bluuebunny/crossref_metadata_2025 huggingface dataset:
Evasion of cGAS and TRIM5 defines pandemic HIV
Authors: Zuliani-Alvarez Lorena , Govasli Morten L. , Rasaiyaah Jane , Monit Chris , Perry Stephen O. , Sumner Rebecca P. , McAlpine-Scott Simon , Dickson Claire , Rifat Faysal K. M. , Hilditch Laura , Miles Richard J. , Bibollet-Ruche Frederic , Hahn Beatrice H. , Boecking Till , Pinotsis Nikos , James Leo C. , Jacques David A. , Towers Greg J.
Published: October 2022

Of the 13 known independent zoonoses of simian immunodeficiency viruses to humans, only one, leading to human immunodeficiency virus (HIV) type 1(M) has become pandemic, causing over 80 million human infections. To understand the specific features associated with pandemic human-to-human HIV spread, we compared replication of HIV-1(M) with non-pandemic HIV-(O) and HIV-2 strains in myeloid cell models. We found that non-pandemic HIV lineages replicate less well than HIV-1(M) owing to activation of cGAS and TRIM5-mediated antiviral responses. We applied phylogenetic and X-ray crystallography structural analyses to identify differences between pandemic and non-pandemic HIV capsids. We found that genetic reversal of two specific amino acid adaptations in HIV-1(M) enables activation of TRIM5, cGAS and innate immune responses. We propose a model in which the parental lineage of pandemic HIV-1(M) evolved a capsid that prevents cGAS and TRIM5 triggering, thereby allowing silent replication in myeloid cells. We hypothesize that this capsid adaptation promotes human-to-human spread through avoidance of innate immune response activation.
Freshwater microbial metagenomes sampled across different water body characteristics, space and time in Israel
Authors: Al-Ashhab Ashraf , Marmen Sophi , Schweitzer-Natan Orna , Bolotin Evgeni , Patil Hemant , Viner-Mozzini Diti , Aharonovich Dikla , Hershberg Ruth , Minz Dror , Carmeli Shmuel , Cytryn Eddie , Sukenik Assaf , Sher Daniel
Published: October 2022

Freshwater bodies are critical components of terrestrial ecosystems. The microbial communities of freshwater ecosystems are intimately linked water quality. These microbes interact with, utilize and recycle inorganic elements and organic matter. Here, we present three metagenomic sequence datasets (total of 182.9 Gbp) from different freshwater environments in Israel. The first dataset is from diverse freshwater bodies intended for different usages – a nature reserve, irrigation and aquaculture facilities, a tertiary wastewater treatment plant and a desert rainfall reservoir. The second represents a two-year time-series, collected during 2013–2014 at roughly monthly intervals, from a water reservoir connected to an aquaculture facility. The third is from several time-points during the winter and spring of 2015 in Lake Kinneret, including a bloom of the cyanobacterium Microcystis sp. These datasets are accompanied by physical, chemical, and biological measurements at each sampling point. We expect that these metagenomes will facilitate a wide range of comparative studies that seek to illuminate new aspects of freshwater microbial ecosystems and inform future water quality management approaches.
Assessing the impact of COVID-19 mass testing in South Tyrol using a semi-parametric growth model
Authors: Ferrari Davide , Stillman Steven , Tonin Mirco
Published: October 2022

Mass antigen testing has been proposed as a possible cost-effective tool to contain the COVID-19 pandemic. We test the impact of a voluntary mass testing campaign implemented in the Italian region of South Tyrol on the spread of the virus in the following months. We do so by using an innovative empirical approach which embeds a semi-parametric growth model—where COVID-19 transmission dynamics are allowed to vary across regions and to be impacted by the implementation of the mass testing campaign—into a synthetic control framework which creates an appropriate control group of other Italian regions. Our results suggest that mass testing campaigns are useful instruments for mitigating the pandemic.
Intronic primers reveal unexpectedly high major histocompatibility complex diversity in Antarctic fur seals
Authors: Tebbe Jonas , Ottensmann Meinolf , Havenstein Katja , Efstratiou Artemis , Lenz Tobias L. , Caspers Barbara A. , Forcada Jaume , Tiedemann Ralph , Hoffman Joseph I.
Published: October 2022

The major histocompatibility complex (MHC) is a group of genes comprising one of the most important components of the vertebrate immune system. Consequently, there has been much interest in characterising MHC variation and its relationship with fitness in a variety of species. Due to the exceptional polymorphism of MHC genes, careful PCR primer design is crucial for capturing all of the allelic variation present in a given species. We therefore developed intronic primers to amplify the full-length 267 bp protein-coding sequence of the MHC class II DQB exon 2 in the Antarctic fur seal. We then characterised patterns of MHC variation among mother–offspring pairs from two breeding colonies and detected 19 alleles among 771 clone sequences from 56 individuals. The distribution of alleles within and among individuals was consistent with a single-copy, classical DQB locus showing Mendelian inheritance. Amino acid similarity at the MHC was significantly associated with genome-wide relatedness, but no relationship was found between MHC heterozygosity and genome-wide heterozygosity. Finally, allelic diversity was several times higher than reported by a previous study based on partial exon sequences. This difference appears to be related to allele-specific amplification bias, implying that primer design can strongly impact the inference of MHC diversity.
Detection of the 40 Hz auditory steady-state response with optically pumped magnetometers
Authors: An Kyung-min , Shim Jeong Hyun , Kwon Hyukchan , Lee Yong-Ho , Yu Kwon-Kyu , Kwon Moonyoung , Chun Woo Young , Hirosawa Tetsu , Hasegawa Chiaki , Iwasaki Sumie , Kikuchi Mitsuru , Kim Kiwoong
Published: October 2022

