bluuebunny/crossref_metadata_2025 huggingface dataset:
Systematic Cross-Biospecimen Evaluation of DNA Extraction Kits for Long- and Short-Read Multi-Metagenomic Sequencing Studies
Authors: Rehner Jacqueline , Schmartz Georges Pierre , Groeger Laura , Dastbaz Jan , Ludwig Nicole , Hannig Matthias , Rupf Stefan , Seitz Berthold , Flockerzi Elias , Berger Tim , Reichert Matthias Christian , Krawczyk Marcin , Meese Eckart , Herr Christian , Bals Robert , Becker Sören L. , Keller Andreas , Müller Rolf
Published: June 2022

High-quality DNA extraction is a crucial step in metagenomic studies. Bias by different isolation kits impairs the comparison across datasets. A trending topic is, however, the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with diseases. We thus collected bile, stool, saliva, plaque, sputum, and conjunctival swab samples and performed DNA extraction with three commercial kits. For each combination of the specimen type and DNA extraction kit, 20-gigabase (Gb) metagenomic data were generated using short-read sequencing. While profiles of the specimen types showed close proximity to each other, we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction kits. No kit outperformed all selected kits on every specimen. We reached consistently good results using the Qiagen QiAamp DNA Microbiome Kit. Depending on the specimen, our data indicate that over 10 Gb of sequencing data are required to achieve sufficient resolution, but DNA-based identification is superior to identification by mass spectrometry. Finally, long-read nanopore sequencing confirmed the results (correlation coefficient > 0.98). Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.
The gender politics of marriage in Ireland
Authors: Earner-Byrne Lindsey
Published: June 2022

It is rare that a book's dedication is quite so apposite to its theme as Maria Luddy and Mary O'Dowd's in their new history of marriage, which reads: ‘For Mary Cullen and Margaret MacCurtain who began it all.’ Indeed, they did, and this tour de force is a fitting testament to the significance of that women's history project started in the 1970s, which has ‘paved the way for all of us who engage with Irish gender history’ (p. xiii). Luddy and O'Dowd, both pioneers in the field in their own right, set themselves the not inconsiderable task of producing ‘an extended study of the history of heterosexual marriage on the island of Ireland from 1660–1925’ (p. 1). The result is a rich, colourful, at times playful, but also often depressing, five-hundred-and-fifty-page study of the most popular sexual bond between men and women in history — marriage. Indeed, that complex institution was obviously on the historical mind because Diane Urquhart's erudite study of Irish divorce from 1800 to 1997 and Sonja Tiernan's deftly navigated history of the marriage equality campaign in Ireland were also published in 2020.
Between Belonging and Identity in Ancient Judaism: The Role of Emotion in the Production of Identity - Reviewed: Kinship, Law and Politics: An Anatomy of Belonging. By Joseph E. David. Cambridge: Cambridge University Press, 2020. Pp. 156. $110.00 (cloth); $88.00 (digital). ISBN: 9781108499682.
Authors: Mermelstein Ari
Published: June 2022

This essay considers the vexed relationship between belonging and identity. Belonging is not an objective or unreflective association but rather an emotional assertion of attachment. That emotional connection is an indispensable component of identity, which, as Joseph David argues inKinship, Law and Politics: An Anatomy of Belonging, is a relationship charged with meaning. Accordingly, the distinction betweenbelongingas a privately held sentiment and thepolitics of belongingoverlooks the fact that the emotions associated with belonging define group membership. Belonging is not a private matter but an emotional relationship that shapes social life, reinforces a group’s identity politics, and finds expression in a group’s practices. Analysis of two case studies from ancient Judaism—the writings of Philo of Alexandria and the sectarian Dead Sea Scrolls—demonstrates the emotional, social, and discursive dimensions of belonging and the role it plays in producing identity. Belonging is not a stable concept but is rather one that assumes different forms depending on the emotional orientation of the group and the particulars of identity politics. For Philo, belonging reflects a universalistic love for all humanity that helps shape an identity embracing Jewish practice and Greek virtue. By contrast, the Dead Sea sect’s antipathy toward all other Jews requires that a sense of belonging express not only love for fellow sectarians but also hate for all outsiders.
NEW APPROACH TO SEPARATE AND DATE SMALL SPORES AND POLLEN FROM LAKE SEDIMENTS IN SEMI-ARID CLIMATES
Authors: Steinhoff Christoph , Pickarski Nadine , Litt Thomas , Hajdas Irka , Welte Caroline , Wurst Peter , Kühne David , Dolf Andreas , Germer Maximilian , Kallmeyer Jens
Published: June 2022

The dating of pollen grains is emerging as the method of choice for lacustrine climate archives that contain few datable macrofossils. Due to the need for high-purity pollen concentrates, new methods are constantly being developed to precisely separate pollen grains. Flow cytometry represents a promising alternative to conventional approaches, enabling the identification of pollen grains through fluorescence and rapid separation for radiocarbon analysis using accelerator mass spectrometry, which has so far been limited to sediments with a high proportion of conifer pollen. We present a revised method for processing large sediment samples, resulting in high-purity pollen and spore concentrates. Using this approach small- to medium-sized pollen and bryophyte spores were isolated from Lake Van sediment samples (Eastern Anatolia, Turkey) in sufficient purity for radiocarbon dating. However, a systematic age discrepancy between pollen and bryophyte spore concentrates was noted. By adapting the chemical and cytometric methods, pure pollen concentrates can be created for sediments with low organic content enabling age determination of climate archives with a low proportion of large pollen or low pollen concentration.
TESTING THE METHODS FOR DETERMINATION OF RADIOCARBON CONTENT IN LIQUID FUELS IN THE GLIWICE RADIOCARBON AND MASS SPECTROMETRY LABORATORY
Authors: Baranyika Jean Baptiste , Piotrowska Natalia , Kłusek Marzena , Michczyński Adam , Pawlyta Jacek
Published: June 2022

Determining the biocomponents in liquid fuels using radiocarbon radioisotope (14C) dating requires sample preparation adaptations to the conditions of the Gliwice Radiocarbon and Mass Spectrometry Laboratory. Liquid scintillation counting (LSC), and accelerator mass spectrometry (AMS) were investigated using six samples, including one 14C-free fuel and modern hydrotreated vegetable oil (HVO). For AMS, samples were prepared using tin capsules for liquids for EA combustion and graphitization in an AGE system. For LSC, liquid fuels were prepared by mixing with purified preheated sand and a benzene synthesis line. Benzene resublimation was also tested. IRMS measurements were also conducted for benzene to account for isotopic fractionation. Sample background measurements using both methods showed good performances by both AMS and LSC without resublimation. Comparable results were also obtained for HVO.
Is it in Colloquial Singapore English
Authors: Gonzales Wilkinson Daniel Wong , Hiramoto Mie , Leimgruber Jakob R. E. , Lim Jun Jie
Published: June 2022

Colloquial Singapore English (CSE, commonly known as Singlish) is a linguistic variety used in Singapore, a Southeast Asian nation home to three major ethnic groups: the Chinese (74.35% of the citizen and permanent resident population), the Malays (13.43%), and the Indians (9%) (Singapore Department of Statistics, 2019). It is one of the best known post-colonial varieties of English and has been documented since the emergence of the field of world Englishes (e.g., Greenbaum, 1988; Richards & Tay, 1977). Linguistically, the grammar and lexicon of CSE are systematically imported from other non-English languages used in the island nation (Leimgruber, 2011). From a creolist perspective, it can be viewed as an English-lexifier creole that contains influences from Sinitic languages such as Hokkien, Cantonese and Mandarin, as well as Malay, Tamil and other varieties in the Singapore language ecology (McWhorter, 2007; Platt, 1975). Several distinct features across various levels of language have been investigated in CSE, including phonetics (Starr & Balasubramaniam, 2019), morphosyntax (Bao, 2010; Bao & Wee, 1999), semantics (Hiramoto & Sato, 2012), and pragmatics (Hiramoto, 2012; Leimgruber, 2016; Lim, 2007).
Can Grid Governance Fix the Party-state's Broken Windows? A Study of Stability Maintenance in Grassroots China
Authors: Xu Jianhua , He Siying
Published: June 2022

Grid governance has been developed by the Chinese party-state to collect intelligence at the grassroots level for the early pre-emption of what it defines as social instability. Using data collected from four months’ participant observation and extensive interviews with personnel who work in the grid governance system in what we call W Street, a location in a second-tier city in southern China, this paper examines how China's grid governance is used for stability maintenance and how in practice the system has become alienated from its original purpose of social control. We find that grid governance is achieved mainly through three mechanisms: intelligence gathering, case coordination and real-time reporting for stability maintenance. We further reveal that while grid governance provides an important infrastructural power for intelligence gathering, the realization of this power could be hindered by contradictory logics among different levels of government. This research not only provides empirical data on how China's grid governance works in practice but also calls for a rethinking of the capacity of China's stability maintenance regime.
Forecasting Eruptions at Poorly Known Volcanoes Using Analogs and Multivariate Renewal Processes
Authors: Wang Ting , Bebbington Mark , Cronin Shane , Carman Joel
Published: June 2022

Forecasting future destructive eruptions from re‐awakening volcanoes remains a challenge, mainly due to a lack of previous event data. This sparks a search for similar volcanoes to provide additional information, especially those with better compiled and understood event records. However, we show that some of the most obviously geologically comparable volcanoes have differing statistical occurrence patterns. Using such matches produces large forecasting uncertainties. We created a statistical tool to identify and test the compatibility of potential analogue volcanoes based on repose‐time characteristics from world‐wide datasets. Selecting analogue volcanoes with compatible behavior for factors being forecast, such as repose time, significantly reduces forecasting uncertainties. Applying this tool to Tongariro volcano (NZ), there is a 5% probability for a Volcanic Explosivity Index (VEI) ≥ 3 explosive eruption in the next 50 years. Using pre‐historic geological records of a smaller available set of analogs, we forecast a 1% probability of a VEI ≥ 4 eruption in the next 50 years.
Plate‐Rate Frictional Behavior of Sediment Inputs to the Hikurangi Subduction Margin: How Does Lithology Control Slow Slip Events?
Authors: Eijsink A. M. , Ikari M. J.
Published: June 2022

The northern Hikurangi subduction margin hosts slow slip events (SSEs), which are exceptionally shallow (<15 km). The sedimentary sequence on the incoming plate is therefore representative of the shallow fault material where the SSEs will take place once they enter the subduction zone. Knowledge about the frictional behavior of these sediments is required to know which lithologies are capable of hosting SSEs, and what mechanisms are causing them. Frictional behavior is material specific and depends on sliding velocity, but it is unknown how these natural sediments behave at plate‐rate velocities. We performed laboratory shearing experiments testing the major lithologies sampled during International Ocean Discovery Program (IODP) Expedition 375, at velocities ranging from the plate convergence rate at the Hikurangi margin (5 cm/year), up to those characteristics of the shallow SSEs (160 and 530 cm/year), under simulated in‐situ as well as standardized conditions. We find that the calcite‐rich pelagic sediments are relatively strong and display the velocity‐weakening frictional behavior required for slip events, whereas other lithologies are weaker and show velocity‐neutral to velocity‐strengthening friction. We observe spontaneous laboratory SSEs in the calcareous pelagic sediments, which show partial locking in between sliding events, consistent with the interpretation of SSEs within the spectrum of slow to fast earthquakes. For the Hikurangi margin, our results suggest that SSE occurrence requires the stronger carbonate‐rich unit to be incorporated into the plate‐boundary fault zone, which we suggest occurs because the rough incoming plate introduces geometrical complexity into the fault zone.
Deep Outer‐Rise Faults in the Southern Mariana Subduction Zone Indicated by a Machine‐Learning‐Based High‐Resolution Earthquake Catalog
Authors: Chen Han , Yang Hongfeng , Zhu Gaohua , Xu Min , Lin Jian , You Qingyu
Published: June 2022

Outer‐rise faults are predominantly concentrated near ocean trenches due to subducted plate bending. These faults play crucial roles in the hydration of subducted plates and the consequent subducting processes. However, it has not yet been possible to develop high‐resolution structures of outer‐rise faults due to the lack of near‐field observations. In this study we deployed an ocean bottom seismometer (OBS) network near the Challenger Deep in the Southernmost Mariana Trench, between December 2016 and June 2017, covering both the overriding and subducting plates. We applied a machine‐learning phase detector (EQTransformer) to the OBS data and found more than 1,975 earthquakes. An identified outer‐rise event cluster revealed an outer‐rise fault penetrating to depths of 50 km, which was inferred as a normal fault based on the extensional depth from tomographic images in the region, shedding new lights on water input at the southmost Mariana subduction zone.
The Role of Atmospheric Blocking in Regulating Arctic Warming
Authors: You Cheng , Tjernström Michael , Devasthale Abhay , Steinfeld Daniel
Published: June 2022

Using ERA5 reanalysis we find positive trends in poleward transport of moisture and heat during 1979–2018 over the winter Barents Sea sector and summer East Siberian Sea sector. The increase in blocking occurrence (blocking days) can explain these trends. Blocking occurrence over the Barents Sea sector significantly increased in the last 40 winters, inducing increasingly stronger poleward transport of moisture and heat. The high linear correlation between poleward energy transports and temperature over the Barents Sea sector suggests that poleward energy transports dominate the regional warming trend there. Meanwhile, in summer, more frequently occurring blocking over the Beaufort Sea sector causes a positive trend of poleward moist and heat transport over the East Siberian Sea sector. The high linear correlation between the blocking occurrence and temperature suggests that the increasing shortwave radiation and subsidence within the more frequently occurring blocking contribute to the regional warming trend.
The Deuterium Isotopic Ratio of Water Released From the Martian Caps as Measured With TGO/NOMAD
Authors: Villanueva Geronimo L. , Liuzzi Giuliano , Aoki Shohei , Stone Shane W. , Brines Adrian , Thomas Ian R. , Lopez‐Valverde Miguel Angel , Trompet Loic , Erwin Justin , Daerden Frank , Ristic Bojan , Smith Michael D. , Mumma Michael J. , Faggi Sara , Kofman Vincent , Robert Séverine , Neary Lori , