bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental and Numerical Study of the Effect of Model Geometric Distortion on Laboratory Modeling of Urban Flooding
Authors: Li Xuefang , Kitsikoudis Vasileios , Mignot Emmanuel , Archambeau Pierre , Pirotton Michel , Dewals Benjamin , Erpicum Sébastien
Published: September 2021

Laboratory studies of urban flooding often use geometrically distorted scale models due to the multi‐scale nature of these specific flows. The possible bias induced by geometric distortion has never been thoroughly investigated with dedicated laboratory experiments. In this study, we combine experimental and computational modeling to systematically assess the influence of the distortion ratio, that is, the ratio of horizontal to vertical scale factors, on upscaled flow depths and discharge partition between streets. Three flow configurations were considered: a street junction, a street bifurcation, and a small synthetic urban district. When the distortion ratio is varied up to a value of about 5, the upscaled flow depths at the model inlets decrease monotonously and the flow discharge in the branch that conveys the largest portion of the flow is greatly enhanced. For equal flow depths at the model outlets and depending on the configuration, the distortion effect induces a variation of the upstream flow depth approximately from ∼4% to ∼17% and a change in outlet discharge partition up to 24 percentage points. For a distortion ratio above 5, both upscaled upstream flow depths and outlet discharge partition tend to stabilize asymptotically. Our study indicates the direction and magnitude of the bias induced by geometric distortion for a broad range of flow cases, which is valuable for offsetting these effects in practical laboratory studies of urban flooding.
Field‐Scale Subsurface Flow Processes Inferred From Continuous Gravity Monitoring During a Sprinkling Experiment
Authors: Reich Marvin , Mikolaj Michal , Blume Theresa , Güntner Andreas
Published: September 2021

Field‐scale subsurface flow processes are difficult to observe and monitor. We investigated the value of gravity time series to identify subsurface flow processes by carrying out a sprinkling experiment in the direct vicinity of a superconducting gravimeter. We demonstrate how different water mass distributions in the subsoil affect the gravity signal and show the benefit of using the shape of the gravity response curve to identify different subsurface flow processes. For this purpose, a simple hydro‐gravimetric model was set up to test different scenarios in an optimization approach, including the processes macropore flow, preferential flow, wetting front advancement (WFA), bypass flow and perched water table rise. Besides the gravity observations, electrical resistivity and soil moisture data were used for evaluation. For the study site, the process combination of preferential flow and WFA led to the best correspondence to the observations in a multi‐criteria assessment. We argue that the approach of combining field‐scale sprinkling experiments in combination with gravity monitoring can be transferred to other sites for process identification, and discuss related uncertainties including limitations of the simple model used here. The study stresses the value of advancing terrestrial gravimetry as an integrative and non‐invasive monitoring technique for assessing hydrological states and dynamics.
MicroRNA-338-3p as a novel therapeutic target for intervertebral disc degeneration
Authors: Jiang Hua , Moro Abu , Wang Jiaqi , Meng Dihua , Zhan Xinli , Wei Qingjun
Published: September 2021

Recent studies have demonstrated the pivotal role played by microRNAs (miRNAs) in the etiopathogenesis of intervertebral disc degeneration (IDD). The study of miRNA intervention in IDD models may promote the advancement of miRNA-based therapeutic strategies. The aim of the current study was to investigate whether intradiscal delivery of miRNA can attenuate IDD development. Our results showed that miR-338-3p expression was significantly increased in the nucleus pulposus (NP) of patients with IDD. Moreover, there was a statistically significant positive correlation between the expression level of miR-338-3p and the severity of IDD. Our functional studies showed that miR-338-3p significantly influenced the expression of extracellular matrix synthesis genes, as well as the proliferation and apoptosis of NP cells. Mechanistically, miR-338-3p aggravated IDD progression by directly targeting SIRT6, a negative regulator of the MAPK/ERK pathway. Intradiscal injection of antagomir-338-3p significantly decelerated IDD development in mouse models. Our study is the first to identify miR-338-3p as a mediator of IDD and thus may be a promising target for rescuing IDD.
Gene expression profiling on effect of aspirin on osteogenic differentiation of periodontal ligament stem cells
Authors: Abd Rahman Fazliny
Published: September 2021

