bluuebunny/crossref_metadata_2025 huggingface dataset:
Eliminating the need for anodic gas separation in CO2 electroreduction systems via liquid-to-liquid anodic upgrading
Authors: Xie Ke , Ozden Adnan , Miao Rui Kai , Li Yuhang , Sinton David , Sargent Edward H.
Published: June 2022

Electrochemical reduction of CO2 to multi-carbon products (C2+), when powered using renewable electricity, offers a route to valuable chemicals and fuels. In conventional neutral-media CO2-to-C2+ devices, as much as 70% of input CO2 crosses the cell and mixes with oxygen produced at the anode. Recovering CO2 from this stream adds a significant energy penalty. Here we demonstrate that using a liquid-to-liquid anodic process enables the recovery of crossed-over CO2 via facile gas-liquid separation without additional energy input: the anode tail gas is directly fed into the cathodic input, along with fresh CO2 feedstock. We report a system exhibiting a low full-cell voltage of 1.9 V and total carbon efficiency of 48%, enabling 262 GJ/ton ethylene, a 46% reduction in energy intensity compared to state-of-art single-stage CO2-to-C2+ devices. The strategy is compatible with today’s highest-efficiency electrolyzers and CO2 catalysts that function optimally in neutral and alkaline electrolytes.
The Landé factors of electrons and holes in lead halide perovskites: universal dependence on the band gap
Authors: Kirstein E. , Yakovlev D. R. , Glazov M. M. , Zhukov E. A. , Kudlacik D. , Kalitukha I. V. , Sapega V. F. , Dimitriev G. S. , Semina M. A. , Nestoklon M. O. , Ivchenko E. L. , Kopteva N. E. , Dirin D. N. , Nazarenko O. , Kovalenko M. V. , Baumann A. , Höcker J. , Dyakonov V. , Bayer M.
Published: June 2022

The Landé or g-factors of charge carriers are decisive for the spin-dependent phenomena in solids and provide also information about the underlying electronic band structure. We present a comprehensive set of experimental data for values and anisotropies of the electron and hole Landé factors in hybrid organic-inorganic (MAPbI3, MAPb(Br0.5Cl0.5)3, MAPb(Br0.05Cl0.95)3, FAPbBr3, FA0.9Cs0.1PbI2.8Br0.2, MA=methylammonium and FA=formamidinium) and all-inorganic (CsPbBr3) lead halide perovskites, determined by pump-probe Kerr rotation and spin-flip Raman scattering in magnetic fields up to 10 T at cryogenic temperatures. Further, we use first-principles density functional theory (DFT) calculations in combination with tight-binding and k ⋅ p approaches to calculate microscopically the Landé factors. The results demonstrate their universal dependence on the band gap energy across the different perovskite material classes, which can be summarized in a universal semi-phenomenological expression, in good agreement with experiment.
Relative, local and global dimension in complex networks
Authors: Peach Robert , Arnaudon Alexis , Barahona Mauricio
Published: June 2022

Dimension is a fundamental property of objects and the space in which they are embedded. Yet ideal notions of dimension, as in Euclidean spaces, do not always translate to physical spaces, which can be constrained by boundaries and distorted by inhomogeneities, or to intrinsically discrete systems such as networks. To take into account locality, finiteness and discreteness, dynamical processes can be used to probe the space geometry and define its dimension. Here we show that each point in space can be assigned a relative dimension with respect to the source of a diffusive process, a concept that provides a scale-dependent definition for local and global dimension also applicable to networks. To showcase its application to physical systems, we demonstrate that the local dimension of structural protein graphs correlates with structural flexibility, and the relative dimension with respect to the active site uncovers regions involved in allosteric communication. In simple models of epidemics on networks, the relative dimension is predictive of the spreading capability of nodes, and identifies scales at which the graph structure is predictive of infectivity. We further apply our dimension measures to neuronal networks, economic trade, social networks, ocean flows, and to the comparison of random graphs.
Order-of-magnitude enhancement in photocurrent generation of Synechocystis sp. PCC 6803 by outer membrane deprivation
Authors: Kusama Shoko , Kojima Seiji , Kimura Ken , Shimakawa Ginga , Miyake Chikahiro , Tanaka Kenya , Okumura Yasuaki , Nakanishi Shuji
Published: June 2022

Biophotovoltaics (BPV) generates electricity from reducing equivalent(s) produced by photosynthetic organisms by exploiting a phenomenon called extracellular electron transfer (EET), where reducing equivalent(s) is transferred to external electron acceptors. Although cyanobacteria have been extensively studied for BPV because of their high photosynthetic activity and ease of handling, their low EET activity poses a limitation. Here, we show an order-of-magnitude enhancement in photocurrent generation of the cyanobacteriumSynechocystissp. PCC 6803 by deprivation of the outer membrane, where electrons are suggested to stem from pathway(s) downstream of photosystem I. A marked enhancement of EET activity itself is verified by rapid reduction of exogenous electron acceptor, ferricyanide. The extracellular organic substances, including reducing equivalent(s), produced by this cyanobacterium serve as respiratory substrates for other heterotrophic bacteria. These findings demonstrate that the outer membrane is a barrier that limits EET. Therefore, depriving this membrane is an effective approach to exploit the cyanobacterial reducing equivalent(s).
The microRNA cluster C19MC confers differentiation potential into trophoblast lineages upon human pluripotent stem cells
Authors: Kobayashi Norio , Okae Hiroaki , Hiura Hitoshi , Kubota Naoto , Kobayashi Eri H. , Shibata Shun , Oike Akira , Hori Takeshi , Kikutake Chie , Hamada Hirotaka , Kaji Hirokazu , Suyama Mikita , Bortolin-Cavaillé Marie-Line , Cavaillé Jérôme , Arima Takahiro
Published: June 2022

The first cell fate commitment during mammalian development is the specification of the inner cell mass and trophectoderm. This irreversible cell fate commitment should be epigenetically regulated, but the precise mechanism is largely unknown in humans. Here, we show that naïve human embryonic stem (hES) cells can transdifferentiate into trophoblast stem (hTS) cells, but primed hES cells cannot. Our transcriptome and methylome analyses reveal that a primate-specific miRNA cluster on chromosome 19 (C19MC) is active in naïve hES cells but epigenetically silenced in primed ones. Moreover, genome and epigenome editing using CRISPR/Cas systems demonstrate that C19MC is essential for hTS cell maintenance and C19MC-reactivated primed hES cells can give rise to hTS cells. Thus, we reveal that C19MC activation confers differentiation potential into trophoblast lineages on hES cells. Our findings are fundamental to understanding the epigenetic regulation of human early development and pluripotency.
Dynamic self-stabilization in the electronic and nanomechanical properties of an organic polymer semiconductor
Authors: Dobryden Illia , Korolkov Vladimir V. , Lemaur Vincent , Waldrip Matthew , Un Hio-Ieng , Simatos Dimitrios , Spalek Leszek J. , Jurchescu Oana D. , Olivier Yoann , Claesson Per M. , Venkateshvaran Deepak
Published: June 2022

The field of organic electronics has profited from the discovery of new conjugated semiconducting polymers that have molecular backbones which exhibit resilience to conformational fluctuations, accompanied by charge carrier mobilities that routinely cross the 1 cm2/Vs benchmark. One such polymer is indacenodithiophene-co-benzothiadiazole. Previously understood to be lacking in microstructural order, we show here direct evidence of nanosized domains of high order in its thin films. We also demonstrate that its device-based high-performance electrical and thermoelectric properties are not intrinsic but undergo rapid stabilization following a burst of ambient air exposure. The polymer’s nanomechanical properties equilibrate on longer timescales owing to an orthogonal mechanism; the gradual sweating-out of residual low molecular weight solvent molecules from its surface. We snapshot the quasistatic temporal evolution of the electrical, thermoelectric and nanomechanical properties of this prototypical organic semiconductor and investigate the subtleties which play on competing timescales. Our study documents the untold and often overlooked story of a polymer device’s dynamic evolution toward stability.
Giant energy-storage density with ultrahigh efficiency in lead-free relaxors via high-entropy design
Authors: Chen Liang , Deng Shiqing , Liu Hui , Wu Jie , Qi He , Chen Jun
Published: June 2022

Next-generation advanced high/pulsed power capacitors rely heavily on dielectric ceramics with high energy storage performance. However, thus far, the huge challenge of realizing ultrahigh recoverable energy storage density (Wrec) accompanied by ultrahigh efficiency (η) still existed and has become a key bottleneck restricting the development of dielectric materials in cutting-edge energy storage applications. Here, we propose a high-entropy strategy to design “local polymorphic distortion” including rhombohedral-orthorhombic-tetragonal-cubic multiphase nanoclusters and random oxygen octahedral tilt, resulting in ultrasmall polar nanoregions, an enhanced breakdown electric field, and delayed polarization saturation. A giant Wrec ~10.06 J cm−3 is realized in lead-free relaxor ferroelectrics, especially with an ultrahigh η ~90.8%, showing breakthrough progress in the comprehensive energy storage performance for lead-free bulk ceramics. This work opens up an effective avenue to design dielectric materials with ultrahigh comprehensive energy storage performance to meet the demanding requirements of advanced energy storage applications.
Climate change reshuffles northern species within their niches
Authors: Antão Laura H. , Weigel Benjamin , Strona Giovanni , Hällfors Maria , Kaarlejärvi Elina , Dallas Tad , Opedal Øystein H. , Heliölä Janne , Henttonen Heikki , Huitu Otso , Korpimäki Erkki , Kuussaari Mikko , Lehikoinen Aleksi , Leinonen Reima , Lindén Andreas , Merilä Päivi , Pietiäinen Hannu , Pöyry Juha , Salemaa Maija , Tonteri Tiina , Vuorio Kristiina , Ovaskainen Otso , Saastamoinen Marjo , Vanhatalo Jarno , Roslin Tomas , Laine Anna-Liisa
Published: June 2022

Climate change is a pervasive threat to biodiversity. While range shifts are a known consequence of climate warming contributing to regional community change, less is known about how species’ positions shift within their climatic niches. Furthermore, whether the relative importance of different climatic variables prompting such shifts varies with changing climate remains unclear. Here we analysed four decades of data for 1,478 species of birds, mammals, butterflies, moths, plants and phytoplankton along a 1,200 km high latitudinal gradient. The relative importance of climatic drivers varied non-uniformly with progressing climate change. While species turnover among decades was limited, the relative position of species within their climatic niche shifted substantially. A greater proportion of species responded to climatic change at higher latitudes, where changes were stronger. These diverging climate imprints restructure a full biome, making it difficult to generalize biodiversity responses and raising concerns about ecosystem integrity in the face of accelerating climate change.
A dimeric proteomimetic prevents SARS-CoV-2 infection by dimerizing the spike protein
Authors: Khatri Bhavesh , Pramanick Ishika , Malladi Sameer Kumar , Rajmani Raju S. , Kumar Sahil , Ghosh Pritha , Sengupta Nayanika , Rahisuddin R. , Kumar Narender , Kumaran S. , Ringe Rajesh P. , Varadarajan Raghavan , Dutta Somnath , Chatterjee Jayanta
Published: June 2022

