bluuebunny/crossref_metadata_2025 huggingface dataset:
Phase controlled synthesis of transition metal carbide nanocrystals by ultrafast flash Joule heating
Authors: Deng Bing , Wang Zhe , Chen Weiyin , Li John Tianci , Luong Duy Xuan , Carter Robert A. , Gao Guanhui , Yakobson Boris I. , Zhao Yufeng , Tour James M.
Published: January 2022

Nanoscale carbides enhance ultra-strong ceramics and show activity as high-performance catalysts. Traditional lengthy carburization methods for carbide syntheses usually result in coked surface, large particle size, and uncontrolled phase. Here, a flash Joule heating process is developed for ultrafast synthesis of carbide nanocrystals within 1 s. Various interstitial transition metal carbides (TiC, ZrC, HfC, VC, NbC, TaC, Cr2C3, MoC, and W2C) and covalent carbides (B4C and SiC) are produced using low-cost precursors. By controlling pulse voltages, phase-pure molybdenum carbides including β-Mo2C and metastable α-MoC1-x and η-MoC1-x are selectively synthesized, demonstrating the excellent phase engineering ability of the flash Joule heating by broadly tunable energy input that can exceed 3000 K coupled with kinetically controlled ultrafast cooling (>104 K s−1). Theoretical calculation reveals carbon vacancies as the driving factor for topotactic transition of carbide phases. The phase-dependent hydrogen evolution capability of molybdenum carbides is investigated with β-Mo2C showing the best performance.
Ultrafast coherent control of a hole spin qubit in a germanium quantum dot
Authors: Wang Ke , Xu Gang , Gao Fei , Liu He , Ma Rong-Long , Zhang Xin , Wang Zhanning , Cao Gang , Wang Ting , Zhang Jian-Jun , Culcer Dimitrie , Hu Xuedong , Jiang Hong-Wen , Li Hai-Ou , Guo Guang-Can , Guo Guo-Ping
Published: January 2022

Operation speed and coherence time are two core measures for the viability of a qubit. Strong spin-orbit interaction (SOI) and relatively weak hyperfine interaction make holes in germanium (Ge) intriguing candidates for spin qubits with rapid, all-electrical coherent control. Here we report ultrafast single-spin manipulation in a hole-based double quantum dot in a germanium hut wire (GHW). Mediated by the strong SOI, a Rabi frequency exceeding 540 MHz is observed at a magnetic field of 100 mT, setting a record for ultrafast spin qubit control in semiconductor systems. We demonstrate that the strong SOI of heavy holes (HHs) in our GHW, characterized by a very short spin-orbit length of 1.5 nm, enables the rapid gate operations we accomplish. Our results demonstrate the potential of ultrafast coherent control of hole spin qubits to meet the requirement of DiVincenzo’s criteria for a scalable quantum information processor.
Comparing ultrastable lasers at 7 × 10−17 fractional frequency instability through a 2220 km optical fibre network
Authors: Schioppo M. , Kronjäger J. , Silva A. , Ilieva R. , Paterson J. W. , Baynham C. F. A. , Bowden W. , Hill I. R. , Hobson R. , Vianello A. , Dovale-Álvarez M. , Williams R. A. , Marra G. , Margolis H. S. , Amy-Klein A. , Lopez O. , Cantin E. , Álvarez-Martínez H. , Le Targat R. , Pottie P. E. , Quintin N. , Legero T. , Häfner S. , Sterr U. , Schwarz R. , Dörscher S. , Lisdat C. , Koke S. , Kuhl A. , Waterholter T. , Benkler E. , Grosche G.
Published: January 2022

Ultrastable lasers are essential tools in optical frequency metrology enabling unprecedented measurement precision that impacts on fields such as atomic timekeeping, tests of fundamental physics, and geodesy. To characterise an ultrastable laser it needs to be compared with a laser of similar performance, but a suitable system may not be available locally. Here, we report a comparison of two geographically separated lasers, over the longest ever reported metrological optical fibre link network, measuring 2220 km in length, at a state-of-the-art fractional-frequency instability of 7 × 10−17 for averaging times between 30 s and 200 s. The measurements also allow the short-term instability of the complete optical fibre link network to be directly observed without using a loop-back fibre. Based on the characterisation of the noise in the lasers and optical fibre link network over different timescales, we investigate the potential for disseminating ultrastable light to improve the performance of remote optical clocks.
Distinct mechanisms orchestrate the contra-polarity of IRK and KOIN, two LRR-receptor-kinases controlling root cell division
Authors: Rodriguez-Furlan Cecilia , Campos Roya , Toth Jessica N. , Van Norman Jaimie M.
Published: January 2022

In plants, cell polarity plays key roles in coordinating developmental processes. Despite the characterization of several polarly localized plasma membrane proteins, the mechanisms connecting protein dynamics with cellular functions often remain unclear. Here, we introduce a polarized receptor, KOIN, that restricts cell divisions in the Arabidopsis root meristem. In the endodermis, KOIN polarity is opposite to IRK, a receptor that represses endodermal cell divisions. Their contra-polar localization facilitates dissection of polarity mechanisms and the links between polarity and function. We find that IRK and KOIN are recognized, sorted, and secreted through distinct pathways. IRK extracellular domains determine its polarity and partially rescue the mutant phenotype, whereas KOIN’s extracellular domains are insufficient for polar sorting and function. Endodermal expression of an IRK/KOIN chimera generates non-cell-autonomous misregulation of root cell divisions that impacts patterning. Altogether, we reveal two contrasting mechanisms determining these receptors’ polarity and link their polarity to cell divisions in root tissue patterning.
MAPK4 promotes triple negative breast cancer growth and reduces tumor sensitivity to PI3K blockade
Authors: Wang Wei , Han Dong , Cai Qinbo , Shen Tao , Dong Bingning , Lewis Michael T. , Wang Runsheng , Meng Yanling , Zhou Wolong , Yi Ping , Creighton Chad J. , Moore David D. , Yang Feng
Published: January 2022