Periodontal ligament (PDL) contains a unique population of mesenchymal stem cells (MSCs), also known as PDL stem cells (PDLSCs). The regenerative properties of PDLSCs hold great potential for its use in stem cells based therapy, particularly for periodontal or bone regeneration. The present study investigated the global gene expression profile in PDLSCs during osteogenic differentiation. MSCs from PDL were isolated from normal permanent human teeth (n = 3). Microarray analysis was used to study the effects of ASA (200, 500, and 1000 μM) on the gene expression profiles in PDLSCs during osteogenic differentiation. Microarray study revealed that ASA was able to modulate PDLSCs gene expression profile. At 200 µM, 315 genes were dysregulated genes (DE), involving 151 upregulated and 164 downregulated genes. At 500 µM, 794 genes were DE, involving of 364 upregulated and 430 downregulated genes. At 1000 µM, the number of DE genes increased to 2035, of which 735 were upregulated and 1300 were downregulated. Bioinformatics analyses of the gene expression data revealed that the majority of DE genes (for 500 and 1000 µM ASA treatment) are involved in osteogenic differentiation. The gene network analysis was carried out using Ingenuity Pathway Analysis (IPA) software, and this revealed that the number of gene groups involved in cell adhesion and extracellular matrix components were increased. This study indicated that ASA could enhance PDLSCs functions and provide evidence for the potential use of ASA with PDLSCs for regenerative dentistry applications, particularly in the areas of periodontal health and regeneration. Periodontal ligament stem cells (PDLSCs) Aspirin (ASA) Microarray Osteogenic
The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole
Authors: Martin Kara , Schmidt Katrin , Toseland Andrew , Boulton Chris A. , Barry Kerrie , Beszteri Bánk , Brussaard Corina P. D. , Clum Alicia , Daum Chris G. , Eloe-Fadrosh Emiley , Fong Allison , Foster Brian , Foster Bryce , Ginzburg Michael , Huntemann Marcel , Ivanova Natalia N. , Kyrpides Nikos C. , Lindquist Erika , Mukherjee Supratim , Palaniappan Krishnaveni , Reddy T. B. K. , Rizkallah Mariam R. , Roux Simon , Timmermans Klaas , Tringe Susannah G. , van de Poll Willem H. , Varghese Neha , Valentin Klaus U. , Lenton Timothy M. , Grigoriev Igor V. , Leggett Richard M. , Moulton Vincent , Mock Thomas
Published: September 2021

Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with prokaryotes as part of complex microbiomes. Although differences in their local species diversity have been estimated, we still have a limited understanding of environmental conditions responsible for compositional differences between local species communities on a large scale from pole to pole. Here, we show, based on pole-to-pole phytoplankton metatranscriptomes and microbial rDNA sequencing, that environmental differences between polar and non-polar upper oceans most strongly impact the large-scale spatial pattern of biodiversity and gene activity in algal microbiomes. The geographic differentiation of co-occurring microbes in algal microbiomes can be well explained by the latitudinal temperature gradient and associated break points in their beta diversity, with an average breakpoint at 14 °C ± 4.3, separating cold and warm upper oceans. As global warming impacts upper ocean temperatures, we project that break points of beta diversity move markedly pole-wards. Hence, abrupt regime shifts in algal microbiomes could be caused by anthropogenic climate change.
Transformation of tenofovir into stable ProTide nanocrystals with long-acting pharmacokinetic profiles
Authors: Cobb Denise A. , Smith Nathan , Deodhar Suyash , Bade Aditya N. , Gautam Nagsen , Shetty Bhagya Laxmi Dyavar , McMillan JoEllyn , Alnouti Yazen , Cohen Samuel M. , Gendelman Howard E. , Edagwa Benson
Published: September 2021

Treatment and prevention of human immunodeficiency virus type one (HIV-1) infection was transformed through widespread use of antiretroviral therapy (ART). However, ART has limitations in requiring life-long daily adherence. Such limitations have led to the creation of long-acting (LA) ART. While nucleoside reverse transcriptase inhibitors (NRTI) remain the ART backbone, to the best of our knowledge, none have been converted into LA agents. To these ends, we transformed tenofovir (TFV) into LA surfactant stabilized aqueous prodrug nanocrystals (referred to as NM1TFV and NM2TFV), enhancing intracellular drug uptake and retention. A single intramuscular injection of NM1TFV, NM2TFV, or a nanoformulated tenofovir alafenamide (NTAF) at 75 mg/kg TFV equivalents to Sprague Dawley rats sustains active TFV-diphosphate (TFV-DP) levels ≥ four times the 90% effective dose for two months. NM1TFV, NM2TFV and NTAF elicit TFV-DP levels of 11,276, 1,651, and 397 fmol/g in rectal tissue, respectively. These results are a significant step towards a LA TFV ProTide.
Vacuum-field-induced THz transport gap in a carbon nanotube quantum dot
Authors: Valmorra F. , Yoshida K. , Contamin L. C. , Messelot S. , Massabeau S. , Delbecq M. R. , Dartiailh M. C. , Desjardins M. M. , Cubaynes T. , Leghtas Z. , Hirakawa K. , Tignon J. , Dhillon S. , Balibar S. , Mangeney J. , Cottet A. , Kontos T.
Published: September 2021

The control of light-matter interaction at the most elementary level has become an important resource for quantum technologies. Implementing such interfaces in the THz range remains an outstanding problem. Here, we couple a single electron trapped in a carbon nanotube quantum dot to a THz resonator. The resulting light-matter interaction reaches the deep strong coupling regime that induces a THz energy gap in the carbon nanotube solely by the vacuum fluctuations of the THz resonator. This is directly confirmed by transport measurements. Such a phenomenon which is the exact counterpart of inhibition of spontaneous emission in atomic physics opens the path to the readout of non-classical states of light using electrical current. This would be a particularly useful resource and perspective for THz quantum optics.
Hecw controls oogenesis and neuronal homeostasis by promoting the liquid state of ribonucleoprotein particles
Authors: Fajner Valentina , Giavazzi Fabio , Sala Simona , Oldani Amanda , Martini Emanuele , Napoletano Francesco , Parazzoli Dario , Cesare Giuliana , Cerbino Roberto , Maspero Elena , Vaccari Thomas , Polo Simona
Published: September 2021

