bluuebunny/crossref_metadata_2025 huggingface dataset:
Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber
Authors: Li Hongbo , Wang Shenhao , Chai Sen , Yang Zhiquan , Zhang Qiqi , Xin Hongjia , Xu Yuanchao , Lin Shengnan , Chen Xinxiu , Yao Zhiwang , Yang Qingyong , Fei Zhangjun , Huang Sanwen , Zhang Zhonghua
Published: February 2022

Structural variants (SVs) represent a major source of genetic diversity and are related to numerous agronomic traits and evolutionary events; however, their comprehensive identification and characterization in cucumber (Cucumis sativus L.) have been hindered by the lack of a high-quality pan-genome. Here, we report a graph-based cucumber pan-genome by analyzing twelve chromosome-scale genome assemblies. Genotyping of seven large chromosomal rearrangements based on the pan-genome provides useful information for use of wild accessions in breeding and genetic studies. A total of ~4.3 million genetic variants including 56,214 SVs are identified leveraging the chromosome-level assemblies. The pan-genome graph integrating both variant information and reference genome sequences aids the identification of SVs associated with agronomic traits, including warty fruits, flowering times and root growth, and enhances the understanding of cucumber trait evolution. The graph-based cucumber pan-genome and the identified genetic variants provide rich resources for future biological research and genomics-assisted breeding.
Tropical cyclone climatology change greatly exacerbates US extreme rainfall–surge hazard
Authors: Gori Avantika , Lin Ning , Xi Dazhi , Emanuel Kerry
Published: February 2022

Tropical cyclones (TCs) are drivers of extreme rainfall and surge, but the current and future TC rainfall–surge joint hazard has not been well quantified. Using a physics-based approach to simulate TC rainfall and storm tides, we show drastic increases in the joint hazard from historical to projected future (SSP5–8.5) conditions. The frequency of joint extreme events (exceeding both hazards’ historical 100-year levels) may increase by 7–36-fold in the southern US and 30–195-fold in the Northeast by 2100. This increase in joint hazard is induced by sea-level rise and TC climatology change; the relative contribution of TC climatology change is higher than that of sea-level rise for 96% of the coast, largely due to rainfall increases. Increasing storm intensity and decreasing translation speed are the main TC change factors that cause higher rainfall and storm tides and up to 25% increase in their dependence.
Large-scale deep multi-layer analysis of Alzheimer’s disease brain reveals strong proteomic disease-related changes not observed at the RNA level
Authors: Johnson Erik C. B. , Carter E. Kathleen , Dammer Eric B. , Duong Duc M. , Gerasimov Ekaterina S. , Liu Yue , Liu Jiaqi , Betarbet Ranjita , Ping Lingyan , Yin Luming , Serrano Geidy E. , Beach Thomas G. , Peng Junmin , De Jager Philip L. , Haroutunian Vahram , Zhang Bin , Gaiteri Chris , Bennett David A. , Gearing Marla , Wingo Thomas S. , Wingo Aliza P. , Lah James J. , Levey Allan I. , Seyfried Nicholas T.
Published: February 2022

The biological processes that are disrupted in the Alzheimer’s disease (AD) brain remain incompletely understood. In this study, we analyzed the proteomes of more than 1,000 brain tissues to reveal new AD-related protein co-expression modules that were highly preserved across cohorts and brain regions. Nearly half of the protein co-expression modules, including modules significantly altered in AD, were not observed in RNA networks from the same cohorts and brain regions, highlighting the proteopathic nature of AD. Two such AD-associated modules unique to the proteomic network included a module related to MAPK signaling and metabolism and a module related to the matrisome. The matrisome module was influenced by the APOE ε4 allele but was not related to the rate of cognitive decline after adjustment for neuropathology. By contrast, the MAPK/metabolism module was strongly associated with the rate of cognitive decline. Disease-associated modules unique to the proteome are sources of promising therapeutic targets and biomarkers for AD.
French crop yield, area and production data for ten staple crops from 1900 to 2018 at county resolution
Authors: Schauberger Bernhard , Kato Hiromi , Kato Tomomichi , Watanabe Daiki , Ciais Philippe
Published: February 2022

Agricultural performance is influenced by environmental conditions, management decisions and economic circumstances. It is important to quantify their respective contribution to allow for detecting major hazards to production, projecting future yields under climate change and deriving adaptation options. For this purpose, time series of agricultural yields with high spatial and long-term temporal resolution are a primary requisite. Here we present a data set of crop performance in France, one of Europe’s major crop producers. The data set comprises ten crops (barley, maize, oats, potatoes, rapeseed, sugarbeet, sunflower, durum wheat, soft wheat and wine) and covers the years 1900 to 2018. It contains harvested area, production and yield data for all 96 French départements (i.e. counties or NUTS3 level) with a total number of 375,264 data points. Entries until 1988 have been digitized manually from statistical yearbooks. The technical validation indicates a high consistency of the data set within itself and with external resources. The data set may contribute to an enhanced understanding of the manifold influences on agricultural performance.
Agent-based models for detecting the driving forces of biomolecular interactions
Authors: Maestri Stefano , Merelli Emanuela , Pettini Marco
Published: February 2022

