bluuebunny/crossref_metadata_2025 huggingface dataset:
CPEB1 directs muscle stem cell activation by reprogramming the translational landscape
Authors: Zeng Wenshu , Yue Lu , Lam Kim S. W. , Zhang Wenxin , So Wai-Kin , Tse Erin H. Y. , Cheung Tom H.
Published: February 2022

Skeletal muscle stem cells, also called Satellite Cells (SCs), are actively maintained in quiescence but can activate quickly upon extrinsic stimuli. However, the mechanisms of how quiescent SCs (QSCs) activate swiftly remain elusive. Here, using a whole mouse perfusion fixation approach to obtain bona fide QSCs, we identify massive proteomic changes during the quiescence-to-activation transition in pathways such as chromatin maintenance, metabolism, transcription, and translation. Discordant correlation of transcriptomic and proteomic changes reveals potential translational regulation upon SC activation. Importantly, we show Cytoplasmic Polyadenylation Element Binding protein 1 (CPEB1), post-transcriptionally affects protein translation during SC activation by binding to the 3′ UTRs of different transcripts. We demonstrate phosphorylation-dependent CPEB1 promoted Myod1 protein synthesis by binding to the cytoplasmic polyadenylation elements (CPEs) within its 3′ UTRs to regulate SC activation and muscle regeneration. Our study characterizes CPEB1 as a key regulator to reprogram the translational landscape directing SC activation and subsequent proliferation.
Kansl1 haploinsufficiency impairs autophagosome-lysosome fusion and links autophagic dysfunction with Koolen-de Vries syndrome in mice
Authors: Li Ting , Lu Dingyi , Yao Chengcheng , Li Tingting , Dong Hua , Li Zhan , Xu Guang , Chen Jiayi , Zhang Hao , Yi Xiaoyu , Zhu Haizhen , Liu Guangqin , Wen Kaiqing , Zhao Haixin , Gao Jun , Zhang Yakun , Han Qiuying , Li Teng , Zhang Weina , Zhao Jie , Li Tao , Bai Zhaofang , Song Moshi , He Xinhua , Zhou Tao , Xia Qing , Li Ailing , Pan Xin
Published: February 2022

Koolen-de Vries syndrome (KdVS) is a rare disorder caused by haploinsufficiency of KAT8 regulatory NSL complex subunit 1 (KANSL1), which is characterized by intellectual disability, heart failure, hypotonia, and congenital malformations. To date, no effective treatment has been found for KdVS, largely due to its unknown pathogenesis. Using siRNA screening, we identified KANSL1 as an essential gene for autophagy. Mechanistic study shows that KANSL1 modulates autophagosome-lysosome fusion for cargo degradation via transcriptional regulation of autophagosomal gene, STX17. Kansl1+/− mice exhibit impairment in the autophagic clearance of damaged mitochondria and accumulation of reactive oxygen species, thereby resulting in defective neuronal and cardiac functions. Moreover, we discovered that the FDA-approved drug 13-cis retinoic acid can reverse these mitophagic defects and neurobehavioral abnormalities in Kansl1+/− mice by promoting autophagosome-lysosome fusion. Hence, these findings demonstrate a critical role for KANSL1 in autophagy and indicate a potentially viable therapeutic strategy for KdVS.
Superresolution concentration measurement realized by sub-shot-noise absorption spectroscopy
Authors: Matsuzaki Korenobu , Tahara Tahei
Published: February 2022

Absorption spectroscopy is one of the most widely used spectroscopic methods. The signal-to-noise ratio in conventional absorption spectroscopy is ultimately limited by the shot noise, which arises from the statistical property of the light used for the measurement. Here we show that the noise in absorption spectra can be suppressed below the shot-noise limit when entangled photon pairs are used for the light source. By combining broadband entangled photon pairs and multichannel detection, we realize the acquisition of sub-shot-noise absorption spectra in the entire visible wavelength. Furthermore, we demonstrate the strength of sub-shot-noise absorption spectroscopy for the identification and quantification of chemical species, which are two primary aims of absorption spectroscopy. For highly diluted binary mixture solutions, sub-shot-noise absorption spectroscopy enables us to determine the concentration of each chemical species with precision beyond the limit of conventional absorption spectroscopy. That is, sub-shot-noise absorption spectroscopy achieves superresolution in concentration measurements.
Unexpectedly minor nitrous oxide emissions from fluvial networks draining permafrost catchments of the East Qinghai-Tibet Plateau
Authors: Zhang Liwei , Zhang Sibo , Xia Xinghui , Battin Tom J. , Liu Shaoda , Wang Qingrui , Liu Ran , Yang Zhifeng , Ni Jinren , Stanley Emily H.
Published: February 2022

Streams and rivers emit substantial amounts of nitrous oxide (N2O) and are therefore an essential component of global nitrogen (N) cycle. Permafrost soils store a large reservoir of dormant N that, upon thawing, can enter fluvial networks and partly degrade to N2O, yet the role of waterborne release of N2O in permafrost regions is unclear. Here we report N2O concentrations and fluxes during different seasons between 2016 and 2018 in four watersheds on the East Qinghai-Tibet Plateau. Thawing permafrost soils are known to emit N2O at a high rate, but permafrost rivers draining the East Qinghai-Tibet Plateau behave as unexpectedly minor sources of atmospheric N2O. Such low N2O fluxes are associated with low riverine dissolved inorganic N (DIN) after terrestrial plant uptake, unfavorable conditions for N2O generation via denitrification, and low N2O yield due to a small ratio of nitrite reductase: nitrous oxide reductase in these rivers. We estimate fluvial N2O emissions of 0.432 − 0.463 Gg N2O-N yr−1 from permafrost landscapes on the entire Qinghai-Tibet Plateau, which is marginal (~0.15%) given their areal contribution to global streams and rivers (0.7%). However, we suggest that these permafrost-affected rivers can shift from minor sources to strong emitters in the warmer future, likely giving rise to the permafrost non-carbon feedback that intensifies warming.
A review of the recent progress in battery informatics
Authors: Ling Chen
Published: February 2022