About 15–20% of breast cancer (BCa) is triple-negative BCa (TNBC), a devastating disease with limited therapeutic options. Aberrations in the PI3K/PTEN signaling pathway are common in TNBC. However, the therapeutic impact of PI3K inhibitors in TNBC has been limited and the mechanism(s) underlying this lack of efficacy remain elusive. Here, we demonstrate that a large subset of TNBC expresses significant levels of MAPK4, and this expression is critical for driving AKT activation independent of PI3K and promoting TNBC cell and xenograft growth. The ability of MAPK4 to bypass PI3K for AKT activation potentially provides a direct mechanism regulating tumor sensitivity to PI3K inhibition. Accordingly, repressing MAPK4 greatly sensitizes TNBC cells and xenografts to PI3K blockade. Altogether, we conclude that high MAPK4 expression defines a large subset or subtype of TNBC responsive to MAPK4 blockage. Targeting MAPK4 in this subset/subtype of TNBC both represses growth and sensitizes tumors to PI3K blockade.
Gut microbiome development in early childhood is affected by day care attendance
Authors: Amir Amnon , Erez-Granat Ortal , Braun Tzipi , Sosnovski Katya , Hadar Rotem , BenShoshan Marina , Heiman Sophia , Abbas-Egbariya Haya , Glick Saar Efrat , Efroni Gilat , Haberman Yael
Published: January 2022

The human gut microbiome develops during the first years of life, followed by a relatively stable adult microbiome. Day care attendance is a drastic change that exposes children to a large group of peers in a diverse environment for prolonged periods, at this critical time of microbial development, and therefore has the potential to affect microbial composition. We characterize the effect of day care on the gut microbial development throughout a single school year in 61 children from 4 different day care facilities, and in additional 24 age-matched home care children (n = 268 samples, median age of entering the study was 12 months). We show that day care attendance is a significant and impactful factor in shaping the microbial composition of the growing child, the specific daycare facility and class influence the gut microbiome, and each child becomes more similar to others in their day care. Furthermore, in comparison to home care children, day care children have a different gut microbial composition, with enrichment of taxa more frequently observed in older populations. Our results provide evidence that daycare may be an external factor that contributes to gut microbiome maturation and make-up in early childhood.
Long-term corrosion monitoring of carbon steels and environmental correlation analysis via the random forest method
Authors: Li Qing , Xia Xiaojian , Pei Zibo , Cheng Xuequn , Zhang Dawei , Xiao Kui , Wu Jun , Li Xiaogang
Published: January 2022

In this work, the atmospheric corrosion of carbon steels was monitored at six different sites (and hence, atmospheric conditions) using Fe/Cu-type atmospheric corrosion monitoring technology over a period of 12 months. After analyzing over 3 million data points, the sensor data were interpretable as the instantaneous corrosion rate, and the atmospheric “corrosivity” for each exposure environment showed highly dynamic changes from the C1 to CX level (according to the ISO 9223 standard). A random forest model was developed to predict the corrosion rate and investigate the impacts of ten “corrosive factors” in dynamic atmospheres. The results reveal rust layer, wind speed, rainfall rate, RH, and chloride concentration, played a significant role in the corrosion process.
High fat diet-induced obesity prolongs critical stages of the spermatogenic cycle in a Ldlr−/−.Leiden mouse model
Authors: Komninos D. , Ramos L. , van der Heijden G. W. , Morrison M. C. , Kleemann R. , van Herwaarden A. E. , Kiliaan A. J. , Arnoldussen I. A. C.
Published: January 2022

Obesity can disturb spermatogenesis and subsequently affect male fertility and reproduction. In our study, we aim to elucidate at which cellular level of adult spermatogenesis the detrimental effects of obesity manifest. We induced high fat diet (HFD) obesity in low-density lipoprotein receptor knock-out Leiden (Ldlr−/−.Leiden) mice, and studied the morphological structure of the testes and histologically examined the proportion of Sertoli cells, spermatocytes and spermatids in the seminiferous tubules. We examined sperm DNA damage and chromatin condensation and measured plasma levels of leptin, testosterone, cholesterol and triglycerides. HFD-induced obesity caused high plasma leptin and abnormal testosterone levels and induced an aberrant intra-tubular organisation (ITO) which is associated with an altered spermatids/spermatocytes ratio (2:1 instead of 3:1). Mice fed a HFD had a higher level of tubules in stages VII + VIII in the spermatogenic cycle. The stages VII + VII indicate crucial processes in spermatogenic development like initiation of meiosis, initiation of spermatid elongation, and release of fully matured spermatids. In conclusion, HFD-induced obese Ldlr−/−.Leiden mice develop an aberrant ITO and alterations in the spermatogenic cycle in crucial stages (stages VII and VII). Thereby, our findings stress the importance of lifestyle guidelines in infertility treatments.
Distinct gut microbiomes in two polar bear subpopulations inhabiting different sea ice ecoregions
Authors: Franz Megan , Whyte Lyle , Atwood Todd C. , Laidre Kristin L. , Roy Denis , Watson Sophie E. , Góngora Esteban , McKinney Melissa A.
Published: January 2022

