bluuebunny/crossref_metadata_2025 huggingface dataset:
The Evolution of a Spacecraft‐Generated Lunar Exosphere
Authors: Prem Parvathy , Hurley Dana M. , Goldstein David B. , Varghese Philip L.
Published: August 2020

Understanding how spacecraft alter planetary environments can offer important insights into key physical processes, as well as being critical to planning mission operations and observations. In this context, it is important to recognize that almost any powered lunar landing will be an active volatile release experiment, due to the release of exhaust gases during descent. This presents both an opportunity to study the interaction of volatiles with the lunar surface and a need to predict how nonindigenous gases are dispersed, and how long they persist in the lunar environment. This work investigates these questions through numerical simulations of the transport of water vapor during a nominal lunar landing and for two lunar days afterward. Simulation results indicate that the water vapor component of spacecraft exhaust is globally redistributed, with a significant amount reaching permanently shadowed regions (cold traps) near the closest pole, where temperatures are sufficiently low that volatiles may remain stable over geological timescales. Exospheric evolution and surface deposition patterns are highly sensitive to desorption activation energy, providing a means to constrain this critical parameter through landed or orbital measurements during future missions. Contamination of cold traps by exhaust gases is likely to scale with exhaust mass and proximity of the landing site to the poles. Exhaust propagation is perhaps the most widespread and long‐lived impact of spacecraft operations on a nominally airless solar system body and should be a key consideration in mission planning and in interpreting measurements made by landed lunar missions, particularly at near‐polar regions.
EGFR/FOXO3a/BIM signaling pathway determines chemosensitivity of BMP4-differentiated glioma stem cells to temozolomide
Authors: Ciechomska Iwona Anna , Gielniewski Bartlomiej , Wojtas Bartosz , Kaminska Bozena , Mieczkowski Jakub
Published: August 2020

Accumulating evidence suggests that glioma stem cells (GSCs), which are rare cells characterized by pluripotency and self-renewal ability, are responsible for glioblastoma (GBM) propagation, recurrence and resistance to therapies. Bone morphogenic proteins (BMPs) induce GSC differentiation, which leads to elimination of GSCs and sensitization of glioma to chemotherapeutics. Alterations in the epidermal growth factor receptor (EGFR) gene are detected in more than half of GBMs; however, the role of EGFR in the chemoresistance of GSCs remains unknown. Here, we examined whether EGFR signaling affects BMP4-induced differentiation of GSCs and their response to the alkylating drug temozolomide (TMZ). We show that BMP4 triggers the SMAD signaling cascade in GSCs independent of the EGFR level. BMP4 downregulated the levels of pluripotency markers (SOX2 and OLIG2) with a concomitant induction of an astrocytic marker (GFAP) and a neuronal marker (β-Tubulin III). However, GSCs with different EGFR levels responded differently to treatments. BMP4-induced differentiation did not enhance sensitivity to TMZ in EGFRlow GSCs, in contrast to EGFRhigh GSCs, which underwent apoptosis. We then identified differences in cell cycle regulation. In EGFRlow cells, BMP4-triggered G1 cell cycle arrest which was not detected in EGFRhigh cells. RNA-seq profiles further highlighted transcriptomic alterations and distinct processes characterizing EGFR-dependent responses in the course of BMP4-induced differentiation. We found that the control of BIM (the pro-apoptotic BCL-2 family protein) by the AKT/FOXO3a axis only operated in BMP4-differentiated EGFRhigh cells upon TMZ treatment.
Reduced axonal caliber and structural changes in a rat model of Fragile X syndrome with a deletion of a K-Homology domain of Fmr1
Authors: Golden Carla E. M. , Yee Yohan , Wang Victoria X. , Harony-Nicolas Hala , Hof Patrick R. , Lerch Jason P. , Buxbaum Joseph D.
Published: August 2020

Fragile X syndrome (FXS) is a neurodevelopmental disorder that is caused by mutations in the FMR1 gene. Neuroanatomical alterations have been reported in both male and female individuals with FXS, yet the morphological underpinnings of these alterations have not been elucidated. In the current study, we found structural changes in both male and female rats that model FXS, some of which are similarly impaired in both sexes, including the superior colliculus and periaqueductal gray, and others that show sex-specific changes. The splenium of the corpus callosum, for example, was only impaired in males. We also found reduced axonal caliber in the splenium, offering a mechanism for its structural changes. Furthermore, we found that overall, male rats have higher brain-wide diffusion than female rats. Our results provide insight into which brain regions are vulnerable to a loss of Fmr1 expression and reveal an impairment at the level of the axon that could cause structural changes in white matter regions.
Cerebrospinal fluid, antineuronal autoantibody, EEG, and MRI findings from 992 patients with schizophreniform and affective psychosis
Authors: Endres Dominique , Meixensberger Sophie , Dersch Rick , Feige Bernd , Stich Oliver , Venhoff Nils , Matysik Miriam , Maier Simon J. , Michel Maike , Runge Kimon , Nickel Kathrin , Urbach Horst , Domschke Katharina , Prüss Harald , Tebartz van Elst Ludger
Published: August 2020

