julilili42/papers huggingface dataset:
Fast In Situ Observation of Atomic Feshbach Resonances by Photoassociative Ionization
2020-03-24

We propose and experimentally investigate a scheme for observing Feshbach resonances in atomic quantum gases in situ and with a high temporal resolution of several tens of nanoseconds. The method is based on the detection of molecular ions, which are optically generated from atom pairs at small interatomic distances. As a test system we use a standard rubidium gas (^{87}Rb) with well known magnetically tunable Feshbach resonances. The fast speed and the high sensitivity of our detection scheme allows us to observe a complete Feshbach resonance within one millisecond and without destroying the gas.
Hemispheric Lateralization of Arithmetic Facts and Magnitude Processing for Two-Digit Numbers
2020-03-24

In the human brain, a (relative) functional asymmetry (i.e., laterality; functional and performance differences between the two cerebral hemispheres) exists for a variety of cognitive domains (e.g., language, visual-spatial processing, etc.). For numerical cognition, both bi-lateral and unilateral processing has been proposed with the retrieval of arithmetic facts postulated as being lateralized to the left hemisphere. In this study, we aimed at evaluating this claim by investigating whether processing of multiplicatively related triplets in a number bisection task (e.g., 12_16_20) in healthy participants (<i>n</i> = 23) shows a significant advantage when transmitted to the right hemisphere only as compared to transmission to the left hemisphere. As expected, a control task revealed that stimulus presentation to the left or both visual hemifields did not increase processing disadvantages of unit-decade incompatible number pairs in magnitude comparison. For the number bisection task, we replicated the multiplicativity effect. However, in contrast to the hypothesis deriving from the triple code model, we did not observe significant hemispheric processing asymmetries for multiplicative items. We suggest that participants resorted to keep number triplets in verbal working memory after perceiving them only very briefly for 150 ms. Rehearsal of the three numbers was probably slow and time-consuming so allowing for interhemispheric communication in the meantime. We suggest that an effect of lateralized presentation may only be expected for early effects when the task is sufficiently easy.
Failure to replicate the JTC-bias in patients with psychotic disorders: A secondary analysis of a baseline assessment of a randomized controlled trial
2020-03-24

Abstract Background: The jumping to conclusions bias (JTC) is considered to be an important causal factor in theoretical models on the formation and maintenance of delusions. However, recent meta-analytic findings show a rather equivocal pattern of results regarding associations between JTC and delusions. Thus, the aim of the present preregistered study is to investigate in a large sample whether the JTC-bias is more pronounced in patients with psychotic disorders in comparison to controls and whether the JTC bias is associated with more severe delusional conviction, persecutory delusions and positive symptoms in general. All hypotheses were pre-specified in the trial proposal.Methods: Patients with psychotic disorders (n = 300) enrolled in a therapy trial and healthy controls (n = 51) conducted a variant of the beads task (fish task) as a measure for the JTC-bias at start of the trial. Further, clinical interviews were used to assess patients’ delusional severity and delusional conviction.Results: There were no statistically significant differences between patients with psychotic disorders (with 53% displaying the JTC-bias) and controls (41%). Furthermore, there were no statistically significant correlations between JTC measures and persecutory delusions, delusional conviction and positive symptoms.Conclusions: We found no evidence for hasty decisions in patients with psychotic disorders, possibly because the fish task induces a more deliberative reasoning style as compared to the traditional beads task. The lack of associations between JTC measures and delusion severity is in line with meta-analytic findings using a wide range of JTC task variants. JTC is not as ubiquitous as previously thought and may only manifest itself in certain situational contexts. Trial Registration: ISRCTN29242879 (isrctn.com), date of registration: April 12th 2006, http://www.isrctn.com/ISRCTN12345678
PGRMC1 in animal breast cancer tissue and blood is associated with increased tumor growth with norethisterone in contrast to progesterone and dydrogesterone: four-arm randomized placebo-controlled xenograft study
2020-03-25