Agent-based modelling and simulation have been effectively applied to the study of complex biological systems, especially when composed of many interacting entities. Representing biomolecules as autonomous agents allows this approach to bring out the global behaviour of biochemical processes as resulting from local molecular interactions. In this paper, we leverage the capabilities of the agent paradigm to construct an in silico replica of the glycolytic pathway; the aim is to detect the role that long-range electrodynamic forces might have on the rate of glucose oxidation. Experimental evidences have shown that random encounters and short-range potentials might not be sufficient to explain the high efficiency of biochemical reactions in living cells. However, while the latest in vitro studies are limited by present-day technology, agent-based simulations provide an in silico support to the outcomes hitherto obtained and shed light on behaviours not yet well understood. Our results grasp properties hard to uncover through other computational methods, such as the effect of electromagnetic potentials on glycolytic oscillations.
Voltage imaging in the olfactory bulb using transgenic mouse lines expressing the genetically encoded voltage indicator ArcLight
Authors: Platisa Jelena , Zeng Hongkui , Madisen Linda , Cohen Lawrence B. , Pieribone Vincent A. , Storace Douglas A.
Published: February 2022

Genetically encoded voltage indicators (GEVIs) allow optical recordings of membrane potential changes in defined cell populations. Transgenic reporter animals that facilitate precise and repeatable targeting with high expression levels would further the use of GEVIs in the in vivo mammalian brain. However, the literature on developing and applying transgenic mouse lines as vehicles for GEVI expression is limited. Here we report the first in vivo experiments using a transgenic reporter mouse for the GEVI ArcLight, which utilizes a Cre/tTA dependent expression system (TIGRE 1.0). We developed two mouse lines with ArcLight expression restricted to either olfactory receptor neurons, or a subpopulation of interneurons located in the granule and glomerular layers in the olfactory bulb. The ArcLight expression in these lines was sufficient for in vivo imaging of odorant responses in single trials using epifluorescence and 2-photon imaging. The voltage responses were odor-specific and concentration-dependent, which supported earlier studies about perceptual transformations carried out by the bulb that used calcium sensors of neural activity. This study demonstrates that the ArcLight transgenic line is a flexible genetic tool that can be used to record the neuronal electrical activity of different cell types with a signal-to-noise ratio that is comparable to previous reports using viral transduction.
Adapting to the pandemic: longitudinal effects of social restrictions on time perception and boredom during the Covid-19 pandemic in Germany
Authors: Wessels Marlene , Utegaliyev Nariman , Bernhard Christoph , Welsch Robin , Oberfeld Daniel , Thönes Sven , von Castell Christoph
Published: February 2022

With the Covid-19 pandemic, many governments introduced nationwide lockdowns that disrupted people’s daily routines and promoted social isolation. We applied a longitudinal online survey to investigate the mid-term effects of the mandated restrictions on the perceived passage of time (PPT) and boredom during and after a strict lockdown in Germany. One week after the beginning of the lockdown in March 2020, respondents reported a slower PPT and increased boredom compared to the pre-pandemic level. However, in the course of the lockdown, PPT accelerated and boredom decreased again until August 2020. Then, in October 2020, when incidence rates sharply rose and new restrictions were introduced, we again observed a slight trend toward a slowing of PPT and an increase of boredom. Our data also show that as the pandemic progressed, respondents adjusted their predictions about the pandemic’s duration substantially upward. In sum, our findings suggest that respondents adapted to the pandemic situation and anticipated it as the new “normal”. Furthermore, we determined perceived boredom and the general emotional state to be predictive of PPT, while depressive symptoms played a minor role.
Energy homeostasis genes modify the association between serum concentrations of IGF-1 and IGFBP-3 and breast cancer risk
Authors: Rodríguez-Valentín Rocío , Torres-Mejía Gabriela , Martínez-Matsushita Louis , Angeles-Llerenas Angélica , Gómez-Flores-Ramos Liliana , Wolff Roger K. , Baumgartner Kathy B. , Hines Lisa M. , Ziv Elad , Flores-Luna Lourdes , Sánchez-Zamorano Luisa Ma. , Ortiz-Panozo Eduardo , Slattery Martha L.
Published: February 2022

Breast cancer is a multifactorial disease in which the interplay among multiple risk factors remains unclear. Energy homeostasis genes play an important role in carcinogenesis and their interactions with the serum concentrations of IGF-1 and IGFBP-3 on the risk of breast cancer have not yet been investigated. The aim of this study was to assess the modifying effect of the genetic variation in some energy homeostasis genes on the association of serum concentrations of IGF-1 and IGFBP-3 with breast cancer risk. We analyzed 78 SNPs from 10 energy homeostasis genes in premenopausal women from the 4-Corner’s Breast Cancer Study (61 cases and 155 controls) and the Mexico Breast Cancer Study (204 cases and 282 controls). After data harmonization, 71 SNPs in HWE were included for interaction analysis. Two SNPs in two genes (MBOAT rs13272159 and NPY rs16131) showed an effect modification on the association between IGF-1 serum concentration and breast cancer risk (Pinteraction < 0.05, adjusted Pinteraction < 0.20). In addition, five SNPs in three genes (ADIPOQ rs182052, rs822391 and rs7649121, CARTPT rs3846659, and LEPR rs12059300) had an effect modification on the association between IGFBP-3 serum concentration and breast cancer risk (Pinteraction < 0.05, adjusted Pinteraction < 0.20). Our findings showed that variants of energy homeostasis genes modified the association between the IGF-1 or IGFBP-3 serum concentration and breast cancer risk in premenopausal women. These findings contribute to a better understanding of this multifactorial pathology.
Organic matter removal in a simultaneous nitrification–denitrification process using fixed-film system
Authors: González-Tineo P. , Aguilar A. , Reynoso A. , Durán U. , Garzón-Zúñiga M. , Meza-Escalante E. , Álvarez L. , Serrano D.
Published: February 2022