Protein tertiary structure mimetics are valuable tools to target large protein–protein interaction interfaces. Here, we demonstrate a strategy for designing dimeric helix-hairpin motifs from a previously reported three-helix-bundle miniprotein that targets the receptor-binding domain (RBD) of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Through truncation of the third helix and optimization of the interhelical loop residues of the miniprotein, we developed a thermostable dimeric helix-hairpin. The dimeric four-helix bundle competes with the human angiotensin-converting enzyme 2 (ACE2) in binding to RBD with 2:2 stoichiometry. Cryogenic-electron microscopy revealed the formation of dimeric spike ectodomain trimer by the four-helix bundle, where all the three RBDs from either spike protein are attached head-to-head in an open conformation, revealing a novel mechanism for virus neutralization. The proteomimetic protects hamsters from high dose viral challenge with replicative SARS-CoV-2 viruses, demonstrating the promise of this class of peptides that inhibit protein–protein interaction through target dimerization.
Understanding occupants’ behaviour, engagement, emotion, and comfort indoors with heterogeneous sensors and wearables
Authors: Gao Nan , Marschall Max , Burry Jane , Watkins Simon , Salim Flora D.
Published: June 2022

We conducted a field study at a K-12 private school in the suburbs of Melbourne, Australia. The data capture contained two elements: First, a 5-month longitudinal field study In-Gauge using two outdoor weather stations, as well as indoor weather stations in 17 classrooms and temperature sensors on the vents of occupant-controlled room air-conditioners; these were collated into individual datasets for each classroom at a 5-minute logging frequency, including additional data on occupant presence. The dataset was used to derive predictive models of how occupants operate room air-conditioning units. Second, we tracked 23 students and 6 teachers in a 4-week cross-sectional study En-Gage, using wearable sensors to log physiological data, as well as daily surveys to query the occupants’ thermal comfort, learning engagement, emotions and seating behaviours. Overall, the combined dataset could be used to analyse the relationships between indoor/outdoor climates and students’ behaviours/mental states on campus, which provide opportunities for the future design of intelligent feedback systems to benefit both students and staff.
CDCDB: A large and continuously updated drug combination database
Authors: Shtar Guy , Azulay Louise , Nizri Omer , Rokach Lior , Shapira Bracha
Published: June 2022

In recent years, due to the complementary action of drug combinations over mono-therapy, the multiple-drugs for multiple-targets paradigm has received increased attention to treat bacterial infections and complex diseases. Although new drug combinations screening has benefited from experimental tests like automated high throughput screening, it is limited due to the large number of possible drug combinations. The task of drug combination screening can be streamlined through computational methods and models. Such models require up-to-date databases; however, existing databases are static and consist of the data collected at the time of their creation. This paper introduces the Continuous Drug Combination Database (CDCDB), a continuously updated drug combination database. The CDCDB includes over 40,795 drug combinations, of which 17,107 are unique combinations consisting of more than 4,129 individual drugs, curated from ClinicalTrials.gov, the FDA Orange Book®, and patents. To create CDCDB, we use various methods, including natural language processing techniques, to improve the process of drug combination discovery, ensuring that our database can be used for drug synergy prediction. Website: https://icc.ise.bgu.ac.il/medical_ai/CDCDB/.
Towards fully automated segmentation of rat cardiac MRI by leveraging deep learning frameworks
Authors: Fernández-Llaneza Daniel , Gondová Andrea , Vince Harris , Patra Arijit , Zurek Magdalena , Konings Peter , Kagelid Patrik , Hultin Leif
Published: June 2022

Automated segmentation of human cardiac magnetic resonance datasets has been steadily improving during recent years. Similar applications would be highly useful to improve and speed up the studies of cardiac function in rodents in the preclinical context. However, the transfer of such segmentation methods to the preclinical research is compounded by the limited number of datasets and lower image resolution. In this paper we present a successful application of deep architectures 3D cardiac segmentation for rats in preclinical contexts which to our knowledge has not yet been reported. We developed segmentation models that expand on the standard U-Net architecture and evaluated models separately trained for systole and diastole phases (2MSA) and a single model trained for all phases (1MSA). Furthermore, we calibrated model outputs using a Gaussian process (GP)-based prior to improve phase selection. The resulting models approach human performance in terms of left ventricular segmentation quality and ejection fraction (EF) estimation in both 1MSA and 2MSA settings (Sørensen-Dice score 0.91 ± 0.072 and 0.93 ± 0.032, respectively). 2MSA achieved a mean absolute difference between estimated and reference EF of 3.5 ± 2.5%, while 1MSA resulted in 4.1 ± 3.0%. Applying GPs to 1MSA enabled automating systole and diastole phase selection. Both segmentation approaches (1MSA and 2MSA) were statistically equivalent. Combined with a proposed cardiac phase selection strategy, our work presents an important first step towards a fully automated segmentation pipeline in the context of rat cardiac analysis.
Depolarization of echo chambers by random dynamical nudge
Authors: Currin Christopher Brian , Vera Sebastián Vallejo , Khaledi-Nasab Ali
Published: June 2022