The central role played by cerebrospinal-fluid (CSF) examinations including antineuronal autoantibody (Ab) testing is increasingly recognized in psychiatry. The rationale of this study was to present a multimodally investigated group of patients. In total, 992 patients were analyzed for CSF alterations: 456 patients with schizophreniform and 536 with affective syndromes. Ab measurement included testing for established antineuronal IgG-Abs against intracellular antigens in serum (Yo/Hu/Ri/cv2[CRMP5]/Ma1/Ma2/SOX1/TR[DNER]/Zic4/amphiphysin/GAD65) and for cell surface antigens in the CSF (NMDAR/AMPA-1/2-R/GABA-B-R/LGI1/CASPR2/DPPX). In 30 patients with “red flags” for autoimmune psychosis, “tissue tests” were performed. Additional diagnostics included MRI and EEG analyses. CSF white-blood-cell counts were increased in 4% and IgG indices in 2%; CSF-specific oligoclonal bands were detected in 4%; overall, 8% displayed signs of neuroinflammation. In addition, 18% revealed increased albumin quotients. Antineuronal Abs against intracellular antigens were detected in serum in 0.6%. Antineuronal Abs against established cell surface antigens were detected in serum of 1% and in the CSF of 0.3% (CSF samples were only questionably positive). Abnormal IgG binding in “tissue tests” was detected in serum of 23% and in CSF of 27%. In total, 92% of the Ab-positive patients demonstrated at least one sign of brain involvement in additional diagnostics using CSF, MRI, EEG, and FDG-PET. In summary, CSF basic analyses revealed signs of blood–brain-barrier dysfunction and neuroinflammation in relevant subgroups of patients. Established antineuronal IgG-Abs were rare in serum and even rarer in the CSF. “Tissue tests” revealed frequent occurrences of Ab-binding; therefore, novel antineuronal Abs could play a relevant role in psychiatry.
Parcel-guided rTMS for depression
Authors: Moreno-Ortega M. , Kangarlu A. , Lee S. , Perera T. , Kangarlu J. , Palomo T. , Glasser M. F. , Javitt D. C.
Published: August 2020

Transcranial magnetic stimulation (TMS) is an approved intervention for treatment-resistant depression (TRD), but current targeting approaches are only partially successful. Our objectives were (1) to examine the feasibility of MRI-guided TMS in the clinical setting using a recently published surface-based, multimodal parcellation in patients with TRD who failed standard TMS (sdTMS); (2) to examine the neurobiological mechanisms and clinical outcomes underlying MRI-guided TMS compared to that of sdTMS. We used parcel-guided TMS (pgTMS) to target the left dorsolateral prefrontal cortex parcel 46. Resting-state functional connectivity (rsfc) was assessed between parcel 46 and predefined nodes within the default mode and visual networks, following both pgTMS and sdTMS. All patients (n = 10) who had previously failed sdTMS responded to pgTMS. Alterations in rsfc between frontal, default mode, and visual networks differed significantly over time between groups. Improvements in symptoms correlated with alterations in rsfc within each treatment group. The outcome of our study supports the feasibility of pgTMS within the clinical setting. Future prospective, double-blind studies of pgTMS vs. sdTMS appear warranted.
A quality improvement project to assess the use of visual aids to improve understanding and motivation in periodontal patients
Authors: Momin Pushpa , Mahmood Sophina
Published: August 2020

Aims

A quality improvement project was carried out in a General Dental Practice in London. The aim was to improve understanding and motivation in periodontal patients.

Methods

Research into interventions in the medical field to improve understanding and motivation amongst patients, lead to the idea of using visual aids to help motivate periodontal patients and to improve their understanding of the disease. The results from the first Plan-Do-Study-Act cycle using visual aids are presented.

Results

After the use of visual aids, patients felt more motivated in maintaining good oral hygiene, felt the visual aids improved their understanding of gum disease and how to take care of their gums and teeth. One hundred percent of patients preferred their diagnosis to be explained to them with visual aids.

Discussion

The project supported the increase in motivation and understanding in periodontal patients. However further data is required to learn more about how visual aids influence patient behaviour, how effective they are in improving patients’ understanding and motivation, and other factors which play a role in this.

Conclusions

The results of this quality improvement project are promising; it has highlighted that visual aids can have a place in the management of periodontitis in general practice.
Measurement of the spin-forbidden dark excitons in MoS2 and MoSe2 monolayers
Authors: Robert C. , Han B. , Kapuscinski P. , Delhomme A. , Faugeras C. , Amand T. , Molas M. R. , Bartos M. , Watanabe K. , Taniguchi T. , Urbaszek B. , Potemski M. , Marie X.
Published: August 2020

Excitons with binding energies of a few hundreds of meV control the optical properties of transition metal dichalcogenide monolayers. Knowledge of the fine structure of these excitons is therefore essential to understand the optoelectronic properties of these 2D materials. Here we measure the exciton fine structure of MoS2 and MoSe2 monolayers encapsulated in boron nitride by magneto-photoluminescence spectroscopy in magnetic fields up to 30 T. The experiments performed in transverse magnetic field reveal a brightening of the spin-forbidden dark excitons in MoS2 monolayer: we find that the dark excitons appear at 14 meV below the bright ones. Measurements performed in tilted magnetic field provide a conceivable description of the neutral exciton fine structure. The experimental results are in agreement with a model taking into account the effect of the exchange interaction on both the bright and dark exciton states as well as the interaction with the magnetic field.
Discovery of EMRE in fungi resolves the true evolutionary history of the mitochondrial calcium uniporter
Authors: Pittis Alexandros A. , Goh Valerie , Cebrian-Serrano Alberto , Wettmarshausen Jennifer , Perocchi Fabiana , Gabaldón Toni
Published: August 2020

Calcium (Ca2+) influx into mitochondria occurs through a Ca2+-selective uniporter channel, which regulates essential cellular processes in eukaryotic organisms. Previous evolutionary analyses of its pore-forming subunits MCU and EMRE, and gatekeeper MICU1, pinpointed an evolutionary paradox: the presence of MCU homologs in fungal species devoid of any other uniporter components and of mt-Ca2+ uptake. Here, we trace the mt-Ca2+ uniporter evolution across 1,156 fully-sequenced eukaryotes and show that animal and fungal MCUs represent two distinct paralogous subfamilies originating from an ancestral duplication. Accordingly, we find EMRE orthologs outside Holoza and uncover the existence of an animal-like uniporter within chytrid fungi, which enables mt-Ca2+ uptake when reconstituted in vivo in the yeast Saccharomyces cerevisiae. Our study represents the most comprehensive phylogenomic analysis of the mt-Ca2+ uptake system and demonstrates that MCU, EMRE, and MICU formed the core of the ancestral opisthokont uniporter, with major implications for comparative structural and functional studies.
Labile carbon limits late winter microbial activity near Arctic treeline
Authors: Sullivan Patrick F. , Stokes Madeline C. , McMillan Cameron K. , Weintraub Michael N.
Published: August 2020

Soil microbial communities remain active during much of the Arctic winter, despite deeply frozen soils. Overwinter microbial activity affects the global carbon (C) budget, nutrient cycling, and vegetation composition. Microbial respiration is highly temperature sensitive in frozen soils, as liquid water and solute availability decrease rapidly with declining temperature. Climate warming and changes in snowpack are leading to warmer Arctic winter soils. Warmer winter soils are thought to yield greater microbial respiration of available C, greater overwinter CO2efflux and greater nutrient availability to plants at thaw. Using field and laboratory observations and experiments, we demonstrate that persistently warm winter soils can lead to labile C starvation and reduced microbial respiration, despite the high C content of most Arctic soils. If winter soils continue to warm, microbial C limitation will reduce expected CO2emissions and alter soil nutrient cycling, if not countered by greater labile C inputs.
Stimulated plasmon polariton scattering
Authors: Wolff C. , Mortensen N. A.
Published: August 2020

Plasmon and phonon polaritons of two-dimensional (2D) and van-der-Waals materials have recently gained substantial interest. Unfortunately, they are notoriously hard to observe in linear response because of their strong confinement, low frequency and longitudinal mode symmetry. Here, we propose an approach of harnessing nonlinear resonant scattering that we call stimulated plasmon polariton scattering (SPPS) in analogy to the opto-acoustic stimulated Brillouin scattering (SBS). We show that SPPS allows to excite, amplify and detect 2D plasmon and phonon polaritons all across the THz-range while requiring only optical components in the near-IR or visible range. We present a coupled-mode theory framework for SPPS and based on this find that SPPS power gains exceed the very top gains observed in on-chip SBS by at least an order of magnitude. This opens exciting possibilities to fundamental studies of 2D materials and will help closing the THz gap in spectroscopy and information technology.
Inhibition of autophagy curtails visual loss in a model of autosomal dominant optic atrophy
Authors: Zaninello Marta , Palikaras Konstantinos , Naon Deborah , Iwata Keiko , Herkenne Stephanie , Quintana-Cabrera Ruben , Semenzato Martina , Grespi Francesca , Ross-Cisneros Fred N. , Carelli Valerio , Sadun Alfredo A. , Tavernarakis Nektarios , Scorrano Luca
Published: August 2020

In autosomal dominant optic atrophy (ADOA), caused by mutations in the mitochondrial cristae biogenesis and fusion protein optic atrophy 1 (Opa1), retinal ganglion cell (RGC) dysfunction and visual loss occur by unknown mechanisms. Here, we show a role for autophagy in ADOA pathogenesis. In RGCs expressing mutated Opa1, active 5’ AMP-activated protein kinase (AMPK) and its autophagy effector ULK1 accumulate at axonal hillocks. This AMPK activation triggers localized hillock autophagosome accumulation and mitophagy, ultimately resulting in reduced axonal mitochondrial content that is restored by genetic inhibition of AMPK and autophagy. In C. elegans, deletion of AMPK or of key autophagy and mitophagy genes normalizes the axonal mitochondrial content that is reduced upon mitochondrial dysfunction. In conditional, RGC specific Opa1-deficient mice, depletion of the essential autophagy gene Atg7 normalizes the excess autophagy and corrects the visual defects caused by Opa1 ablation. Thus, our data identify AMPK and autophagy as targetable components of ADOA pathogenesis.
Identification of a likely pathogenic structural variation in the LAMA1 gene by Bionano optical mapping
Authors: Chen Min , Zhang Min , Qian Yeqing , Yang Yanmei , Sun Yixi , Liu Bei , Wang Liya , Dong Minyue
Published: August 2020