Swine wastewater treatment is a complex challenge, due to the high organic matter (OM) and nitrogen (N) concentrations which require an efficient process. This study focused on evaluating two different support media for OM and N removal from an Upflow Anaerobic Sludge Blanket (UASB) reactor fed with swine wastewater. Maximum specific nitrification (MSNA) and denitrification (MSDA) activity test for both biofilm and suspended biomass were carried out using as supports: polyurethane foam (R1) and polyethylene rings (R2). The results showed that R2 system was more efficiently than R1, reaching OM removal of 77 ± 8% and N of 98 ± 4%, attributed to higher specific denitrifying activity recorded (5.3 ± 0.34 g NO3-N/g TVS∙h). Furthermore, 40 ± 5% of the initial N in the wastewater could have been transformed into molecular nitrogen through SND, of which only 10 ± 1% was volatilized. In this sense, MSDA tests indicated that suspended biomass was responsible for at least 70% of N removal and only 20% can be attributed to biofilm. SND could be confirmed with the analysis of microbial diversity, due to the presence of the genus Pseudomonas dominated the prokaryotic community of the system in 54.4%.
Abnormal corneal nerve morphology and brain volume in patients with schizophrenia
Authors: Ponirakis Georgios , Ghandi Reem , Ahmed Amani , Gad Hoda , Petropoulos Ioannis N. , Khan Adnan , Elsotouhy Ahmed , Vattoth Surjith , Alshawwaf Mahmoud K. M. , Khoodoruth Mohamed Adil Shah , Ramadan Marwan , Bhagat Anjushri , Currie James , Mahfoud Ziyad , Al Hamad Hanadi , Own Ahmed , M. Haddad Peter , Alabdulla Majid , Malik Rayaz A. , Woodruff Peter W.
Published: February 2022

Neurodevelopmental and neurodegenerative pathology occur in Schizophrenia. This study compared the utility of corneal confocal microscopy (CCM), an ophthalmic imaging technique with MRI brain volumetry in quantifying neuronal pathology and its relationship to cognitive dysfunction and symptom severity in schizophrenia. Thirty-six subjects with schizophrenia and 26 controls underwent assessment of cognitive function, symptom severity, CCM and MRI brain volumetry. Subjects with schizophrenia had lower cognitive function (P ≤ 0.01), corneal nerve fiber density (CNFD), length (CNFL), branch density (CNBD), CNBD:CNFD ratio (P < 0.0001) and cingulate gyrus volume (P < 0.05) but comparable volume of whole brain (P = 0.61), cortical gray matter (P = 0.99), ventricle (P = 0.47), hippocampus (P = 0.10) and amygdala (P = 0.68). Corneal nerve measures and cingulate gyrus volume showed no association with symptom severity (P = 0.35–0.86 and P = 0.50) or cognitive function (P = 0.35–0.86 and P = 0.49). Corneal nerve measures were not associated with metabolic syndrome (P = 0.61–0.64) or diabetes (P = 0.057–0.54). The area under the ROC curve distinguishing subjects with schizophrenia from controls was 88% for CNFL, 84% for CNBD and CNBD:CNFD ratio, 79% for CNFD and 73% for the cingulate gyrus volume. This study has identified a reduction in corneal nerve fibers and cingulate gyrus volume in schizophrenia, but no association with symptom severity or cognitive dysfunction. Corneal nerve loss identified using CCM may act as a rapid non-invasive surrogate marker of neurodegeneration in patients with schizophrenia.
Suppression of non-selected solutions as a possible brain mechanism for ambiguity resolution in the word fragment task completion task
Authors: Kireev Maxim , Korotkov Alexander , Masharipov Ruslan , Zheltyakova Maya , Cherednichenko Denis , Gershkovich Valeria , Moroshkina Nadezhda , Slioussar Natalia , Allakhverdov Victor , Chernigovskaya Tatiana
Published: February 2022

Brain systems dealing with multiple meanings of ambiguous stimuli are relatively well studied, while the processing of non-selected meanings is less investigated in the neurophysiological literature and provokes controversy between existing theories. It is debated whether these meanings are actively suppressed and, if yes, whether suppression characterizes any task that involves alternative solutions or only those tasks that emphasize semantic processing or the existence of alternatives. The current functional MRI event-related study used a modified version of the word fragment completion task to reveal brain mechanisms involved in implicit processing of the non-selected solutions of ambiguous fragments. The stimuli were pairs of fragmented adjectives and nouns. Noun fragments could have one or two solutions (resulting in two words with unrelated meanings). Adjective fragments had one solution and created contexts strongly suggesting one solution for ambiguous noun fragments. All fragmented nouns were presented twice during the experiment (with two different adjectives). We revealed that ambiguity resolution was associated with a reduced BOLD signal within several regions related to language processing, including the anterior hippocampi and amygdala and posterior lateral temporal cortex. Obtained findings were interpreted as resulting from brain activity inhibition, which underlies a hypothesized mechanism of suppression of non-selected solutions.
The gut virome in two indigenous populations from Malaysia
Authors: Lee Chuen Zhang , Zoqratt Muhammad Zarul Hanifah Md , Phipps Maude E. , Barr Jeremy J. , Lal Sunil K. , Ayub Qasim , Rahman Sadequr
Published: February 2022

The human gut contains a complex microbiota dominated by bacteriophages but also containing other viruses and bacteria and fungi. There are a growing number of techniques for the extraction, sequencing, and analysis of the virome but currently no standardized protocols. This study established an effective workflow for virome analysis to investigate the virome of stool samples from two understudied ethnic groups from Malaysia: the Jakun and Jehai Orang Asli. By using the virome extraction and analysis workflow with the Oxford Nanopore Technology, long-read sequencing successfully captured close to full-length viral genomes. The virome composition of the two indigenous Malaysian communities were remarkably different from those found in other parts of the world. Additionally, plant viruses found in the viromes of these individuals were attributed to traditional food-seeking methods. This study establishes a human gut virome workflow and extends insights into the healthy human gut virome, laying the groundwork for comparative studies.
A wave finite element approach for modelling wave transmission through laminated plate junctions
Authors: Aimakov Nurkanat , Tanner Gregor , Chronopoulos Dimitrios
Published: February 2022