In social networks, users often engage with like-minded peers. This selective exposure to opinions might result in echo chambers, i.e., political fragmentation and social polarization of user interactions. When echo chambers form, opinions have a bimodal distribution with two peaks on opposite sides. In certain issues, where either extreme positions contain a degree of misinformation, neutral consensus is preferable for promoting discourse. In this paper, we use an opinion dynamics model that naturally forms echo chambers in order to find a feedback mechanism that bridges these communities and leads to a neutral consensus. We introduce the random dynamical nudge (RDN), which presents each agent with input from a random selection of other agents’ opinions and does not require surveillance of every person’s opinions. Our computational results in two different models suggest that the RDN leads to a unimodal distribution of opinions centered around the neutral consensus. Furthermore, the RDN is effective both for preventing the formation of echo chambers and also for depolarizing existing echo chambers. Due to the simple and robust nature of the RDN, social media networks might be able to implement a version of this self-feedback mechanism, when appropriate, to prevent the segregation of online communities on complex social issues.
Evidence for content-dependent timing of real-life events during COVID-19 crisis
Authors: Taub Keren , Abeles Dekel , Yuval-Greenberg Shlomit
Published: June 2022

How do people estimate the time of past events? A prominent hypothesis suggests that there are multiple timing systems which operate in parallel, depending on circumstances. However, quantitative evidence supporting this hypothesis focused solely on short time-scales (seconds to minutes) and lab-produced events. Furthermore, these studies typically examined the effect of the circumstance and the psychological state of the participant rather than the content of the timed events. Here, we provide, for the first time, support for multiple content-based timing systems when estimating the time of real-life events over long time-scales. The study was conducted during the COVID-19 crisis, which provided a rare opportunity to examine real-life time perception when many were exposed to similar meaningful events. Participants (N = 468) were asked to retrospectively estimate the time that has passed since prominent events, that were either related or unrelated to the pandemic. Results showed an overall time-inflation, which was decreased for events related to the pandemic. This indicates that long-term subjective timing of real-life events exists in multiple systems, which are affected not only by circumstances, but also by content.
Plasma extracellular vesicles bearing PD-L1, CD40, CD40L or TNF-RII are significantly reduced after treatment of AIDS-NHL
Authors: Martínez Laura E. , Lensing Shelly , Chang Di , Magpantay Larry I. , Mitsuyasu Ronald , Ambinder Richard F. , Sparano Joseph A. , Martínez-Maza Otoniel , Epeldegui Marta
Published: June 2022

Emerging evidence shows that tumor cells secrete extracellular vesicles (EVs) that carry bioactive cell surface markers, such as programmed death-ligand 1 (PD-L1), which can modulate immune responses and inhibit anti-tumor responses, potentially playing a role in lymphomagenesis and in promoting the growth of these cancers. In this study, we investigated the role of EVs expressing cell surface molecules associated with B cell activation and immune regulation. We measured levels of EVs derived from plasma from 57 subjects with AIDS-related non-Hodgkin lymphoma (AIDS-NHL) enrolled in the AIDS Malignancies Consortium (AMC) 034 clinical trial at baseline and post-treatment with rituximab plus concurrent infusional EPOCH chemotherapy. We found that plasma levels of EVs expressing PD-L1, CD40, CD40L or TNF-RII were significantly reduced after cancer treatment. AIDS-NHL patients with the diffuse large B cell lymphoma (DLBCL) tumor subtype had decreased plasma levels of EVs bearing PD-L1, compared to those with Burkitt’s lymphoma. CD40, CD40L and TNF-RII-expressing EVs showed a significant positive correlation with plasma levels of IL-10, CXCL13, sCD25, sTNF-RII and IL-18. Our results suggest that patients with AIDS-NHL have higher levels of EVs expressing PD-L1, CD40, CD40L or TNF-RII in circulation before cancer treatment and that levels of these EVs are associated with levels of biomarkers of microbial translocation and inflammation.
Changes in biceps brachii muscle hardness assessed by a push-in meter and strain elastography after eccentric versus concentric contractions
Authors: Murayama Mitsuyoshi , Inami Takayuki , Shima Norihiro , Yoneda Tsugutake , Nosaka Kazunori
Published: June 2022

Changes in biceps brachii muscle hardness assessed by a push-in meter (PM) and strain elastography (SE) were compared between eccentric (ECC) and concentric contractions (CON) of the elbow flexors to test the hypothesis that muscle hardness would increase greater after ECC. Ten men performed 5 sets of 10 ECC with their non-dominant arms and 5 sets of 10 CON with their dominant arms using a dumbbell corresponding to 50% of maximum voluntary isometric contraction (MVIC) force at 90º elbow flexion. Before and 1–4 days after the exercise, MVIC force, elbow joint angles, upper-arm circumference, and muscle soreness as muscle damage makers, and biceps brachii muscle hardness at maximally extended elbow joint by PM and SE were measured. Changes in these measures over time were compared between ECC and CON. All muscle damage markers showed greater changes after ECC than CON (p < 0.001). Muscle hardness assessed by PM and SE increased (p < 0.05) and peaked at 4 days post-ECC with 154.4 ± 90.0% (PM) and 156.2 ± 64.2% (SE) increases from the baseline, but did not change significantly after CON. The changes in muscle hardness post-ECC were correlated between PM and SE (r = 0.752, p < 0.001). A correlation (p < 0.001) between the normalized changes in resting elbow joint angle and changes in muscle hardness assessed by PM (r = − 0.772) or SE (r = − 0.745) was also found. These results supported the hypothesis and suggest that the increases in muscle hardness after ECC were associated with muscle damage (increased muscle stiffness), and PM and SE detected muscle hardness changes similarly.
Relationship between smoking and postoperative complications of cervical spine surgery: a systematic review and meta-analysis
Authors: Zheng Li-ming , Zhang Zhi-wen , Wang Wei , Li Yang , Wen Feng
Published: June 2022