Recent advances in Bionano optical mapping (BOM) provide a great insight into the determination of structural variants (SVs), but its utility in identification of clinical likely pathogenic variants needs to be further demonstrated and proved. In a family with two consecutive pregnancies affected with ventriculomegaly, a splicing likely pathogenic variant at the LAMA1 locus (NM_005559: c. 4663 + 1 G > C) inherited from the father was identified in the proband by whole-exome sequencing, and no other pathogenic variant associated with the clinical phenotypes was detected. SV analysis by BOM revealed an ~48 kb duplication at the LAMA1 locus in the maternal sample. Real-time quantitative PCR and Sanger sequencing further confirmed the duplication as c.859-153_4806 + 910dup. Based on these variants, we hypothesize that the fetuses have Poretti-Boltshauser syndrome (PBS) presenting with ventriculomegaly. With the ability to determine single nucleotide variants and SVs, the strategy adopted here might be useful to detect cases missed by current routine screening methods. In addition, our study may broaden the phenotypic spectrum of fetuses with PBS.
Pathway-specific model estimation for improved pathway annotation by network crosstalk
Authors: Castresana-Aguirre Miguel , Sonnhammer Erik L. L.
Published: August 2020

Pathway enrichment analysis is the most common approach for understanding which biological processes are affected by altered gene activities under specific conditions. However, it has been challenging to find a method that efficiently avoids false positives while keeping a high sensitivity. We here present a new network-based method ANUBIX based on sampling random gene sets against intact pathway. Benchmarking shows that ANUBIX is considerably more accurate than previous network crosstalk based methods, which have the drawback of modelling pathways as random gene sets. We demonstrate that ANUBIX does not have a bias for finding certain pathways, which previous methods do, and show that ANUBIX finds biologically relevant pathways that are missed by other methods.
Inhibition of Wnt signaling pathway suppresses radiation-induced dermal fibrosis
Authors: Lee Dong Won , Lee Won Jai , Cho Jaeho , Yun Chae-Ok , Roh Hyun , Chang Hsien Pin , Roh Tai Suk , Lee Ju Hee , Lew Dae Hyun
Published: August 2020

Progressive fibrosis of the dermal tissues is a challenging complication of radiotherapy whose underlying mechanism is not fully understood, and there are few available treatments. The canonical Wnt/β-catenin signaling pathway plays an important role in fibrosis as well as in the epithelial-to-mesenchymal transition (EMT). We investigated whether inhibition of Wnt/β-catenin signaling with sLRP6E1E2, a molecule that binds to extracellular Wnt ligands, ameliorated radiation-induced fibrosis both in vitro and in vivo. Radiation with a single dose of 2 Gy not only facilitated fibrosis in cultured human dermal fibroblasts via activation of the Wnt/β-catenin pathway but also initiated EMT in cultured keratinocytes, developing collagen-producing mesenchymal cells. sLRP6E1E2-expressing adenovirus treatment exerted anti-fibrotic activity in irradiated cultured dermal fibroblasts and keratinocytes. In a mouse model, a single fraction of 15 Gy was delivered to the dorsal skins of 36 mice randomized into three groups: those receiving PBS, those receiving control adenovirus, and those receiving decoy Wnt receptor-expressing adenovirus (dE1-k35/sLRP6E1E2). The mice were observed for 16 weeks, and excessive deposition of type I collagen was suppressed by sLRP6E1E2-expressing adenovirus treatment. These results demonstrate that the modulation of the Wnt/β-catenin pathway has the potential to decrease the severity of radiation-induced dermal fibrosis.
Developmental changes in the accessible chromatin, transcriptome and Ascl1-binding correlate with the loss in Müller Glial regenerative potential
Authors: VandenBosch Leah S. , Wohl Stefanie G. , Wilken Matthew S. , Hooper Marcus , Finkbeiner Connor , Cox Kristen , Chipman Laura , Reh Thomas A.
Published: August 2020

Diseases and damage to the retina lead to losses in retinal neurons and eventual visual impairment. Although the mammalian retina has no inherent regenerative capabilities, fish have robust regeneration from Müller glia (MG). Recently, we have shown that driving expression of Ascl1 in adult mouse MG stimulates neural regeneration. The regeneration observed in the mouse is limited in the variety of neurons that can be derived from MG; Ascl1-expressing MG primarily generate bipolar cells. To better understand the limits of MG-based regeneration in mouse retinas, we used ATAC- and RNA-seq to compare newborn progenitors, immature MG (P8-P12), and mature MG. Our analysis demonstrated developmental differences in gene expression and accessible chromatin between progenitors and MG, primarily in neurogenic genes. Overexpression of Ascl1 is more effective in reprogramming immature MG, than mature MG, consistent with a more progenitor-like epigenetic landscape in the former. We also used ASCL1 ChIPseq to compare the differences in ASCL1 binding in progenitors and reprogrammed MG. We find that bipolar-specific accessible regions are more frequently linked to bHLH motifs and ASCL1 binding. Overall, our analysis indicates a loss of neurogenic gene expression and motif accessibility during glial maturation that may prevent efficient reprogramming.
Insights on small molecule binding to the Hv1 proton channel from free energy calculations with molecular dynamics simulations
Authors: Lim Victoria T. , Geragotelis Andrew D. , Lim Nathan M. , Freites J. Alfredo , Tombola Francesco , Mobley David L. , Tobias Douglas J.
Published: August 2020

Hv1 is a voltage-gated proton channel whose main function is to facilitate extrusion of protons from the cell. The development of effective channel blockers for Hv1 can lead to new therapeutics for the treatment of maladies related to Hv1 dysfunction. Although the mechanism of proton permeation in Hv1 remains to be elucidated, a series of small molecules have been discovered to inhibit Hv1. Here, we computed relative binding free energies of a prototypical Hv1 blocker on a model of human Hv1 in an open state. We used alchemical free energy perturbation techniques based on atomistic molecular dynamics simulations. The results support our proposed open state model and shed light on the preferred tautomeric state of the channel blocker. This work lays the groundwork for future studies on adapting the blocker molecule for more effective inhibition of Hv1.
A micro-bioimpedance meter for monitoring insulin bioavailability in personalized diabetes therapy
Authors: Arpaia Pasquale , Cesaro Umberto , Frosolone Mirco , Moccaldi Nicola , Taglialatela Maurizio
Published: August 2020

