bluuebunny/crossref_metadata_2025 huggingface dataset:
Biological impact of ultraviolet-B radiation on spider mites and its application in integrated pest management
Authors: Osakabe Masahiro
Published: January 2021

Many plant-dwelling mites reside on lower leaf surfaces. The biological impact of solar ultraviolet-B (UV-B) radiation on spider mites has been demonstrated over the last decade. Due to the serious problem of acaricide resistance in spider mites, the development of alternative control methods and establishment of an integrated pest management (IPM) strategy are urgently needed, especially for greenhouse horticultural crops such as strawberries. A physical control method for spider mites using UV-B lamps (UV-B method) has been established. Using the UV-B method, simultaneous control of spider mites and powdery mildew, a major disease, is possible, making it is a favorable IPM strategy. Here, I introduce general findings regarding the biological impact of UV radiation on spider mites and phytoseiid mites, useful natural enemies for biological control, over the last decade, including dose response, effective wavelengths, and photoreactivation. Moreover, I introduce the application of UV-B to spider mite control in strawberry greenhouses, including the possibility of concurrent use with biological control via phytoseiid mites, and discuss its possible contributions to IPM.
Robotic Bronchoscopy for the Diagnosis of Peripheral Lung Nodules: a Review
Authors: Puchalski Jonathan
Published: January 2021

Purpose of Review

Conventional bronchoscopy has limitations based on an inability to accurately reach and reliably diagnose peripheral lesions with many studies having a yield of less than 50%. Although newer technology such as virtual bronchoscopy, use of smaller bronchoscopes, peripheral endobronchial ultrasound, and electromagnetic navigation may have some improvements and a better safety profile, oftentimes transthoracic or surgical biopsies are required to establish a diagnosis and rule out malignancy. The purpose of this review is to highlight the potential benefits of robotic bronchoscopy, the latest in technological advances for this very common medical issue.

Recent Findings

Recently published early studies suggest the yield of robotic bronchoscopy may surpass 90%. Studies performed in cadavers and humans suggest robotic bronchoscopic platforms are better than currently existing bronchoscopic modalities for lung nodule diagnosis and have a favorable safety profile.

Although additional multi-center randomized clinical trials are needed, robotic bronchoscopy appears poised to supplement current bronchoscopic techniques for establishing a diagnosis of pulmonary nodules.
Should COVID-19 Mother Breastfeed her Newborn Child? A Literature Review on the Safety of Breastfeeding for Pregnant Women with COVID-19
Authors: Bhatt Harshil
Published: January 2021

Purpose of Review

Breastfeeding is beneficial to both the newborn and the mother. During the COVID-19 pandemic, concerns have been raised on whether the SARS-CoV-2 virus could be transmitted from COVID-19 positive mother to the newborn through breastmilk. The purpose of this review is to examine the available evidence on the risks of transmission of infection from COVID-19 mothers to their newborns through breastfeeding.

Recent Findings

Data is very limited in this regard, with only a few smaller case series, and case reports have been published so far. In most of the studies, breastmilk samples from COVID-19 mothers tested negative for the virus. In the case reports where the virus was detected in breastmilk and the infants were diagnosed with COVID-19, it remained unclear whether the disease was transmitted through breastmilk or direct contact or through delivery. Another hypothesis is that the viral antibodies could pass to the newborn passively through breastmilk of COVID-19 positive mothers and give immunity to the child, but data is minimal.

Based on the currently available limited evidence and recognizing the benefits of breastfeeding, it may be concluded that if the health of the mother and her newborn allows, direct breastfeeding or extracted breastmilk should be encouraged by the healthcare providers after a careful discussion of the risks of vertical transmission to the mother and her family. Preventive measures should be taken by COVID-19 mothers to prevent droplet transmission of infection to the infants while breastfeeding.
Genetic programming with separability detection for symbolic regression
Authors: Liu Wei-Li , Yang Jiaquan , Zhong Jinghui , Wang Shibin
Published: January 2021

Genetic Programming (GP) is a popular and powerful evolutionary optimization algorithm that has a wide range of applications such as symbolic regression, classification and program synthesis. However, existing GPs often ignore the intrinsic structure of the ground truth equation of the symbolic regression problem. To improve the search efficacy of GP on symbolic regression problems by fully exploiting the intrinsic structure information, this paper proposes a genetic programming with separability detection technique (SD-GP). In the proposed SD-GP, a separability detection method is proposed to detect additive separable characteristics of input features from the observed data. Then based on the separability detection results, a chromosome representation is proposed, which utilizes multiple sub chromosomes to represent the final solution. Some sub chromosomes are used to construct separable sub functions by using separate input features, while the other sub chromosomes are used to construct sub functions by using all input features. The final solution is the weighted sum of all sub functions, and the optimal weights of sub functions are obtained by using the least squares method. In this way, the structure information can be learnt and the global search ability of GP can be maintained. Experimental results on synthetic problems with differing characteristics have demonstrated that the proposed SD-GP can perform better than several state-of-the-art GPs in terms of the success rate of finding the optimal solution and the convergence speed.
Breaking and mining-induced stress evolution of overlying strata in the working face of a steeply dipping coal seam
Authors: Chi Xiaolou , Yang Ke , Wei Zhen
Published: January 2021

The breaking features and stress distribution of overlying strata in a steeply dipping coal seam (SDCS) differ significantly from those in a near-horizontal one. In this study, the laws governing the evolution of vertical stress release and shear stress concentration in the overlying strata of coal seams with different dip angles are derived via numerical simulation, rock mechanics tests, acoustic emissions, and field measurements. Thus, the stress-driven dynamic evolution of the overlying strata structure, in which a shear stress arch forms, is determined. Upon breaking the lower part of the overlying strata, the shear stress transfers rapidly to the upper part of the working face. The damaged zone of the overlying strata migrates upward along the dip direction of the working face. The gangue in the lower part of the working face is compacted, leading to an increase in vertical stress. As the dip angle of the coal seam increases, the overlying strata fail suddenly under the action of shear stresses. Finally, the behavioral response of the overlying strata driven by shear stresses in the longwall working face of an SDCS is identified and analyzed in detail. The present research findings reveal the laws governing the behavior of mine pressure in the working face of an SDCS, which in turn can be used to establish the respective on-site guidance.
Ta-Doped Sb2Te Allows Ultrafast Phase-Change Memory with Excellent High-Temperature Operation Characteristics
Authors: Xue Yuan , Yan Shuai , Lv Shilong , Song Sannian , Song Zhitang
Published: January 2021

Phase-change memory (PCM) has considerable promise for new applications based on von Neumann and emerging neuromorphic computing systems. However, a key challenge in harnessing the advantages of PCM devices is achieving high-speed operation of these devices at elevated temperatures, which is critical for the efficient processing and reliable storage of data at full capacity. Herein, we report a novel PCM device based on Ta-doped antimony telluride (Sb2Te), which exhibits both high-speed characteristics and excellent high-temperature characteristics, with an operation speed of 2 ns, endurance of > 106 cycles, and reversible switching at 140 °C. The high coordination number of Ta and the strong bonds between Ta and Sb/Te atoms contribute to the robustness of the amorphous structure, which improves the thermal stability. Furthermore, the small grains in the three-dimensional limit lead to an increased energy efficiency and a reduced risk of layer segregation, reducing the power consumption and improving the long-term endurance. Our findings for this new Ta–Sb2Te material system can facilitate the development of PCMs with improved performance and novel applications.
Bacteria-Mediated Synergistic Cancer Therapy: Small Microbiome Has a Big Hope
Authors: Lou Xinyu , Chen Zhichao , He Zhonggui , Sun Mengchi , Sun Jin
Published: January 2021

The use of bacteria to specifically migrate to cancerous tissue and elicit an antitumor immune response provides a promising platform against cancer with significantly high potency. With dozens of clinical trials underway, some researchers hold the following views: “humans are nearing the first commercial live bacteria therapeutic.” However, the facultative anaerobe Salmonella typhimurium VNP20009, which is particularly safe and shows anticancer effects in preclinical studies, had failed in a phase I clinical trial due to low tumor regression and undesired dose-dependent side effects. This is almost certain to disappoint people’s inflated expectations, but it is noted that recent state-of-the-art research has turned attention to bacteria-mediated synergistic cancer therapy (BMSCT). In this review, the foundation of bacteria-mediated bio-therapy is outlined. Then, we summarize the potential benefits and challenges of bacterial bio-therapy in combination with different traditional anticancer therapeutic modalities (chemotherapy, photothermal therapy, reactive oxygen and nitrogen species therapy, immunotherapy, or prodrug-activating therapy) in the past 5 years. Next, we discuss multiple administration routes of BMSCT, highlighting potentiated antitumor responses and avoidance of potential side effects. Finally, we envision the opportunities and challenges for BMSCT development, with the purpose of inspiring medicinal scientists to widely utilize the microbiome approach in patient populations.
A Bulk-Heterostructure Nanocomposite Electrolyte of Ce0.8Sm0.2O2-δ–SrTiO3 for Low-Temperature Solid Oxide Fuel Cells
Authors: Cai Yixiao , Chen Yang , Akbar Muhammad , Jin Bin , Tu Zhengwen , Mushtaq Naveed , Wang Baoyuan , Qu Xiangyang , Xia Chen , Huang Yizhong
Published: January 2021

Since colossal ionic conductivity was detected in the planar heterostructures consisting of fluorite and perovskite, heterostructures have drawn great research interest as potential electrolytes for solid oxide fuel cells (SOFCs). However, so far, the practical uses of such promising material have failed to materialize in SOFCs due to the short circuit risk caused by SrTiO3. In this study, a series of fluorite/perovskite heterostructures made of Sm-doped CeO2 and SrTiO3 (SDC–STO) are developed in a new bulk-heterostructure form and evaluated as electrolytes. The prepared cells exhibit a peak power density of 892 mW cm−2 along with open circuit voltage of 1.1 V at 550 °C for the optimal composition of 4SDC–6STO. Further electrical studies reveal a high ionic conductivity of 0.05–0.14 S cm−1 at 450–550 °C, which shows remarkable enhancement compared to that of simplex SDC. Via AC impedance analysis, it has been shown that the small grain-boundary and electrode polarization resistances play the major roles in resulting in the superior performance. Furthermore, a Schottky junction effect is proposed by considering the work functions and electronic affinities to interpret the avoidance of short circuit in the SDC–STO cell. Our findings thus indicate a new insight to design electrolytes for low-temperature SOFCs.
Developing the FILL+ Tool to Reliably Classify Classroom Practices Using Lecture Recordings
Authors: Kinnear George , Smith Steph , Anderson Ross , Gant Thomas , MacKay Jill R D , Docherty Pamela , Rhind Susan , Galloway Ross
Published: January 2021