To determine whether smoking has adverse effects on postoperative complications following spine cervical surgery (PROSPERO 2021: CRD42021269648). We searched PubMed, Embase, Cochrane Library, and Web of Science through 13 July 2021 for cohort and case–control studies that investigated the effect of smoking on postoperative complications after cervical spine surgery. Two researchers independently screened the studies and extracted data according to the selection criteria. The meta-analysis included 43 studies, including 27 case–control studies and 16 cohort studies, with 10,020 patients. Pooled estimates showed that smoking was associated with overall postoperative complications (effect estimate [ES] = 1.99, 95% confidence interval [CI]: 1.62–2.44, p < 0.0001), respiratory complications (ES = 2.70, 95% CI: 1.62–4.49, p < 0.0001), reoperation (ES = 2.06, 95% CI: 1.50–2.81, p < 0.0001), dysphagia (ES = 1.49, 95% CI: 1.06–2.10, p = 0.022), wound infection (ES = 3.21, 95% CI: 1.62–6.36, p = 0.001), and axial neck pain (ES = 1.98, 95% CI: 1.25–3.12, p = 0.003). There were no significant differences between the smoking and nonsmoking groups in terms of fusion (ES = 0.97, 95% CI: 0.94–1.00, p = 0.0097), operation time (weighted mean difference [WMD] = 0.08, 95% CI: −5.54 to 5.71, p = 0.977), estimated blood loss (WMD = −5.31, 95% CI: −148.83 to 139.22, p = 0.943), length of hospital stay (WMD = 1.01, 95% CI: −2.17 to 4.20, p = 0.534), Visual Analog Scale-neck pain score (WMD = −0.19, 95% CI: −1.19 to 0.81, p = 0.707), Visual Analog Scale-arm pain score (WMD = −0.50, 95% CI: −1.53 to 0.53, p = 0.343), Neck Disability Index score (WMD = 11.46, 95% CI: −3.83 to 26.76, p = 0.142), or Japanese Orthopedic Association Scores (WMD = −1.75, 95% CI: −5.27 to 1.78, p = 0.332). Compared with nonsmokers, smokers seem to be more significantly associated with overall complications, respiratory complications, reoperation, longer hospital stay, dysphagia, wound infection and axial neck pain after cervical spine surgery. It is essential to provide timely smoking cessation advice and explanation to patients before elective cervical spine surgery.
Analysis of immune related gene expression profiles and immune cell components in patients with Barrett esophagus
Authors: Shi Lin , Guo Renwei , Chen Zhuo , Jiao Ruonan , Zhang Shuangshuang , Xiong Xuanxuan
Published: June 2022

Barrett's esophagus (BE) is a well-known precancerous condition of esophageal adenocarcinoma. However, the immune cells and immune related genes involved in BE development and progression are not fully understood. Therefore, our study attempted to investigate the roles of immune cells and immune related genes in BE patients. The raw gene expression data were downloaded from the GEO database. The limma package in R was used to screen differentially expressed genes (DEGs). Then we performed the least absolute shrinkage and selection operator (LASSO) and random forest (RF) analyses to screen key genes. The proportion of infiltrated immune cells was evaluated using the CIBERSORT algorithm between BE and normal esophagus (NE) samples. The spearman index was used to show the correlations of immune genes and immune cells. Receiver operating characteristic (ROC) curves were used to assess the diagnostic value of key genes in BE. A total of 103 differentially expressed immune-related genes were identified between BE samples and normal samples. Then, 7 genes (CD1A, LTF, FABP4, PGC, TCF7L2, INSR,SEMA3C) were obtained after Lasso analysis and RF modeling. CIBERSORT analysis revealed that resting CD4 T memory cells and gamma delta T cells were present at significantly lower levels in BE samples. Moreover, plasma cell and regulatory T cells were present at significantly higher levels in BE samples than in NE samples. INSR had the highest AUC values in ROC analysis. We identified 7 immune related genes and 4 different immune cells in our study, that may play vital roles in the occurrence and development of BE. Our findings improve the understanding of the molecular mechanisms of BE.
Semaphorin 3A regulates alveolar bone remodeling on orthodontic tooth movement
Authors: Kamei Hirokazu , Ishii Takenobu , Nishii Yasushi
Published: June 2022

Semaphorin 3A (Sema3A) promotes osteoblast differentiation and inhibits osteoclast differentiation. In the present study, we observed the regulation of alveolar bone remodeling by Sema3A during orthodontic tooth movement (OTM). Four inflammatory cytokines (IL-1β, IL-6, TNFα, and INF-γ) involved in OTM were applied to osteoblasts in vitro, and Sema3A expression was determined by reverse-transcription quantitative polymerase chain reaction (RT-qPCR). In vivo, springs were attached to the maxillary first molars of C56BL/6J mice (OTM model) and the localization of Sema3A was confirmed by immunofluorescent. Recombinant Sema3A (rSema3A) was locally injected into the OTM model. Inflammatory cytokine localization in the OTM model was confirmed by immunohistochemistry. In vivo, more Sema3A was observed on the tension side in the OTM group. Injection of rSema3A into the OTM model increased mineralization on the tension side and decreased the number of osteoclasts on the compression side. In vitro, IL-1β significantly increased Sema3A mRNA levels. Immunohistochemistry for IL-1β in vivo showed more concentrated staining in the periodontal ligament on the tension side than on the compression side. In summary, our findings revealed the distribution of Sema3A in the periodontal ligament and demonstrated that rSema3A administration promotes bone formation and inhibits bone resorption during OTM.
Characterization of intestinal microbiota in normal weight and overweight Border Collie and Labrador Retriever dogs
Authors: Morelli Giada , Patuzzi Ilaria , Losasso Carmen , Ricci Antonia , Contiero Barbara , Andrighetto Igino , Ricci Rebecca
Published: June 2022

Obesity in dogs is an emerging issue that affects canine health and well-being. Its development is ascribed to several factors, including genetic predisposition and dietary management, and recent evidence suggests that intestinal microbiota may be involved as well. Previous works have shown obesity to be linked to significant changes in gut microbiota composition in humans and mice, but only limited information is available on the role played by canine gut microbiota. The aim of this exploratory study was to investigate whether composition of canine faecal microbiota may be influenced by overweight condition and breed. All the enrolled companion dogs were young adults, intact, healthy, and fed commercial extruded pet food; none had received antibiotics, probiotics or immunosuppressant drugs in the previous six months. Labrador Retriever (LR) and Border Collie (BC) were chosen as reference breeds and Body Condition Score (BCS) on a 9-point scale as reference method for evaluating body fat. The faecal microbial communities of 15 lean (BCS 4–5/9; 7 LRs and 8 BCs) and 14 overweight (BCS > 5/9; 8 LRs and 6 BCs) family dogs were analysed using 16S rRNA gene sequencing. Moreover, for each dog, the daily intake of energy (kcal/d) and dietary macronutrients (g/d) were calculated according to an accurate feeding history collection.FirmicutesandBacteroidetesresulted the predominant phyla (51.5 ± 10.0% and 33.4 ± 8.5%, respectively) in all dogs. Bioinformatic and statistical analysis revealed that no bacterial taxon differed significantly based on body condition, except for genusAllisonella(p < 0.05); BC gut microbiota was richer (p < 0.05) in bacteria belonging to phylaActinobacteria(familyCoriobacteriaceaein particular) andFirmicutes(AllobaculumandRoseburiagenera). No remarkable differences were recorded either for diversity indices (i.e., alpha diversity,p > 0.10) or for divergence within the sample set (i.e., beta diversity,p > 0.05). PERMANOVA tests performed on single factors demonstrated the tendency of dietary protein to influence the recruited dogs’ microbiota beta-diversity at amplicon sequence variant level (p = 0.08). In conclusion, the faecal microbiota of dogs involved in this exploratory study showed no major variations based on body condition. However, our findings suggested that certain bacterial taxa previously acknowledged in obesity-related studies may be detected in dissimilar amounts depending on canine breed.
Microvascular imaging of the unstained human superior colliculus using synchrotron-radiation phase-contrast microtomography
Authors: Lee Ju Young , Mack Andreas F. , Shiozawa Thomas , Longo Renata , Tromba Giuliana , Scheffler Klaus , Hagberg Gisela E.
Published: June 2022

Characterizing the microvasculature of the human brain is critical to advance understanding of brain vascular function. Most methods rely on tissue staining and microscopy in two-dimensions, which pose several challenges to visualize the three-dimensional structure of microvessels. In this study, we used an edge-based segmentation method to extract the 3D vasculature from synchrotron radiation phase-contrast microtomography (PC-μCT) of two unstained, paraffin-embedded midbrain region of the human brain stem. Vascular structures identified in PC-μCT were validated with histology of the same specimen. Using the Deriche-Canny edge detector that was sensitive to the boundary between tissue and vascular space, we could segment the vessels independent of signal variations in PC-μCT images. From the segmented volumetric vasculature, we calculated vessel diameter, vessel length and volume fraction of the vasculature in the superior colliculi. From high resolution images, we found the most frequent vessel diameter to be between 8.6–10.2 µm. Our findings are consistent with the known anatomy showing two types of vessels with distinctive morphology: peripheral collicular vessels and central collicular vessels. The proposed method opens up new possibilities for vascular research of the central nervous system using synchrotron radiation PC-μCT of unstained human tissue.
FABP5 deletion in nociceptors augments endocannabinoid signaling and suppresses TRPV1 sensitization and inflammatory pain
Authors: Bogdan Diane M. , Studholme Keith , DiBua Adriana , Gordon Chris , Kanjiya Martha P. , Yu Mei , Puopolo Michelino , Kaczocha Martin
Published: June 2022

The endocannabinoid anandamide (AEA) produces antinociceptive effects by activating cannabinoid receptor 1 (CB1). However, AEA also serves as an agonist at transient receptor potential vanilloid receptor 1 (TRPV1) in nociceptive sensory neurons, which may exacerbate pain. This potential functional duality is highlighted by the failure of an inhibitor of the AEA catabolic enzyme fatty acid amide hydrolase (FAAH) to afford pain relief in a clinical trial. Consequently, it remains to be determined whether elevating AEA levels in nociceptors leads to antinociceptive or pro-nociceptive effects. Fatty acid binding protein 5 (FABP5) is an intracellular carrier that mediates AEA transport to FAAH for inactivation. Leveraging the abundant expression of FABP5 in TRPV1+ nociceptors, we employed a conditional knockout strategy to demonstrate that FABP5 deletion in nociceptors augments AEA levels, resulting in the emergence of antinociceptive effects mediated by CB1. Mechanistically, FABP5 deletion suppresses inflammation- and nerve growth factor-mediated TRPV1 sensitization via CB1, an effect mediated by calcineurin. Unexpectedly, inhibition of FAAH failed to blunt TRPV1 sensitization, uncovering functionally distinct outputs resulting from FABP5 and FAAH inhibition. Collectively, our results demonstrate that FABP5 serves a key role in governing endocannabinoid signaling in nociceptors to disrupt TRPV1 sensitization and pain, and position FABP5 as a therapeutic target for the development of analgesics.
Predicting early failure of quantum cascade lasers during accelerated burn-in testing using machine learning
Authors: Aydinkarahaliloglu Cagri , Jatar Shashank , Wang Xiaojun , Fong Mary , Gupta Vijay , Troccoli Mariano , Hoffman Anthony J.
Published: June 2022

Device life time is a significant consideration in the cost of ownership of quantum cascade lasers (QCLs). The life time of QCLs beyond an initial burn-in period has been studied previously; however, little attention has been given to predicting premature device failure where the device fails within several hundred hours of operation. Here, we demonstrate how standard electrical and optical device measurements obtained during an accelerated burn-in process can be used in a simple support vector machine to predict premature failure with high confidence. For every QCL that fails, at least one of the measurements is classified as belonging to a device that will fail prematurely—as much as 200 h before the actual failure of the device. Furthermore, for devices that are operational at the end of the burn-in process, the algorithm correctly classifies all the measurements. This work will influence future device analysis and could lead to insights on the physical mechanisms of premature failure in QCLs.
Metagenomic assembled plasmids of the human microbiome vary across disease cohorts
Authors: Stockdale S. R. , Harrington R. S. , Shkoporov A. N. , Khokhlova E. V. , Daly K. M. , McDonnell S. A. , O’Reagan O. , Nolan J. A. , Sheehan D. , Lavelle A. , Draper L. A. , Shanahan F. , Ross R. P. , Hill C.
Published: June 2022

We compiled a human metagenome assembled plasmid (MAP) database and interrogated differences across multiple studies that were originally designed to investigate the composition of the human microbiome across various lifestyles, life stages and events. This was performed as plasmids enable bacteria to rapidly expand their functional capacity through mobilisation, yet their contribution to human health and disease is poorly understood. We observed that inter-sample β-diversity differences of plasmid content (plasmidome) could distinguish cohorts across a multitude of conditions. We also show that reduced intra-sample plasmidome α-diversity is consistent amongst patients with inflammatory bowel disease (IBD) and Clostridioides difficile infections. We also show that faecal microbiota transplants can restore plasmidome diversity. Overall plasmidome diversity, specific plasmids, and plasmid-encoded functions can all potentially act as biomarkers of IBD or its severity. The human plasmidome is an overlooked facet of the microbiome and should be integrated into investigations regarding the role of the microbiome in promoting health or disease. Including MAP databases in analyses will enable a greater understanding of the roles of plasmid-encoded functions within the gut microbiome and will inform future human metagenome analyses.
Investigating the association of environmental exposures and all-cause mortality in the UK Biobank using sparse principal component analysis
Authors: Mamouei Mohammad , Zhu Yajie , Nazarzadeh Milad , Hassaine Abdelaali , Salimi-Khorshidi Gholamreza , Cai Yutong , Rahimi Kazem
Published: June 2022

Multicollinearity refers to the presence of collinearity between multiple variables and renders the results of statistical inference erroneous (Type II error). This is particularly important in environmental health research where multicollinearity can hinder inference. To address this, correlated variables are often excluded from the analysis, limiting the discovery of new associations. An alternative approach to address this problem is the use of principal component analysis. This method, combines and projects a group of correlated variables onto a new orthogonal space. While this resolves the multicollinearity problem, it poses another challenge in relation to interpretability of results. Standard hypothesis testing methods can be used to evaluate the association of projected predictors, called principal components, with the outcomes of interest, however, there is no established way to trace the significance of principal components back to individual variables. To address this problem, we investigated the use of sparse principal component analysis which enforces a parsimonious projection. We hypothesise that this parsimony could facilitate the interpretability of findings. To this end, we investigated the association of 20 environmental predictors with all-cause mortality adjusting for demographic, socioeconomic, physiological, and behavioural factors. The study was conducted in a cohort of 379,690 individuals in the UK. During an average follow-up of 8.05 years (3,055,166 total person-years), 14,996 deaths were observed. We used Cox regression models to estimate the hazard ratio (HR) and 95% confidence intervals (CI). The Cox models were fitted to the standardised environmental predictors (a) without any transformation (b) transformed with PCA, and (c) transformed with SPCA. The comparison of findings underlined the potential of SPCA for conducting inference in scenarios where multicollinearity can increase the risk of Type II error. Our analysis unravelled a significant association between average noise pollution and increased risk of all-cause mortality. Specifically, those in the upper deciles of noise exposure have between 5 and 10% increased risk of all-cause mortality compared to the lowest decile.
Simple and effective serum-free medium for sustained expansion of bovine satellite cells for cell cultured meat
Authors: Stout Andrew J. , Mirliani Addison B. , Rittenberg Miriam L. , Shub Michelle , White Eugene C. , Yuen John S. K. , Kaplan David L.
Published: June 2022