Magnetoencephalography (MEG) is a functional neuroimaging technique that noninvasively detects the brain magnetic field from neuronal activations. Conventional MEG measures brain signals using superconducting quantum interference devices (SQUIDs). SQUID-MEG requires a cryogenic environment involving a bulky non-magnetic Dewar flask and the consumption of liquid helium, which restricts the variability of the sensor array and the gap between the cortical sources and sensors. Recently, miniature optically pumped magnetometers (OPMs) have been developed and commercialized. OPMs do not require cryogenic cooling and can be placed within millimeters from the scalp. In the present study, we arranged six OPM sensors on the temporal area to detect auditory-related brain responses in a two-layer magnetically shielded room. We presented the auditory stimuli of 1 kHz pure-tone bursts with 200 ms duration and obtained the M50 and M100 components of auditory-evoked fields. We delivered the periodic stimuli with a 40 Hz repetition rate and observed the gamma-band power changes and inter-trial phase coherence of auditory steady-state responses at 40 Hz. We found that the OPM sensors have a performance comparable to that of conventional SQUID-MEG sensors, and our results suggest the feasibility of using OPM sensors for functional neuroimaging and brain–computer interface applications.
Radiative heat transfer between two carbon nanotubes
Authors: Nefedov Igor S. , Davidovich Michael V. , Glukhova Olga E. , Slepchenkov Michael M. , Rubi J. Miguel
Published: October 2022

We analyze the radiative heat transfer between two parallel and infinitely long carbon nanotubes (CNTs). The radiative heat exchange is due to the difference between the Poynting vectors generated by the fluctuating currents when the CNTs are at different temperatures. The radiated and absorbed Poynting vectors are expressed in terms of the correlations of the electromagnetic fields obtained from the Green’s function and the fluctuation-dissipation theorem for the current density. The analysis takes into account the scattering of the fields by the nanotubes. We show that the radiative heat transfer depends not only on the distance between nanotubes, but also on their chiralities and thus on their semiconducting or metallic nature, which would allow the design of nanostructures for optimal radiative heat exchange.
Vortex-electromagnetic-wave-based ISAR imaging for high-speed maneuvering targets
Authors: Bu Lijun , Zhu Yongzhong , Chen Yijun , Yang Yufei , Zang Yadan
Published: October 2022

Vortex electromagnetic wave (VEMW) carrying orbital angular momentum (OAM), which is expected to introduce additional degrees of freedom in inverse synthetic aperture radar(ISAR) imaging. However, the current research about maneuvering targets is based on the "stop go" hypothesis, which does not apply to high-speed motion scenarios due to the intrapulse movement of the target. To improve the imaging quality, this letter proposes a VEMW-based high-speed maneuvering targets imaging method. Firstly, the ISAR imaging scenario of high-speed target is established. According to the spatial geometric relationship between radar and maneuvering target, the vortex echo is deduced and its characteristics are analyzed. Subsequently, a frequency modulation rate estimation method considering both calculation efficiency and high precision is proposed to realize the accurate estimation of target speed. Then, an adaptive azimuth image compensation method based on minimum entropy is proposed. Through the setting of threshold, the number of component signals in linear frequency modulation (LFM) signal is determined and compensated successively. Finally, the range profile and azimuth profile are combined to reconstruct the three-dimensional information. The simulation results demonstrate that this work can effectively eliminate the influence of high-speed motion on range and azimuth profile, also benefit the development of ISAR imaging technique of high-speed maneuvering targets.
Intercellular interaction mechanisms promote diversity in intracellular ATP concentration in Escherichia coli populations
Authors: Nakatani Ryo J. , Itabashi Masahiro , Yamada Takahiro G. , Hiroi Noriko F. , Funahashi Akira
Published: October 2022

In fluctuating environments, many microorganisms acquire phenotypic heterogeneity as a survival tactic to increase the likelihood of survival of the overall population. One example of this interindividual heterogeneity is the diversity of ATP concentration among members ofEscherichia colipopulations under glucose deprivation. Despite the importance of such environmentally driven phenotypic heterogeneity, how the differences in intracellular ATP concentration emerge among individualE. coliorganisms is unknown. In this study, we focused on the mechanism through which individualE. coliachieve high intracellular ATP concentrations. First, we measured the ATP retained byE. coliover time when cultured at low (0.1 mM) and control (22.2 mM) concentrations of glucose and obtained the chronological change in ATP concentrations. Then, by comparing these chronological change of ATP concentrations and analyzing whether stochastic state transitions, periodic oscillations, cellular age, and intercellular communication—which have been reported as molecular biological mechanisms for generating interindividual heterogeneity—are involved, we showed that the appearance of high ATP-holding individuals observed amongE. colican be explained only by intercellular transmission. By performing metabolomic analysis of post-culture medium, we revealed a significant increase in the ATP, especially at low glucose, and that the number ofE. colithat retain significantly higher ATP can be controlled by adding large amounts of ATP to the medium, even in populations cultured under control glucose concentrations. These results reveal for the first time that ATP-mediated intercellular transmission enables some individuals inE. colipopulations grown at low glucose to retain large amounts of ATP.
Optimal settings and advantages of drones as a tool for canopy arthropod collection
Authors: Madden Jamie C. , Brisson-Curadeau Émile , Gillung Jessica P. , Bird David M. , Elliott Kyle H.
Published: October 2022