Batteries are of paramount importance for the energy storage, consumption, and transportation in the current and future society. Recently machine learning (ML) has demonstrated success for improving lithium-ion technologies and beyond. This in-depth review aims to provide state-of-art achievements in the interdisciplinary field of ML and battery research and engineering, the battery informatics. We highlight a crucial hurdle in battery informatics, the availability of battery data, and explain the mitigation of the data scarcity challenge with a detailed review of recent achievements. This review is concluded with a perspective in this new but exciting field.
African fermented foods: overview, emerging benefits, and novel approaches to microbiome profiling
Authors: Obafemi Yemisi D. , Oranusi Solomon U. , Ajanaku Kolawole O. , Akinduti Paul A. , Leech John , Cotter Paul D.
Published: February 2022

Traditional fermented foods are of major importance with respect to the socio-economic growth, food security, nutrition, and health of African consumers. In several African countries, traditional fermentation processes provide a means of food preservation, improving the shelf life and adding to the nutrients in the food products. As with any fermented foods, the associated food microbiota is of great importance and interest. Recent studies on the microbiome of African fermented foods using high-throughput DNA sequencing techniques have revealed the presence of diverse microbial populations of fundamental, technological, and commercial interest that could be harnessed to further improve health, food safety, and quality. This review provides an overview of African fermented foods, their microbiota, and the health-promoting potential of these foods and microbes.
Comparing the thermal stability of 10-carboxy-, 10-methyl-, and 10-catechyl-pyranocyanidin-3-glucosides and their precursor, cyanidin-3-glucoside
Authors: Voss Danielle M. , Miyagusuku-Cruzado Gonzalo , Giusti M. Mónica
Published: February 2022

Pyranoanthocyanins are vibrant, naturally derived pigments formed by the reaction of an anthocyanin with a cofactor containing a partially negatively charged carbon. This study compared the thermal stability and degradation products of 10-carboxy-pyranocyanidin-3-glucoside (pyruvic acid cofactor), 10-methyl-pyranocyanidin-3-glucoside (acetone cofactor), and 10-catechyl-pyranocyanidin-3-glucoside (caffeic acid cofactor) with their anthocyanin precursor to evaluate the role of the pyranoanthocyanin C10 substitution on stability. Pyranoanthocyanins exhibited absorbance half-lives ~2.1–8.6 times greater than cyanidin-3-glucoside, with ~15–52% of their original pigment remaining after 12 h of 90 °C heating at pH 3.0. 10-Methyl-pyranocyanidin-3-glucoside was the most stable (p < 0.01) based on UHPLC-PDA analysis, while 10-catechyl-pyranocyanidin-3-glucoside had the most stable color in part due to contribution from a colored degradation compound. Protocatechuic acid formed in all heated samples, which suggested a similar degradation mechanism among pigments. In conclusion, the C10 substitution impacted the extent of pyranoanthocyanin stability and the degradation compounds formed.
Perceiving societal pressure to be happy is linked to poor well-being, especially in happy nations
Authors: Dejonckheere Egon , Rhee Joshua J. , Baguma Peter K. , Barry Oumar , Becker Maja , Bilewicz Michał , Castelain Thomas , Costantini Giulio , Dimdins Girts , Espinosa Agustín , Finchilescu Gillian , Friese Malte , Gastardo-Conaco Maria Cecilia , Gómez Angel , González Roberto , Goto Nobuhiko , Halama Peter , Hurtado-Parrado Camilo , Jiga-Boy Gabriela M. , Karl Johannes A. , Novak Lindsay , Ausmees Liisi , Loughnan Steve , Mastor Khairul A. , McLatchie Neil , Onyishi Ike E. , Rizwan Muhammad , Schaller Mark , Serafimovska Eleonora , Suh Eunkook M. , Swann William B. , Tong Eddie M. W. , Torres Ana , Turner Rhiannon N. , Vinogradov Alexander , Wang Zhechen , Yeung Victoria Wai-lan , Amiot Catherine E. , Boonyasiriwat Watcharaporn , Peker Müjde , Van Lange Paul A. M. , Vauclair Christin-Melanie , Kuppens Peter , Bastian Brock
Published: February 2022

Happiness is a valuable experience, and societies want their citizens to be happy. Although this societal commitment seems laudable, overly emphasizing positivity (versus negativity) may create an unattainable emotion norm that ironically compromises individual well-being. In this multi-national study (40 countries; 7443 participants), we investigate how societal pressure to be happy and not sad predicts emotional, cognitive and clinical indicators of well-being around the world, and examine how these relations differ as a function of countries’ national happiness levels (collected from the World Happiness Report). Although detrimental well-being associations manifest for an average country, the strength of these relations varies across countries. People’s felt societal pressure to be happy and not sad is particularly linked to poor well-being in countries with a higher World Happiness Index. Although the cross-sectional nature of our work prohibits causal conclusions, our findings highlight the correlational link between social emotion valuation and individual well-being, and suggest that high national happiness levels may have downsides for some.
Optimisation of self-healing of bio-foamed concrete bricks pores using Bacillus tequilensis under different temperature and CO2 curing conditions
Authors: Alshalif Abdullah F. , Juki M. Irwan , Tajarudin Husnul Azan , Othman N. , Al-Gheethi Adel Ali , Shamsudin S. , Altowayti Wahid , Sabah Saddam Abo
Published: February 2022

