tired" by Katherine Mansfield and "Sleepy" by Anton Chekhov

This article aims to examine the mind style of suffering protagonists in A. Chekhov's "Sleepy" and K. Mansfield's "The Child-Who-Was-Tired" in cognitive stylistic tradition (Semino 2002, 2006). The stories represent an interesting case of "Chekhovian influence" in Mansfield's works in connection with the similarities in plot and setting. The analysis will demonstrate how cognitive stylistic approach to narrative fiction can advance literary interpretation by identifying the aspects of characterization of fiction individuals through their language, thoughts and behavior.
Selection Correction in Panel Data Models: An Application to the Estimation of Females' Wage Equations

In recent years a number of panel estimators have been suggested for sample selection models, where both the selection equation and the equation of interest contain individual effects which are correlated with the explanatory variables. Not many studies exist that use these methods in practise. We present and compare alternative estimators, and apply them to a typical problem in applied econometrics: the estimation of the wage returns to experience for females. We discuss the assumptions each estimator imposes on the data, and the problems that occur in our applications. This should be particularly useful to practitioners who consider using such estimators in their own application. All estimators rely on the assumption of strict exogeneity of regressors in the equation of interest, conditional on individual specific effects and the selection mechanism. This assumption is likely to be violated in many applications. Also, life history variables are often measured with error in survey data sets, because they contain a retrospective component. We show how this particular measurement error, and not strict exogeneity can be taken into account within the estimation methods discussed.
Machine Vision for an Intelligent Tutor

This paper presents a facial expression analysis system that performs recognition and emotional classification of human facial expression from a full-face image. The system consists of four main components. The first component performs face detection in an unstructured image using Artificial Neural Network. The second component is face recognition using Principal Component Analysis. The third component is facial feature extraction, which converts pixel base facial information into high-level geometry information. The fourth component is a fuzzy facial expression classifier. People’s facial features are analyzed logically and a decision unit is used to classify the expression. The system was implemented using extensions of existing algorithms and a new fuzzy approach to the classification of facial expressions.
Phylogenetic relationships and diversity of bat-associated Leptospira and the histopathological evaluation of these infections in bats from Grenada, West Indies

Bats can harbor zoonotic pathogens, but their status as reservoir hosts for Leptospira bacteria is unclear. During 2015–2017, kidneys from 47 of 173 bats captured in Grenada, West Indies, tested PCR-positive for Leptospira. Sequence analysis of the Leptospira rpoB gene from 31 of the positive samples showed 87–91% similarity to known Leptospira species. Pairwise and phylogenetic analysis of sequences indicate that bats from Grenada harbor as many as eight undescribed Leptospira genotypes that are most similar to known pathogenic Leptospira, including known zoonotic serovars. Warthin-Starry staining revealed leptospiral organisms colonizing the renal tubules in 70% of the PCR-positive bats examined. Mild inflammatory lesions in liver and kidney observed in some bats were not significantly correlated with renal Leptospira PCR-positivity. Our findings suggest that Grenada bats are asymptomatically infected with novel and diverse Leptospira genotypes phylogenetically related to known pathogenic strains, supporting the hypothesis that bats may be reservoirs for zoonotic Leptospira.
Does squatting need attention?—A dual-task study on cognitive resources in resistance exercise

Introduction Accumulating evidence shows that acute resistance exercises and long-term resistance training positively influence cognitive functions, but the underlying mechanisms have been rarely investigated. One explanatory approach assumes that the execution of resistance exercises requires higher cognitive processes which, in turn, lead to an ‘indirect’ training of higher cognitive functions. However, current knowledge on the engagement of higher cognitive functions during the execution of resistance exercises is relatively sparse. Hence, the purpose of this study was to examine to what extent cognitive resources are needed to perform a resistance exercise in the form of barbell back squatting. Methods Twenty-four young adults performed a cognitive task (serial subtraction of 7’s) during standing and during barbell back squatting on a Smith machine. The total number and the number of correct responses were analyzed and taken as indicators of the cognitive load imposed by the experimental condition (squatting) and the control condition (standing). Additionally, participants’ perceived exertion, mean heart rate, and the number of squats they were able to perform were assessed. Results While accuracy scores were found not to be significantly different between conditions, the numbers of total and of correct responses were significantly lower during squatting than during standing. Additionally, during squatting a higher number of total answers was given in the fifth set compared to the first set. We attribute this phenomenon to a learning effect. Furthermore, there was no statistically significant correlation between cognitive measures and perceived exertion. Conclusion Results suggest that perceived exertion cannot explain the higher dual-task costs observed during squatting. They rather reflect that more cognitive resources are needed to perform low-load barbell back squats than during standing. However, further research is necessary to confirm and generalize these findings.