The growing field of aeroecology is limited by difficulties associated with sampling in the air column. Aerial insects are particularly hard to sample, despite being the main prey in the air column, with some recent studies attempting to use drones as a collection method. We conducted a study to determine the optimal drone settings for collecting insects above the canopy, where drones are seldom used. By attaching a net to the body of a small, commercial drone, we tested yield from different height, speed, and net settings in wetlands, as well as compared insect diversity across different habitat canopies. Height was the most important setting; grazing the canopy yielded significantly more insects than flying one meter above it. Speed, drone type, and net size did not influence the number of insects caught per trial. Wetland canopies had higher abundance, diversity, and species richness in its arthropod populations compared to forest canopies or lakes. Compared to the yield of Lindgren funnels—a traditional sampling method in entomology—drones captured higher diversity and abundance of insects in a fraction of the time. This study confirms that drones are an efficient and accurate way to collect canopy arthropods.
Mg segregation at inclined facets of pyramidal inversion domains in GaN:Mg
Authors: Persson Axel R. , Papamichail Alexis , Darakchieva Vanya , Persson Per O. Å.
Published: October 2022

Structural defects in Mg-doped GaN were analyzed using high-resolution scanning transmission electron microscopy combined with electron energy loss spectroscopy. The defects, in the shape of inverted pyramids, appear at high concentrations of incorporated Mg, which also lead to a reduction in free-hole concentration in Mg doped GaN. Detailed analysis pinpoints the arrangement of atoms in and around the defects and verify the presence of a well-defined layer of Mg at all facets, including the inclined facets. Our observations have resulted in a model of the pyramid-shaped defect, including structural displacements and compositional replacements, which is verified by image simulations. Finally, the total concentration of Mg atoms bound to these defects were evaluated, enabling a correlation between inactive and defect-bound dopants.
Flexible embryonic shell allies large offspring size and anti-predatory protection in viviparous snails
Authors: Sulikowska-Drozd A. , Maltz T. K. , Janiszewska K.
Published: October 2022

The evolutionary conflicts between viviparous reproductive mode and skeleton shape may occur whenever the space available for embryo development or delivery is limited by hard inflexible structures of a parent (bones, shell, etc.). In tetrapods, offspring size is at odds with female locomotion efficiency, which results in obstetric selection. We suggest a similar relationship for viviparous gastropods, where spacious canal needed for embryo delivery may interfere with anti-predatory role of narrow and toothed shell aperture. We explored this hypothesis in the group of viviparous land snails (Clausiliidae, subfamily Phaedusinae), known for complex apertural barriers protecting the shell interior. Most of the shell structure modifications we recorded facilitate the delivery of embryos but simultaneously reduce the safeguard of a narrow shell opening. However, we also observed highly flexible embryonic shells that may withstand squeezing between apertural barriers during birth. We investigated the microstructure of these flexible embryonic shells, compared to the typical hard shells of clausiliid embryos, which are rigid and unpliable already in the genital tract of the parent. Our results suggest that the unusual flexibility, which is related to a low number of organomineral layers in the shell, evolved in two phylogenetically distant lineages of Phaedusinae. This adaptation reduces mechanical constraints for birth of the neonates but allows to maintain the protective function of the apertural barriers.
Small-scale (sub-organ and cellular level) alpha-particle dosimetry methods using an iQID digital autoradiography imaging system
Authors: Peter Robin , Sandmaier Brenda M. , Dion Michael P. , Frost Sofia H. L. , Santos Erlinda B. , Kenoyer Aimee , Hamlin Donald K. , Wilbur D. Scott , Stewart Robert D. , Fisher Darrell R. , Vetter Kai , Seo Youngho , Miller Brian W.
Published: October 2022

Targeted radiopharmaceutical therapy with alpha-particle emitters (αRPT) is advantageous in cancer treatment because the short range and high local energy deposition of alpha particles enable precise radiation delivery and efficient tumor cell killing. However, these properties create sub-organ dose deposition effects that are not easily characterized by direct gamma-ray imaging (PET or SPECT). We present a computational procedure to determine the spatial distribution of absorbed dose from alpha-emitting radionuclides in tissues using digital autoradiography activity images from an ionizing-radiation quantum imaging detector (iQID). Data from 211At-radioimmunotherapy studies for allogeneic hematopoietic cell transplantation in a canine model were used to develop these methods. Nine healthy canines were treated with 16.9–30.9 MBq 211At/mg monoclonal antibodies (mAb). Lymph node biopsies from early (2–5 h) and late (19–20 h) time points (16 total) were obtained, with 10–20 consecutive 12-µm cryosections extracted from each and imaged with an iQID device. iQID spatial activity images were registered within a 3D volume for dose-point-kernel convolution, producing dose-rate maps. The accumulated absorbed doses for high- and low-rate regions were 9 ± 4 Gy and 1.2 ± 0.8 Gy from separate dose-rate curves, respectively. We further assess uptake uniformity, co-registration with histological pathology, and requisite slice numbers to improve microscale characterization of absorbed dose inhomogeneities in αRPT.
Membrane mediated phase separation of the bacterial nucleoid occlusion protein Noc
Authors: Babl Leon , Merino-Salomón Adrián , Kanwa Nishu , Schwille Petra
Published: October 2022