The self-healing of bio-concrete cracks and pores have been utilised worldwide to improve the properties of bio-concrete using different types of bacteria. Meanwhile, no published research was conducted to heal bio-foamed concrete bricks (B-FCB) pores using Bacillus tequilensis. Previous studies focused on the concentration of bacteria and neglect other factors that could affect the healing process. This research aimed to optimise the healing ratio of B-FCB pores using four factors: B. tequilensis concentration, concrete density, temperature and CO2 concentration. Initial water absorption (IWA) and water absorption (WA) were used as responses in statistical methods, namely, factorial and response surface methodology (RSM). B. tequilensis species was isolated from cement kiln dust, produced in a powder form, then subjected to simulate test using a special medium consisting of foamed concrete materials to check the survival ability in B-FCB. SEM, EDX, and XRD were used to investigate the healing process of B-FCB pores. The results revealed that the decrement ratios of IWA and WA of B-FCB were 52.8% and 29.1% compared to FCB, respectively. SEM results reflect the healing that occurred in B-FCB pores, mostly healed via precipitation of CaCO3 as demonstrated on the XRD results.
Structural properties of Bi thin film grown on Si (111) by quasi-van der Waals epitaxy
Authors: Chou Chieh , Wu Bo-Xun , Lin Hao-Hsiung
Published: February 2022

Crystallinity of an 80-nm-thick bismuth thin film grown on Si (111) substrate by MBE was investigated. The highly (0003) textured Bi film contains two twinning domains with different bilayer stacking sequences. The basic lattice parameters c and a as well as b, the bilayer thickness, of the two domains were determined from a series of X-ray diffraction (XRD) measurements, and found that the differences are within 0.1% as compared with those of bulk Bi reported in literature, suggesting that the Bi film has been nearly fully relaxed. From the XRD φ-scans of asymmetric Bi (01–14), (10–15), (11–26) planes and Si (220) plane as well as selected area electron diffraction patterns and electron back scatter diffraction pole figures, we confirmed the well registration between the lattices of Si and Bi lattice, i.e. the ω angle difference between Bi[0003] and Si[111] and the φ angle difference between Bi[01–14] and Si[220] are 0.056° and 0.25°, respectively, and thus concluded that the growth is a quasi-van der Waals epitaxy.
Impact of local and systemic antimicrobials on leukocyte- and platelet rich fibrin: an in vitro study
Authors: Siawasch S. A. M. , Andrade C. , Castro A. B. , Teughels W. , Temmerman A. , Quirynen M.
Published: February 2022

The aim of this study was to evaluate the effect of local and systemic administration of antimicrobials to leukocyte- and platelet-rich fibrin (L-PRF). For part A, 16 tubes of venous blood were collected from each of eight systemically healthy subjects. Prior to blood centrifugation, 12 of the 16 tubes were injected with 0.125 ml, 0.25 ml or 0.50 ml metronidazole solution. One set of L-PRF membranes was used to assess the release of vascular endothelial growth factor AB, platelet-derived growth factor, transforming growth factor beta 1, and bone morphogenetic protein 2 at indicated time points. The metronidazole release over time by L-PRF membranes was also evaluated. The remaining L-PRF membranes were placed on the surface of agar plates inoculated with three different periodontal pathogens to determine their antibacterial activity. For part B, another six subjects were enrolled with three subjects taking 2 g amoxicillin and three subjects 500 mg metronidazole as prophylaxis prior to a periodontal treatment. Before and 2 h after consuming one of the prescribed antimicrobials, three tubes of blood were collected for preparing L-PRF membranes. These membranes were used to measure the antibacterial activity against periodontal pathogens. No statistically significant difference could be found in the release of growth factors between L-PRF membranes with and without incorporation of metronidazole solution. The release of metronidazole could be detected up to day 3, however with the highest concentration during the first 4 h. This concentration was dose dependent. The antibacterial capacity of L-PRF membranes increased significantly for both the systemic intake, and after the addition of metronidazole solution to the blood tubes before centrifugation, the latter again dose dependent. The antibacterial capacity of L-PRF against the periodontal pathogens tested can significantly be enhanced by the addition of antimicrobials, without disadvantage for the release of growth factors.
Catchment memory explains hydrological drought forecast performance
Authors: Sutanto Samuel Jonson , Van Lanen Henny A. J.
Published: February 2022

Hydrological drought forecasts outperform meteorological ones, which is anticipated coming from catchment memory. Yet, the importance of catchment memory in explaining hydrological drought forecast performance has not been studied. Here, we use the Baseflow Index (BFI) and the groundwater Recession Coefficient (gRC), which through the streamflow, give information on the catchment memory. Performance of streamflow drought forecasts was evaluated using the Brier Score (BS) for rivers across Europe. We found that BS is negatively correlated with BFI, meaning that rivers with high BFI (large memory) yield better drought prediction (low BS). A significant positive correlation between gRC and BS demonstrates that catchments slowly releasing groundwater to streams (low gRC), i.e. large memory, generates higher drought forecast performance. The higher performance of hydrological drought forecasts in catchments with relatively large memory (high BFI and low gRC) implies that Drought Early Warning Systems have more potential to be implemented there and will appear to be more useful.
Distance-based clustering using QUBO formulations
Authors: Matsumoto Nasa , Hamakawa Yohei , Tatsumura Kosuke , Kudo Kazue
Published: February 2022