An on-chip transducer, for monitoring noninvasively the insulin bio-availability in real time after administration in clinical diabetology, is proposed. The bioavailability is assessed as insulin decrease in situ after administration by means of local impedance measurement. Inter-and-intra individual reproducibility is enhanced by a personalized model, specific for the subject, identified and validated during each insulin administration. Such a real-time noninvasive bioavailability measurement allows to increase the accuracy of insulin bolus administration, by attenuating drawbacks of glycemic swings significantly. In the first part of this paper, the concept, the architecture, and the operation of the transducer, as well as details about its prototype, are illustrated. Then, the metrological characterization and validation are reported in laboratory, in vitro on eggplants, ex vivo on pig abdominal non-perfused muscle, and in vivo on a human subject, using injection as a reference subcutaneous delivery of insulin. Results of significant intra-individual reproducibility in vitro and ex vivo point out noteworthy scenarios for assessing insulin bioavailability in clinical diabetology.
Probing the influence of graphene oxide sheets size on the performance of label-free electrochemical biosensors
Authors: Eissa Shimaa , N’diaye Jeanne , Brisebois Patrick , Izquierdo Ricardo , Tavares Ana C. , Siaj Mohamed
Published: August 2020

The integration of graphene materials into electrochemical biosensing platforms has gained significant interest in recent years. Bulk quantities of graphene can be synthesized by oxidation of graphite to graphite oxide and subsequent exfoliation to graphene oxide (GO). However, the size of the resultant GO sheets changes from the parent graphite yielding a polydispersed solution of sizes ranging from a few nanometers to tens of micrometers. Here, we investigate the direct effect of GO sheets sizes on biosensor performance. We separated different GO sheets sizes, and we characterized them via atomic force, scanning electron, Raman and X-ray photoelectron spectroscopies and solid state nuclear magnetic resonance (NMR). As proof of concept, the sensing performance of these GO samples was probed using a well-known ssDNA aptasensor against microcystin-LR toxin and an immunosensor against β-lactoglobulin. The resulting aptasensors and immunosensors are fabricated by using covalent attachment and physical adsorption. We found that the aptasensors fabricated using physical adsorption, the binding signal variation was dramatically increased with increasing the GO sheet size. In contrast, for the aptasensor fabricated using covalent immobilization, the binding signal variation decreased with increasing GO sheet size. However, for the β-lactoglobulin immunosensors, the optimum signals were observed at intermediate GO sheet size. GO sheet size could enhance or inhibit the sensitivity of the graphene-based electrochemical sensors. Our results demonstrate that controlling the size of GO sheets may have a profound impact in specific biosensing applications.
The influence of hydrodynamic exposure on carbon storage and nutrient retention in eelgrass (Zostera marina L.) meadows on the Swedish Skagerrak coast
Authors: Dahl Martin , Asplund Maria E. , Björk Mats , Deyanova Diana , Infantes Eduardo , Isaeus Martin , Nyström Sandman Antonia , Gullström Martin
Published: August 2020

Cold-temperate seagrass (Zostera marina) meadows provide several important ecosystem services, including trapping and storage of sedimentary organic carbon and nutrients. However, seagrass meadows are rapidly decreasing worldwide and there is a pressing need for protective management of the meadows and the organic matter sinks they create. Their carbon and nutrient storage potential must be properly evaluated, both at present situation and under future climate change impacts. In this study, we assessed the effect of wave exposure on sedimentary carbon and nitrogen accumulation using existing data from 53 Z. marina meadows at the Swedish west coast. We found that meadows with higher hydrodynamic exposure had larger absolute organic carbon and nitrogen stocks (at 0–25 cm depth). This can be explained by a hydrodynamically induced sediment compaction in more exposed sites, resulting in increased sediment density and higher accumulation (per unit volume) of sedimentary organic carbon and nitrogen. With higher sediment density, the erosion threshold is assumed to increase, and as climate change-induced storms are predicted to be more common, we suggest that wave exposed meadows can be more resilient toward storms and might therefore be even more important as carbon- and nutrient sinks in the future.
Experimental realization of controlled quantum teleportation of arbitrary qubit states via cluster states
Authors: Kumar Abhijeet , Haddadi Saeed , Pourkarimi Mohammad Reza , Behera Bikash K. , Panigrahi Prasanta K.
Published: August 2020

Controlled quantum teleportation involves a third party as a controller for the teleportation of state. Here, we present the novel protocols for controlling teleportation of the arbitrary two-qubit and three-qubit states through five-qubit and seven-qubit cluster states respectively. In these schemes, Alice sends the arbitrary qubit states to the remote receiver Bob through the cluster states as quantum channels under the control of Charlie. Bob can recover the mentioned states by making appropriate unitary operations, and we point out that the efficiency in our schemes is 100%. In the process of our analysis, we find the classical communication cost in our protocols is remarkably reduced when compared to the previous protocols. We perform the experimental realization of the above protocols on “IBM 16 Melbourne” quantum computer and “IBM quantum simulator” and we calculate the fidelity. We also examine the security analysis against Charlie, and these schemes which we considered here are secure against Charlie’s attacks.
In-situ monitoring of an organic sample with electric field determination during cold plasma jet exposure
Authors: Slikboer Elmar , Sobota Ana , Garcia-Caurel Enric , Guaitella Olivier
Published: August 2020