Lectures are a commonly used teaching method in higher education, but there is significant debate about the relative merits of different classroom practices. Various classroom observation tools have been developed to try to give insight into these practices, beyond the simple dichotomy of “traditional lecturing versus active learning”. Here we review of a selection of classroom observation protocols from an ethological perspective and describe how this informed the development of a new protocol, FILL+. We demonstrate that FILL+ can be applied reliably by undergraduate students after minimal training. We analysed a sample of 208 lecture recordings from Mathematics, Physics, and Veterinary Medicine and found a wide variety of classroom practices, e.g. on average lecturers spent 2.1% (± 2.6%) of the time asking questions, and 79.3% (± 19%) of the lecture talking, but individuals varied considerably. The FILL+ protocol has the potential to be widely used, both in research on effective teaching practices, and in informing discussion of pedagogical approaches within institutions and disciplines.
An in vitro model for investigation of vitamin A effects on wound	healing
Authors: Neghab Hoda Keshmiri , Soheilifar Mohammad Hasan , Djavid Gholamreza Esmaeeli
Published: January 2021

Abstract. Wound healing consists of a series of highly orderly overlapping processes characterized by hemostasis, inflammation, proliferation, and remodeling. Prolongation or interruption in each phase can lead to delayed wound healing or a non-healing chronic wound. Vitamin A is a crucial nutrient that is most beneficial for the health of the skin. The present study was undertaken to determine the effect of vitamin A on regeneration, angiogenesis, and inflammation characteristics in an in vitro model system during wound healing. For this purpose, mouse skin normal fibroblast (L929), human umbilical vein endothelial cell (HUVEC), and monocyte/macrophage-like cell line (RAW 264.7) were considered to evaluate proliferation, angiogenesis, and anti-inﬂammatory responses, respectively. Vitamin A (0.1–5 μM) increased cellular proliferation of L929 and HUVEC (p < 0.05). Similarly, it stimulated angiogenesis by promoting endothelial cell migration up to approximately 4 fold and interestingly tube formation up to 8.5 fold (p < 0.01). Furthermore, vitamin A treatment was shown to decrease the level of nitric oxide production in a dose-dependent effect (p < 0.05), exhibiting the anti-inflammatory property of vitamin A in accelerating wound healing. These results may reveal the therapeutic potential of vitamin A in diabetic wound healing by stimulating regeneration, angiogenesis, and anti-inﬂammation responses.
Spatial Variability of the Snowmelt‐Albedo Feedback in Antarctica
Authors: Jakobs C. L. , Reijmer C. H. , van den Broeke M. R. , van de Berg W. J. , van Wessem J. M.
Published: January 2021

Surface melt is an important process for the stability of ice shelves, and therewith the Antarctic ice sheet. In Antarctica, absorption of solar radiation is mostly the largest energy source for surface melt, which is further enhanced by the snowmelt‐albedo feedback (SMAF): Refrozen snow has a lower albedo than new snow, which causes it to absorb more solar radiation, further increasing the energy available for surface melt. This feedback has previously been shown to increase surface melt by approximately a factor of 2.5 at Neumayer Station in East Antarctica. In this study, we use a regional climate model to quantify SMAF for the entire Antarctic ice sheet. We find that it is most effective on ice shelves in East Antarctica, and is less important in the Antarctic Peninsula and on the Ross and Filchner‐Ronne ice shelves. We identify a relationship between SMAF and average summer 2 m air temperatures, and find that SMAF is most important around 265 ± 2 K. On a subseasonal scale, we identify several parameters that contribute to SMAF: the length of dry periods, the time between significant snowfall events and snowmelt events, and prevailing temperatures. We then apply the same temperature dependency of SMAF to the Greenland ice sheet and find that it is potentially active in a narrow band around the ice sheet, and finally discuss how the importance of SMAF could change in a warming climate.
Structural basis for voltage-sensor trapping of the cardiac sodium channel by a deathstalker scorpion toxin
Authors: Jiang Daohua , Tonggu Lige , Gamal El-Din Tamer M. , Banh Richard , Pomès Régis , Zheng Ning , Catterall William A.
Published: January 2021

Voltage-gated sodium (NaV) channels initiate action potentials in excitable cells, and their function is altered by potent gating-modifier toxins. The α-toxin LqhIII from the deathstalker scorpion inhibits fast inactivation of cardiac NaV1.5 channels with IC50 = 11.4 nM. Here we reveal the structure of LqhIII bound to NaV1.5 at 3.3 Å resolution by cryo-EM. LqhIII anchors on top of voltage-sensing domain IV, wedged between the S1-S2 and S3-S4 linkers, which traps the gating charges of the S4 segment in a unique intermediate-activated state stabilized by four ion-pairs. This conformational change is propagated inward to weaken binding of the fast inactivation gate and favor opening the activation gate. However, these changes do not permit Na+ permeation, revealing why LqhIII slows inactivation of NaV channels but does not open them. Our results provide important insights into the structural basis for gating-modifier toxin binding, voltage-sensor trapping, and fast inactivation of NaV channels.
Nanoscale decoupling of electronic nematicity and structural anisotropy in FeSe thin films
Authors: Ren Zheng , Li Hong , Zhao He , Sharma Shrinkhala , Wang Ziqiang , Zeljkovic Ilija
Published: January 2021