In computer science, clustering is a technique for grouping data. Ising machines can solve distance-based clustering problems described by quadratic unconstrained binary optimization (QUBO) formulations. A typical simple method using an Ising machine makes each cluster size equal and is not suitable for clustering unevenly distributed data. We propose a new clustering method that provides better performance than the simple method, especially for unevenly distributed data. The proposed method is a hybrid algorithm including an iterative process that comprises solving a discrete optimization problem with an Ising machine and calculating parameters with a general-purpose computer. To minimize the communication overhead between the Ising machine and the general-purpose computer, we employed a low-latency Ising machine implementing the simulated bifurcation algorithm with a field-programmable gate array attached to a local server. The proposed method results in clustering 200 unevenly distributed data points with a clustering score 18% higher than that of the simple method. The discrete optimization with 2000 variables is performed 100 times per iteration, and the overhead time is reduced to approximately 20% of the total execution time. These results suggest that hybrid algorithms using Ising machines can efficiently solve practical optimization problems.
The effect of a hydrolyzed protein diet on the fecal microbiota in cats with chronic enteropathy
Authors: Kathrani Aarti , Yen Sandi , Swann Jonathan R. , Hall Edward J.
Published: February 2022

The effect of a hydrolyzed protein diet on the fecal microbiota has not been studied in feline chronic enteropathy (CE). Our study aimed to (1) compare the fecal microbiota of cats with CE to control cats with no gastrointestinal signs and (2) determine the effect of a hydrolyzed protein diet on the fecal microbiota of cats with CE and whether this differs between dietary responders and non-responders. The fecal microbiome of cats with CE (n = 36) showed decreased α-diversity in terms of genus richness (P = 0.04) and increased β-diversity in terms of Bray–Curtis Dissimilarity (P < 0.001) compared to control cats (n = 14).Clostridiumwas the only genera significantly over-represented in cats with CE compared to control cats (adjustedP < 0.1). After 6-weeks of feeding the diet, fifteen cats were classified as responders and 18 as non-responders, based on clinical signs. At the genus level, α-diversity was increased in non-responders versus responders at diagnosis, but decreased after dietary intervention in both groups (P < 0.05). At the family level, non-responders became increasingly dissimilar after dietary intervention (P = 0.012). In general, the abundance of bacteria decreased with feeding a hydrolyzed diet, with the genera most significantly affected being more frequently observed in non-responders.Bifidobacteriumwas the only genus that increased significantly in abundance post-diet and this effect was observed in both responders and non-responders. BothOscillibacterandDesulfovibrionaceae_unclassifiedwere most abundant in non-responders at diagnosis but were rarely observed post diet in neither responders nor non-responders. Cats with CE had similar microbiota changes to those described in human inflammatory bowel disease. Whether the presence ofOscillibacterandDesulfovibrionaceae_unclassifiedare indicators of non-response to the diet at diagnosis requires further investigation. Despite the hydrolyzed diet reducing α-diversity in all cats with CE, this did not resolve gastrointestinal signs in some cats. However, responders metabolized the diet in a similar manner, reflected by sustained β-diversity, while the microbiome of non-responders became increasingly dissimilar compared to diagnosis at the family level. Therefore, the microbiome may not be as tightly regulated in cats with CE that are non-responders and therefore, these cats would require additional therapy for remission of clinical signs.
Constant output characteristics and design methodology of double side LC compensated capacitive power transfer
Authors: Xiong Qiao , Shao Ying , Sun Pan , Sun Jun , Rong Enguo , Liang Yan
Published: February 2022

Capacitive power transfer (CPT) has been verified to be capable of transferring a power level as high as inductive power transfer (IPT) recently, and has its own merits. It is a well complement of IPT in near-field wireless power transfer (WPT). This paper gives a newly designed method of realizing both constant output voltage (COV) and constant output current (COC) modes of double side LC compensated CPT. Firstly, through analysis of basic circuit characteristics, the conditions for both of the two modes are deduced theoretically. Especially, one merit of the method is that the conditions indicate a very clear relationship between the compensation components forming resonant tanks. Another merit is that the couple capacitors also participate in resonant tanks. Different from the COV mode, the COC mode can theoretically reach zero phase angle condition simultaneously. Based on these conditions, the parameter design methodology is proposed. Besides, an efficient model of double side LC compensated CPT is built, and the optimum load is calculated theoretically to guide the design course. Finally, the results of both simulations and experiments demonstrate high consistency with the theoretical analysis.
Body composition, physical fitness and cardiovascular risk factors in 9-year-old children
Authors: Henriksson Pontus , Sandborg Johanna , Henström Maria , Delisle Nyström Christine , Ek Evelina , Ortega Francisco B. , Löf Marie
Published: February 2022