Specialised ribonucleoprotein (RNP) granules are a hallmark of polarized cells, like neurons and germ cells. Among their main functions is the spatial and temporal modulation of the activity of specific mRNA transcripts that allow specification of primary embryonic axes. While RNPs composition and role are well established, their regulation is poorly defined. Here, we demonstrate that Hecw, a newly identified Drosophila ubiquitin ligase, is a key modulator of RNPs in oogenesis and neurons. Hecw depletion leads to the formation of enlarged granules that transition from a liquid to a gel-like state. Loss of Hecw activity results in defective oogenesis, premature aging and climbing defects associated with neuronal loss. At the molecular level, reduced ubiquitination of the Fmrp impairs its translational repressor activity, resulting in altered Orb expression in nurse cells and Profilin in neurons.
Community and single cell analyses reveal complex predatory interactions between bacteria in high diversity systems
Authors: Cohen Yossi , Pasternak Zohar , Müller Susann , Hübschmann Thomas , Schattenberg Florian , Sivakala Kunjukrishnan Kamalakshi , Abed-Rabbo Alfred , Chatzinotas Antonis , Jurkevitch Edouard
Published: September 2021

A fundamental question in community ecology is the role of predator–prey interactions in food-web stability and species coexistence. Although microbial microcosms offer powerful systems to investigate it, interrogating the environment is much more arduous. Here, we show in a 1-year survey that the obligate predators Bdellovibrio and like organisms (BALOs) can regulate prey populations, possibly in a density-dependent manner, in the naturally complex, species-rich environments of wastewater treatment plants. Abundant as well as rarer prey populations are affected, leading to an oscillating predatory landscape shifting at various temporal scales in which the total population remains stable. Shifts, along with differential prey range, explain co-existence of the numerous predators through niche partitioning. We validate these sequence-based findings using single-cell sorting combined with fluorescent hybridization and community sequencing. Our approach should be applicable for deciphering community interactions in other systems.
COVID-19 patients age, comorbidity profiles and clinical presentation related to the SARS-CoV-2 UK-variant spread in the Southeast of France
Authors: Courjon Johan , Contenti Julie , Demonchy Elisa , Levraut Jacques , Barbry Pascal , Rios Géraldine , Dellamonica Jean , Chirio David , Bonnefoy Caroline , Giordanengo Valérie , Carles Michel
Published: September 2021

The variant 20I/501Y.V1, associated to a higher risk of transmissibility, emerged in Nice city (Southeast of France, French Riviera) during January 2021. The pandemic has resumed late December 2020 in this area. A high incidence rate together with a fast turn-over of the main circulating variants, provided us the opportunity to analyze modifications in clinical profile and outcome traits. We performed an observational study in the University hospital of Nice from December 2020 to February 2021. We analyzed data of sequencing of SARS-CoV-2 from the sewage collector and PCR screening from all positive samples at the hospital. Then, we described the characteristics of all COVID-19 patients admitted in the emergency department (ED) (n = 1247) and those hospitalized in the infectious diseases ward or ICU (n = 232). The UK-variant was absent in this area in December, then increasingly spread in January representing 59% of the PCR screening performed mid-February. The rate of patients over 65 years admitted to the ED decreased from 63 to 50% (p = 0.001). The mean age of hospitalized patients in the infectious diseases ward decreased from 70.7 to 59.2 (p < 0.001) while the proportion of patients without comorbidity increased from 16 to 42% (p = 0.007). Spread of the UK-variant in the Southeast of France affects younger and healthier patients.
Effect of arbuscular mycorrhizal fungi on the physiological functioning of maize under zinc-deficient soils
Authors: Saboor Abdul , Ali Muhammad Arif , Danish Subhan , Ahmed Niaz , Fahad Shah , Datta Rahul , Ansari Mohammad Javed , Nasif Omaima , Rahman Muhammad Habib ur , Glick Bernard R.
Published: September 2021

Zinc (Zn) deficiency can severely inhibit plant growth, yield, and enzymatic activities. Zn plays a vital role in various enzymatic activities in plants. Arbuscular mycorrhizal fungi (AMF) play a crucial role in improving the plant’s Zn nutrition and mitigating Zn stress effects on plants. The current study was conducted to compare the response of inoculated and non-inoculated maize (YH 1898) in the presence of different levels of zinc under greenhouse conditions under a Zn deficient condition. There were two mycorrhizal levels (i.e., M + with mycorrhizae, M- without mycorrhizae) and five Zn levels (i.e., 0, 1.5, 3, 6, and 12 mg kg-1), with three replicates following completely randomized design. At the vegetative stage (before tillering), biochemical, physiological, and agronomic attributes were measured. The results showed that maize plants previously inoculated with AMF had higher gaseous exchange traits, i.e., a higher stomatal conductance rate, favoring an increased photosynthetic rate. Improvement in antioxidant enzyme activity was also observed in inoculated compared to non-inoculated maize plants. Moreover, AMF inoculation also played a beneficial role in nutrients availability and its uptake by plants. Higher Zn12 (12 mg Zn kg-1 soil) treatment accumulated a higher Zn concentration in soil, root, and shoot in AMF-inoculated than in non-inoculated maize plants. These results are consistent with mycorrhizal symbiosis beneficial role for maize physiological functioning in Zn deficient soil conditions. Additionally, AMF inoculation mitigated the stress conditions and assisted nutrient uptake by maize.
Direct visualization of the effect of DNA structure and ionic conditions on HU–DNA interactions
Authors: Lin Szu-Ning , Dame Remus T. , Wuite Gijs J. L.
Published: September 2021