Progesterone receptor membrane component 1 (PGRMC1) is mediating strong breast cancer cell proliferation induced by certain synthetic progestogens which we have shown within already published <i>in vitro</i> studies. Aim was now to use an animal model, to compare tumor growth using progesterone and its isomer dydrogesterone with norethisterone, which elicited in our <i>in vitro</i> studies the strongest proliferating effect. For the first time, we wanted to investigate if growth can be correlated both with blood concentrations and tissue expression of PGRMC1 to identify if PGRMC1 could be a new tumor marker. Prospective, randomized, blinded, placebo-controlled four-arm study (45-50 days); PGRMC1-transfected or empty-vector T47D- and MCF7-xenotransplants were each treated with estradiol (E2) +placebo; E2 + progesterone; E2 + norethisterone; E2 + dydrogesterone; blood PGRMC1 assessed by a novel ELISA, tissue expression by immunohistochemistry. PGRMC1-transfected tumors further increased with E2 + norethisterone but not with E2-dydrogesterone or E2-progesterone. In both PGRMC1-xenograft groups (T47D, MCF7) with E2/norethisterone, the blood concentrations and tissue expression of PGRMC1 were higher than in all other 14 groups (<i>p</i> < .05), with positive significant correlation between blood PGRMCI concentrations and tissue PGRMC1 expression. In the presence of PGRMC1, certain progestogens could increase the growth of breast tumor, which now also should be tested in clinical studies.
Sponging of glutamate at the outer plasma membrane surface reveals roles for glutamate in development
2020-03-25

SUMMARY Plants use electrical and chemical signals for systemic communication. Herbivory, for instance, appears to trigger local apoplasmic glutamate accumulation, systemic electrical signals and calcium waves that travel to report insect damage to neighboring leaves and initiate defense. To monitor extra- and intracellular glutamate concentrations in plants, we generated Arabidopsis lines expressing genetically encoded fluorescent glutamate sensors. In contrast to cytosolically localized sensors, extracellularly displayed variants inhibited plant growth and proper development. Phenotypic analyses of high-affinity display sensor lines revealed that root meristem development, particularly the quiescent center (QC), number of lateral roots, vegetative growth and floral architecture were impacted. Notably, the severity of the phenotypes was positively correlated with the affinity of the display sensors, intimating that their ability to sequester glutamate at the surface of the plasma membrane was responsible for the defects. Root growth defects were suppressed by supplementing culture media with low levels of glutamate. Together, the data indicate that sequestration of glutamate at the cell surface either disrupts the supply of glutamate to meristematic cells and/or impairs localized glutamatergic signaling important for developmental processes. SIGNIFICANCE STATEMENT Glutamate is an important signaling molecule in animals and plants. The affinity-dependent effects of surface-displayed glutamate sensors on plant development intimate that glutamate levels in the vicinity of the plasma membrane play important roles in signaling in plants.
The motor neuron-like cell line NSC-34 and its parent cell line N18TG2 have glycogen that is degraded under cellular stress
2020-03-25

Abstract Brain glycogen has a long and versatile history: Primarily regarded as an evolutionary remnant, it was then thought of as an unspecific emergency fuel store. A dynamic role for glycogen in normal brain function has been proposed later but exclusively attributed to astrocytes, its main storage site. Neuronal glycogen had long been neglected, but came into focus when sensitive technical methods allowed quantification of glycogen at low concentration range and the detection of glycogen metabolizing enzymes in cells and cell lysates. Recently, an active role of neuronal glycogen and even its contribution to neuronal survival could be demonstrated. Our studies continue these investigations on the function and regulation of neuronal glycogen metabolism. We demonstrate the presence of an active glycogen metabolism in the neuronal cell lines NSC-34 and N18TG2 and the mobilization of the glycogen stores under hypoxia, oxidative and acidic metabolic stress. The key enzyme in glycogen degradation is glycogen phosphorylase. Neurons express only the brain isoform (GPBB) that is supposed to be activated primarily by the allosteric activator AMP and less by covalent phosphorylation via the cAMP cascade. Our results indicate that neuronal glycogen is not degraded upon hormone action but by factors lowering the energy charge of the cells directly.
The natural history of progressive fibrosing interstitial lung diseases
2020-03-26