Pockels-based Mueller polarimetry is presented as a novel diagnostic technique for studying time and space-resolved and in-situ the interaction between an organic sample (a layer of onion cells) and non-thermal atmospheric pressure plasma. The effect of plasma is complex, as it delivers electric field, radicals, (UV) radiation, non-uniform in time nor in space. This work shows for the first time that the plasma-surface interaction can be characterized through the induced electric field in an electro-optic crystal (birefringence caused by the Pockels effect) while at the same moment the surface evolution of the targeted sample is monitored (depolarization) which is attached to the crystal. As Mueller polarimetry allows for separate detection of depolarization and birefringence, it is possible to decouple the entangled effects of the plasma. In the sample three spatial regions are identified where the surface evolution of the sample differs. This directly relates to the spatial in-homogeneity of the plasma at the surface characterized through the detected electric field. The method can be applied in the future to investigate plasma-surface interactions for various targets ranging from bio-films, to catalytic surfaces and plastics/polymers.
The conversion of forestland into agricultural land without appropriate measures to conserve SOM leads to the degradation of physical and rheological soil properties
Authors: Tolimir Miodrag , Kresović Branka , Životić Ljubomir , Dragović Snežana , Dragović Ranko , Sredojević Zorica , Gajić Boško
Published: August 2020

This study was conducted to compare soil particle density (ρs), soil total porosity (TP), liquid limit (LL), plastic limit (PL), and plasticity index, and their relations with soil organic matter (SOM), of non-carbonate silty clay Fluvisols under different land uses. Three neighboring land uses were studied: native deciduous forest, arable land, and meadow, managed in the same way for more than 100 years. Soil was collected from 27 soil profiles and from three depths (0–15, 15–30 and 30–45 cm). Land use caused statistically significant but different impacts on soil properties, particularly in the topsoil. The forest topsoil measured the lowest ρs and bulk density (ρb) but the highest SOM and soil water content at PL, compared to meadow and arable soil. Statistically significant linear relationship was observed with the SOM content and ρs (− 0.851**), ρb (− 0.567**), calculated TP (0.567**) and measured TP (− 0.280**). There was a nonlinear relationship between SOM and LL (0.704**) and PL (0.845**) at the topsoil. The findings suggested that SOM content strongly affected ρs, ρb, TP, LL and LP. This regional study showed that the conversion of forestland into agricultural land without appropriate measures to conserve SOM leads to the degradation of physical and rheological soil properties.
Principles of computer-controlled linear motion applied to an open-source affordable liquid handler for automated micropipetting
Authors: Florian David C. , Odziomek Mateusz , Ock Cerie L. , Chen Hannah , Guelcher Scott A.
Published: August 2020

OTTO is an open-source automated liquid handler that can be fabricated at a cost of $1,500 using off-the-shelf and 3D-printable parts as an alternative to commercial devices. Open-source approaches have been applied to build syringe pumps, centrifuges, and other laboratory equipment. These devices are affordable but generally rely on a single motor to perform simple operations and thus do not fully utilize the potential of the Maker Movement. Open-source linear actuators and microcontrollers enable the fabrication of more complex laboratory instruments that rely on 3D positioning and accurate dispensing of fluids, such as automated liquid handlers. These instruments can be built rapidly and affordably, thereby providing access to highly reproducible sample preparation for common biological assays such as qPCR. We applied the design principles of speed and accuracy, unattended automation, and open-source components to build an automated liquid handler that controls micropipetting of liquids in 3D space at speeds and positional resolutions required for qPCR. In benchmarking studies, OTTO showed accuracy and sample preparation times comparable to manual qPCR. The ability to control linear motion and liquid dispensing using affordable off-the-shelf and 3D-printable parts can facilitate the adoption of open-source automated liquid handlers for qPCR, bioplotting, and other bioinstrumentation applications.
Salmonella enterica serovar Typhi exposure elicits ex vivo cell-type-specific epigenetic changes in human gut cells
Authors: Sztein Marcelo B. , Bafford Andrea C. , Salerno-Goncalves Rosângela
Published: August 2020

Salmonella enterica serovar Typhi (S. Typhi) causes substantial morbidity and mortality worldwide, particularly among young children. Humans develop an array of mucosal immune responses following S. Typhi infection. Whereas the cellular mechanisms involved in S. Typhi infection have been intensively studied, very little is known about the early chromatin modifications occurring in the human gut microenvironment that influence downstream immune responses. To address this gap in knowledge, cells isolated from human terminal ileum exposed ex vivo to the wild-type S. Typhi strain were stained with a 33-metal-labeled antibody panel for mass cytometry analyses of the early chromatin modifications modulated by S. Typhi. We measured the cellular levels of 6 classes of histone modifications, and 1 histone variant in 11 major cell subsets (i.e., B, CD3 + T, CD4 + T, CD8 + T, NK, TCR-γδ, Mucosal associated invariant (MAIT), and NKT cells as well as monocytes, macrophages, and epithelial cells). We found that arginine methylation might regulate the early-differentiation of effector-memory CD4+ T-cells following exposure to S. Typhi. We also found S. Typhi-induced post-translational modifications in histone methylation and acetylation associated with epithelial cells, NKT, MAIT, TCR-γδ, Monocytes, and CD8 + T-cells that are related to both gene activation and silencing.
Integrative analyses of transcriptomics and metabolomics upon seed germination of foxtail millet in response to salinity
Authors: Pan Jiaowen , Li Zhen , Dai Shaojun , Ding Hanfeng , Wang Qingguo , Li Xiaobo , Ding Guohua , Wang Pengfei , Guan Yanan , Liu Wei
Published: August 2020