Architectural DNA–binding proteins are involved in many important DNA transactions by virtue of their ability to change DNA conformation. Histone-like protein from E. coli strain U93, HU, is one of the most studied bacterial architectural DNA–binding proteins. Nevertheless, there is still a limited understanding of how the interactions between HU and DNA are affected by ionic conditions and the structure of DNA. Here, using optical tweezers in combination with fluorescent confocal imaging, we investigated how ionic conditions affect the interaction between HU and DNA. We directly visualized the binding and the diffusion of fluorescently labelled HU dimers on DNA. HU binds with high affinity and exhibits low mobility on the DNA in the absence of Mg2+; it moves 30-times faster and stays shorter on the DNA with 8 mM Mg2+ in solution. Additionally, we investigated the effect of DNA tension on HU–DNA complexes. On the one hand, our studies show that binding of HU enhances DNA helix stability. On the other hand, we note that the binding affinity of HU for DNA in the presence of Mg2+ increases at tensions above 50 pN, which we attribute to force-induced structural changes in the DNA. The observation that HU diffuses faster along DNA in presence of Mg2+ compared to without Mg2+ suggests that the free energy barrier for rotational diffusion along DNA is reduced, which can be interpreted in terms of reduced electrostatic interaction between HU and DNA, possibly coinciding with reduced DNA bending.
Control of membrane protein homeostasis by a chaperone-like glial cell adhesion molecule at multiple subcellular locations
Authors: Xu Haijin , Isenmann Sandra , López-Hernández Tania , Estévez Raúl , Lukacs Gergely L. , Apaja Pirjo M.
Published: September 2021

The significance of crosstalks among constituents of plasma membrane protein clusters/complexes in cellular proteostasis and protein quality control (PQC) remains incompletely understood. Examining the glial (enriched) cell adhesion molecule (CAM), we demonstrate its chaperone-like role in the biosynthetic processing of the megalencephalic leukoencephalopathy with subcortical cyst 1 (MLC1)-heteromeric regulatory membrane protein complex, as well as the function of the GlialCAM/MLC1 signalling complex. We show that in the absence of GlialCAM, newly synthesized MLC1 molecules remain unfolded and are susceptible to polyubiquitination-dependent proteasomal degradation at the endoplasmic reticulum. At the plasma membrane, GlialCAM regulates the diffusional partitioning and endocytic dynamics of cluster members, including the ClC-2 chloride channel and MLC1. Impaired folding and/or expression of GlialCAM or MLC1 in the presence of diseases causing mutations, as well as plasma membrane tethering compromise the functional expression of the cluster, leading to compromised endo-lysosomal organellar identity. In addition, the enlarged endo-lysosomal compartments display accelerated acidification, ubiquitinated cargo-sorting and impaired endosomal recycling. Jointly, these observations indicate an essential and previously unrecognized role for CAM, where GliaCAM functions as a PQC factor for the MLC1 signalling complex biogenesis and possess a permissive role in the membrane dynamic and cargo sorting functions with implications in modulations of receptor signalling.
Copper-binding ligands in deep-sea pore waters of the Pacific Ocean and potential impacts of polymetallic nodule mining on the copper cycle
Authors: Paul Sophie A. L. , Zitoun Rebecca , Noowong Ann , Manirajah Mythili , Koschinsky Andrea
Published: September 2021

The release of potentially toxic metals, such as copper (Cu), into the water column is of concern during polymetallic nodule mining. The bioavailability and thus toxicity of Cu is strongly influenced by its speciation which is dominated by organic ligand (L) complexation in seawater, with L-complexes being considered less bioavailable than free Cu2+. The presence of CuL-complexes in deep-sea sediments has, however, not been systematically studied in the context of deep-sea mining. We thus analyzed the Cu-binding L concentration ([L]) in deep-sea pore waters of two polymetallic nodule provinces in the Pacific Ocean, the Peru Basin and the Clarion-Clipperton-Zone, using competitive ligand equilibration–adsorptive stripping voltammetry. The pore-water dissolved Cu concentration ([dCu]) ranged from 3 to 96 nM, generally exceeding bottom water concentrations (4–44 nM). Based on fitting results from ProMCC and Excel, Cu was predominantly complexed by L (3–313 nM) in bottom waters and undisturbed pore waters. We conclude that processes like deep-sea mining are unlikely to cause a release of toxic Cu2+ concentrations ([Cu2+]) to the seawater as > 99% Cu was organically complexed in pore waters and the [Cu2+] was < 6 pM for 8 of 9 samples. Moreover, the excess of L found especially in shallow pore waters implied that even with a Cu release through mining activities, Cu2+ likely remains beneath toxic thresholds.
Emerging of new bioartificial corticospinal motor synergies using a robotic additional thumb
Authors: Rossi Simone , Salvietti Gionata , Neri Francesco , Romanella Sara M. , Cinti Alessandra , Sinigaglia Corrado , Ulivelli Monica , Lisini Baldi Tommaso , Santarnecchi Emiliano , Prattichizzo Domenico
Published: September 2021