Gut microbiomes were analyzed by 16S rRNA gene metabarcoding for polar bears (Ursus maritimus) from the southern Beaufort Sea (SB), where sea ice loss has led to increased use of land-based food resources by bears, and from East Greenland (EG), where persistent sea ice has allowed hunting of ice-associated prey nearly year-round. SB polar bears showed a higher number of total (940 vs. 742) and unique (387 vs. 189) amplicon sequence variants and higher inter-individual variation compared to EG polar bears. Gut microbiome composition differed significantly between the two subpopulations and among sex/age classes, likely driven by diet variation and ontogenetic shifts in the gut microbiome. Dietary tracer analysis using fatty acid signatures for SB polar bears showed that diet explained more intrapopulation variation in gut microbiome composition and diversity than other tested variables, i.e., sex/age class, body condition, and capture year. Substantial differences in the SB gut microbiome relative to EG polar bears, and associations between SB gut microbiome and diet, suggest that the shifting foraging habits of SB polar bears tied to sea ice loss may be altering their gut microbiome, with potential consequences for nutrition and physiology.
A systematic review and meta-analysis of the catastrophic costs incurred by tuberculosis patients
Authors: Ghazy Ramy Mohamed , El Saeh Haider M. , Abdulaziz Shaimaa , Hammouda Esraa Abdellatif , Elzorkany Amira Mohamed , Khidr Heba , Zarif Nardine , Elrewany Ehab , Abd ElHafeez Samar
Published: January 2022

One of the strategies of the World Health Organization End Tuberculosis (TB) was to reduce the catastrophic costs incurred by TB-affected families to 0% by 2020.Catastrophic cost is defined by the total cost related to TB management exceeding 20% of the annual pre-TB household income. This study aimed to estimate the pooled proportion of TB affected households who incurred catastrophic costs. We searched PubMed, SciELO, Scopus, Embase, Google Scholar, ProQuest, SAGE, and Web of Science databases according to Preferred Reporting Items of the Systematic Reviews and Meta-Analysis (PRISMA) guidelines till November 20, 2020. Eligible studies were identified and data on catastrophic costs due to TB were extracted. We performed a meta-analysis to generate the pooled proportion of patients with TB facing catastrophic costs. From 5114 studies identified, 29 articles were included in the final analysis. The pooled proportion of patients faced catastrophic costs was (43%, 95% CI [34–51]). Meta-regression revealed that country, drug sensitivity, and Human immune-deficiency Virus (HIV) co-infection were the main predictors of such costs. Catastrophic costs incurred by drug sensitive, drug resistant, and HIV co-infection were 32%, 81%, and 81%, respectively. The catastrophic costs incurred were lower among active than passive case findings (12% vs. 30%). Half (50%) of TB-affected households faced catastrophic health expenditure at 10% cut-off point. The financial burden of patients seeking TB diagnosis and treatment continues to be a worldwide impediment. Therefore, the End TB approach should rely on socioeconomic support and cost-cutting initiatives.

PROSPERO registration: CRD42020221283.
Prone versus supine free-breathing for right-sided whole breast radiotherapy
Authors: Fargier-Bochaton Odile , Wang Xinzhuo , Dipasquale Giovanna , Laouiti Mohamed , Kountouri Melpomeni , Gorobets Olena , Nguyen Nam P. , Miralbell Raymond , Vinh-Hung Vincent
Published: January 2022

Prone setup has been advocated to improve organ sparing in whole breast radiotherapy without impairing breast coverage. We evaluate the dosimetric advantage of prone setup for the right breast and look for predictors of the gain. Right breast cancer patients treated in 2010–2013 who had a dual supine and prone planning were retrospectively identified. A penalty score was computed from the mean absolute dose deviation to heart, lungs, breasts, and tumor bed for each patient's supine and prone plan. Dosimetric advantage of prone was assessed by the reduction of penalty score from supine to prone. The effect of patients' characteristics on the reduction of penalty was analyzed using robust linear regression. A total of 146 patients with right breast dual plans were identified. Prone compared to supine reduced the penalty score in 119 patients (81.5%). Lung doses were reduced by 70.8%, from 4.8 Gy supine to 1.4 Gy prone. Among patient's characteristics, the only significant predictors were the breast volumes, but no cutoff could identify when prone would be less advantageous than supine. Prone was associated with a dosimetric advantage in most patients. It sets a benchmark of achievable lung dose reduction.