We used data from the INBUILD and INPULSIS trials to investigate the natural history of progressive fibrosing interstitial lung diseases (ILDs). Subjects in the two INPULSIS trials had a clinical diagnosis of idiopathic pulmonary fibrosis (IPF) while subjects in the INBUILD trial had a progressive fibrosing ILD other than IPF and met protocol-defined criteria for ILD progression despite management. Using data from the placebo groups, we compared the rate of decline in forced vital capacity (FVC) (mL·year −1 ) and mortality over 52 weeks in the INBUILD trial with pooled data from the INPULSIS trials. The adjusted mean annual rate of decline in FVC in the INBUILD trial (n=331) was similar to that observed in the INPULSIS trials (n=423) (−192.9 mL·year −1 and −221.0 mL·year −1 , respectively; nominal p-value=0.19). The proportion of subjects who had a relative decline in FVC &gt;10% predicted at Week 52 was 48.9% in the INBUILD trial and 48.7% in the INPULSIS trials, and the proportion who died over 52 weeks was 5.1% in the INBUILD trial and 7.8% in the INPULSIS trials. A relative decline in FVC &gt;10% predicted was associated with an increased risk of death in the INBUILD trial (hazard ratio 3.64) and the INPULSIS trials (hazard ratio 3.95). These findings indicate that patients with fibrosing ILDs other than IPF, who are progressing despite management, have a subsequent clinical course similar to patients with untreated IPF, with a high risk of further ILD progression and early mortality.
Underhydration Is Associated with Obesity, Chronic Diseases, and Death Within 3 to 6 Years in the U.S. Population Aged 51–70 Years
2020-03-26

Nationally representative data from the National Health and Nutrition Examination Survey (NHANES) indicate that over 65% of adults aged 51–70 years in the U.S. do not meet hydration criteria. They have hyponatremia (serum sodium &lt; 135 mmol/L) and/or underhydration (serum sodium &gt;145 mmol/L, spot urine volume &lt;50 mL, and/or spot urine osmolality ≥500 mmol/kg). To explore potential public health implications of not meeting hydration criteria, data from the NHANES 2009–2012 and National Center for Health Statistics Linked Mortality Files for fasting adults aged 51–70 years (sample n = 1200) were used to determine if hyponatremia and/or underhydration were cross-sectionally associated with chronic health conditions and/or longitudinally associated with chronic disease mortality. Underhydration accounted for 97% of the population group not meeting hydration criteria. In weighted multivariable adjusted Poisson models, underhydration was significantly associated with increased prevalence of obesity, high waist circumference, insulin resistance, diabetes, low HDL, hypertension, and metabolic syndrome. Over 3–6 years of follow-up, 33 chronic disease deaths occurred in the sample, representing an estimated 1,084,144 deaths in the U.S. Alongside chronic health conditions, underhydration was a risk factor for an estimated 863,305 deaths. Independent of the chronic health conditions evaluated, underhydration was a risk factor for 128,107 deaths. In weighted multivariable Cox models, underhydration was associated with 4.21 times greater chronic disease mortality (95% CI: 1.29–13.78, p = 0.019). Zero chronic disease deaths were observed for people who met the hydration criteria and did not already have a chronic condition in 2009–2012. Further work should consider effects of underhydration on population health.
Rotation-activity relations and flares of M dwarfs with K2 long- and short-cadence data
2020-03-26

Using light curves obtained by the K2 mission, we study the relation between stellar rotation and magnetic activity with special focus on stellar flares. Our sample comprises 56 bright and nearby M dwarfs observed by K2 during campaigns C0-C18 in long- and short-cadence mode. We derive rotation periods for 46 M dwarfs and measure photometric activity indicators such as amplitude of the rotational signal, standard deviation of the light curves, and the basic flare properties (flare rate, flare energy, flare duration, and flare amplitude). We found 1662 short-cadence flares, 363 of which have a long-cadence counterpart with flare energies of up to 5.6 × 10 34 erg. The flare amplitude, duration, and frequency derived from the short-cadence light curves differ significantly from those derived from the long-cadence data. The analysis of the short-cadence light curves results in a flare rate that is 4.6 times higher than the long-cadence data. We confirm the abrupt change in activity level in the rotation-activity relation at a critical period of ~10 d when photometric activity diagnostics are used. This change is most drastic in the flare duration and frequency for short-cadence data. Our flare studies revealed that the highest flare rates are not found among the fastest rotators and that stars with the highest flare rates do not show the most energetic flares. We found that the superflare frequency ( E ≥ 5 × 10 34 erg) for the fast-rotating M stars is twice higher than for solar like stars in the same period range. By fitting the cumulative FFD, we derived a power-law index of α = 1.84 ± 0.14, consistent with previous M dwarf studies and the value found for the Sun.
Ten simple rules for providing effective bioinformatics research support
2020-03-26