Liquid–liquid phase separation is a fundamental biophysical process to organize eukaryotic and prokaryotic cytosols. While many biomolecular condensates are formed in the vicinity of, or even on lipid membranes, little is known about the interaction of protein condensates and lipid bilayers. In this study, we characterize the recently unknown phase behavior of the bacterial nucleoid occlusion protein Noc. We find that, similarly to other ParB-like proteins, CTP binding tightly regulates Noc’s propensity to phase separate. As CTP-binding and hydrolysis also allows Noc to bind and spread on membranes, we furthermore establish Noc condensates as model system to investigate how lipid membranes can influence protein condensation and vice versa. Last, we show that Noc condensates can recruit FtsZ to the membrane, while this does not happen in the non-phase separated state. These findings suggest a new model of Noc mediated nucleoid occlusion, with membrane-mediated liquid–liquid phase separation as underlying principle of complex formation and regulation thereof.
Promising SARS-CoV-2 main protease inhibitor ligand-binding modes evaluated using LB-PaCS-MD/FMO
Authors: Hengphasatporn Kowit , Harada Ryuhei , Wilasluck Patcharin , Deetanya Peerapon , Sukandar Edwin R. , Chavasiri Warinthorn , Suroengrit Aphinya , Boonyasuppayakorn Siwaporn , Rungrotmongkol Thanyada , Wangkanont Kittikhun , Shigeta Yasuteru
Published: October 2022

Parallel cascade selection molecular dynamics-based ligand binding-path sampling (LB-PaCS-MD) was combined with fragment molecular orbital (FMO) calculations to reveal the ligand path from an aqueous solution to the SARS-CoV-2 main protease (Mpro) active site and to customise a ligand-binding pocket suitable for delivering a potent inhibitor. Rubraxanthone exhibited mixed-inhibition antiviral activity against SARS-CoV-2 Mpro, relatively low cytotoxicity, and high cellular inhibition. However, the atomic inhibition mechanism remains ambiguous. LB-PaCS-MD/FMO is a hybrid ligand-binding evaluation method elucidating how rubraxanthone interacts with SARS-CoV-2 Mpro. In the first step, LB-PaCS-MD, which is regarded as a flexible docking, efficiently samples a set of ligand-binding pathways. After that, a reasonable docking pose of LB-PaCS-MD is evaluated by the FMO calculation to elucidate a set of protein–ligand interactions, enabling one to know the binding affinity of a specified ligand with respect to a target protein. A possible conformation was proposed for rubraxanthone binding to the SARS-CoV-2 Mpro active site, and allosteric inhibition was elucidated by combining blind docking with k-means clustering. The interaction profile, key binding residues, and considerable interaction were elucidated for rubraxanthone binding to both Mpro sites. Integrated LB-PaCS-MD/FMO provided a more reasonable complex structure for ligand binding at the SARS-CoV-2 Mpro active site, which is vital for discovering and designing antiviral drugs.
Efficacy, according to urodynamics, of OnabotulinumtoxinA compared with antimuscarinic drugs, for neurogenic detrusor overactivity: a systematic review and network meta-analysis
Authors: Xu Rui , Yang Tong-Xin , Fang Ke-Wei , Wang Guang , Li Pei
Published: October 2022

To summarize the differences in urodynamic outcomes between oral antimuscarinic drugs and OnabotulinumtoxinA, and finding a therapy that maintains good urodynamics in neurogenic detrusor overactivity (NDO). We conducted a literature search of EMBASE and PubMed, with the language limited to English. In the analysis, all of the published randomized trials of OnabotulinumtoxinA or antimuscarinic drugs used to treat NDO were found and the results were finally obtained through Bayesian model analysis. A total of 12 RCTs and 2208 patients were included. OnabotulinumtoxinA 300U was superior to other drugs in terms of MCC, volume at IDC, and Pdetmax endpoints. OnabotulinumtoxinA 200U was more effective on the urodynamic endpoint of BC than other drugs or doses of OnabotulinumtoxinA. According to the MCC urodynamic results, oxybutynin, solifenacin 10 mg, and tolterodine 4 mg also had positive effects. OnabotulinumtoxinA 300U, 200U and 100U were better in improving the urodynamic results of NDO, and the current evidence also shows that selective injection of onabotulinumtoxinA can effectively improve the urodynamic results.
Gender inequality in source country modifies sex differences in stroke incidence in Canadian immigrants
Authors: Vyas Manav V. , Fang Jiming , Kapral Moira K. , Yu Amy Y. X. , Austin Peter C.
Published: October 2022

Research suggests that gender inequality, measured using the gender inequality index (GII), influences stroke mortality in women compared to men. We examine how source country GII modifies the rate of ischemic stroke in women compared to men after immigration to Canada, a country with low gender inequality. We used linked health data and immigration records of 452,089, stroke-free immigrants aged 40–69 year who migrated from 123 countries. Over 15 years of follow-up, 5991 (1.3%) had an incident ischemic stroke. We demonstrate (a) a lower adjusted rate of stroke in women compared to men (hazard ratio 0.64; 95% CI 0.61–0.67); (b) that sex differences in stroke incidence were modified by source country GII, as the hazard of stroke in women vs. men attenuated by a factor of 1.06 for every 0.1 increase in the GII of the source country (Psex*GII = 0.002); and (c) migration to a country with low GII attenuates the adverse effect of source country GII on sex differences in stroke incidence. Evaluating pathways through which source country gender inequality differentially influences stroke risk in immigrant women compared to men could help develop strategies to mitigate the effects of early-life gender inequality on stroke risk.
Impact of CaSO4-rich soil on Miocene surface preservation and Quaternary sinuous to meandering channel forms in the hyperarid Atacama Desert
Authors: Ritter Benedikt , Diederich-Leicher Julia L. , Binnie Steven A. , Stuart Finlay M. , Wennrich Volker , Bolten Andreas , Dunai Tibor J.
Published: October 2022

