bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractOrthosteric 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

AbstractWe 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

AbstractL-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

AbstractThe 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

AbstractLife 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

AbstractApplying 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

AbstractThe 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

AbstractTo 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

AbstractThe 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

AbstractWe 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

AbstractNo 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

AbstractIntracytoplasmic 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

AbstractIn 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

AbstractIn 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

AbstractHerba 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.