It is likely that when using an artificially augmented hand with six fingers, the natural five plus a robotic one, corticospinal motor synergies controlling grasping actions might be different. However, no direct neurophysiological evidence for this reasonable assumption is available yet. We used transcranial magnetic stimulation of the primary motor cortex to directly address this issue during motor imagery of objects’ grasping actions performed with or without the Soft Sixth Finger (SSF). The SSF is a wearable robotic additional thumb patented for helping patients with hand paresis and inherent loss of thumb opposition abilities. To this aim, we capitalized from the solid notion that neural circuits and mechanisms underlying motor imagery overlap those of physiological voluntary actions. After a few minutes of training, healthy humans wearing the SSF rapidly reshaped the pattern of corticospinal outputs towards forearm and hand muscles governing imagined grasping actions of different objects, suggesting the possibility that the extra finger might rapidly be encoded into the user’s body schema, which is integral part of the frontal-parietal grasping network. Such neural signatures might explain how the motor system of human beings is open to very quickly welcoming emerging augmentative bioartificial corticospinal grasping strategies. Such an ability might represent the functional substrate of a final common pathway the brain might count on towards new interactions with the surrounding objects within the peripersonal space. Findings provide a neurophysiological framework for implementing augmentative robotic tools in humans and for the exploitation of the SSF in conceptually new rehabilitation settings.
Deep saliency models learn low-, mid-, and high-level features to predict scene attention
Authors: Hayes Taylor R. , Henderson John M.
Published: September 2021

Deep saliency models represent the current state-of-the-art for predicting where humans look in real-world scenes. However, for deep saliency models to inform cognitive theories of attention, we need to knowhowdeep saliency models prioritize different scene features to predict where people look. Here we open the black box of three prominent deep saliency models (MSI-Net, DeepGaze II, and SAM-ResNet) using an approach that models the association between attention, deep saliency model output, and low-, mid-, and high-level scene features. Specifically, we measured the association between each deep saliency model and low-level image saliency, mid-level contour symmetry and junctions, and high-level meaning by applying a mixed effects modeling approach to a large eye movement dataset. We found that all three deep saliency models were most strongly associated with high-level and low-level features, but exhibited qualitatively different feature weightings and interaction patterns. These findings suggest that prominent deep saliency models are primarily learning image features associated with high-level scene meaning and low-level image saliency and highlight the importance of moving beyond simply benchmarking performance.
Brick Strex: a robust device built of LEGO bricks for mechanical manipulation of cells
Authors: Mäntylä Elina , Ihalainen Teemu O.
Published: September 2021

Cellular forces, mechanics and other physical factors are important co-regulators of normal cell and tissue physiology. These cues are often misregulated in diseases such as cancer, where altered tissue mechanics contribute to the disease progression. Furthermore, intercellular tensile and compressive force-related signaling is highlighted in collective cell behavior during development. However, the mechanistic understanding on the role of physical forces in regulation of cellular physiology, including gene expression and signaling, is still lacking. This is partly because studies on the molecular mechanisms of force transmission require easily controllable experimental designs. These approaches should enable both easy mechanical manipulation of cells and, importantly, readouts ranging from microscopy imaging to biochemical assays. To achieve a robust solution for mechanical manipulation of cells, we developed devices built of LEGO bricks allowing manual, motorized and/or cyclic cell stretching and compression studies. By using these devices, we show that$$\upbeta$$β-catenin responds differentially to epithelial monolayer stretching and lateral compression, either localizing more to the cell nuclei or cell–cell junctions, respectively. In addition, we show that epithelial compression drives cytoplasmic retention and phosphorylation of transcription coregulator YAP1. We provide a complete part listing and video assembly instructions, allowing other researchers to build and use the devices in cellular mechanics-related studies.
Tunable X-ray dark-field imaging for sub-resolution feature size quantification in porous media
Authors: Blykers Benjamin K. , Organista Caori , Boone Matthieu N. , Kagias Matias , Marone Federica , Stampanoni Marco , Bultreys Tom , Cnudde Veerle , Aelterman Jan
Published: September 2021

X-ray computed micro-tomography typically involves a trade-off between sample size and resolution, complicating the study at a micrometer scale of representative volumes of materials with broad feature size distributions (e.g. natural stones). X-ray dark-field tomography exploits scattering to probe sub-resolution features, promising to overcome this trade-off. In this work, we present a quantification method for sub-resolution feature sizes using dark-field tomograms obtained by tuning the autocorrelation length of a Talbot grating interferometer. Alumina particles with different nominal pore sizes (50 nm and 150 nm) were mixed and imaged at the TOMCAT beamline of the SLS synchrotron (PSI) at eighteen correlation lengths, covering the pore size range. The different particles cannot be distinguished by traditional absorption µCT due to their very similar density and the pores being unresolved at typical image resolutions. Nevertheless, by exploiting the scattering behavior of the samples, the proposed analysis method allowed to quantify the nominal pore sizes of individual particles. The robustness of this quantification was proven by reproducing the experiment with solid samples of alumina, and alumina particles that were kept separated. Our findings demonstrate the possibility to calibrate dark-field image analysis to quantify sub-resolution feature sizes, allowing multi-scale analyses of heterogeneous materials without subsampling.
Late stage 3 chronic kidney disease is an independent risk factor for sarcopenia, but not proteinuria
Authors: An Jung Nam , Kim Jwa-Kyung , Lee Hyung-Seok , Kim Sung Gyun , Kim Hyung Jik , Song Young Rim
Published: September 2021