The independent associations of body composition and physical fitness components with cardiovascular disease (CVD) risk factors in childhood are not fully understood. Thus, this cross-sectional study examined the independent associations of body composition and physical fitness with CVD risk factors in Swedish 9-year-old children (n = 411). Unadjusted linear regression analyses showed that body mass index (BMI), % fat mass and fat mass index were all positively associated with systolic and diastolic blood pressure, Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) and Metabolic Syndrome (MetS) score (all β ≥ 0.229,P ≤ 0.001). These associations were virtually unaffected by adjustments for basic covariates (child’s age and sex, maternal educational level and maternal BMI), fat-free mass and physical fitness. Fat-free mass index had generally weak associations with CVD risk factors and no associations were statistically significant after adjustments (allP > 0.27). Greater cardiorespiratory fitness and motor fitness were associated with lower HOMA-IR and MetS score in unadjusted models (all β ≤ − 0.158,P ≤ 0.039) but not after adjustments for basic covariates and body composition. These findings indicate that cardiovascular health promotion in childhood may focus on the maintenance of a healthy fat mass.
Two entry tunnels in mouse TAAR9 suggest the possibility of multi-entry tunnels in olfactory receptors
Authors: Xu ZhengRong , Guo LingNa , Qian XiaoYun , Yu ChenJie , Li ShengJu , Zhu ChengWen , Ma XiaoFeng , Li Hui , Zhu GuangJie , Zhou Han , Dai WenXuan , Li Qian , Gao Xia
Published: February 2022

Orthosteric binding sites of olfactory receptors have been well understood for ligand-receptor interactions. However, a lack of explanation for subtle differences in ligand profile of olfactory receptors even with similar orthosteric binding sites promotes more exploration into the entry tunnels of the receptors. An important question regarding entry tunnels is the number of entry tunnels, which was previously believed to be one. Here, we used TAAR9 that recognizes important biogenic amines such as cadaverine, spermine, and spermidine as a model for entry tunnel study. We identified two entry tunnels in TAAR9 and described the residues that form the tunnels. In addition, we found two vestibular binding pockets, each located in one tunnel. We further confirmed the function of two tunnels through site-directed mutagenesis. Our study challenged the existing views regarding the number of entry tunnels in the subfamily of olfactory receptors and demonstrated the possible mechanism how the entry tunnels function in odorant recognition.
Three-dimensional deep learning to automatically generate cranial implant geometry
Authors: Wu Chieh-Tsai , Yang Yao-Hung , Chang Yau-Zen
Published: February 2022

We present a 3D deep learning framework that can generate a complete cranial model using a defective one. The Boolean subtraction between these two models generates the geometry of the implant required for surgical reconstruction. There is little or no need for post-processing to eliminate noise in the implant model generated by the proposed approach. The framework can be used to meet the repair needs of cranial imperfections caused by trauma, congenital defects, plastic surgery, or tumor resection. Traditional implant design methods for skull reconstruction rely on the mirror operation. However, these approaches have great limitations when the defect crosses the plane of symmetry or the patient's skull is asymmetrical. The proposed deep learning framework is based on an enhanced three-dimensional autoencoder. Each training sample for the framework is a pair consisting of a cranial model converted from CT images and a corresponding model with simulated defects on it. Our approach can learn the spatial distribution of the upper part of normal cranial bones and use flawed cranial data to predict its complete geometry. Empirical research on simulated defects and actual clinical applications shows that our framework can meet most of the requirements of cranioplasty.
Association of L-type amino acid transporter 1 (LAT1) with the immune system and prognosis in invasive breast cancer
Authors: Kurozumi Sasagu , Kaira Kyoichi , Matsumoto Hiroshi , Kurosumi Masafumi , Yokobori Takehiko , Kanai Yoshikatsu , Sekine Chikako , Honda Chikako , Katayama Ayaka , Furuya Mio , Shiino Sho , Makiguchi Takaya , Mongan Nigel P. , Rakha Emad A. , Oyama Tetsunari , Fujii Takaaki , Shirabe Ken , Horiguchi Jun
Published: February 2022

L-type amino acid transporter 1 (LAT1), also referred to as SLC7A5, is believed to regulate tumor metabolism and be associated with tumor proliferation. In invasive breast cancer, we clinicopathologically investigated the utility of LAT1 expression. LAT1 expression was evaluated via immunohistochemistry analyses in 250 breast cancer patients undergoing long-term follow-up. We assessed the relationships between LAT1 expression and patient outcomes and clinicopathological factors. Breast cancer-specific survival stratified by LAT1 expression was assessed. Human epidermal growth factor receptor 2 (HER2)-positive patients with metastasis received trastuzumab therapy. The density of tumor-infiltrating lymphocytes (TILs) was evaluated according to the International Working Group guidelines. In the current study, high LAT1 expression was significantly correlated with estrogen receptor (ER) negativity, progesterone receptor negativity, high histological grade, increased TILs, and programmed death ligand 1 positivity. Among the ER-positive and HER2-negative patients, high LAT1 was an independent indicator of poor outcomes (hazard ratio (HR) = 2.97; 95% confidence interval (CI), 1.16–7.62; p = 0.023). Moreover, high LAT1 expression was an independent poor prognostic factor in luminal B-like breast cancer with aggressive features (HR = 3.39; 95% CI 1.35–8.52; p = 0.0094). In conclusion, high LAT1 expression could be used to identify a subgroup of invasive breast cancer characterized by aggressive behavior and high tumor immunoreaction. Our findings suggest that LAT1 might be a candidate therapeutic target for breast cancer patients, particularly those with luminal B-like type breast cancer.
Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater and a use-case in the metropolitan area of Thessaloniki, Greece
Authors: Pechlivanis Nikolaos , Tsagiopoulou Maria , Maniou Maria Christina , Togkousidis Anastasis , Mouchtaropoulou Evangelia , Chassalevris Taxiarchis , Chaintoutis Serafeim C. , Petala Maria , Kostoglou Margaritis , Karapantsios Thodoris , Laidou Stamatia , Vlachonikola Elisavet , Chatzidimitriou Anastasia , Papadopoulos Agis , Papaioannou Nikolaos , Dovas Chrysostomos I. , Argiriou Anagnostis , Psomopoulos Fotis
Published: February 2022