Salinity stress has become an expanding threat to food security worldwide. Revealing the mechanisms of salinity tolerance in plants has immense significance. Foxtail millet (Setaria italica L.) has been regarded as a model crop for exploring mechanisms under stress, considering its extreme adaptation abilities to adverse ecologies. In present study, two foxtail millet cultivars of Yugu2 and An04 with contrasting salt tolerance properties were investigated through integrative analyses of transcriptomics and metabolomics. In the transcriptomics results, 8887 and 12,249 DEGs were identified in Yugu2 and An04 in response to salinity, respectively, and 3149 of which were overlapped between two varieties. These salinity-responsive genes indicated that ion transport, redox homeostasis, phytohormone metabolism, signaling and secondary metabolism were enriched in Yugu2 by GO and KEGG analyses. The integrative omics analysis implied that phenylpropanoid, flavonoid and lignin biosynthesis pathways, and lysophospholipids were vital in determining the foxtail millet salinity tolerance. Importantly, the tolerance of Yugu2 attributed to higher efficiencies of ion channel and antioxidant system. All these provide a comprehensive regulatory network of foxtail millet to cope with salinity, and shed some lights on salt tolerance which is relevant for other cereal crops.
The P-glycoprotein repertoire of the equine parasitic nematode Parascaris univalens
Authors: Gerhard Alexander P. , Krücken Jürgen , Heitlinger Emanuel , Janssen I. Jana I. , Basiaga Marta , Kornaś Sławomir , Beier Céline , Nielsen Martin K. , Davis Richard E. , Wang Jianbin , von Samson-Himmelstjerna Georg
Published: August 2020

P-glycoproteins (Pgp) have been proposed as contributors to the widespread macrocyclic lactone (ML) resistance in several nematode species including a major pathogen of foals, Parascaris univalens. Using new and available RNA-seq data, ten different genomic loci encoding Pgps were identified and characterized by transcriptome-guided RT-PCRs and Sanger sequencing. Phylogenetic analysis revealed an ascarid-specific Pgp lineage, Pgp-18, as well as two paralogues of Pgp-11 and Pgp-16. Comparative gene expression analyses in P. univalens and Caenorhabditis elegans show that the intestine is the major site of expression but individual gene expression patterns were not conserved between the two nematodes. In P. univalens, PunPgp-9, PunPgp-11.1 and PunPgp-16.2 consistently exhibited the highest expression level in two independent transcriptome data sets. Using RNA-Seq, no significant upregulation of any Pgp was detected following in vitro incubation of adult P. univalens with ivermectin suggesting that drug-induced upregulation is not the mechanism of Pgp-mediated ML resistance. Expression and functional analyses of PunPgp-2 and PunPgp-9 in Saccharomyces cerevisiae provide evidence for an interaction with ketoconazole and ivermectin, but not thiabendazole. Overall, this study established reliable reference gene models with significantly improved annotation for the P. univalens Pgp repertoire and provides a foundation for a better understanding of Pgp-mediated anthelmintic resistance.
ApcMin/+ tumours and normal mouse small intestines show linear metabolite concentration and DNA cytosine hydroxymethylation gradients from pylorus to colon
Authors: Madhu Basetti , Uribe-Lewis Santiago , Bachman Martin , Murrell Adele , Griffiths John R.
Published: August 2020

Topographical variations of metabolite concentrations have been reported in the duodenum, jejunum and ileum of the small intestine, and in human intestinal tumours from those regions, but there are no published metabolite concentrations measurements correlated with linear position in the mouse small intestine or intestinal tumours. Since DNA methylation dynamics are influenced by metabolite concentrations, they too could show linear anatomical variation. We measured metabolites by HR-MAS 1H NMR spectroscopy and DNA cytosine modifications by LC/MS, in normal small intestines of C57BL/6J wild-type mice, and in normal and tumour samples from ApcMin/+ mice. Wild-type mouse intestines showed approximately linear, negative concentration gradations from the pylorus (i.e. the junction with the stomach) of alanine, choline compounds, creatine, leucine and valine. ApcMin/+ mouse tumours showed negative choline and valine gradients, but a positive glycine gradient. 5-Hydroxymethylcytosine showed a positive gradient in the tumours. The linear gradients we found along the length of the mouse small intestine and in tumours contrast with previous reports of discrete concentration changes in the duodenum, jejunum and ileum. To our knowledge, this is also the first report of a systematic measurement of global levels of DNA cytosine modification in wild-type and ApcMin/+ mouse small intestine.
Molecular characterization of pyridoxine 5′-phosphate oxidase and its pathogenic forms associated with neonatal epileptic encephalopathy
Authors: Barile Anna , Nogués Isabel , di Salvo Martino L. , Bunik Victoria , Contestabile Roberto , Tramonti Angela
Published: August 2020