In a material prone to a nematic instability, anisotropic strain in principle provides a preferred symmetry-breaking direction for the electronic nematic state to follow. This is consistent with experimental observations, where electronic nematicity and structural anisotropy typically appear hand-in-hand. In this work, we discover that electronic nematicity can be locally decoupled from the underlying structural anisotropy in strain-engineered iron-selenide (FeSe) thin films. We use heteroepitaxial molecular beam epitaxy to grow FeSe with a nanoscale network of modulations that give rise to spatially varying strain. We map local anisotropic strain by analyzing scanning tunneling microscopy topographs, and visualize electronic nematic domains from concomitant spectroscopic maps. While the domains form so that the energy of nemato-elastic coupling is minimized, we observe distinct regions where electronic nematic ordering fails to flip direction, even though the underlying structural anisotropy is locally reversed. The findings point towards a nanometer-scale stiffness of the nematic order parameter.
Group 2i Isochrysidales produce characteristic alkenones reflecting sea ice distribution
Authors: Wang Karen Jiaxi , Huang Yongsong , Majaneva Markus , Belt Simon T. , Liao Sian , Novak Joseph , Kartzinel Tyler R. , Herbert Timothy D. , Richter Nora , Cabedo-Sanz Patricia
Published: January 2021

Alkenones are biomarkers produced solely by algae in the order Isochrysidales that have been used to reconstruct sea surface temperature (SST) since the 1980s. However, alkenone-based SST reconstructions in the northern high latitude oceans show significant bias towards warmer temperatures in core-tops, diverge from other SST proxies in down core records, and are often accompanied by anomalously high relative abundance of the C37 tetra-unsaturated methyl alkenone (%C37:4). Elevated %C37:4 is widely interpreted as an indicator of low sea surface salinity from polar water masses, but its biological source has thus far remained elusive. Here we identify a lineage of Isochrysidales that is responsible for elevated C37:4 methyl alkenone in the northern high latitude oceans through next-generation sequencing and lab-culture experiments. This Isochrysidales lineage co-occurs widely with sea ice in marine environments and is distinct from other known marine alkenone-producers, namely Emiliania huxleyi and Gephyrocapsa oceanica. More importantly, the %C37:4 in seawater filtered particulate organic matter and surface sediments is significantly correlated with annual mean sea ice concentrations. In sediment cores from the Svalbard region, the %C37:4 concentration aligns with the Greenland temperature record and other qualitative regional sea ice records spanning the past 14 kyrs, reflecting sea ice concentrations quantitatively. Our findings imply that %C37:4 is a powerful proxy for reconstructing sea ice conditions in the high latitude oceans on thousand- and, potentially, on million-year timescales.
Efficient assembly of nanopore reads via highly accurate and intact error correction
Authors: Chen Ying , Nie Fan , Xie Shang-Qian , Zheng Ying-Feng , Dai Qi , Bray Thomas , Wang Yao-Xin , Xing Jian-Feng , Huang Zhi-Jian , Wang De-Peng , He Li-Juan , Luo Feng , Wang Jian-Xin , Liu Yi-Zhi , Xiao Chuan-Le
Published: January 2021

Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection.
Hydroxamic acid-modified peptide microarrays for profiling isozyme-selective interactions and inhibition of histone deacetylases
Authors: Moreno-Yruela Carlos , Bæk Michael , Vrsanova Adela-Eugenie , Schulte Clemens , Maric Hans M. , Olsen Christian A.
Published: January 2021

Histones control gene expression by regulating chromatin structure and function. The posttranslational modifications (PTMs) on the side chains of histones form the epigenetic landscape, which is tightly controlled by epigenetic modulator enzymes and further recognized by so-called reader domains. Histone microarrays have been widely applied to investigate histone–reader interactions, but not the transient interactions of Zn2+-dependent histone deacetylase (HDAC) eraser enzymes. Here, we synthesize hydroxamic acid-modified histone peptides and use them in femtomolar microarrays for the direct capture and detection of the four class I HDAC isozymes. Follow-up functional assays in solution provide insights into their suitability to discover HDAC substrates and inhibitors with nanomolar potency and activity in cellular assays. We conclude that similar hydroxamic acid-modified histone peptide microarrays and libraries could find broad application to identify class I HDAC isozyme-specific substrates and facilitate the development of isozyme-selective HDAC inhibitors and probes.
Autophagy sustains glutamate and aspartate synthesis in Saccharomyces cerevisiae during nitrogen starvation
Authors: Liu Kuanqing , Sutter Benjamin M. , Tu Benjamin P.
Published: January 2021

Autophagy catabolizes cellular constituents to promote survival during nutrient deprivation. Yet, a metabolic comprehension of this recycling operation, despite its crucial importance, remains incomplete. Here, we uncover a specific metabolic function of autophagy that exquisitely adjusts cellular metabolism according to nitrogen availability in the budding yeast Saccharomyces cerevisiae. Autophagy enables metabolic plasticity to promote glutamate and aspartate synthesis, which empowers nitrogen-starved cells to replenish their nitrogen currency and sustain macromolecule synthesis. Our findings provide critical insights into the metabolic basis by which autophagy recycles cellular components and may also have important implications in understanding the role of autophagy in diseases such as cancer.
The origin of the Moon’s Earth-like tungsten isotopic composition from dynamical and geochemical modeling
Authors: Fischer Rebecca A. , Zube Nicholas G. , Nimmo Francis
Published: January 2021

The Earth and Moon have identical or very similar isotopic compositions for many elements, including tungsten. However, canonical models of the Moon-forming impact predict that the Moon should be made mostly of material from the impactor, Theia. Here we evaluate the probability of the Moon inheriting its Earth-like tungsten isotopes from Theia in the canonical giant impact scenario, using 242 N-body models of planetary accretion and tracking tungsten isotopic evolution, and find that this probability is <1.6–4.7%. Mixing in up to 30% terrestrial materials increases this probability, but it remains <10%. Achieving similarity in stable isotopes is also a low-probability outcome, and is controlled by different mechanisms than tungsten. The Moon’s stable isotopes and tungsten isotopic composition are anticorrelated due to redox effects, lowering the joint probability to significantly less than 0.08–0.4%. We therefore conclude that alternate explanations for the Moon’s isotopic composition are likely more plausible.
Terahertz pulse shaping using diffractive surfaces
Authors: Veli Muhammed , Mengu Deniz , Yardimci Nezih T. , Luo Yi , Li Jingxi , Rivenson Yair , Jarrahi Mona , Ozcan Aydogan
Published: January 2021

Recent advances in deep learning have been providing non-intuitive solutions to various inverse problems in optics. At the intersection of machine learning and optics, diffractive networks merge wave-optics with deep learning to design task-specific elements to all-optically perform various tasks such as object classification and machine vision. Here, we present a diffractive network, which is used to shape an arbitrary broadband pulse into a desired optical waveform, forming a compact and passive pulse engineering system. We demonstrate the synthesis of various different pulses by designing diffractive layers that collectively engineer the temporal waveform of an input terahertz pulse. Our results demonstrate direct pulse shaping in terahertz spectrum, where the amplitude and phase of the input wavelengths are independently controlled through a passive diffractive device, without the need for an external pump. Furthermore, a physical transfer learning approach is presented to illustrate pulse-width tunability by replacing part of an existing network with newly trained diffractive layers, demonstrating its modularity. This learning-based diffractive pulse engineering framework can find broad applications in e.g., communications, ultra-fast imaging and spectroscopy.
ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function
Authors: Zhou Qiling , Yu Miao , Tirado-Magallanes Roberto , Li Bin , Kong Lingshi , Guo Mingrui , Tan Zi Hui , Lee Sanghoon , Chai Li , Numata Akihiko , Benoukraf Touati , Fullwood Melissa Jane , Osato Motomi , Ren Bing , Tenen Daniel G.
Published: January 2021

CCCTC binding factor (CTCF) is an important factor in the maintenance of chromatin–chromatin interactions, yet the mechanism regulating its binding to chromatin is unknown. We demonstrate that zinc finger protein 143 (ZNF143) is a key regulator for CTCF-bound promoter–enhancer loops. In the murine genome, a large percentage of CTCF and ZNF143 DNA binding motifs are distributed 37 bp apart in the convergent orientation. Furthermore, deletion of ZNF143 leads to loss of CTCF binding on promoter and enhancer regions associated with gene expression changes. CTCF-bound promoter–enhancer loops are also disrupted after excision of ZNF143. ZNF143-CTCF-bound promoter–enhancer loops regulate gene expression patterns essential for maintenance of murine hematopoietic stem and progenitor cell integrity. Our data suggest a common feature of gene regulation is that ZNF143 is a critical factor for CTCF-bound promoter–enhancer loops.
FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation
Authors: Ramírez-Aportela Erney , Maluenda David , Fonseca Yunior C. , Conesa Pablo , Marabini Roberto , Heymann J. Bernard , Carazo Jose Maria , Sorzano Carlos Oscar S.
Published: January 2021

In recent years, advances in cryoEM have dramatically increased the resolution of reconstructions and, with it, the number of solved atomic models. It is widely accepted that the quality of cryoEM maps varies locally; therefore, the evaluation of the maps-derived structural models must be done locally as well. In this article, a method for the local analysis of the map-to-model fit is presented. The algorithm uses a comparison of two local resolution maps. The first is the local FSC (Fourier shell correlation) between the full map and the model, while the second is calculated between the half maps normally used in typical single particle analysis workflows. We call the quality measure “FSC-Q”, and it is a quantitative estimation of how much of the model is supported by the signal content of the map. Furthermore, we show that FSC-Q may be helpful to detect overfitting. It can be used to complement other methods, such as the Q-score method that estimates the resolvability of atoms.
Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet-induced diabetes
Authors: Rodrigues Richard R. , Gurung Manoj , Li Zhipeng , García-Jaramillo Manuel , Greer Renee , Gaulke Christopher , Bauchinger Franziska , You Hyekyoung , Pederson Jacob W. , Vasquez-Perez Stephany , White Kimberly D. , Frink Briana , Philmus Benjamin , Jump Donald B. , Trinchieri Giorgio , Berry David , Sharpton Thomas J. , Dzutsev Amiran , Morgun Andrey , Shulzhenko Natalia
Published: January 2021