The COVID-19 pandemic represents an unprecedented global crisis necessitating novel approaches for, amongst others, early detection of emerging variants relating to the evolution and spread of the virus. Recently, the detection of SARS-CoV-2 RNA in wastewater has emerged as a useful tool to monitor the prevalence of the virus in the community. Here, we propose a novel methodology, called lineagespot, for the monitoring of mutations and the detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing (NGS). Our proposed method was tested and evaluated using NGS data produced by the sequencing of 14 wastewater samples from the municipality of Thessaloniki, Greece, covering a 6-month period. The results showed the presence of SARS-CoV-2 variants in wastewater data. lineagespot was able to record the evolution and rapid domination of the Alpha variant (B.1.1.7) in the community, and allowed the correlation between the mutations evident through our approach and the mutations observed in patients from the same area and time periods. lineagespot is an open-source tool, implemented in R, and is freely available on GitHub and registered on bio.tools.
Microbial epibiotic community of the deep-sea galatheid squat lobster Munidopsis alvisca
Authors: Leinberger Janina , Milke Felix , Christodoulou Magdalini , Poehlein Anja , Caraveo-Patiño Javier , Teske Andreas , Brinkhoff Thorsten
Published: February 2022

Life at hydrothermal vent sites is based on chemosynthetic primary producers that supply heterotrophic microorganisms with substrates and generate biomass for higher trophic levels. Often, chemoautotrophs associate with the hydrothermal vent megafauna. To investigate attached bacterial and archaeal communities on deep-sea squat lobsters, we collected ten specimens from a hydrothermal vent in the Guaymas Basin (Gulf of California). All animals were identified as Munidopsis alvisca via morphological and molecular classification, and intraspecific divergence was determined. Amplicon sequencing of microbial DNA and cDNA revealed significant differences between microbial communities on the carapaces of M. alvisca and those in ambient sea water. Major epibiotic bacterial taxa were chemoautotrophic Gammaproteobacteria, such as Thiotrichaceae and Methylococcaceae, while archaea were almost exclusively represented by sequences affiliated with Ca. Nitrosopumilus. In sea water samples, Marine Group II and III archaea and organoheterotrophic Alphaproteobacteria, Flavobacteriia and Planctomycetacia were more dominant. Based on the identified taxa, we assume that main metabolic processes, carried out by M. alvisca epibiota, include ammonia, methane and sulphide oxidation. Considering that M. alvisca could benefit from sulphide detoxification by its epibiota, and that attached microbes are supplied with a stable habitat in proximity to substrate-rich hydrothermal fluids, a mutualistic host-microbe relationship appears likely.
Field emission microscope for a single fullerene molecule
Authors: Yanagisawa Hirofumi , Bohn Markus , Goschin Florian , Seitsonen Ari P. , Kling Matthias F.
Published: February 2022

Applying strong direct current (DC) electric fields on the apex of a sharp metallic tip, electrons can be radially emitted from the apex to vacuum. Subsequently, they magnify the nanoscopic information on the apex, which serves as a field emission microscope (FEM). When depositing molecules on such a tip, peculiar electron emission patterns such as clover leaves appear. These phenomena were first observed seventy years ago. However, the source of these emission patterns has not yet been identified owing to the limited experimental information about molecular configurations on a tip. Here, we used fullerene molecules and characterized the molecule-covered tip by an FEM. In addition to the experiments, simulations were performed to obtain optimized molecular configurations on a tip. Both results indicate that the molecules, the source of the peculiar emission patterns, appear on a molecule layer formed on the tip under strong DC electric fields. Furthermore, the simulations revealed that these molecules are mostly isolated single molecules forming single-molecule-terminated protrusions. Upon the excellent agreements in both results, we concluded that each emission pattern originates from a single molecule. Our work should pave the way to revive old-fashioned electron microscopy as a powerful tool for investigating a single molecule.
Topological data analysis gives two folding paths in HP35(nle-nle), double mutant of villin headpiece subdomain
Authors: Ichinomiya Takashi
Published: February 2022

The folding dynamics of proteins is a primary area of interest in protein science. We carried out topological data analysis (TDA) of the folding process of HP35(nle-nle), a double-mutant of the villin headpiece subdomain. Using persistent homology and non-negative matrix factorization, we reduced the dimension of protein structure and investigated the flow in the reduced space. We found this protein has two folding paths, distinguished by the pairings of inter-helix residues. Our analysis showed the excellent performance of TDA in capturing the formation of tertiary structure.
A meta-analysis of Th1 and Th2 cytokine profiles differentiating tuberculous from malignant pleural effusion
Authors: Zeng Yulin , Wang Liwei , Zhou Hai , Qi Yu
Published: February 2022