Cell-cultured meat offers the potential for a more sustainable, ethical, resilient, and healthy food system. However, research and development has been hindered by the lack of serum-free media that enable the robust expansion of relevant cells (e.g., muscle satellite cells) over multiple passages. Recently, a low-cost serum-free media (B8) was described for pluripotent stem cells. Here, B8 is adapted for bovine satellite cells through the addition of a single component, recombinant albumin, which renders it suitable for long-term satellite cell expansion without sacrificing myogenicity. This new media (Beefy-9) maintains cell growth over the entire period tested (seven passages), with an average doubling time of 39 h. Along with demonstrated efficacy for bovine cells, Beefy-9 offers a promising starting-point for developing serum-free media for other meat-relevant species. Ultimately, this work offers a foundation for escaping cultured meat research’s reliance on serum, thereby accelerating the field.
RAISING is a high-performance method for identifying random transgene integration sites
Authors: Wada Yusaku , Sato Tomoo , Hasegawa Hiroo , Matsudaira Takahiro , Nao Naganori , Coler-Reilly Ariella L. G. , Tasaka Tomohiko , Yamauchi Shunsuke , Okagawa Tomohiro , Momose Haruka , Tanio Michikazu , Kuramitsu Madoka , Sasaki Daisuke , Matsumoto Nariyoshi , Yagishita Naoko , Yamauchi Junji , Araya Natsumi , Tanabe Kenichiro , Yamagishi Makoto , Nakashima Makoto , Nakahata Shingo , Iha Hidekatsu , Ogata Masao , Muramatsu Masamichi , Imaizumi Yoshitaka , Uchimaru Kaoru , Miyazaki Yasushi , Konnai Satoru , Yanagihara Katsunori , Morishita Kazuhiro , Watanabe Toshiki , Yamano Yoshihisa , Saito Masumichi
Published: June 2022

Both natural viral infections and therapeutic interventions using viral vectors pose significant risks of malignant transformation. Monitoring for clonal expansion of infected cells is important for detecting cancer. Here we developed a novel method of tracking clonality via the detection of transgene integration sites. RAISING (Rapid Amplification of Integration Sites without Interference by Genomic DNA contamination) is a sensitive, inexpensive alternative to established methods. Its compatibility with Sanger sequencing combined with our CLOVA (Clonality Value) software is critical for those without access to expensive high throughput sequencing. We analyzed samples from 688 individuals infected with the retrovirus HTLV-1, which causes adult T-cell leukemia/lymphoma (ATL) to model our method. We defined a clonality value identifying ATL patients with 100% sensitivity and 94.8% specificity, and our longitudinal analysis also demonstrates the usefulness of ATL risk assessment. Future studies will confirm the broad applicability of our technology, especially in the emerging gene therapy sector.
Male mating strategies to counter sexual conflict in spiders
Authors: Zhang Shichang , Yu Long , Tan Min , Tan Noeleen Y. L. , Wong Xaven X. B. , Kuntner Matjaž , Li Daiqin
Published: June 2022

When sexual conflict selects for reproductive strategies that only benefit one of the sexes, evolutionary arms races may ensue. Female sexual cannibalism is an extreme manifestation of sexual conflict. Here we test two male mating strategies aiming at countering sexual cannibalism in spiders. The “better charged palp” hypothesis predicts male selected use of the paired sexual organ (palp) containing more sperm for their first copulation. The “fast sperm transfer” hypothesis predicts accelerated insemination when cannibalism is high. Our comparative tests on five orbweb spider species with varying levels of female sexual cannibalism and sexual size dimorphism (SSD) reveal that males choose the palp with more sperm for the first copulation with cannibalistic females and that males transfer significantly more sperm if females are cannibalistic or when SSD is biased. By supporting the two hypotheses, these results provide credibility for male mating syndrome. They, however, open new questions, namely, how does a male differentiate sperm quantities between his palps? How does he perform palp choice after assessing his cannibalistic partner? By conducting follow-up experiments onNephilengys malabarensis, we reveal that it is sperm volume detection, rather than left-right palp dominance, that plays prominently in male palp choice.
Protective effects of camellia and olive oils against cognitive impairment via gut microbiota-brain communication in rats
Authors: Chen Sheng-Yi , Weng Ming-Hung , Li Zih-Ying , Wang Guan-Yu , Yen Gow-Chin
Published: June 2022

The camellia oil (PCO) and olive oil consumption effectively improved mild cognitive impairment (MCI) by altering the relationship between the biochemical parameters and gut microbiota; PCO treatment in particularly.
X-ray absorption near-edge spectroscopy of antimony complexed with organic molecules: a theoretical interpretation
Authors: Chen Haoze , Zhong Wen , Jing Chuanyong
Published: June 2022

The shoulder feature for the white line (Sb K-edge) was ascribed to metal–ligand charge transfer transitions from Sb 1s to the unoccupied states of the carbon chains. Longer distance for charge transfer caused lower intensity of the shoulder peak.
A highly sensitive colorimetric sensing platform based on silver nanocomposites for alkaline phosphatase
Authors: Wang Wei-Feng , Nsanzamahoro Stanislas , Zhang Ying , Wang Cheng-Bo , Shi Yan-Ping , Yang Jun-Li
Published: June 2022

Alkaline phosphatase (ALP) plays significant roles in regulating intracellular processes and is an important biomarker connected to several diseases.
An air-stable, well-defined palladium–BIAN–NHC chloro dimer: a fast-activating, highly efficient catalyst for cross-coupling
Authors: Zhang Jin , Li Tao , Li Xue , Zhang Gaopeng , Fang Shuai , Yan Wenxuan , Li Xiangyang , Yang Xiufang , Ma Yangmin , Szostak Michal
Published: June 2022

We report palladium–BIAN–NHC chloro dimer complex, [Pd(BIAN–IPr)(μ-Cl)Cl]2. This rapidly activating catalyst merges the reactive properties of palladium chloro dimers, [Pd(NHC)(μ-Cl)Cl]2, with the attractive structural features of the BIAN framework.
Clarifying notes on the bonding analysis adopted by the energy decomposition analysis
Authors: Bickelhaupt F. Matthias , Fonseca Guerra Célia , Mitoraj Mariusz , Sagan F. , Michalak Artur , Pan Sudip , Frenking Gernot
Published: June 2022

We correct misunderstandings and misleading statements in recent criticisms of the energy decomposition analysis (EDA) and show its versatility in understanding chemical bonds in a physically sound manner.