The Atacama Desert is the driest and oldest desert on Earth. Despite the abundance evidence for long-term landscape stability, there are subtle signs of localised fluvial erosion and deposition since the onset of hyperaridity in the rock record. In the dry core of the Atacama Desert, pluvial episodes allowed antecedent drainage to incise into uplifting fault scarps, which in turn generated sinuous to meandering channels. Incision of ancient alluvial fan surfaces occurred during intermittent fluvial periods, albeit without signs of surface erosion. Fluvial incision during predominantly hyperarid climate periods is evident from these channels in unconsolidated alluvium. The absence of dense vegetation to provide bank stability and strength led us to investigate the potential role of regionally ubiquitous CaSO4-rich surface cover. This has enabled the preservation of Miocene surfaces and we hypothesize that it provided the required bank stability by adding strength to the upper decimetre to meter of incised alluvium to allow high sinuosity of stream channels to form during pluvial episodes in the Quaternary.
A novel technique to overcome fluid flow influence in carbon quantum dots/paper-based analytical devices
Authors: Zoghi Sepideh , Rahmandoust Moones
Published: October 2022

Paper-based analytical devices are promising choices for rapid tests and lab-on-chip detection techniques. Carbon quantum dots (CQDs), on the other hand, are biocompatible nanomaterials, which are industrially promising, due to their fast and cost-effective gram-scale synthesis techniques, as well as their significantly high and stable photoluminescence (PL) properties, which are durable and reliable over a year. However, there have been limitations in the entrapment of CQDs on cellulose papers in a way that their PL is not influenced by the flowing of the CQDs with the stream of analyte fluid, making the sensors less accurate at very low concentrations of liquid analytes. Therefore, in this investigation, a polyvinyl alcohol/alkaline-based method was systematically generated and developed to entrap CQDs inside a 3D crystalline matrix on paper, in a way that they can be used directly as probes for a simple drop-and-detect method. As a proof of concept, N/P-doped CQD on cellulose paper was used to make fluorescent paper-based analytical devices for identifying traces of Hg2+ of around 100 ppb. The designed sensor was tested over several months, to study its durability and functionality over long periods, for potential industrial applications.
Screening and characterization of vaginal fluid donations for vaginal microbiota transplantation
Authors: Yockey Laura J. , Hussain Fatima Aysha , Bergerat Agnes , Reissis Alexandra , Worrall Daniel , Xu Jiawu , Gomez Isabella , Bloom Seth M. , Mafunda Nomfuneko A. , Kelly Julia , Kwon Douglas S. , Mitchell Caroline M.
Published: October 2022

Bacterial vaginosis (BV), the overgrowth of diverse anaerobic bacteria in the vagina, is the most common cause of vaginal symptoms worldwide. BV frequently recurs after antibiotic therapy, and the best probiotic treatments only result in transient changes from BV-associated states to “optimal” communities dominated by a single species of Lactobacillus. Therefore, additional treatment strategies are needed to durably alter vaginal microbiota composition for patients with BV. Vaginal microbiota transplantation (VMT), the transfer of vaginal fluid from a healthy person with an optimal vaginal microbiota to a recipient with BV, has been proposed as one such alternative. However, VMT carries potential risks, necessitating strict safety precautions. Here, we present an FDA-approved donor screening protocol and detailed methodology for donation collection, storage, screening, and analysis of VMT material. We find that Lactobacillus viability is maintained for over six months in donated material stored at − 80 °C without glycerol or other cryoprotectants. We further show that species-specific quantitative PCR for L. crispatus and L. iners can be used as a rapid initial screening strategy to identify potential donors with optimal vaginal microbiomes. Together, this work lays the foundation for designing safe, reproducible trials of VMT as a treatment for BV.
Immunity-based Ebola optimization search algorithm for minimization of feature extraction with reduction in digital mammography using CNN models
Authors: Oyelade Olaide N. , Ezugwu Absalom E.
Published: October 2022

Feature classification in digital medical images like mammography presents an optimization problem which researchers often neglect. The use of a convolutional neural network (CNN) in feature extraction and classification has been widely reported in the literature to have achieved outstanding performance and acceptance in the disease detection procedure. However, little emphasis is placed on ensuring that only discriminant features extracted by the convolutional operations are passed on to the classifier, to avoid bottlenecking the classification operation. Unfortunately, since this has been left unaddressed, a subtle performance impairment has resulted from this omission. Therefore, this study is devoted to addressing these drawbacks using a metaheuristic algorithm to optimize the number of features extracted by the CNN, so that suggestive features are applied for the classification process. To achieve this, a new variant of the Ebola-based optimization algorithm is proposed, based on the population immunity concept and the use of a chaos mapping initialization strategy. The resulting algorithm, called the immunity-based Ebola optimization search algorithm (IEOSA), is applied to the optimization problem addressed in the study. The optimized features represent the output from the IEOSA, which receives the noisy and unfiltered detected features from the convolutional process as input. An exhaustive evaluation of the IEOSA was carried out using classical and IEEE CEC benchmarked functions. A comparative analysis of the performance of IEOSA is presented, with some recent optimization algorithms. The experimental result showed that IEOSA performed well on all the tested benchmark functions. Furthermore, IEOSA was then applied to solve the feature enhancement and selection problem in CNN for better prediction of breast cancer in digital mammography. The classification accuracy returned by the IEOSA method showed that the new approach improved the classification process on detected features when using CNN models.
Intrinsic individual variation in daily activity onset and plastic responses on temporal but not spatial scales in female great tits
Authors: Meijdam Marjolein , Müller Wendt , Eens Marcel
Published: October 2022