Western diet (WD) is one of the major culprits of metabolic disease including type 2 diabetes (T2D) with gut microbiota playing an important role in modulating effects of the diet. Herein, we use a data-driven approach (Transkingdom Network analysis) to model host-microbiome interactions under WD to infer which members of microbiota contribute to the altered host metabolism. Interrogation of this network pointed to taxa with potential beneficial or harmful effects on host’s metabolism. We then validate the functional role of the predicted bacteria in regulating metabolism and show that they act via different host pathways. Our gene expression and electron microscopy studies show that two species from Lactobacillus genus act upon mitochondria in the liver leading to the improvement of lipid metabolism. Metabolomics analyses revealed that reduced glutathione may mediate these effects. Our study identifies potential probiotic strains for T2D and provides important insights into mechanisms of their action.
Hepatitis B virus rigs the cellular metabolome to avoid innate immune recognition
Authors: Zhou Li , He Rui , Fang Peining , Li Mengqi , Yu Haisheng , Wang Qiming , Yu Yi , Wang Fubing , Zhang Yi , Chen Aidong , Peng Nanfang , Lin Yong , Zhang Rui , Trilling Mirko , Broering Ruth , Lu Mengji , Zhu Ying , Liu Shi
Published: January 2021

Glucose metabolism and innate immunity evolved side-by-side. It is unclear if and how the two systems interact with each other during hepatitis B virus (HBV) infections and, if so, which mechanisms are involved. Here, we report that HBV activates glycolysis to impede retinoic acid-inducible gene I (RIG-I)-induced interferon production. We demonstrate that HBV sequesters MAVS from RIG-I by forming a ternary complex including hexokinase (HK). Using a series of pharmacological and genetic approaches, we provide in vitro and in vivo evidence indicating that HBV suppresses RLR signaling via lactate dehydrogenase-A-dependent lactate production. Lactate directly binds MAVS preventing its aggregation and mitochondrial localization during HBV infection. Therefore, we show that HK2 and glycolysis-derived lactate have important functions in the immune escape of HBV and that energy metabolism regulates innate immunity during HBV infection.
LTD is involved in the formation and maintenance of rat hippocampal CA1 place-cell fields
Authors: Ashby Donovan M. , Floresco Stan B. , Phillips Anthony G. , McGirr Alexander , Seamans Jeremy K. , Wang Yu Tian
Published: January 2021

Hippocampal synaptic plasticity includes both long-term potentiation (LTP) and long-term depression (LTD) of synaptic strength, and has been implicated in shaping place field representations that form upon initial exposure to a novel environment. However, direct evidence causally linking either LTP or LTD to place fields remains limited. Here, we show that hippocampal LTD regulates the acute formation and maintenance of place fields using electrophysiology and blocking specifically LTD in freely-moving rats. We also show that exploration of a novel environment produces a widespread and pathway specific de novo synaptic depression in the dorsal hippocampus. Furthermore, disruption of this pathway-specific synaptic depression alters both the dynamics of place field formation and the stability of the newly formed place fields, affecting spatial memory in rats. These results suggest that activity-dependent synaptic depression is required for the acquisition and maintenance of novel spatial information.
Machine learned features from density of states for accurate adsorption energy prediction
Authors: Fung Victor , Hu Guoxiang , Ganesh P. , Sumpter Bobby G.
Published: January 2021

Materials databases generated by high-throughput computational screening, typically using density functional theory (DFT), have become valuable resources for discovering new heterogeneous catalysts, though the computational cost associated with generating them presents a crucial roadblock. Hence there is a significant demand for developing descriptors or features, in lieu of DFT, to accurately predict catalytic properties, such as adsorption energies. Here, we demonstrate an approach to predict energies using a convolutional neural network-based machine learning model to automatically obtain key features from the electronic density of states (DOS). The model, DOSnet, is evaluated for a diverse set of adsorbates and surfaces, yielding a mean absolute error on the order of 0.1 eV. In addition, DOSnet can provide physically meaningful predictions and insights by predicting responses to external perturbations to the electronic structure without additional DFT calculations, paving the way for the accelerated discovery of materials and catalysts by exploration of the electronic space.
Single-cell transcriptome profiling of the vaginal wall in women with severe anterior vaginal prolapse
Authors: Li Yaqian , Zhang Qing-Yang , Sun Bao-Fa , Ma Yidi , Zhang Ye , Wang Min , Ma Congcong , Shi Honghui , Sun Zhijing , Chen Juan , Yang Yun-Gui , Zhu Lan
Published: January 2021

Anterior vaginal prolapse (AVP) is the most common form of pelvic organ prolapse (POP) and has deleterious effects on women’s health. Despite recent advances in AVP diagnosis and treatment, a cell atlas of the vaginal wall in AVP has not been constructed. Here, we employ single-cell RNA-seq to construct a transcriptomic atlas of 81,026 individual cells in the vaginal wall from AVP and control samples and identify 11 cell types. We reveal aberrant gene expression in diverse cell types in AVP. Extracellular matrix (ECM) dysregulation and immune reactions involvement are identified in both non-immune and immune cell types. In addition, we find that several transcription factors associated with ECM and immune regulation are activated in AVP. Furthermore, we reveal dysregulated cell–cell communication patterns in AVP. Taken together, this work provides a valuable resource for deciphering the cellular heterogeneity and the molecular mechanisms underlying severe AVP.
Spatiotemporal profiling of cytosolic signaling complexes in living cells by selective proximity proteomics
Authors: Ke Mi , Yuan Xiao , He An , Yu Peiyuan , Chen Wendong , Shi Yu , Hunter Tony , Zou Peng , Tian Ruijun
Published: January 2021

Signaling complexes are often organized in a spatiotemporal manner and on a minute timescale. Proximity labeling based on engineered ascorbate peroxidase APEX2 pioneered in situ capture of spatiotemporal membrane protein complexes in living cells, but its application to cytosolic proteins remains limited due to the high labeling background. Here, we develop proximity labeling probes with increased labeling selectivity. These probes, in combination with label-free quantitative proteomics, allow exploring cytosolic protein assemblies such as phosphotyrosine-mediated protein complexes formed in response to minute-scale EGF stimulation. As proof-of-concept, we systematically profile the spatiotemporal interactome of the EGFR signaling component STS1. For STS1 core complexes, our proximity proteomics approach shows comparable performance to affinity purification-mass spectrometry-based temporal interactome profiling, while also capturing additional—especially endosomally-located—protein complexes. In summary, we provide a generic approach for exploring the interactome of mobile cytosolic proteins in living cells at a temporal resolution of minutes.
How the anisotropy of surface oxide formation influences the transient activity of a surface reaction
Authors: Winkler P. , Zeininger J. , Suchorski Y. , Stöger-Pollach M. , Zeller P. , Amati M. , Gregoratti L. , Rupprechter G.
Published: January 2021

Scanning photoelectron microscopy (SPEM) and photoemission electron microscopy (PEEM) allow local surface analysis and visualising ongoing reactions on a µm-scale. These two spatio-temporal imaging methods are applied to polycrystalline Rh, representing a library of well-defined high-Miller-index surface structures. The combination of these techniques enables revealing the anisotropy of surface oxidation, as well as its effect on catalytic hydrogen oxidation. In the present work we observe, using locally-resolved SPEM, structure-sensitive surface oxide formation, which is summarised in an oxidation map and quantitatively explained by the novel step density (SDP) and step edge (SEP) parameters. In situ PEEM imaging of ongoing H2 oxidation allows a direct comparison of the local reactivity of metallic and oxidised Rh surfaces for the very same different stepped surface structures, demonstrating the effect of Rh surface oxides. Employing the velocity of propagating reaction fronts as indicator of surface reactivity, we observe a high transient activity of Rh surface oxide in H2 oxidation. The corresponding velocity map reveals the structure-dependence of such activity, representing a direct imaging of a structure-activity relation for plenty of well-defined surface structures within one sample.
Dose-dependent response to infection with SARS-CoV-2 in the ferret model and evidence of protective immunity
Authors: Ryan Kathryn A. , Bewley Kevin R. , Fotheringham Susan A. , Slack Gillian S. , Brown Phillip , Hall Yper , Wand Nadina I. , Marriott Anthony C. , Cavell Breeze E. , Tree Julia A. , Allen Lauren , Aram Marilyn J. , Bean Thomas J. , Brunt Emily , Buttigieg Karen R. , Carter Daniel P. , Cobb Rebecca , Coombes Naomi S. , Findlay-Wilson Steve J. , Godwin Kerry J. , Gooch Karen E. , Gouriet Jade , Halkerston Rachel , Harris Debbie J. , Hender Thomas H. , Humphries Holly E. , Hunter Laura , Ho Catherine M. K. , Kennard Chelsea L. , Leung Stephanie , Longet Stephanie , Ngabo Didier , Osman Karen L. , Paterson Jemma , Penn Elizabeth J. , Pullan Steven T. , Rayner Emma , Skinner Oliver , Steeds Kimberley , Taylor Irene , Tipton Tom , Thomas Stephen , Turner Carrie , Watson Robert J. , Wiblin Nathan R. , Charlton Sue , Hallis Bassam , Hiscox Julian A. , Funnell Simon , Dennis Mike J. , Whittaker Catherine J. , Catton Michael G. , Druce Julian , Salguero Francisco J. , Carroll Miles W.
Published: January 2021

There is a vital need for authentic COVID-19 animal models to enable the pre-clinical evaluation of candidate vaccines and therapeutics. Here we report a dose titration study of SARS-CoV-2 in the ferret model. After a high (5 × 106 pfu) and medium (5 × 104 pfu) dose of virus is delivered, intranasally, viral RNA shedding in the upper respiratory tract (URT) is observed in 6/6 animals, however, only 1/6 ferrets show similar signs after low dose (5 × 102 pfu) challenge. Following sequential culls pathological signs of mild multifocal bronchopneumonia in approximately 5–15% of the lung is seen on day 3, in high and medium dosed groups. Ferrets re-challenged, after virus shedding ceased, are fully protected from acute lung pathology. The endpoints of URT viral RNA replication & distinct lung pathology are observed most consistently in the high dose group. This ferret model of SARS-CoV-2 infection presents a mild clinical disease.
Publisher Correction: Autophagy facilitates adaptation of budding yeast to respiratory growth by recycling serine for one-carbon metabolism
Authors: May Alexander I. , Prescott Mark , Ohsumi Yoshinori
Published: January 2021

A Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20648-5
Microscopic mechanism of unusual lattice thermal transport in TlInTe2
Authors: Pal Koushik , Xia Yi , Wolverton Chris
Published: January 2021

We investigate the microscopic mechanism of ultralow lattice thermal conductivity (κl) of TlInTe2 and its weak temperature dependence using a unified theory of lattice heat transport, that considers contributions arising from the particle-like propagation as well as wave-like tunneling of phonons. While we use the Peierls–Boltzmann transport equation (PBTE) to calculate the particle-like contributions (κl(PBTE)), we explicitly calculate the off-diagonal (OD) components of the heat-flux operator within a first-principles density functional theory framework to determine the contributions (κl(OD)) arising from the wave-like tunneling of phonons. At each temperature, T, we anharmonically renormalize the phonon frequencies using the self-consistent phonon theory including quartic anharmonicity, and utilize them to calculate κl(PBTE) and κl(OD). With the combined inclusion of κl(PBTE), κl(OD), and additional grain-boundary scatterings, our calculations successfully reproduce the experimental results. Our analysis shows that large quartic anharmonicity of TlInTe2 (a) strongly hardens the low-energy phonon branches, (b) diminishes the three-phonon scattering processes at finite T, and (c) recovers the weaker than T−1 decay of the measured κl.
Emergence and control of complex behaviors in driven systems of interacting qubits with dissipation
Authors: Andreev A. V. , Balanov A. G. , Fromhold T. M. , Greenaway M. T. , Hramov A. E. , Li W. , Makarov V. V. , Zagoskin A. M.
Published: January 2021

Progress in the creation of large-scale, artificial quantum coherent structures demands the investigation of their nonequilibrium dynamics when strong interactions, even between remote parts, are non-perturbative. Analysis of multiparticle quantum correlations in a large system in the presence of decoherence and external driving is especially topical. Still, the scaling behavior of dynamics and related emergent phenomena are not yet well understood. We investigate how the dynamics of a driven system of several quantum elements (e.g., qubits or Rydberg atoms) changes with increasing number of elements. Surprisingly, a two-element system exhibits chaotic behaviors. For larger system sizes, a highly stochastic, far from equilibrium, hyperchaotic regime emerges. Its complexity systematically scales with the size of the system, proportionally to the number of elements. Finally, we demonstrate that these chaotic dynamics can be efficiently controlled by a periodic driving field. The insights provided by our results indicate the possibility of a reduced description for the behavior of a large quantum system in terms of the transitions between its qualitatively different dynamical regimes. These transitions are controlled by a relatively small number of parameters, which may prove useful in the design, characterization, and control of large artificial quantum structures.
Spiny mouse (Acomys): an emerging research organism for regenerative medicine with applications beyond the skin
Authors: Gaire Janak , Varholick Justin A. , Rana Sabhya , Sunshine Michael D. , Doré Sylvain , Barbazuk W. Brad , Fuller David D. , Maden Malcolm , Simmons Chelsey S.
Published: January 2021

The spiny mouse (Acomys species) has emerged as an exciting research organism due to its remarkable ability to undergo scarless regeneration of skin wounds and ear punches. Excitingly, Acomys species demonstrate scar-free healing in a wide-range of tissues beyond the skin. In this perspective article, we discuss published findings from a variety of tissues to highlight how this emerging research organism could shed light on numerous clinically relevant human diseases. We also discuss the challenges of working with this emerging research organism and suggest strategies for future Acomys-inspired research.
Author Correction: Salmonella enterica serovar Typhi exposure elicits ex vivo cell-type-specific epigenetic changes in human gut cells
Authors: Sztein Marcelo B. , Bafford Andrea C. , Salerno-Goncalves Rosângela
Published: January 2021

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Author Correction: Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates with Proliferation Arrest and Differentiation
Authors: López de la Oliva Amada R. , Campos-Sandoval José A. , Gómez-García María C. , Cardona Carolina , Martín-Rufián Mercedes , Sialana Fernando J. , Castilla Laura , Bae Narkhyun , Lobo Carolina , Peñalver Ana , García-Frutos Marina , Carro David , Enrique Victoria , Paz José C. , Mirmira Raghavendra G. , Gutiérrez Antonia , Alonso Francisco J. , Segura Juan A. , Matés José M. , Lubec Gert , Márquez Javier
Published: January 2021

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Strong and tunable spin–orbit interaction in a single crystalline InSb nanosheet
Authors: Chen Yuanjie , Huang Shaoyun , Pan Dong , Xue Jianhong , Zhang Li , Zhao Jianhua , Xu H. Q.
Published: January 2021

A dual-gate InSb nanosheet field-effect device is realized and is used to investigate the physical origin and the controllability of the spin–orbit interaction in a narrow bandgap semiconductor InSb nanosheet. We demonstrate that by applying a voltage over the dual gate, efficiently tuning of the spin–orbit interaction in the InSb nanosheet can be achieved. We also find the presence of an intrinsic spin–orbit interaction in the InSb nanosheet at zero dual-gate voltage and identify its physical origin as a build-in asymmetry in the device layer structure. Having a strong and controllable spin–orbit interaction in an InSb nanosheet could simplify the design and realization of spintronic deceives, spin-based quantum devices, and topological quantum devices.