We present a numerical method for computing reflection and transmission coefficients at joints connecting composite laminated plates. The method is based on modelling joints with finite elements with boundary conditions given by the solutions of the wave finite element method for the plates in the infinite half-spaces connected to the joint. There are no restrictions on the number of plates, inter-plate angles, and material parameters of individual layers forming the composite. An L-shaped laminated plate junction is discussed in more detail. Comparisons of numerically predicted scattering coefficients with semi-analytical solutions for the selected structures are presented. The results obtained are essential for statistical energy analysis and dynamical energy analysis based calculations of the wave energy distribution in full built-up structure.
The sodium–glucose cotransporter 2 inhibitor ipragliflozin improves liver function and insulin resistance in Japanese patients with type 2 diabetes
Authors: Okura Tsuyoshi , Fujioka Yohei , Nakamura Risa , Kitao Sonoko , Ito Yuichi , Anno Mari , Matsumoto Kazuhisa , Shoji Kyoko , Matsuzawa Kazuhiko , Izawa Shoichiro , Okura Hiroko , Ueta Etsuko , Kato Masahiko , Imamura Takeshi , Taniguchi Shin-ichi , Yamamoto Kazuhiro
Published: February 2022

Sodium–glucose cotransporter 2 inhibitor (SGLT2i) treatment is a therapeutic approach for type 2 diabetes mellitus (T2DM). Some reports have shown that SGLT2i treatment improves insulin resistance; however, few studies have evaluated insulin resistance by the glucose clamp method. Hepatic insulin clearance (HIC) is a new pathophysiological mechanism of T2DM. The effect of SGLT2i treatment on hepatic insulin clearance and insulin resistance is not well known. We investigated the effect of SGLT2i treatment on insulin resistance, insulin secretion, incretin levels, body composition, and hepatic insulin clearance. We conducted a meal tolerance test (MTT) and a hyperinsulinemic-euglycemic clamp test in 9 T2DM patients. Ipragliflozin (50 mg/day) was administered, and the MTT and clamp test were performed after 4 months. We calculated HIC as the postprandial C-peptide AUC-to-insulin AUC ratio. We also measured GLP-1, GIP, and glucagon levels during the MTT. Body weight and HbA1c were decreased, although not significantly, after 4 months of treatment. Postprandial glucose, fasting insulin and postprandial insulin were significantly decreased. Insulin resistance with the glucose clamp was not changed, but the HOMA-IR and insulin sensitivity indices were significantly improved. Incretin and glucagon levels were not changed. Hepatic insulin clearance was significantly increased, but whole-body insulin clearance was not changed. The FIB-4 index and fatty liver index were significantly reduced. The HOMA-beta and insulinogenic indices were not changed, but the C-peptide index was significantly increased. Although the number of patients was small, these results suggested that SGLT2i treatment improved liver function, decreased hepatic insulin resistance, and increased hepatic insulin clearance, despite the small weight reduction.
Wave attenuation through forests under extreme conditions
Authors: van Wesenbeeck Bregje K. , Wolters Guido , Antolínez José A. A. , Kalloe Sudarshini A. , Hofland Bas , de Boer Wiebe P. , Çete Ceylan , Bouma Tjeerd J.
Published: February 2022

Worldwide, communities are facing increasing flood risk, due to more frequent and intense hazards and rising exposure through more people living along coastlines and in flood plains. Nature-based Solutions (NbS), such as mangroves, and riparian forests, offer huge potential for adaptation and risk reduction. The capacity of trees and forests to attenuate waves and mitigate storm damages receives massive attention, especially after extreme storm events. However, application of forests in flood mitigation strategies remains limited to date, due to lack of real-scale measurements on the performance under extreme conditions. Experiments executed in a large-scale flume with a willow forest to dissipate waves show that trees are hardly damaged and strongly reduce wave and run-up heights, even when maximum wave heights are up to 2.5 m. It was observed for the first time that the surface area of the tree canopy is most relevant for wave attenuation and that the very flexible leaves limitedly add to effectiveness. Overall, the study shows that forests can play a significant role in reducing wave heights and run-up under extreme conditions. Currently, this potential is hardly used but may offer future benefits in achieving more adaptive levee designs.
Comparison of clinical outcomes between carbon ion radiotherapy and X-ray radiotherapy for reirradiation in locoregional recurrence of rectal cancer
Authors: Chung Seung Yeun , Takiyama Hirotoshi , Kang Jae Hyun , Chang Jee Suk , Min Byung Soh , Tsuji Hiroshi , Yamada Shigeru , Koom Woong Sub
Published: February 2022

Carbon ion radiotherapy (CIRT) has garnered interest for the treatment of locoregional rectal cancer recurrence. No study has compared CIRT and X-ray radiotherapy (XRT) for reirradiation (reRT) in such cases. We analyzed and compared the clinical outcomes such as local control, overall survival, and late toxicity rate between CIRT and XRT, for treating locoregional rectal cancer recurrence. Patients with rectal cancer who received reRT to the pelvis by CIRT or XRT from March 2005 to July 2019 were included. The CIRT treatment schedule was 70.4 Gy (relative biological effectiveness) in 16 fractions. For the XRT group, the median reRT dose was 50 Gy (range 25–62.5 Gy) with a median of 25 fractions (range 3–33). Thirty-five and 31 patients received CIRT and XRT, respectively. Tumour and treatment characteristics such as recurrence location and chemotherapy treatment differed between the two groups. CIRT showed better control of local recurrence (adjusted hazard ratio [HR] 0.17; p = 0.002), better overall survival (HR 0.30; p = 0.004), and lower severe late toxicity rate (HR 0.15; p = 0.015) than XRT. CIRT was effective for treating locoregional rectal cancer recurrence, with high rates of local control and survival, and a low late severe toxicity rate.
Integrated physiological, proteomic, and metabolomic analyses of pecan cultivar ‘Pawnee’ adaptation to salt stress
Authors: Jiao Yun , Zhang Jianhong , Pan Cunde
Published: February 2022