To clarify the predominance of Th1 or Th2 immune responses in malignant and tuberculous pleural effusion (MPE and TPE, respectively), we performed a meta-analysis of previously published results of the levels of Th1/Th2 cytokines associated with these two types of pleural effusion to evaluate the use of Th1/Th2 cytokine profiles in distinguishing TPE from MPE. We searched the PubMed and EMBASE databases for studies indexed from 2000 to March 2021. We included studies that (a) diagnosed TPE and MPE based on culture or pleural tissue biopsy and that (b) compared levels of Th1/Th2 cytokines between TPE and MPE. Pooled data based on a random-effects model or fixed-effects model and standardized mean differences (SMDs) across studies were used to compare TPE and MPE. We also performed Egger’s test to assess publication bias. Of 917 identified studies, a total of 42 studies were selected for the meta-analysis. Compared with MPE subjects, TPE subjects had a significantly higher level of TNF-α [2.22, (1.60–2.84)], an elevated level of IFN-γ [3.30, (2.57–4.40)] in pleural effusion, a situation where the Th1 immune response dominated. Conversely, the levels of interleukin-4 (IL-4) and IL-10 (Th2 cytokines) were higher in the MPE subjects than in the TPE subjects, showing statistically nonsignificant tiny effects [−0.15, (−0.94 to 0.63) and −0.04, (−0.21 to 0.12), respectively]. We confirmed that TPE, a situation in which the Th1 cytokines are predominant. The slight preponderance of Th2 cytokines in MPE, which is not convincing enough to prove.
Facemasks and ferrous metallurgy: improving gasification reactivity of low-volatile coals using waste COVID-19 facemasks for ironmaking application
Authors: Stewart Daniel J. C. , Fisher Lucy V. , Warwick Michael E. A. , Thomson David , Barron Andrew R.
Published: February 2022

The global pandemic response to COVID-19 has led to the generation of huge volumes of unrecyclable plastic waste from single use disposable face coverings. Rotary hearth furnaces can be used to recover Zn and Fe from non-recyclable steelmaking by-product dusts, and waste plastic material such as facemasks could be utilized as a supplementary reductant for the rotary hearth furnace (RHF), but their fibrous form makes milling and processing to appropriate sizing for RHF application extremely challenging. A scalable method of grinding facemasks to powder by melting and mixing with Welsh coal dust reported herein provides a solution to both environmental challenges. The melt-blended PPE/coal dust shows a dramatically improved CO2 gasification reactivity (Ea = 133–159 kJmol−1) when compared to the untreated coal (Ea = 183–246 kJmol−1), because of improved pore development in the coal during the pyrolysis stage of heating and the catalytic activity of the CaO based ash present in the facemask plastic. The results are promising for the application of waste facemasks in recycling steelmaking by-product dusts in rotary hearth furnaces and may also be suitable for direct injection to the blast furnace subject to further study.
A COVID-19 vaccination model for Aotearoa New Zealand
Authors: Steyn Nicholas , Plank Michael J. , Binny Rachelle N. , Hendy Shaun C. , Lustig Audrey , Ridings Kannan
Published: February 2022

We develop a mathematical model to estimate the effect of New Zealand’s vaccine rollout on the potential spread and health impacts of COVID-19. The main purpose of this study is to provide a basis for policy advice on border restrictions and control measures in response to outbreaks that may occur during the vaccination roll-out. The model can be used to estimate the theoretical population immunity threshold, which represents a point in the vaccine rollout at which border restrictions and other controls could be removed and only small, occasional outbreaks would take place. We find that, with a basic reproduction number of 6, approximately representing the Delta variant of SARS-CoV-2, and under baseline vaccine effectiveness assumptions, reaching the population immunity threshold would require close to 100% of the total population to be vaccinated. Since this coverage is not likely to be achievable in practice, relaxing controls completely would risk serious health impacts. However, the higher vaccine coverage is, the more collective protection the population has against adverse health outcomes from COVID-19, and the easier it will become to control outbreaks. There remains considerable uncertainty in model outputs, in part because of the potential for the evolution of new variants. If new variants arise that are more transmissible or vaccine resistant, an increase in vaccine coverage will be needed to provide the same level of protection.
Effects of dexmedetomidine on surgery for type A acute aortic dissection outcome
Authors: Cheng Yu-Ting , Lee Kuang-Tso , Chang Chih-Hsiang , Wu Victor Chien-Chia , Chan Yi-Shin , Chen Dong-Yi , Chu Pao-Hsien , Chou An-Hsun , Liu Kuo-Sheng , Chen Shao-Wei
Published: February 2022

No study has evaluated the effect of dexmedetomidine in patients who received surgery for type A aortic dissection. This is the first study to evaluate the effect of dexmedetomidine in aortic dissection patients. This study was executed using data from the Chang Gung Research Database in Taiwan. The CGRD contains the multi‐institutional standardized electronic medical records from seven Chang Gung Memorial hospitals, the largest medical system in Taiwan. We retrospectively evaluate patients who received surgery for acute type A aortic dissection between January 2014 and December 2018. Overall, 511 patients were included, of whom 104 has received dexmedetomidine infusion in the postoperative period. One-to-two propensity score-matching yielded 86 cases in the dexmedetomidine group and 158 cases in the non-dexmedetomidine group. The in-hospital mortality and composite outcome including all-cause mortality, acute kidney injury, delirium, postoperative atrial fibrillation, and respiratory failure, were considered primary outcomes. The in-hospital mortality and composite outcome were similar between groups. The risk of Acute Kidney Injury Network stage 3 acute kidney injury was significantly lower in the dexmedetomidine group than in the non-dexmedetomidine group (8.1% vs 19.0%; OR, 0.38; 95% CI, 0.17–0.86; p = 0.020. The risk of newly-onset dialysis was also significantly lower in the dexmedetomidine group than in the non-dexmedetomidine group (4.7% vs 13.3%; OR, 0.32; 95% CI, 0.11–0.90; p = 0.031). Post-operative dexmedetomidine infusion significantly reduced the rate of severe acute kidney injury and newly-onset dialysis in patients who received surgery for acute type A aortic dissection.
Treatment with MG132 prevents spontaneous activation of rat oocyte in culture and promotes embryonic development after intracytoplasmic sperm injection
Authors: Nakagawa Yuki , Kaneko Takehito
Published: February 2022