Trial registration: ClinicalTrials.gov NCT02237469, HUGProne, September 11, 2014, retrospectively registered.
Analysis of coal face stability of lower coal seam under repeated mining in close coal seams group
Authors: Xiong Yu , Kong Dezhong , Wen Zhijie , Wu Guiyi , Liu Qinzhi
Published: January 2022

Aiming at the problem of coal face failure of lower coal seam under the influence of repeated mining in close coal seams, with the working face 17,101 as a background, the coal samples mechanics test clarified the strength characteristics of the coal face under repeated mining, through similar simulation experiments, the development of stable roof structure and surrounding rock cracks under repeated mining of close coal seams are further explored. And based on this, establish a coal face failure mechanics model to comprehensively analyze the influence of multiple roof structural instabilities on the stability of the coal face. Finally, numerical simulation is used to further supplement and verify the completeness and rationality of similar simulation experiment and theoretical analysis results. The results show that: affected by repeated mining disturbances, the cracks in the coal face are relatively developed, the strength of the coal body is reduced, and the coal face is more prone to failure under the same roof pressure; During the mining of coal seam 17#, the roofs of different layers above the stope form two kinds of "arch" structures and one kind of “voussoir beam” structure, and there are three different degrees of frequent roof pressure phenomenon, which is easy to cause coal face failure; Under repeated mining of close coal seams, the roof pressure acting on the coal face is not large. The main controlling factor of coal face failure is the strength of the coal body, and the form of coal face failure is mostly the shear failure of soft coal. The research results can provide a theoretical basis for coal face failure under similar conditions.
Active earth pressure against flexible retaining wall for finite soils under the drum deformation mode
Authors: Hu Weidong , Zhu Xinnian , Zeng Yongqing , Liu Xiaohong , Peng Chucai
Published: January 2022

A reasonable method is proposed to calculate the active earth pressure of finite soils based on the drum deformation mode of the flexible retaining wall close to the basement’s outer wall. The flexible retaining wall with cohesionless sand is studied, and the ultimate failure angle of finite soils close to the basement’s outer wall is obtained using the Coulomb theory. Soil arch theory is led to get the earth pressure coefficient in the subarea using the trace line of minor principal stress of circular arc after stress deflection. The soil layers at the top and bottom part of the retaining wall are restrained when the drum deformation occurs, and the soil layers are in a non-limit state. The linear relationship between the wall movement’s magnitude and the mobilization of the internal friction angle and the wall friction anger is presented. The level layer analysis method is modified to propose the resultant force of active earth pressure, the action point’s height, and the pressure distribution. Model tests are carried out to emulate the process of drum deformation and soil rupture with limited width. Through image analysis, it is found that the failure angle of soil within the limited width is larger than that of infinite soil. With the increase of the aspect ratio, the failure angle gradually reduces and tends to be constant. Compared with the test results, it is shown that the horizontal earth pressure reduces with the reduction of the aspect ratio within critical width, and the resultant force decreases with the increase of the limit state region under the same ratio. The middle part of the distribution curve is concave. The active earth pressure strength decreases less than Coulomb’s value, the upper and lower soil layers are in the non-limit state, and the active earth pressure strength is more than Coulomb’s value.
Suppression of lipopolysaccharide-induced corneal opacity by hepatocyte growth factor
Authors: Elbasiony Elsayed , Cho WonKyung , Mittal Sharad K. , Chauhan Sunil K.
Published: January 2022

Keratitis induced by bacterial toxins, including lipopolysaccharide (LPS), is a major cause of corneal opacity and vision loss. Our previous study demonstrates hepatocyte growth factor (HGF) promotes epithelial wound healing following mechanical corneal injury. Here, we investigated whether HGF has the capacity to suppress infectious inflammatory corneal opacity using a new model of LPS-induced keratitis. Keratitis, induced by two intrastromal injections of LPS on day 1 and 4 in C57BL/6 mice, resulted in significant corneal opacity for up to day 10. Following keratitis induction, corneas were topically treated with 0.1% HGF or PBS thrice daily for 5 days. HGF-treated mice showed a significantly smaller area of corneal opacity compared to PBS-treated mice, thus improving corneal transparency. Moreover, HGF treatment resulted in suppression of α-SMA expression, compared to PBS treatment. HGF-treated corneas showed normalized corneal structure and reduced expression of pro-inflammatory cytokine, demonstrating that HGF restores corneal architecture and immune quiescence in corneas with LPS-induced keratitis. These findings offer novel insight into the potential application of HGF-based therapies for the prevention and treatment of infection-induced corneal opacity.
A novel molecular diagnostic method for the gut content analysis of Philaenus DNA
Authors: Rodrigues Isabel , Ramos Vítor , Benhadi-Marín Jacinto , Moreno Aránzazu , Fereres Alberto , Pereira José Alberto , Baptista Paula
Published: January 2022

Philaenus spumarius is a vector of Xylella fastidiosa, one of the most dangerous plants pathogenic bacteria worldwide. There is currently no control measure against this pathogen. Thus, the development of vector control strategies, like generalist predators, such as spiders, could be essential to limit the spread of this vector-borne pathogen. In this study, a polymerase chain reaction (PCR)-based approach was developed to principally detect DNA of P. spumarius in the spider’s gut. Accordingly, 20 primer pairs, targeting the mitochondrial cytochrome oxidase I (COI) and cytochrome b (cytB) genes, were tested for specificity, sensitivity, and efficiency in detecting P. spumarius DNA. Overall, two primer sets, targeting COI gene (COI_Ph71F/COI_Ph941R) and the cytB gene (cytB_Ph85F/cytB_Ph635R), showed the highest specificity and sensitivity, being able to amplify 870 pb and 550 bp fragments, respectively, with P. spumarius DNA concentrations 100-fold lower than that of the DNA of non-target species. Among these two primer sets, the cytB_Ph85F/cytB_Ph635R was able to detect P. spumarius in the spider Xysticus acerbus, reaching 50% detection success 82 h after feeding. The feasibility of this primer set to detect predation of P. spumarius by spiders was confirmed in the field, where 20% of the collected spiders presented positive amplifications.
The AtMYB60 transcription factor regulates stomatal opening by modulating oxylipin synthesis in guard cells
Authors: Simeoni Fabio , Skirycz Aleksandra , Simoni Laura , Castorina Giulia , de Souza Leonardo Perez , Fernie Alisdair R. , Alseekh Saleh , Giavalisco Patrick , Conti Lucio , Tonelli Chiara , Galbiati Massimo
Published: January 2022