Most epidemiologic studies assessing the relationship between chronic kidney disease (CKD) and sarcopenia have been performed in dialysis patients. This study aimed to evaluate the relationship between estimated glomerular filtration rate (eGFR), proteinuria, and sarcopenia in patients with non-dialysis-dependent CKD. A total of 892 outpatients who did not show any rapid changes in renal function were enrolled in this observational cohort study. We measured the muscle mass using bioimpedance analysis and handgrip strength (HGS), and sarcopenia was defined as low HGS and low muscle mass. Sarcopenia was found in 28.1% of the patients and its prevalence decreased as the body mass index (BMI) increased; however, in patients with BMI ≥ 23 kg/m2, the prevalence did not increase with BMI. As eGFR decreased, the lean tissue index and HGS significantly decreased. However, the eGFR did not affect the fat tissue index. The risk of sarcopenia increased approximately 1.6 times in patients with eGFR < 45 mL/min/1.73 m2. However, proteinuria was not associated with sarcopenia. With a decrease in eGFR, the lean muscle mass and muscle strength decreased, and the prevalence of sarcopenia increased. In patients with late stage 3 CKD, further assessment of body composition and screening for sarcopenia may be needed.
Highly efficient CRISPR/Cas9 system in Plasmodium falciparum using Cas9-expressing parasites and a linear donor template
Authors: Nishi Tsubasa , Shinzawa Naoaki , Yuda Masao , Iwanaga Shiroh
Published: September 2021

The CRISPR/Cas9 system is a powerful genetic engineering technology for Plasmodium falciparum. We here report further improvement of the CRISPR/Cas9 system by combining the Cas9-expressing parasite with a liner donor template DNA. The Cas9-expressing parasite was generated by inserting the cas9 gene in the genome by double crossover recombination. The site-directed mutagenesis and the fusion of fluorescence protein was achieved within two weeks with high efficiency (> 85%), by transfecting the schizonts of the Cas9-expressing parasite with the liner donor template and the plasmid carrying the sgRNAs. Notably, there were neither off-target mutations in the resultant transgenic parasites nor unexpected recombination, that are the technical problems of the current CRISPR/Cas9 system. Furthermore, with our system, two genes on different chromosomes were successfully modified in single transfection. Because of its high efficiency and robustness, our improved CRISPR/Cas9 system will become a standard technique for genetic engineering of P. falciparum, which dramatically advances future studies of this parasite.
Early outcome detection for COVID-19 patients
Authors: Sîrbu Alina , Barbieri Greta , Faita Francesco , Ferragina Paolo , Gargani Luna , Ghiadoni Lorenzo , Priami Corrado
Published: September 2021

With the outbreak of COVID-19 exerting a strong pressure on hospitals and health facilities, clinical decision support systems based on predictive models can help to effectively improve the management of the pandemic. We present a method for predicting mortality for COVID-19 patients. Starting from a large number of clinical variables, we select six of them with largest predictive power, using a feature selection method based on genetic algorithms and starting from a set of COVID-19 patients from the first wave. The algorithm is designed to reduce the impact of missing values in the set of variables measured, and consider only variables that show good accuracy on validation data. The final predictive model provides accuracy larger than 85% on test data, including a new patient cohort from the second COVID-19 wave, and on patients with imputed missing values. The selected clinical variables are confirmed to be relevant by recent literature on COVID-19.
Translating synthetic natural language to database queries with a polyglot deep learning framework
Authors: Bazaga Adrián , Gunwant Nupur , Micklem Gos
Published: September 2021

The number of databases as well as their size and complexity is increasing. This creates a barrier to use especially for non-experts, who have to come to grips with the nature of the data, the way it has been represented in the database, and the specific query languages or user interfaces by which data are accessed. These difficulties worsen in research settings, where it is common to work with many different databases. One approach to improving this situation is to allow users to pose their queries in natural language. In this work we describe a machine learning framework, Polyglotter, that in a general way supports the mapping of natural language searches to database queries. Importantly, it does not require the creation of manually annotated data for training and therefore can be applied easily to multiple domains. The framework is polyglot in the sense that it supports multiple different database engines that are accessed with a variety of query languages, including SQL and Cypher. Furthermore Polyglotter supports multi-class queries. Good performance is achieved on both toy and real databases, as well as a human-annotated WikiSQL query set. Thus Polyglotter may help database maintainers make their resources more accessible.
Axial length and its associations in the Ural Very Old Study
Authors: Bikbov Mukharram M. , Kazakbaeva Gyulli M. , Rakhimova Ellina M. , Rusakova Iuliia A. , Fakhretdinova Albina A. , Tuliakova Azaliia M. , Panda-Jonas Songhomitra , Gilmanshin Timur R. , Zainullin Rinat M. , Bolshakova Natalia I. , Safiullina Kamilia R. , Gizzatov Ainur V. , Ponomarev Ildar P. , Yakupova Dilya F. , Baymukhametov Nail E. , Nikitin Nikolay A. , Jonas Jost B.
Published: September 2021