The pecan is a salt-alkali-tolerant plant, and its fruit and wood have high economic value. This study aimed to explore the molecular mechanisms responsible for salt stress tolerance in the pecan grown under hydroponic conditions to simulate salt stress. The results showed that the photosynthetic rate (Pn) was reduced in response to salt stress, while the intercellular carbon dioxide concentrations (Ci) increased. The response of the pecan to salt stress was measured using iTRAQ (isobaric tags for relative or absolute quantitation) and LC/MS (liquid chromatography and mass spectrometry) non-targeted metabolomics technology. A total of 198 differentially expressed proteins (65 down-regulated and 133 up-regulated) and 538 differentially expressed metabolites (283 down-regulated and 255 up-regulated) were identified after exposure to salt stress for 48 h. These genes were associated with 21 core pathways, shown by Kyoto Encyclopedia of Genes and Genomes annotation and enrichment, including the metabolic pathways involved in nucleotide sugar and amino sugar metabolism, amino acid biosynthesis, starch and sucrose metabolism, and phenylpropane biosynthesis. In addition, analysis of interactions between the differentially expressed proteins and metabolites showed that two key nodes of the salt stress regulatory network, L-fucose and succinate, were up-regulated and down-regulated, respectively, suggesting that these metabolites may be significant for adaptations to salt stress. Finally, several key proteins were further verified by parallel reaction monitoring. In conclusion, this study used physiological, proteomic, and metabolomic methods to provide an important preliminary foundation for improving the salt tolerance of pecans.
Insights and genetic features of extended-spectrum beta-lactamase producing Escherichia coli isolates from two hospitals in Ghana
Authors: Mahazu Samiratu , Sato Wakana , Ayibieke Alafate , Prah Isaac , Hayashi Takaya , Suzuki Toshihiko , Iwanaga Shiroh , Ablordey Anthony , Saito Ryoichi
Published: February 2022

Recently, the emergence and rapid dissemination of extended-spectrum beta-lactamase (ESBL)-producing bacteria, particularly of the family Enterobacteriaceae, has posed serious healthcare challenges. Here, we determined the antimicrobial susceptibility and genetic characteristics of 164 Escherichia coli strains isolated from infected patients in two hospitals in Ghana. In total, 102 cefotaxime-resistant isolates (62.2%) were identified as ESBL-producers. Multilocus sequence typing of the ESBL-producers identified 20 different sequence types (STs) with ST131 (n = 25, 24.5%) as the dominant group. Other detected STs included ST410 (n = 21, 20.6%) and ST617 (n = 19, 18.6%). All identified ESBL-producers harbored blaCTX-M-14, blaCTX-M-15, or blaCTX-M-27, with blaCTX-M-15 (n = 96, 94.1%) being the most predominant ESBL allele. Further analysis showed that the immediate genetic environment around blaCTX-M-15 is conserved within blaCTX-M-15 containing strains. Five of the 25 ST131 isolates were clustered with clade A, one with sub-clade C1, and 19 with the dominant sub-clade C2. The results show that fluoroquinolone-resistant, blaCTX-M-14- and blaCTX- M-15-producing ESBL E. coli ST131 strains belonging to clade A and sub-clades C1 and C2 are disseminating in Ghanaian hospitals. To the best of our knowledge, this is the first report of the ST131 phylogeny in Ghana.
Deep learning based diagnosis for cysts and tumors of jaw with massive healthy samples
Authors: Yu Dan , Hu Jiacong , Feng Zunlei , Song Mingli , Zhu Huiyong
Published: February 2022

We aimed to develop an explainable and reliable method to diagnose cysts and tumors of the jaw with massive panoramic radiographs of healthy peoples based on deep learning, since collecting and labeling massive lesion samples are time-consuming, and existing deep learning-based methods lack explainability. Based on the collected 872 lesion samples and 10,000 healthy samples, a two-branch network was proposed for classifying the cysts and tumors of the jaw. The two-branch network is firstly pretrained on massive panoramic radiographs of healthy peoples, then is trained for classifying the sample categories and segmenting the lesion area. Totally, 200 healthy samples and 87 lesion samples were included in the testing stage. The average accuracy, precision, sensitivity, specificity, and F1 score of classification are 88.72%, 65.81%, 66.56%, 92.66%, and 66.14%, respectively. The average accuracy, precision, sensitivity, specificity, and F1 score of classification will reach 90.66%, 85.23%, 84.27%, 93.50%, and 84.74%, if only classifying the lesion samples and healthy samples. The proposed method showed encouraging performance in the diagnosis of cysts and tumors of the jaw. The classified categories and segmented lesion areas serve as the diagnostic basis for further diagnosis, which provides a reliable tool for diagnosing jaw tumors and cysts.
Identification and selection of healthy spermatozoa in heterozygous carriers of the Phe508del-variant of the CFTR-gene in assisted reproduction
Authors: De Geyter Julie , Gallati-Kraemer Sabina , Zhang Hong , De Geyter Christian
Published: February 2022