In a variety of species, individuals appear to be consistent in the daily timing of their activity onset. Such consistent among-individual differences can result from both intrinsic factors, as individuals may e.g. differ genetically, and extrinsic factors, as the environment may vary on spatial and temporal scales. However, previous studies typically did not differentiate between their respective contributions on individual variation in the timing of activities. Here, we repeatedly measured the onset of activity in female great tits (Parus major) on consecutive days during the egg laying phase of the breeding season in four consecutive years. Subsequently, we used a variance partitioning analysis in order to determine which part of the total variation could be attributed to intrinsic (female identity) and extrinsic (nest box identity) factors. Overall, 27% of the total variation could be attributed to female identity. In addition, we found temporal variation in the activity onset, indicating that individuals can plastically adjust their timing. Yet despite their general ability to change the timing of activities over time, spatial environmental factors did not contribute significantly to the observed variation. Individuals may choose a habitat that matches the preferred timing of activities, or might not benefit from adjusting their timing to environmental factors that might vary on spatial scales.
Changes in the raffinose family oligosaccharides content in the lentil and common bean seeds during malting and mashing processes
Authors: Gasiński Alan , Kawa-Rygielska Joanna , Mikulski Dawid , Kłosowski Grzegorz
Published: October 2022

Raffinose family oligosaccharides (RFOs) are sugars, which are considered anti-nutritional substances, which are not digestible by human gastric enzymes and can lead to flatulence. Legume seeds are often rich in these compounds, which can be cumbersome for many people, such as vegetarians or the population of developing countries, whose diets consists of large amounts of these food products. In this study, simple procedures used around the world in the brewing industry (malting and mashing) were used to determine, whether these processes could be applied to popular legume seeds (lentil and bean) to reduce the RFOs content. Acquired malts and worts were characterised by radically decreased concentration (up to 90%) of most ubiquitous RFOs, such as raffinose and stachyose.
miR-4653-3p overexpression is associated with a poor prognosis of pancreatic ductal adenocarcinoma via HIPK2 downregulation
Authors: Hirabayashi Kenichi , Miyazawa Masaki , Takanashi Yumi , Morimachi Masashi , Kawanishi Aya , Saika Tsubasa , Nakagohri Toshio , Nakamura Naoya
Published: October 2022

Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignant tumor. Several upregulated and downregulated microRNAs (miRNAs) are associated with invasiveness, tumorigenesis, and prognosis of PDAC. Herein, using in situ hybridization, we evaluated miR-4653-3p expression and pancreatic intraepithelial neoplasia (PanIN) and the association between miR-4653-3p expression and clinicopathological factors in PDAC patients. The miR-4653-3p target was also identified. Ninety PDAC cases, including 30 each with normal pancreatic ducts, low-grade PanINs, and high-grade PanINs, were evaluated. miR-4653-3p expression increased in the order—normal pancreatic duct, low-grade PanIN, high-grade PanIN, and PDAC—with no expression detected in normal pancreatic duct. High expression significantly correlated with advanced pathological T stage, lymph node metastasis, advanced Union for International Cancer Control stage, perineural invasion, venous involvement, and shorter overall and disease-specific survival. Homeodomain Interacting Protein Kinase 2 (HIPK2) was identified as a miR-4653-3p target based on mRNA microarray analysis and database screening. In MIA PaCa-2 cells, miR-4653-3p significantly downregulated HIPK2 expression. HIPK2 expression, unlike that of miR-4653-3p, decreased in the order—normal pancreatic duct, low-grade PanIN, high-grade PanIN, and PDAC. Low HIPK2 expression was associated with shorter overall and disease-specific survival in PDAC patients. Thus, miR-4653-3p associates with tumorigenesis and worse prognosis, partly by reducing HIPK2 expression.
Pooled image-base screening of mitochondria with microraft isolation distinguishes pathogenic mitofusin 2 mutations
Authors: Yenkin Alex L. , Bramley John C. , Kremitzki Colin L. , Waligorski Jason E. , Liebeskind Mariel J. , Xu Xinyuan E. , Chandrasekaran Vinay D. , Vakaki Maria A. , Bachman Graham W. , Mitra Robi D. , Milbrandt Jeffrey D. , Buchser William J.
Published: October 2022

Most human genetic variation is classified as variants of uncertain significance. While advances in genome editing have allowed innovation in pooled screening platforms, many screens deal with relatively simple readouts (viability, fluorescence) and cannot identify the complex cellular phenotypes that underlie most human diseases. In this paper, we present a generalizable functional genomics platform that combines high-content imaging, machine learning, and microraft isolation in a method termed “Raft-Seq”. We highlight the efficacy of our platform by showing its ability to distinguish pathogenic point mutations of the mitochondrial regulator Mitofusin 2, even when the cellular phenotype is subtle. We also show that our platform achieves its efficacy using multiple cellular features, which can be configured on-the-fly. Raft-Seq enables a way to perform pooled screening on sets of mutations in biologically relevant cells, with the ability to physically capture any cell with a perturbed phenotype and expand it clonally, directly from the primary screen.
Cftr deletion in mouse epithelial and immune cells differentially influence the intestinal microbiota
Authors: Scull Callie E. , Luo Meng , Jennings Scott , Taylor Christopher M. , Wang Guoshun
Published: October 2022

Cystic fibrosis (CF) is a life-threatening genetic disorder, caused by mutations in the CF transmembrane-conductance regulator gene (cftr) that encodes CFTR, a cAMP-activated chloride and bicarbonate channel. Clinically, CF lung disease dominates the adult patient population. However, its gastrointestinal illness claims the early morbidity and mortality, manifesting as intestinal dysbiosis, inflammation and obstruction. As CF is widely accepted as a disease of epithelial dysfunction, it is unknown whether CFTR loss-of-function in immune cells contributes to these clinical outcomes. Using cftr genetic knockout and bone marrow transplantation mouse models, we performed 16S rRNA gene sequencing of the intestinal microbes. Here we show that cftr deletion in both epithelial and immune cells collectively influence the intestinal microbiota. However, the immune defect is a major factor determining the dysbiosis in the small intestine, while the epithelial defect largely influences that in the large intestine. This finding revises the current concept by suggesting that CF epithelial defect and immune defect play differential roles in CF intestinal disease.
Atomic-scale tuning of ultrathin memristors
Authors: Goul Ryan , Marshall Angelo , Seacat Sierra , Peelaers Hartwin , Robles Hernandez Francisco C. , Wu Judy Z.
Published: October 2022