To assess the distribution of axial length as surrogate for myopia and its determinants in an old population, we performed the Ural Very Old Study as a population-based cohort study. Out of 1882 eligible individuals aged 85 + years, the Ural Very Old Study performed in an urban and rural region in Bashkortostan/Russia included 1526 (81.1%) individuals undergoing ophthalmological and medical examinations with sonographic axial length measurement. Biometric data were available for 717 (47.0%) individuals with a mean age of 88.0 ± 2.6 years (range 85–98 years; 25%). Mean axial length was 23.1 ± 1.1 mm (range 19.37–28.89 mm). Prevalences of moderate myopia (axial length 24.5–< 26.5 mm) and high myopia (axial length ≥ 26.5 mm) were 47/717 (6.6%; 95% CI 4.7, 8.4) and 10/717 (1.4%; 95% CI 0.5, 2.3), respectively. In multivariable analysis, longer axial length was associated (coefficient of determination r2 0.25) with taller body height (standardized regression coefficient beta:0.16;non-standardized regression coefficient B: 0.02; 95% confidence interval (CI) 0.01, 0.03; P < 0.001), higher level of education (beta: 0.12; B: 0.07; 95% CI 0.02, 0.11; P = 0.002), and lower corneal refractive power (beta: − 0.35; B: − 0.23; 95% CI − 0.28, − 0.18; P < 0.001). Higher prevalence of moderate myopia, however not of high myopia, was associated with higher educational level (OR 1.39; 95% CI 1.09, 1.68; P = 0.007) and lower corneal refractive power (OR 0.77; 95% CI 0.63, 0.94; P = 0.01). In this old study population, prevalence of moderate axial myopia (6.6% versus 9.7%) was lower than, and prevalence of high axial myopia (1.4% versus 1.4%) was similar as, in a corresponding study on a younger population from the same Russian region. Both myopia prevalence rates were higher than in rural Central India (1.5% and 0.4%, respectively). As in other, younger, populations, axial length and moderate myopia prevalence increased with higher educational level, while high myopia prevalence was independent of the educational level.
Modeling of the fracture energy on the finite element simulation in Ti6Al4V alloy machining
Authors: Bermudo Gamboa Carolina , Andersson Tobias , Svensson Daniel , Trujillo Vilches Francisco Javier , Martín-Béjar Sergio , Sevilla Hurtado Lorenzo
Published: September 2021

One of the main problems that exists when working with Finite Element Methods (FEM) applied to machining processes is the lack of adequate experimental data for simulating the material properties. Moreover, for damage models based on fracture energy, the correct selection of the energy value is critical for the chip formation process. It is usually difficult to obtain the fracture energy values and requires complex tests. In this work, an analysis of the influence of this fracture energy on the cutting force and the chip generation process has been carried out for different sets of cutting parameters. The aim is to present an empirical relationship, that allows selecting the fracture energy based on the cutting force and cutting parameters. The work is based on a FEM model of an orthogonal turning process for Ti6Al4V alloy using Abaqus/Explicit and the fracture energy empirical relation. This work shows that it is necessary to adjust the fracture energy for each combination of cutting conditions, to be able to fit the experimental results. The cutting force and the chip geometry are analyzed, showing how the developed model adapts to the experimental results. It shows that as the cutting speed and the feed increase, the fracture energy value that best adapts to the model decreases. The evolution shows a more pronounced decrease related to the feed increment and high cutting speed.
A multi-cantilever beam low-frequency FBG acceleration sensor
Authors: Hong Li , Sun Rui , Qiu Zhongchao , Han Zhiming , Li Yanan
Published: September 2021

The acquisition of 2–50 Hz low-frequency vibration signals is of great significance for the monitoring researches on engineering seismology, bridges & dams, oil & gas exploration, etc. A multi-cantilever beam low-frequency FBG acceleration sensor is proposed against the low sensitivity that predominates in the low-frequency vibration measurement by FBG acceleration sensors. Structural parameters of the sensor is subjected to simulation analysis and optimization design using the ANSYS software; the real sensor is developed based on the simulation results in the following manner: Three rectangular of the cantilever beams are evenly arranged around the mass block at 120°to improve the sensitivity and alleviate the transverse crosstalk of sensor; in the end, a performance test is performed on the sensor. According to the research findings, the sensor, whose natural frequency is approximately 64 Hz, is applicable for monitoring the low-frequency vibration signals within the range 16–54 Hz. The sensor sensitivity is approximately $$87.955\,{\text{pm/m}}\;{\text{s}}^{ - 2}$$

87.955

pm/m

s

-
2

, the linearity being greater than 99%, the transverse interference immunity being lower than 2.58%, and the dynamic range being up to 86 dB. The findings offer a reference for developing sensor of the same type and further improving the sensitivity of fiber optic acceleration sensor.
Comparison of proton pump inhibitors and histamine 2 receptor antagonists for stress ulcer prophylaxis in the intensive care unit
Authors: Song Myung Jin , Kim Seok , Boo Dachung , Park Changhyun , Yoo Sooyoung , Yoon Ho Il , Cho Young-Jae
Published: September 2021