The pathogenic variant Phe508del of the CFTR-gene is the most frequent cause of cystic fibrosis (CF). Whereas male CF-patients are infertile due to bilateral agenesis of the efferent ducts, the fertility status of male heterozygous carriers is uncertain. We aimed at demonstrating the involvement of the CFTR-ion channel during sperm capacitation and to potentially select variant-free spermatozoa in heterozygous carriers of the CFTR-variant using flow cytometry (FC). Using FC and sorting, single cell polymerase chain reaction, immuno-fluorescent staining an experimental study was performed on nine fertile semen donors and three heterozygous infertile men carrying the Phe508del gene variant. Chemical inhibition of CFTR interfered with sperm capacitation. Most viable spermatozoa of heterozygous carriers of the Phe508del variant of the CFTR-gene show immune-fluorescent CFTR. Sperm capacitation in Phe508del carriers was similar to that in healthy semen donors. Distribution of the Phe508del allele in trio data of CF-affected families corresponded to the expected recessive inheritance pattern. Infertility in Phe508del heterozygous men is unlikely to be caused by the pathogenic variant although some contribution cannot be excluded. Normal sperm capacitation in carriers of pathogenic variants of the Phe508del-gene may in part explain the high prevalence of a potentially lethal recessive disorder.
Climate drives long-term change in Antarctic Silverfish along the western Antarctic Peninsula
Authors: Corso Andrew D. , Steinberg Deborah K. , Stammerjohn Sharon E. , Hilton Eric J.
Published: February 2022

Over the last half of the 20th century, the western Antarctic Peninsula has been one of the most rapidly warming regions on Earth, leading to substantial reductions in regional sea ice coverage. These changes are modulated by atmospheric forcing, including the Amundsen Sea Low (ASL) pressure system. We utilized a novel 25-year (1993–2017) time series to model the effects of environmental variability on larvae of a keystone species, the Antarctic Silverfish (Pleuragramma antarctica). Antarctic Silverfish use sea ice as spawning habitat and are important prey for penguins and other predators. We show that warmer sea surface temperature and decreased sea ice are associated with reduced larval abundance. Variability in the ASL modulates both sea surface temperature and sea ice; a strong ASL is associated with reduced larvae. These findings support a narrow sea ice and temperature tolerance for adult and larval fish. Further regional warming predicted to occur during the 21st century could displace populations of Antarctic Silverfish, altering this pelagic ecosystem.
Cortical neural dynamics unveil the rhythm of natural visual behavior in marmosets
Authors: Kaneko Takaaki , Komatsu Misako , Yamamori Tetsuo , Ichinohe Noritaka , Okano Hideyuki
Published: February 2022

Numerous studies have shown that the visual system consists of functionally distinct ventral and dorsal streams; however, its exact spatial-temporal dynamics during natural visual behavior remain to be investigated. Here, we report cerebral neural dynamics during active visual exploration recorded by an electrocorticographic array covering the entire lateral surface of the marmoset cortex. We found that the dorsal stream was activated before the primary visual cortex with saccades and followed by the alteration of suppression and activation signals along the ventral stream. Similarly, the signal that propagated from the dorsal to ventral visual areas was accompanied by a travelling wave of low frequency oscillations. Such signal dynamics occurred at an average of 220 ms after saccades, which corresponded to the timing when whole-brain activation returned to background levels. We also demonstrated that saccades could occur at any point of signal flow, indicating the parallel computation of motor commands. Overall, this study reveals the neural dynamics of active vision, which are efficiently linked to the natural rhythms of visual exploration.
Physiology can predict animal activity, exploration, and dispersal
Authors: Wu Nicholas C. , Seebacher Frank
Published: February 2022

Physiology can underlie movement, including short-term activity, exploration of unfamiliar environments, and larger scale dispersal, and thereby influence species distributions in an environmentally sensitive manner. We conducted meta-analyses of the literature to establish, firstly, whether physiological traits underlie activity, exploration, and dispersal by individuals (88 studies), and secondly whether physiological characteristics differed between range core and edges of distributions (43 studies). We show that locomotor performance and metabolism influenced individual movement with varying levels of confidence. Range edges differed from cores in traits that may be associated with dispersal success, including metabolism, locomotor performance, corticosterone levels, and immunity, and differences increased with increasing time since separation. Physiological effects were particularly pronounced in birds and amphibians, but taxon-specific differences may reflect biased sampling in the literature, which also focussed primarily on North America, Europe, and Australia. Hence, physiology can influence movement, but undersampling and bias currently limits general conclusions.
Macrophage migration inhibitory factor is overproduced through EGR1 in TET2low resting monocytes
Authors: Pronier Elodie , Imanci Aygun , Selimoglu-Buet Dorothée , Badaoui Bouchra , Itzykson Raphael , Roger Thierry , Jego Chloé , Naimo Audrey , Francillette Maëla , Breckler Marie , Wagner-Ballon Orianne , Figueroa Maria E. , Aglave Marine , Gautheret Daniel , Porteu Françoise , Bernard Olivier A. , Vainchenker William , Delhommeau François , Solary Eric , Droin Nathalie M.
Published: February 2022