Defects of vitamin B6 metabolism are responsible for severe neurological disorders, such as pyridoxamine 5′-phosphate oxidase deficiency (PNPOD; OMIM: 610090), an autosomal recessive inborn error of metabolism that usually manifests with neonatal-onset severe seizures and subsequent encephalopathy. At present, 27 pathogenic mutations of the gene encoding human PNPO are known, 13 of which are homozygous missense mutations; however, only 3 of them have been characterised with respect to the molecular and functional properties of the variant enzyme forms. Moreover, studies on wild type and variant human PNPOs have so far largely ignored the regulation properties of this enzyme. Here, we present a detailed characterisation of the inhibition mechanism of PNPO by pyridoxal 5′-phosphate (PLP), the reaction product of the enzyme. Our study reveals that human PNPO has an allosteric PLP binding site that plays a crucial role in the enzyme regulation and therefore in the regulation of vitamin B6 metabolism in humans. Furthermore, we have produced, recombinantly expressed and characterised several PNPO pathogenic variants responsible for PNPOD (G118R, R141C, R225H, R116Q/R225H, and X262Q). Such replacements mainly affect the catalytic activity of PNPO and binding of the enzyme substrate and FMN cofactor, leaving the allosteric properties unaltered.
Risk factors for the deterioration of periventricular–intraventricular hemorrhage in preterm infants
Authors: Wu Tian , Wang Yan , Xiong Tao , Huang Sheng , Tian Tian , Tang Jun , Mu Dezhi
Published: August 2020

Preterm infants with periventricular–intraventricular hemorrhage (PV–IVH) have a high risk of neurological sequelae, with severity depending on the severity of the PV–IVH. Previous studies on the pathogenesis of PV–IVH have focused mainly on comparisons of perinatal risk factors between patients with and without PV–IVH. Notably, most cases of PV–IVH occur within the first 3 days after birth, and the condition may worsen within 1 week following the initial diagnosis. However, the risk factors that contribute to the deterioration of PV–IVH have not been investigated. In this cohort study, 514 PV–IVH infants with a gestational age (GA) < 32 weeks were enrolled. The dependent variable was initially diagnosed as mild PV–IVH (grade I or II) that subsequently progressed to severe PV–IVH (grade III or IV) within 1 week. A stepwise forward multivariate logistic regression model was adopted to select potential or related factors that affected the deterioration of PV–IVH in preterm infants. Overall, 42 of the 514 infants with PV–IVH (8.2%) showed deterioration within 1 week. The results showed that maternal lower genital tract infection (OR 3.73, 95% CI 1.75–7.95) was an independent risk factor for PV–IVH deterioration. Higher GA (OR 0.62, 95% CI 0.48–0.80) was a protective factor. Our results suggest that maternal lower genital tract infection and a lower GA may contribute to PV–IVH deterioration in preterm infants.
Spatial regression analysis of MR diffusion reveals subject-specific white matter changes associated with repetitive head impacts in contact sports
Authors: Asselin Patrick D. , Gu Yu , Merchant-Borna Kian , Abar Beau , Wright David W. , Qiu Xing , Bazarian Jeff J.
Published: August 2020

Repetitive head impacts (RHI) are a growing concern due to their possible neurocognitive effects, with research showing a season of RHI produce white matter (WM) changes seen on neuroimaging. We conducted a secondary analysis of diffusion tensor imaging (DTI) data for 28 contact athletes to compare WM changes. We collected pre-season and post-season DTI scans for each subject, approximately 3 months apart. We collected helmet data for the athletes, which we correlated with DTI data. We adapted the SPatial REgression Analysis of DTI (SPREAD) algorithm to conduct subject-specific longitudinal DTI analysis, and developed global inferential tools using functional norms and a novel robustpvalue combination test. At the individual level, most detected injured regions (93.3%) were associated with decreased FA values. Using meta-analysis techniques to combine injured regions across subjects, we found the combined injured region at the group level occupied the entire WM skeleton, suggesting the WM damage location is subject-specific. Several subject-specific functional summaries of SPREAD-detected WM change, e.g., the$${L}^{\infty }$$L∞norm, significantly correlated with helmet impact measures, e.g. cumulative unweighted rotational acceleration (adjustedp = 0.0049), time between hits rotational acceleration (adjustedpvalue 0.0101), and time until DTI rotational acceleration (adjustedp = 0.0084), suggesting RHIs lead to WM changes.
Artificially induced MAIT cells inhibit M. bovis BCG but not M. tuberculosis during in vivo pulmonary infection
Authors: Yu Huifeng , Yang Amy , Derrick Steven , Mak Jeffrey Y. W. , Liu Ligong , Fairlie David P. , Cowley Siobhan
Published: August 2020

There is significant interest in targeting MAIT cells with immunostimulatory agents to enhance immune responses. Mycobacterium tuberculosis (M. tb.) is a pervasive respiratory disease that could benefit from treatments that augment immunity. Here we investigate the role of MAIT cells in M. tb. infection and the potential for MAIT cell-targeted immunotherapy to control bacterial burdens. We find that MAIT cells fail to substantially accumulate in the lungs during murine pulmonary M. bovis BCG and M. tb. infections but this defect is overcome by intranasal installation of a TLR2/6 agonist and a MAIT cell antigen. Although artificially induced MAIT cells produce important cytokines in both infections, they control BCG but not M. tb. growth in the lungs. Correspondingly, M. tb.-infected mouse macrophages are relatively resistant to MAIT cell antimicrobial activities in vitro. Thus, MAIT cell antigen-mediated immunotherapy for M. tb. presents a complex challenge.