Stomata are epidermal pores formed by pairs of specialized guard cells, which regulate gas exchanges between the plant and the atmosphere. Modulation of transcription has emerged as an important level of regulation of stomatal activity. The AtMYB60 transcription factor was previously identified as a positive regulator of stomatal opening, although the details of its function remain unknown. Here, we propose a role for AtMYB60 as a negative modulator of oxylipins synthesis in stomata. The atmyb60-1 mutant shows reduced stomatal opening and accumulates increased levels of 12-oxo-phytodienoic acid (12-OPDA), jasmonic acid (JA) and jasmonoyl-l-isoleucine (JA-Ile) in guard cells. We provide evidence that 12-OPDA triggers stomatal closure independently of JA and cooperatively with abscisic acid (ABA) in atmyb60-1. Our study highlights the relevance of oxylipins metabolism in stomatal regulation and indicates AtMYB60 as transcriptional integrator of ABA and oxylipins responses in guard cells.
Interfacial reactions in lithia-based cathodes depending on the binder in the electrode and salt in the electrolyte
Authors: Im Hee Jeong , Park Yong Joon
Published: January 2022

Lithia (Li2O)-based cathodes, utilizing oxygen redox reactions for obtaining capacity, exhibit higher capacity than commercial cathodes. However, they are highly reactive owing to superoxides formed during charging, and they enable more active parasitic (side) reactions at the cathode/electrolyte and cathode/binder interfaces than conventional cathodes. This causes deterioration of the electrochemical performance limiting commercialization. To address these issues, the binder and salt for electrolyte were replaced in this study to reduce the side reaction of the cells containing lithia-based cathodes. The commercially used polyvinylidene fluoride (PVDF) binder and LiPF6 salt in the electrolyte easily generate such reactions, and the subsequent reaction between PVDF and LiOH (from decomposition of lithia) causes slurry gelation and agglomeration of particles in the electrode. Moreover, the fluoride ions from PVDF promote side reactions, and LiPF6 salt forms POF3 and HF, which cause side reactions owing to hydrolysis in organic solvents containing water. However, the polyacrylonitrile (PAN) binder and LiTFSI salt decrease these side reactions owing to their high stability with lithia-based cathode. Further, thickness of the interfacial layer was reduced, resulting in decreased impedance value of cells containing lithia-based cathodes. Consequently, for the same lithia-based cathodes, available capacity and cyclic performance were increased owing to the effects of PAN binder and LiTFSI salt in the electrolyte.
Structure of alumina glass
Authors: Hashimoto Hideki , Onodera Yohei , Tahara Shuta , Kohara Shinji , Yazawa Koji , Segawa Hiroyo , Murakami Motohiko , Ohara Koji
Published: January 2022

The fabrication of novel oxide glass is a challenging topic in glass science. Alumina (Al2O3) glass cannot be fabricated by a conventional melt–quenching method, since Al2O3 is not a glass former. We found that amorphous Al2O3 synthesized by the electrochemical anodization of aluminum metal shows a glass transition. The neutron diffraction pattern of the glass exhibits an extremely sharp diffraction peak owing to the significantly dense packing of oxygen atoms. Structural modeling based on X-ray/neutron diffraction and NMR data suggests that the average Al–O coordination number is 4.66 and confirms the formation of OAl3 triclusters associated with the large contribution of edge-sharing Al–O polyhedra. The formation of edge-sharing AlO5 and AlO6 polyhedra is completely outside of the corner-sharing tetrahedra motif in Zachariasen’s conventional glass formation concept. We show that the electrochemical anodization method leads to a new path for fabricating novel single-component oxide glasses.
Change in the optic nerve sheath diameter after deflation of a pneumatic tourniquet: a prospective observational study
Authors: Kim Ha-Jung , Kim Yeon Ju , Kim Jiyoung , Kim Hyungtae , Ro Young-Jin , Koh Won Uk
Published: January 2022

Applying a pneumatic tourniquet provides surgeons with a bloodless surgical field. However, application of the tourniquet induces various physiological changes. We evaluated the effect of tourniquet deflation on the intracranial pressure by using ultrasonography to measure the optic nerve sheath diameter (ONSD) in patients undergoing lower limb surgery. The ONSD was measured in 20 patients at five time points: after anesthetic induction (T0) and immediately before (T1), immediately after (T2), 5 min after (T3), and 10 min after tourniquet deflation (T4). Hemodynamic and respiratory variables were recorded. The ONSD showed significant differences at each point (P < 0.001). The ONSDs at T2 and T3 were significantly greater than that at T1 (P = 0.0007 and < 0.0001, respectively). The change in the end-tidal carbon dioxide partial pressure (EtCO2) was similar to the change in the ONSD. The change in the ONSD was significantly correlated with the change in the EtCO2 after tourniquet deflation (r = 0.484, P = 0.030). In conclusion, the ONSD, as an indicator of intracranial pressure, increased after tourniquet deflation in patients undergoing lower limb surgery. This was correlated with an increased EtCO2 and arterial carbon dioxide partial pressure.