Proton pump inhibitors (PPIs), followed by histamine 2 receptor antagonists (H2RAs), are the most commonly used drugs to prevent gastrointestinal bleeding in critically ill patients through stress ulcer prophylaxis. The relative efficacy and drug-related adverse events of PPIs and H2RAs remain unclear. In this retrospective, observational, comparative cohort study, PPIs and H2RAs for stress ulcer prophylaxis in critically ill patients were compared using a common data model. After propensity matching, 935 patients from each treatment group (PPI or H2RA) were selected. The PPI group had a significantly higher 90-day mortality than the H2RA group (relative risk: 1.28; P = 0.01). However, no significant inter-group differences in the risk of clinically important gastrointestinal bleeding were observed. Moreover, there were no significant differences between the groups concerning the risk of pneumonia or Clostridioides difficile infection, which are known potential adverse events related to these drugs. Subgroup analysis of patients with high disease severity were consistent with those of the total propensity score-matched population. These findings do not support the current recommendations, which prefer PPIs for gastrointestinal bleeding prophylaxis in the intensive care unit.
Antifungal features and properties of chitosan/sandalwood oil Pickering emulsion coating stabilized by appropriate cellulose nanofiber dosage for fresh fruit application
Authors: Wardana Ata Aditya , Koga Arisa , Tanaka Fumina , Tanaka Fumihiko
Published: September 2021

A novel composite edible coating film was developed from 0.8% chitosan (CS) and 0.5% sandalwood oil (SEO). Cellulose nanofibers (CNFs) were used as a stabilizer agent of oil-in-water Pickering emulsion. We found four typical groups of CNF level-dependent emulsion stabilization, including (1) unstable emulsion in the absence of CNFs; (2) unstable emulsion (0.006–0.21% CNFs); (3) stable emulsion (0.24–0.31% CNFs); and (4) regular emulsion with the addition of surfactant. Confocal laser scanning microscopy was performed to reveal the characteristics of droplet diameter and morphology. Antifungal tests against Botrytis cinerea and Penicillium digitatum, between emulsion coating stabilized with CNFs (CS-SEOpick) and CS or CS-SEO was tested. The effective concentration of CNFs (0.24%) may improve the performance of CS coating and maintain CS-SEO antifungal activity synergistically confirmed with a series of assays (in vitro, in vivo, and membrane integrity changes). The incorporation of CNFs contributed to improve the functional properties of CS and SEO-loaded CS including light transmission at UV and visible light wavelengths and tensile strength. Atomic force microscopy and scanning electron microscopy were employed to characterize the biocompatibility of each coating film formulation. Emulsion-CNF stabilized coating may have potential applications for active coating for fresh fruit commodities.
Integrating magnetic capabilities to intracellular chips for cell trapping
Authors: Arjona María Isabel , González-Manchón Consuelo , Durán Sara , Duch Marta , del Real Rafael P. , Kadambi Abhinav , Agusil Juan Pablo , Redondo-Horcajo Mariano , Pérez-García Lluïsa , Gómez Elvira , Suárez Teresa , Plaza José Antonio
Published: September 2021

Current microtechnologies have shown plenty of room inside a living cell for silicon chips. Microchips as barcodes, biochemical sensors, mechanical sensors and even electrical devices have been internalized into living cells without interfering their cell viability. However, these technologies lack from the ability to trap and preconcentrate cells in a specific region, which are prerequisites for cell separation, purification and posterior studies with enhanced sensitivity. Magnetic manipulation of microobjects, which allows a non-contacting method, has become an attractive and promising technique at small scales. Here, we show intracellular Ni-based chips with magnetic capabilities to allow cell enrichment. As a proof of concept of the potential to integrate multiple functionalities on a single device of this technique, we combine coding and magnetic manipulation capabilities in a single device. Devices were found to be internalized by HeLa cells without interfering in their viability. We demonstrated the tagging of a subpopulation of cells and their subsequent magnetic trapping with internalized barcodes subjected to a force up to 2.57 pN (for magnet-cells distance of 4.9 mm). The work opens the venue for future intracellular chips that integrate multiple functionalities with the magnetic manipulation of cells.
Histone-like nucleoid-structuring protein (H-NS) regulatory role in antibiotic resistance in Acinetobacter baumannii
Authors: Rodgers Deja , Le Casin , Pimentel Camila , Tuttobene Marisel R. , Subils Tomás , Escalante Jenny , Nishimura Brent , Vescovi Eleonora García , Sieira Rodrigo , Bonomo Robert A. , Tolmasky Marcelo E. , Ramirez Maria Soledad
Published: September 2021

In the multidrug resistant (MDR) pathogen Acinetobacter baumannii the global repressor H-NS was shown to modulate the expression of genes involved in pathogenesis and stress response. In addition, H-NS inactivation results in an increased resistance to colistin, and in a hypermotile phenotype an altered stress response. To further contribute to the knowledge of this key transcriptional regulator in A. baumannii behavior, we studied the role of H-NS in antimicrobial resistance. Using two well characterized A. baumannii model strains with distinctive resistance profile and pathogenicity traits (AB5075 and A118), complementary transcriptomic and phenotypic approaches were used to study the role of H-NS in antimicrobial resistance, biofilm and quorum sensing gene expression. An increased expression of genes associated with β-lactam resistance, aminoglycosides, quinolones, chloramphenicol, trimethoprim and sulfonamides resistance in the Δhns mutant background was observed. Genes codifying for efflux pumps were also up-regulated, with the exception of adeFGH. The wild-type transcriptional level was restored in the complemented strain. In addition, the expression of biofilm related genes and biofilm production was lowered when the transcriptional repressor was absent. The quorum network genes aidA, abaI, kar and fadD were up-regulated in Δhns mutant strains. Overall, our results showed the complexity and scope of the regulatory network control by H-NS (genes involved in antibiotic resistance and persistence). These observations brings us one step closer to understanding the regulatory role of hns to combat A. baumannii infections.