Somatic mutation in TET2 gene is one of the most common clonal genetic events detected in age-related clonal hematopoiesis as well as in chronic myelomonocytic leukemia (CMML). In addition to being a pre-malignant state, TET2 mutated clones are associated with an increased risk of death from cardiovascular disease, which could involve cytokine/chemokine overproduction by monocytic cells. Here, we show in mice and in human cells that, in the absence of any inflammatory challenge, TET2 downregulation promotes the production of MIF (macrophage migration inhibitory factor), a pivotal mediator of atherosclerotic lesion formation. In healthy monocytes, TET2 is recruited to MIF promoter and interacts with the transcription factor EGR1 and histone deacetylases. Disruption of these interactions as a consequence of TET2-decreased expression favors EGR1-driven transcription of MIF gene and its secretion. MIF favors monocytic differentiation of myeloid progenitors. These results designate MIF as a chronically overproduced chemokine and a potential therapeutic target in patients with clonal TET2 downregulation in myeloid cells.
Synthesis of α,β-unsaturated ketones through nickel-catalysed aldehyde-free hydroacylation of alkynes
Authors: Rhlee Joon Ho , Maiti Saikat , Lee Jeong Woo , Lee Ho Seung , Bakhtiyorzoda Ismoili Ahror , Lee Soochan , Park Jaehyun , Kang Seok Ju , Kim Yung Sam , Seo Jeong Kon , Myung Kyungjae , Choe Wonyoung , Hong Sung You
Published: February 2022

α,β-Unsaturated ketones are common feedstocks for the synthesis of fine chemicals, pharmaceuticals, and natural products. Transition metal-catalysed hydroacylation reactions of alkynes using aldehydes have been recognised as an atom-economical route to access α,β-unsaturated ketones through chemoselective aldehydic C–H activation. However, the previously reported hydroacylation reactions using rhodium, cobalt, or ruthenium catalysts require chelating moiety-bearing aldehydes to prevent decarbonylation of acyl-metal-hydride complexes. Herein, we report a nickel-catalysed anti-Markovnikov selective coupling process to afford non-tethered E-enones from terminal alkynes and S-2-pyridyl thioesters in the presence of zinc metal as a reducing agent. Utilization of a readily available thioester as an acylating agent and water as a proton donor enables the mechanistically distinctive and aldehyde-free hydroacylation of terminal alkynes. This non-chelation-controlled approach features mild reaction conditions, high step economy, and excellent regio- and stereoselectivity.
Integrated quantum polariton interferometry
Authors: Nigro Davide , D’Ambrosio Vincenzo , Sanvitto Daniele , Gerace Dario
Published: February 2022

Exciton-polaritons are hybrid radiation-matter elementary excitations that, thanks to their strong nonlinearities, enable a plethora of physical phenomena ranging from room temperature condensation to superfluidity. While polaritons are usually exploited in a high-density regime, evidence for quantum correlations at the level of few excitations has been recently reported, thus suggesting the possibility of using these systems for quantum information purposes. Here we show that integrated circuits of propagating single polaritons can be arranged to build deterministic quantum logic gates in which the two-particle interaction energy plays a crucial role. Besides showing their prospective potential for photonic quantum computation, we also show that these systems can be exploited for metrology purposes, as for instance to precisely measure the magnitude of the polariton-polariton interaction at the two-body level. Our results will motivate the development of practical quantum polaritonic devices in prospective quantum technologies.
Environmental structure impacts microbial composition and secondary metabolism
Authors: Junkins Emily N , McWhirter Joseph B , McCall Laura-Isobel , Stevenson Bradley S
Published: February 2022

Determining the drivers of microbial community assembly is a central theme of microbial ecology, and chemical ecologists seek to characterize how secondary metabolites mediate these assembly patterns. Environmental structure affects how communities assemble and what metabolic pathways aid in that assembly. Here, we bridged these two perspectives by addressing the chemical drivers of community assembly within a spatially structured landscape with varying oxygen availability. We hypothesized that structured environments would favor higher microbial diversity and metabolite diversity. We anticipated that the production of a compound would be more advantageous in a structured environment (less mixing) compared to an unstructured environment (more mixing), where the molecule would have a diminished local effect. We observed this to be partially true in our experiments: structured environments had similar microbial diversity compared to unstructured environments but differed significantly in the metabolites produced. We also found that structured environments selected for communities with higher evenness, rather than communities with higher richness. This supports the idea that when characterizing the drivers of community assembly, it matters less about who is there and more about what they are doing. Overall, these data contribute to a growing effort to approach microbial community assembly with interdisciplinary tools and perspectives.
Genomic analysis of focal nodular hyperplasia with associated hepatocellular carcinoma unveils its malignant potential: a case report
Authors: Ercan Caner , Coto-Llerena Mairene , Gallon John , Fourie Lana , Marinucci Mattia , Hess Gabriel F. , Vosbeck Jürg , Taha-Mehlitz Stephanie , Boldanova Tuyana , Meier Marie-Anne , Tzankov Alexandar , Matter Matthias S. , Hoffmann Martin H. K. , Di Tommaso Luca , von Flüe Markus , Ng Charlotte K. Y. , Heim Markus H. , Soysal Savas D. , Terracciano Luigi M. , Kollmar Otto , Piscuoglio Salvatore
Published: February 2022

Background

Focal nodular hyperplasia (FNH) is typically considered a benign tumor of the liver without malignant potential. The co-occurrence of FNH and hepatocellular carcinoma (HCC) has been reported in rare cases. In this study we sought to investigate the clonal relationship between these lesions in a patient with FNH-HCC co-occurrence.

Methods

A 74-year-old female patient underwent liver tumor resection. The resected nodule was subjected to histologic analyses using hematoxylin and eosin stain and immunohistochemistry. DNA extracted from microdissected FNH and HCC regions was subjected to whole exome sequencing. Clonality analysis were performed using PyClone.

Results

Histologic analysis reveals that the nodule consists of an FNH and two adjoining HCC components with distinct histopathological features. Immunophenotypic characterization and genomic analyses suggest that the FNH is clonally related to the HCC components, and is composed of multiple clones at diagnosis, that are likely to have progressed to HCC through clonal selection and/or the acquisition of additional genetic events.