Trial registration: ClinicalTrials.gov (NCT03782077).
Automated prediction of the clinical impact of structural copy number variations
Authors: Gažiová M. , Sládeček T. , Pös O. , Števko M. , Krampl W. , Pös Z. , Hekel R. , Hlavačka M. , Kucharík M. , Radvánszky J. , Budiš J. , Szemes T.
Published: January 2022

Copy number variants (CNVs) play an important role in many biological processes, including the development of genetic diseases, making them attractive targets for genetic analyses. The interpretation of the effect of these structural variants is a challenging problem due to highly variable numbers of gene, regulatory, or other genomic elements affected by the CNV. This led to the demand for the interpretation tools that would relieve researchers, laboratory diagnosticians, genetic counselors, and clinical geneticists from the laborious process of annotation and classification of CNVs. We designed and validated a prediction method (ISV; Interpretation of Structural Variants) that is based on boosted trees which takes into account annotations of CNVs from several publicly available databases. The presented approach achieved more than 98% prediction accuracy on both copy number loss and copy number gain variants while also allowing CNVs being assigned “uncertain” significance in predictions. We believe that ISV’s prediction capability and explainability have a great potential to guide users to more precise interpretations and classifications of CNVs.
Mechanisms of dispersal and colonisation in a wind-borne cereal pest, the haplodiploid wheat curl mite
Authors: Laska Alicja , Przychodzka Anna , Puchalska Ewa , Lewandowski Mariusz , Karpicka-Ignatowska Kamila , Skoracka Anna
Published: January 2022

Dispersal and colonisation determine the survival and success of organisms, and influence the structure and dynamics of communities and ecosystems in space and time. Both affect the gene flow between populations, ensuring sufficient level of genetic variation and improving adaptation abilities. In haplodiploids, such as Aceria tosichella (wheat curl mite, WCM), a population may be founded even by a single unfertilised female, so there is a risk of heterozygosity loss (i.e. founder effect). It may lead to adverse outcomes, such as inbreeding depression. Yet, the strength of the founder effect partly depends on the genetic variation of the parental population. WCM is an economically important pest with a great invasive potential, but its dispersal and colonisation mechanisms were poorly studied before. Therefore, here we assessed WCM dispersal and colonisation potential in relation to the genetic variation of the parental population. We checked whether this potential may be linked to specific pre-dispersal actions (e.g. mating before dispersal and collective behaviour). Our study confirms that dispersal strategies of WCM are not dependent on heterozygosity in the parental population, and the efficient dispersal of this species depends on collective movement of fertilised females.
Isolation, characterization, molecular analysis and application of bacteriophage DW-EC to control Enterotoxigenic Escherichia coli on various foods
Authors: Dewanggana Marta Nisita , Evangeline Clare , Ketty Maurita Delia , Waturangi Diana Elizabeth , Yogiara  , Magdalena Stella
Published: January 2022

Among food preservation methods, bacteriophage treatment can be a viable alternative method to overcome the drawbacks of traditional approaches. Bacteriophages are naturally occurring viruses that are highly specific to their hosts and have the capability to lyse bacterial cells, making them useful as biopreservation agents. This study aims to characterize and determine the application of bacteriophage isolated from Indonesian traditional Ready-to-Eat (RTE) food to control EnterotoxigenicEscherichia coli(ETEC) population in various foods. Phage DW-EC isolated from Indonesian traditional RTE food called dawet with ETEC as its host showed a positive result by the formation of plaques (clear zone) in the bacterial host lawn. Transmission electron microscopy (TEM) results also showed that DW-EC can be suspected to belong to theMyoviridaefamily. Molecular characterization and bioinformatic analysis showed that DW-EC exhibited characteristics as promising biocontrol agents in food samples. Genes related to the lytic cycle, such as lysozyme and tail fiber assembly protein, were annotated. There were also no signs of lysogenic genes among the annotation results. The resulting PHACTS data also indicated that DW-EC was leaning toward being exclusively lytic. DW-EC significantly reduced the ETEC population (P ≤ 0.05) in various food samples after two different incubation times (1 day and 6 days) in chicken meat (80.93%; 87.29%), fish meat (63.78%; 87.89%), cucumber (61.42%; 71.88%), tomato (56.24%; 74.51%), and lettuce (46.88%; 43.38%).
Digital health tools for the passive monitoring of depression: a systematic review of methods
Authors: De Angel Valeria , Lewis Serena , White Katie , Oetzmann Carolin , Leightley Daniel , Oprea Emanuela , Lavelle Grace , Matcham Faith , Pace Alice , Mohr David C. , Dobson Richard , Hotopf Matthew
Published: January 2022

The use of digital tools to measure physiological and behavioural variables of potential relevance to mental health is a growing field sitting at the intersection between computer science, engineering, and clinical science. We summarised the literature on remote measuring technologies, mapping methodological challenges and threats to reproducibility, and identified leading digital signals for depression. Medical and computer science databases were searched between January 2007 and November 2019. Published studies linking depression and objective behavioural data obtained from smartphone and wearable device sensors in adults with unipolar depression and healthy subjects were included. A descriptive approach was taken to synthesise study methodologies. We included 51 studies and found threats to reproducibility and transparency arising from failure to provide comprehensive descriptions of recruitment strategies, sample information, feature construction and the determination and handling of missing data. The literature is characterised by small sample sizes, short follow-up duration and great variability in the quality of reporting, limiting the interpretability of pooled results. Bivariate analyses show consistency in statistically significant associations between depression and digital features from sleep, physical activity, location, and phone use data. Machine learning models found the predictive value of aggregated features. Given the pitfalls in the combined literature, these results should be taken purely as a starting point for hypothesis generation. Since this research is ultimately aimed at informing clinical practice, we recommend improvements in reporting standards including consideration of generalisability and reproducibility, such as wider diversity of samples, thorough reporting methodology and the reporting of potential bias in studies with numerous features.
Diacylglyceryl-N,N,N-trimethylhomoserine-dependent lipid remodeling in a green alga, Chlorella kessleri
Authors: Oishi Yutaro , Otaki Rie , Iijima Yukari , Kumagai Eri , Aoki Motohide , Tsuzuki Mikio , Fujiwara Shoko , Sato Norihiro
Published: January 2022

Membrane lipid remodeling contributes to the environmental acclimation of plants. In the green lineage, a betaine lipid, diacylglyceryl-N,N,N-trimethylhomoserine (DGTS), is included exclusively among green algae and nonflowering plants. Here, we show that the green alga Chlorella kessleri synthesizes DGTS under phosphorus-deficient conditions through the eukaryotic pathway via the ER. Simultaneously, phosphatidylcholine and phosphatidylethanolamine, which are similar to DGTS in their zwitterionic properties, are almost completely degraded to release 18.1% cellular phosphorus, and to provide diacylglycerol moieties for a part of DGTS synthesis. This lipid remodeling system that substitutes DGTS for extrachloroplast phospholipids to lower the P-quota operates through the expression induction of the BTA1 gene. Investigation of this lipid remodeling system is necessary in a wide range of lower green plants for a comprehensive understanding of their phosphorus deficiency acclimation strategies.
Primordial mimicry induces morphological change in Escherichia coli
Authors: Lu Hui , Aida Honoka , Kurokawa Masaomi , Chen Feng , Xia Yang , Xu Jian , Li Kai , Ying Bei-Wen , Yomo Tetsuya
Published: January 2022

The morphology of primitive cells has been the subject of extensive research. A spherical form was commonly presumed in prebiotic studies but lacked experimental evidence in living cells. Whether and how the shape of living cells changed are unclear. Here we exposed the rod-shaped bacterium Escherichia coli to a resource utilization regime mimicking a primordial environment. Oleate was given as an easy-to-use model prebiotic nutrient, as fatty acid vesicles were likely present on the prebiotic Earth and might have been used as an energy resource. Six evolutionary lineages were generated under glucose-free but oleic acid vesicle (OAV)-rich conditions. Intriguingly, fitness increase was commonly associated with the morphological change from rod to sphere and the decreases in both the size and the area-to-volume ratio of the cell. The changed cell shape was conserved in either OAVs or glucose, regardless of the trade-offs in carbon utilization and protein abundance. Highly differentiated mutations present in the genome revealed two distinct strategies of adaption to OAV-rich conditions, i.e., either directly targeting the cell wall or not. The change in cell morphology of Escherichia coli for adapting to fatty acid availability supports the assumption of the primitive spherical form.
DAF-2c signaling promotes taste avoidance after starvation in Caenorhabditis elegans by controlling distinct phospholipase C isozymes
Authors: Tomioka Masahiro , Jang Moon Sun , Iino Yuichi
Published: January 2022

Previously, we reported that DAF-2c, an axonal insulin receptor isoform in Caenorhabditis elegans, acts in the ASER gustatory neuron to regulate taste avoidance learning, a process in which worms learn to avoid salt concentrations experienced during starvation. Here, we show that secretion of INS-1, an insulin-like peptide, after starvation conditioning is sufficient to drive taste avoidance via DAF-2c signaling. Starvation conditioning enhances the salt-triggered activity of AIA neurons, the main sites of INS-1 release, which potentially promotes feedback signaling to ASER to maintain DAF-2c activity during taste avoidance. Genetic studies suggest that DAF-2c–Akt signaling promotes high-salt avoidance via a decrease in PLCβ activity. On the other hand, the DAF-2c pathway promotes low-salt avoidance via PLCε and putative Akt phosphorylation sites on PLCε are essential for taste avoidance. Our findings imply that animals disperse from the location at which they experience starvation by controlling distinct PLC isozymes via DAF-2c.
Viscoelastic parameterization of human skin cells characterize material behavior at multiple timescales
Authors: Parvini Cameron H. , Cartagena-Rivera Alexander X. , Solares Santiago D.
Published: January 2022

Countless biophysical studies have sought distinct markers in the cellular mechanical response that could be linked to morphogenesis, homeostasis, and disease. Here, an iterative-fitting methodology visualizes the time-dependent viscoelastic behavior of human skin cells under physiologically relevant conditions. Past investigations often involved parameterizing elastic relationships and assuming purely Hertzian contact mechanics, which fails to properly account for the rich temporal information available. We demonstrate the performance superiority of the proposed iterative viscoelastic characterization method over standard open-search approaches. Our viscoelastic measurements revealed that 2D adherent metastatic melanoma cells exhibit reduced elasticity compared to their normal counterparts—melanocytes and fibroblasts, and are significantly less viscous than fibroblasts over timescales spanning three orders of magnitude. The measured loss angle indicates clear differential viscoelastic responses across multiple timescales between the measured cells. This method provides insight into the complex viscoelastic behavior of metastatic melanoma cells relevant to better understanding cancer metastasis and aggression.
Interannual temperature variability is a principal driver of low-frequency fluctuations in marine fish populations
Authors: van der Sleen Peter , Zuidema Pieter A. , Morrongiello John , Ong Jia Lin J. , Rykaczewski Ryan R. , Sydeman William J. , Di Lorenzo Emanuele , Black Bryan A.
Published: January 2022