Continuous device downsizing and circuit complexity have motivated atomic-scale tuning of memristors. Herein, we report atomically tunable Pd/M1/M2/Al ultrathin (<2.5 nm M1/M2 bilayer oxide thickness) memristors using in vacuo atomic layer deposition by controlled insertion of MgO atomic layers into pristine Al2O3 atomic layer stacks guided by theory predicted Fermi energy lowering leading to a higher high state resistance (HRS) and a reduction of oxygen vacancy formation energy. Excitingly, memristors with HRS and on/off ratio increasing exponentially with M1/M2 thickness in the range 1.2–2.4 nm have been obtained, illustrating tunneling mechanism and tunable on/off ratio in the range of 10–104. Further dynamic tunability of on/off ratio by electric field is possible by designing of the atomic M2 layer and M1/M2 interface. This result probes ways in the design of memristors with atomically tunable performance parameters.
Addition of GAC caps and ozonation to conventional filters for improved organics and disinfection by-product reduction
Authors: Bridgehouse Emily , Armour John , Taylor-Edmonds Liz , Andrews Robert C. , McKie Michael J.
Published: October 2022

An examination of shallow GAC filter caps to promote biological filtration without requiring costly full filter bed media replacements.
High-field asymmetric waveform ion mobility spectrometry for xylene isomer separation assisted by helium-chemical modifiers
Authors: Du Xiaoxia , Wang Yifei , Zeng Hongda , Zeng Hao , Chen Zhencheng , Li Hua
Published: October 2022

We propose a combined helium-chemical modifier method for a faster and more convenient separation and detection of xylene isomers. The method employs high-field asymmetric waveform ion mobility spectrometry to investigate the separation and identification of three xylene isomers. This study introduces a novel concept and method for the separation and identification of xylene isomers.
Evaluation of propylene glycol methyl ether as a potential challenge agent for leak detection of liquid and headspace from closed system drug transfer devices using Fourier transform infrared spectroscopy
Authors: Westbrook Emily G. , Doepke Amos , Streicher Robert P.
Published: October 2022

Choosing an appropriate surrogate of hazardous drugs for use in testing Closed System Drug-Transfer Devices (CSTDs) is a challenging endeavor with many factors that must be considered.
Research progress of stimuli-responsive ZnO-based nanomaterials in biomedical applications
Authors: Weng Zhenzhen , Xu Yingying , Gao Jie , Wang Xiaolei
Published: October 2022

Herein, the emerging advances in some exogenous stimuli and endogenous stimuli responsive systems of ZnO-based nanomaterials in biomedical applications are highlighted, while their advantages and directions for improvement are also pointed out.
Interfacial engineering of heterostructured Fe-Ni3S2/Ni(OH)2nanosheets with tailored d-band center for enhanced oxygen evolution catalysis
Authors: Li Gao , Ma Zhanfeng , Li Weirong , Nie Yuhang , Pei Lang , Zhong Jiasong , Miao Qian , Hu Mao-Lin , Wen Xin
Published: October 2022

The OER catalytic activities of Fe-Ni3S2nanosheets can be well manipulated by tailoring the d band center positions via interfacial engineering strategy.
An insight into the bridging role of Co3O4 in MOF-derived binary metal oxide modified sheet-like g-C3N4 for photo-assisted peroxymonosulfate activation
Authors: Wang Guangfu , Huang Danlian , Cheng Min , Chen Sha , Zhang Gaoxia , Du Li , Lei Lei , Chen Yashi , Li Ruijin , Liu Yang
Published: October 2022

Structurally complementary MOF-derived binary metal oxide modified layered g-C3N4 is synthesized by hydrothermal treatment and co-pyrolysis. This article focuses on exploring the synergy of photocatalysis and PMS activation mediated by Co3O4.
Enhanced oxygen activation on an atomically dispersed Au catalyst with dual active sites for room-temperature formaldehyde oxidation
Authors: Li Huixia , Fang Shaofan , Jiang Guimin , Zhang Zuotai
Published: October 2022

Formaldehyde (HCHO) is known to be a hazardous indoor air pollutant.
Ceramic membrane bioreactor for low carbon source wastewater treatment: process design performance and membrane fouling
Authors: Wang Kai , Xu Xiaoyu , Ma Xujiao , Cheng Xiquan , Zhang Yingjie , Ma Jun
Published: October 2022

Anaerobic/aerobic/anaerobic–membrane bioreactor (AOA–MBR) has a very good treatment effect for low C/N wastewater, which is easy to clean.
Antibiotic removal by metal–organic framework and 2D nanomaterial based polyetherimide mixed matrix membranes using a membrane bioreactor
Authors: Sonawane Amol Vijay , Murthy Z. V. P.
Published: October 2022

The ZIF-8, MoS2 and h-BN based PEI MMMs are fabricated to investigate their removal performance for antibiotics (favipiravir, ivermectin and azithromycin) using the MBR system. The MMMs show significant removal of antibiotics from synthetic wastewater.
The association between serum vitamin A and NAFLD among US adults varied in different BMI groups: a cross-sectional study
Authors: Zhang Kaiwen , Nulali Jiayida , Zhang Caoxu , Chen Yingchao , Cheng Jing , Shi Xiaye , Zhu Chunfang , Lu Yingli , Wang Ningjian , Han Bing
Published: October 2022