Conclusion

To the best of our knowledge, our work is the first study showing a clonal relationship between FNH and HCC. We show that FNH may possess the capability to undergo malignant transformation and to progress to HCC in very rare cases.
LC-MS/MS methodology development and validation for the screening and quantification of five antibiotics in water
Authors: Nunes M. João , Paz Victória , Cordas Cristina M. , Noronha João Paulo , Branco Luís C.
Published: February 2022

A screening LC-MS/MS method was established for five antibiotics. The optimization and validation proved that it is suitable for the identification and quantification. The utility for the removal process of antibiotics from water was proven.
Preliminaryin vivostudy of biodegradable PLA–PEU–PLA anti-adhesion membranes in a rat Achilles tendon model of peritendinous adhesions
Authors: Hadda Zebiri , Hélène Van Den Berghe , Tom Paunet , Aurélie Wolf-Mandroux , Audrey Bethry , Hubert Taillades , Noël Yohan Jean , Pirot Nelly , Catherine Botteron , Michel Chammas , Pierre-Emmanuel Chammas , Xavier Garric
Published: February 2022

In vivoevaluation of PLA–PEU–PLA membranes (D-PACO) for the prevention of peritendinous adhesions.
Metal imidazolate sulphate frameworks as a variation of zeolitic imidazolate frameworks
Authors: Noh Kyungkyou , Sim Jaeung , Kim Jonghoon , Kim Jaheon
Published: February 2022

Both imidazolate and sulphate ions can connect metal ions to give extended structures resembling zeolitic imidazolate frameworks.
Electrochemical control of the RWGS reaction over Ni nanoparticles deposited on yttria stabilized zirconia
Authors: Zagoraios Dimitrios , Kokkinou Nikoletta , Kyriakou Georgios , Katsaounis Alexandros
Published: February 2022

Transition metal oxides are promising candidates for the activation of the reverse water gas shift (RWGS) reaction.
Gardenia jasminoides J. Ellis extract alleviated white matter damage through promoting the differentiation of oligodendrocyte precursor cells via suppressing neuroinflammation
Authors: Zang Caixia , Liu Hui , Ju Cheng , Yuan Fangyu , Ning Jingwen , Shang Meiyu , Bao Xiuqi , Yu Yang , Yao Xinsheng , Zhang Dan
Published: February 2022

Gardenia jasminoides J. Ellis extract alleviated white matter damage through the promotion of OPC proliferation and differentiation, resulting in improved neuron and myelin function.
Color tunable aerogels/sponge-like structures developed from fine fiber membranes
Authors: Villarreal Alexa , Barbosa Raul , Bose Saptasree , Srivastava Bhupendra B. , Padilla-Gainza Victoria , Lozano Karen
Published: February 2022

The development of macroscopic aerogels from 1D systems, such as nanofibers, has resulted in a novel pathway to obtain porous and lightweight architectures.
Failure mechanism of solid-state electrolyte Li10GeP2S12 in a moist atmosphere: a first-principles study
Authors: Zhang Jin , Huang Li , Gu Xiao
Published: February 2022

Reaction mechanism of Li10GeP2S12 hydrolysis in a moist atmosphere to generate H2S gas.
Domain wall motion driven by a wide range of current in coupled soft/hard ferromagnetic nanowires
Authors: Yu Ziyang , Gong Bin , Xiong Lun , Du Xinran , Wei Chenhuinan , Xiong Rui , Lu Zhihong , Zhang Yue
Published: February 2022

A double FM nanowire system composed of two FM nanowires with distinct magnetic anisotropy constants (the lower DW is induced to move under the injection of current, and the upper one is also dragged to move by the interlayer magnetostatic coupling).
Acid-, mechano- and photochromic molecular switches based on a spiropyran derivative for rewritable papers
Authors: Yang Yuhui , Chen Yilong , Li Yuqing , Wang Zhaohui , Zhao Huimin
Published: February 2022

In this work, we report a novel acid-, photo- and mechanochromic material based on a spiropyran (SP) derivative.
Cobalt-catalyzed cascade hydroalkenylation of 1,6-enynes with chalcones
Authors: Pan Chunxiang , Wang Gaowei , Zhao Hengyuan , Ni Jianxiao , Fan Ruifeng , Zhou Yongyun , Zhu Yuanbin , Wu Shiyuan , Fan Baomin
Published: February 2022

An efficient stereoselective cobalt-catalyzed hydrovinylative cyclization of 1,6-enynes with chalcones to obtain functionalized pyrrolidines has been developed.
2,11-Dimethoxyldipyridopurinone as an efficient reducing visible-light photocatalyst for organic transformations
Authors: Wan Yameng , Liu Qingfeng , Wu Hao , Zhang Zhiguo , Zhang Guisheng
Published: February 2022

2,11-Dimethoxyldipyridopurinone (DP4) was demonstrated as a potent reducing visible-light PC that can efficiently catalyze three prototypic photoreactions: the redox-neutral, net oxidative and reductive reactions via oxidative-quenching mechanisms.
DFT-based study of the structural, optoelectronic, mechanical and magnetic properties of Ti3AC2 (A = P, As, Cd) for coating applications
Authors: Khalil R. M. Arif , Hussain Muhammad Iqbal , Luqman Nadia , Hussain Fayyaz , Rana Anwar Manzoor , Akhtar Muhammad Saeed , Mehmood Rana Farhat
Published: February 2022

The first-principles approach has used the Perdew–Burke–Ernzerhof exchange-correlation functional of generalized gradient approximation along with the Hubbard parameter to study various properties of titanium-based MAX materials Ti3AC2 (A = P, As, Cd).