Marine fish populations commonly exhibit low-frequency fluctuations in biomass that can cause catch volatility and thus endanger the food and economic security of dependent coastal societies. Such variability has been linked to fishing intensity, demographic processes and environmental variability, but our understanding of the underlying drivers remains poor for most fish stocks. Our study departs from previous findings showing that sea surface temperature (SST) is a significant driver of fish somatic growth variability and that life-history characteristics mediate population-level responses to environmental variability. We use autoregressive models to simulate how fish populations integrate SST variability over multiple years depending on fish life span and trophic position. We find that simulated SST-driven population dynamics can explain a significant portion of observed low-frequency variability in independent observations of fisheries landings around the globe. Predictive skill, however, decreases with increasing fishing pressure, likely due to demographic truncation. Using our modelling approach, we also show that increases in the mean and variance of SST could amplify biomass volatility and lessen its predictability in the future. Overall, biological integration of high-frequency SST variability represents a null hypothesis with which to explore the drivers of low-frequency population change across upper-trophic marine species.
UVC inactivation of pathogenic samples suitable for cryo-EM analysis
Authors: Depelteau Jamie S. , Renault Ludovic , Althof Nynke , Cassidy C. Keith , Mendonça Luiza M. , Jensen Grant J. , Resch Guenter P. , Briegel Ariane
Published: January 2022

Cryo-electron microscopy has become an essential tool to understand structure and function of biological samples. Especially for pathogens, such as disease-causing bacteria and viruses, insights gained by cryo-EM can aid in developing cures. However, due to the biosafety restrictions of pathogens, samples are often treated by chemical fixation to render the pathogen inert, affecting the ultrastructure of the sample. Alternatively, researchers use in vitro or ex vivo models, which are non-pathogenic but lack the complexity of the pathogen of interest. Here we show that ultraviolet-C (UVC) radiation applied at cryogenic temperatures can be used to eliminate or dramatically reduce the infectivity of Vibrio cholerae and the bacterial virus, the ICP1 bacteriophage. We show no discernable structural impact of this treatment of either sample using two cryo-EM methods: cryo-electron tomography followed by sub-tomogram averaging, and single particle analysis (SPA). Additionally, we applied the UVC irradiation to the protein apoferritin (ApoF), which is a widely used test sample for high-resolution SPA studies. The UVC-treated ApoF sample resulted in a 2.1 Å structure indistinguishable from an untreated published map. This research demonstrates that UVC treatment is an effective and inexpensive addition to the cryo-EM sample preparation toolbox.
Fluorescence lifetime DNA-PAINT for multiplexed super-resolution imaging of cells
Authors: Oleksiievets Nazar , Sargsyan Yelena , Thiele Jan Christoph , Mougios Nikolaos , Sograte-Idrissi Shama , Nevskyi Oleksii , Gregor Ingo , Opazo Felipe , Thoms Sven , Enderlein Jörg , Tsukanov Roman
Published: January 2022

DNA point accumulation for imaging in nanoscale topography (DNA-PAINT) is a powerful super-resolution technique highly suitable for multi-target (multiplexing) bio-imaging. However, multiplexed imaging of cells is still challenging due to the dense and sticky environment inside a cell. Here, we combine fluorescence lifetime imaging microscopy (FLIM) with DNA-PAINT and use the lifetime information as a multiplexing parameter for targets identification. In contrast to Exchange-PAINT, fluorescence lifetime PAINT (FL-PAINT) can image multiple targets simultaneously and does not require any fluid exchange, thus leaving the sample undisturbed and making the use of flow chambers/microfluidic systems unnecessary. We demonstrate the potential of FL-PAINT by simultaneous imaging of up to three targets in a cell using both wide-field FLIM and 3D time-resolved confocal laser scanning microscopy (CLSM). FL-PAINT can be readily combined with other existing techniques of multiplexed imaging and is therefore a perfect candidate for high-throughput multi-target bio-imaging.
Selective control of synaptically-connected circuit elements by all-optical synapses
Authors: Prakash Mansi , Murphy Jeremy , St Laurent Robyn , Friedman Nina , Crespo Emmanuel L. , Bjorefeldt Andreas , Pal Akash , Bhagat Yuvraj , Kauer Julie A. , Shaner Nathan C. , Lipscombe Diane , Moore Christopher I. , Hochgeschwender Ute
Published: January 2022

Understanding percepts, engrams and actions requires methods for selectively modulating synaptic communication between specific subsets of interconnected cells. Here, we develop an approach to control synaptically connected elements using bioluminescent light: Luciferase-generated light, originating from a presynaptic axon terminal, modulates an opsin in its postsynaptic target. Vesicular-localized luciferase is released into the synaptic cleft in response to presynaptic activity, creating a real-time Optical Synapse. Light production is under experimenter-control by introduction of the small molecule luciferin. Signal transmission across this optical synapse is temporally defined by the presence of both the luciferin and presynaptic activity. We validate synaptic Interluminescence by multi-electrode recording in cultured neurons and in mice in vivo. Interluminescence represents a powerful approach to achieve synapse-specific and activity-dependent circuit control in vivo.