Life scientists are increasingly turning to high-throughput sequencing technologies in their research programs, owing to the enormous potential of these methods. In a parallel manner, the number of core facilities that provide bioinformatics support are also increasing. Notably, the generation of complex large datasets has necessitated the development of bioinformatics support core facilities that aid laboratory scientists with cost-effective and efficient data management, analysis, and interpretation. In this article, we address the challenges-related to communication, good laboratory practice, and data handling-that may be encountered in core support facilities when providing bioinformatics support, drawing on our own experiences working as support bioinformaticians on multidisciplinary research projects. Most importantly, the article proposes a list of guidelines that outline how these challenges can be preemptively avoided and effectively managed to increase the value of outputs to the end user, covering the entire research project lifecycle, including experimental design, data analysis, and management (i.e., sharing and storage). In addition, we highlight the importance of clear and transparent communication, comprehensive preparation, appropriate handling of samples and data using monitoring systems, and the employment of appropriate tools and standard operating procedures to provide effective bioinformatics support.
Ape cultures do not require behaviour copying
2020-03-26

Abstract While culture is widespread in the animal kingdom, human culture has been claimed to be special due to being cumulative. It is currently debated which cognitive abilities support cumulative culture, but behavioural form copying is one of the main abilities proposed. One important source of contention is the presence or absence of behaviour copying in our closest living relatives, non-human great apes (apes) – especially given that their behaviour does not show clear signs of cumulation. Those who claim that apes copy behaviour often base this claim on the existence of stable ape cultures in the wild. We developed an individual-based model to test whether ape cultural patterns can emerge in absence of any behaviour copying, when only allowing for a well-supported alternative social learning mechanism, socially mediated reinnovation, where only the frequency of reinnovation is under social influence, but the form of the behaviour is not. Our model reflects wild ape life conditions, including physiological and behavioural needs, demographic and spatial features, and possible genetic and ecological variation between populations. Our results show that, under a wide range of values of parameters, we can reproduce the defining features of wild ape cultural patterns. Overall, our results show that ape cultures can emerge and stabilise without behaviour copying. Ape cultures do not show the signatures of behaviour copying abilities, lending support to the notion that behaviour copying is, among apes, unique in the human lineage. It therefore remains an open question when and why behaviour copying evolved in hominins.
Queer(ed) Pedagogies: A Critical Perspective
2020-03-26

Abstract Current political controversies concerning progressive concepts of sex education in schools lead to an often openly aggressive dispute about the handling of identity concepts, understandings of gender, and knowledge in school and extracurricular contexts. In addition to general emancipatory concepts which emphasise diversity and tolerance, the discussion increasingly considers queer-theoretical interventions. This article outlines the axiological questions of a queer pedagogy, and offers insights into practices which might emerge as a result of such considerations. At the same time, it formulates theoretical questions of a queer pedagogy as they pertain to a more general theory of educational processes, and which concern not only the practice of teaching and learning, but also the formation of educational theory.
Enhancing CO2-Valorization Using Clostridium autoethanogenum for Sustainable Fuel and Chemicals Production
2020-03-27

Acetogenic bacteria can convert waste gases into fuels and chemicals. Design of bioprocesses for waste carbon valorization requires quantification of steady-state carbon flows. Here, steady-state quantification of autotrophic chemostats containing Clostridium autoethanogenum grown on CO<sub>2</sub> and H<sub>2</sub> revealed that captured carbon (460 ± 80 mmol/gDCW/day) had a significant distribution to ethanol (54 ± 3 C-mol% with a 2.4 ± 0.3 g/L titer). We were impressed with this initial result, but also observed limitations to biomass concentration and growth rate. Metabolic modeling predicted culture performance and indicated significant metabolic adjustments when compared to fermentation with CO as the carbon source. Moreover, modeling highlighted flux to pyruvate, and subsequently reduced ferredoxin, as a target for improving CO<sub>2</sub> and H<sub>2</sub> fermentation. Supplementation with a small amount of CO enabled co-utilization with CO<sub>2</sub>, and enhanced CO<sub>2</sub> fermentation performance significantly, while maintaining an industrially relevant product profile. Additionally, the highest specific flux through the Wood-Ljungdahl pathway was observed during co-utilization of CO<sub>2</sub> and CO. Furthermore, the addition of CO led to superior CO<sub>2</sub>-valorizing characteristics (9.7 ± 0.4 g/L ethanol with a 66 ± 2 C-mol% distribution, and 540 ± 20 mmol CO<sub>2</sub>/gDCW/day). Similar industrial processes are commercial or currently being scaled up, indicating CO-supplemented CO<sub>2</sub> and H<sub>2</sub> fermentation has high potential for sustainable fuel and chemical production. This work also provides a reference dataset to advance our understanding of CO<sub>2</sub> gas fermentation, which can contribute to mitigating climate change.
Cross-site and cross-platform variability of automated patch clamp assessments of drug effects on human cardiac currents in recombinant cells
2020-03-27

Abstract Automated patch clamp (APC) instruments enable efficient evaluation of electrophysiologic effects of drugs on human cardiac currents in heterologous expression systems. Differences in experimental protocols, instruments, and dissimilar site procedures affect the variability of IC 50 values characterizing drug block potency. This impacts the utility of APC platforms for assessing a drug’s cardiac safety margin. We determined variability of APC data from multiple sites that measured blocking potency of 12 blinded drugs (with different levels of proarrhythmic risk) against four human cardiac currents (hERG [I Kr ], hCav1.2 [L-Type I Ca ], peak hNav1.5, [Peak I Na ], late hNav1.5 [Late I Na ]) with recommended protocols (to minimize variance) using five APC platforms across 17 sites. IC 50 variability (25/75 percentiles) differed for drugs and currents (e.g., 10.4-fold for dofetilide block of hERG current and 4-fold for mexiletine block of hNav1.5 current). Within-platform variance predominated for 4 of 12 hERG blocking drugs and 4 of 6 hNav1.5 blocking drugs. hERG and hNav1.5 block. Bland-Altman plots depicted varying agreement across APC platforms. A follow-up survey suggested multiple sources of experimental variability that could be further minimized by stricter adherence to standard protocols. Adoption of best practices would ensure less variable APC datasets and improved safety margins and proarrhythmic risk assessments.
The chemokine CXCL14 mediates platelet function and migration via direct interaction with CXCR4
2020-03-27

Abstract Aims Beyond classical roles in thrombosis and haemostasis, it becomes increasingly clear that platelets contribute as key players to inflammatory processes. The involvement of platelets in these processes is often mediated through a variety of platelet-derived chemokines which are released upon activation and act as paracrine and autocrine factors. In this study, we investigate CXCL14, a newly described platelet chemokine and its role in thrombus formation as well as monocyte and platelet migration. In addition, we examine the chemokine receptor CXCR4 as a possible receptor for CXCL14 on platelets. Furthermore, with the use of artificially generated platelets derived from induced pluripotent stem cells (iPSC), we investigate the importance of CXCR4 for CXCL14-mediated platelet functions. Methods and results In this study, we showed that CXCL14 deficient platelets reveal reduced thrombus formation under flow compared with wild-type platelets using a standardized flow chamber. Addition of recombinant CXCL14 normalized platelet-dependent thrombus formation on collagen. Furthermore, we found that CXCL14 is a chemoattractant for platelets and mediates migration via CXCR4. CXCL14 promotes platelet migration of platelets through the receptor CXCR4 as evidenced by murine CXCR4-deficient platelets and human iPSC-derived cultured platelets deficient in CXCR4. We found that CXCL14 directly interacts with the CXCR4 as verified by immunoprecipitation and confocal microscopy. Conclusions Our results reveal CXCL14 as a novel platelet-derived chemokine that is involved in thrombus formation and platelet migration. Furthermore, we identified CXCR4 as principal receptor for CXCL14, an interaction promoting platelet migration.