Intracytoplasmic sperm injection (ICSI) is an effective reproductive technique for obtaining rat offspring using preserved sperm with low or no motility. However, rat oocytes undergo spontaneous activation immediately after retrieval from the oviduct and poorly develop after ICSI unless it is performed quickly. Here, we evaluated whether treatment with MG132, the proteasome inhibitor, suppresses the spontaneous activation of oocytes before and during ICSI. After retrieval from the oviducts, the rate of development into morula and blastocyst from the oocytes cultured in vitro for 1 h prior to ICSI significantly decreased compared with that from the control oocytes subject to ICSI without culture (7% versus 36%). However, a higher proportion of oocytes treated with MG132 for 0, 1, and 3 h before and during ICSI developed into morulae and blastocysts (70%, 60%, and 52%, respectively). Offspring were obtained from oocytes treated with MG132 for 0 and 1 h before and during ICSI (percentage: 31%). Altogether, MG132 could suppress the spontaneous activation of rat oocytes and increase embryonic development after ICSI.
Relationship between physical activity and cognitive functioning among older Indian adults
Authors: Kumar Manish , Srivastava Shobhit , Muhammad T.
Published: February 2022

In a culturally different and low-resource setting, where lifestyle habits, including dietary pattern and physical activities differ from those in high-income countries, the association between physical activity and cognition is expected to differ. We aimed to investigate the association between physical activity and cognitive functioning after controlling for potential confounders among older adults in India. Furthermore, gender differences in this relationship were analyzed. Using a national-level data from the Longitudinal Ageing Study in India (2017–2018), this paper employed propensity score matching (PSM) approach to examine the association between physical activities and cognitive functioning among Indian older adults. Cognitive impairment was measured through five broad domains (memory, orientation, arithmetic function, executive function, and object naming). We limit our sample to older adults aged 60 + years, and our final dataset contains 31,464 participants (men = 16,366, and women = 15,098). The results indicated that older adults who engaged in frequent physical activity have greater cognitive functioning than older adults without physical activity after adjusting for various individual, health, lifestyle, and household factors. This association holds true for both older men and older women. The results from the PSM revealed that the cognitive function score was increased by 0.98 and 1.32 points for the frequently physically active older men and women population, respectively. The results demonstrate the possible beneficial effects of frequent physical activity on cognitive functioning among older adults. Thus, regular physical activity can be considered as an effective lifestyle factor to promote healthy cognitive aging.
Scaling up and down of 3-D floating-point data in quantum computation
Authors: Xu Meiyu , Lu Dayong , Sun Xiaoyun
Published: February 2022

In the past few decades, quantum computation has become increasingly attractive due to its remarkable performance. Quantum image scaling is considered a common geometric transformation in quantum image processing, however, the quantum floating-point data version of which does not exist. Is there a corresponding scaling for 2-D and 3-D floating-point data? The answer is yes. In this paper, we present a quantum scaling up and down scheme for floating-point data by using trilinear interpolation method in 3-D space. This scheme offers better performance (in terms of the precision of floating-point numbers) for realizing the quantum floating-point algorithms than previously classical approaches. The Converter module we proposed can solve the conversion of fixed-point numbers to floating-point numbers of arbitrary size data with $$p+q$$

p
+
q

qubits based on IEEE-754 format, instead of 32-bit single-precision, 64-bit double-precision and 128-bit extended-precision. Usually, we use nearest-neighbor interpolation and bilinear interpolation to achieve quantum image scaling algorithms, which are not applicable in high-dimensional space. This paper proposes trilinear interpolation of floating-point data in 3-D space to achieve quantum algorithms of scaling up and down for 3-D floating-point data. Finally, the quantum scaling circuits of 3-D floating-point data are designed.
Transcriptomic and metabolomic analysis reveals the difference between large and small flower taxa of Herba Epimedii during flavonoid accumulation
Authors: Qin Weihan , Yang Yong , Wang Yunhong , Zhang Xiaomei , Liu Xiang
Published: February 2022

Herba Epimedii, as a traditional Chinese herb, is divided into large and small flower taxa, and can invigorate sexuality and strengthen muscles and bones. Herba Epimedii is rich in flavonoids, which largely contribute to its medicinal benefits. In our previous studies, we have found that the flavonoids content was much more in small than large flower taxa. To further identify molecular mechanisms of flavonoids metabolism in Herba Epimedii, combined metabolome and transcriptomic analyses were performed to profile leaves and flowers. Association analysis revealed that the expression of genes involved in flavonoid biosynthesis showed significant differences between small and large flower taxa. Eleven flavonols significantly increased in small compared to large flower taxa. Moreover, genes encoding O-methyltransferase played crucial roles in flavonoids metabolism by an integrated analysis. Taken together, these data highlight the breeding tendency of small flower taxa to improve the quality of Herba Epimedii.