The association between serum vitamin A (VA) and non-alcoholic fatty liver disease (NAFLD) has not been adequately studied.
Acidic Stigma maydis polysaccharides protect against podocyte injury in membranous nephropathy by maintenance of glomerular filtration barrier integrity and gut-kidney axis
Authors: Wang Xizhu , Dong Yifei , Bao Zhijie , Lin Songyi
Published: October 2022

MN mice models were induced by C-BSA, and we found that acidic stigma maydis polysaccharides  maintained the integrity of the glomerular filtration barrier by promoting slit diaphragm proteins expression and PI3K/AKT signaling.
Live and pasteurized Akkermansia muciniphila attenuate hyperuricemia in mice through modulating uric acid metabolism, inflammation, and gut microbiota
Authors: Zhang Lihua , Liu Jiaxiu , Jin Tong , Qin Ningbo , Ren Xiaomeng , Xia Xiaodong
Published: October 2022

Live and pasteurized Akkermansia muciniphila attenuate hyperuricemia in mice through modulating uric acid synthesis and excretion, inflammation and the gut environment.
Porous ionic liquids: beyond the bounds of free volume in a fluid phase
Authors: Avila Jocasta , Clark Ryan , Pádua Agilio A. H. , Costa Gomes Margarida
Published: October 2022

After reviewing the synthesis, characterization and applications of 150+ porous suspensions, we conclude that type III porous liquids are either suspensions of MOFs in ionic liquids and liquid polymers or of decorated MOFs in molecular solvents.
Partially oxidised boron nitride as a 2D nanomaterial for nanofiltration applications
Authors: Doménech Natalia García , Coogan Áine , Purcell-Milton Finn , Casasín García María Luisa , Arjona Adrián Sanz , Cabré Marc Brunet , Rafferty Aran , McKelvey Kim , Dunne Peter , Gun'ko Yurii K.
Published: October 2022

Here, we report the preparation, characterisation and testing of highly promising nanofiltration membranes produced from partially oxidised BN (BNOx) 2D nanosheets.
Preparation of ultra-stable and environmentally friendly CsPbBr3@ZrO2/PS composite films for white light-emitting diodes
Authors: Shi Jindou , Wang Minqiang , Wang Hao , Zhang Chen , Ji Yongqiang , Wang Junnan , Zhou Yun , Bhatti Arshad Saleem
Published: October 2022

Organic–inorganic dual-encapsulated CsPbBr3@ZrO2/PS CFs are both thermally stable and environmentally friendly, and the assembled white LEDs exhibit long-term working stability.
Toward highly efficient bifunctional electrocatalysts for zinc–air batteries: from theoretical prediction to a ternary FeCoNi design
Authors: Tang Wenhao , He Jialin , Teng Kewei , Gao Lei , Qi Ruiyu , Deng Yirui , Liu Ruiping , Li Ang , Fu Huadong , Wang Chang-an
Published: October 2022

A novel electrocatalyst of hollow nitrogen-doped carbon tubes with coexisting M–N–C single atoms and alloy nanoparticles (denoted FexCoyNiz@hNCTs) shows excellent bifunctional electrocatalytic performances.
Porous biscuit-like nanoplate FeNb11O29−x@C for lithium-ion storage and oxygen evolution
Authors: Fu Hongliang , Lian Yue , Bai Yongqing , Wang Zhifeng , Hu Yongfeng , Zhao Jing , Zhang Huaihao
Published: October 2022

A bifunctional nanocomposite, FeNb11O29−x@C, formed by morphology control (porous biscuit-like nanoplates and carbon layers) and microstructure modification (oxygen vacancies and lattice defects), displays high rate performance and a low overpotential in LIBs and the OER.
Tetraamidoindolyl calix[4]arene as a selective ion pair receptor for LiCl
Authors: Kim Seung Hyeon , Yeon Yerim , Lee Areum , Lynch Vincent M. , He Qing , Sessler Jonathan L. , Kim Sung Kuk
Published: October 2022

A calix[4]arene (1) functionalized with amidoindole groups on the upper rim and with propyl groups on the lower rim extracts LiCl and LiBr selectively.
Effect of electric field on coalescence of an oil-in-water emulsion stabilized by surfactant: a molecular dynamics study
Authors: Wang Yudou , Li Shiyan , Zhang Yuanwu , Zhang Zhenlei , Yuan Shundong , Wang Diansheng
Published: October 2022

The microscopic mechanisms of electrocoalescence of O/W emulsions stabilized by surfactant were analyzed from the electric dipole moment of the surfactant, the interaction between surfactant and oil molecules and the deformation of the surfactant.
Anisole hydrodeoxygenation over Ni–Co bimetallic catalyst: a combination of experimental, kinetic and DFT study
Authors: Kumar Adarsh , Jindal Meenu , Rawat Shivam , Sahoo Abhisek , Verma Rahul , Chandra Devesh , Kumar Sagar , Thallada Bhaskar , Yang Bin
Published: October 2022

High reducible distorted bimetallic sites with medium size in Ni5Co5-AC promoted the production of cyclohexanol by hydrogenation of anisole and subsequent cleavage of C6H11O–CH3 bond.
Influence of TiCN addition on the microstructures and mechanical properties of the AZ31 alloy
Authors: Li Qi-feng , Qiu Wei , Xie Wen , Huang Wei-ying , Zhou Li-bo , Ren Yan-jie , Chen Jian , Yao Mao-hai , Xiong Ai-hu , Chen Wei
Published: October 2022

The microstructure and mechanical properties of extruded AZ31 + xTiCN (x = 0, 0.4, 0.8, 1.2 wt%) were investigated, and the strengthening mechanism was discussed.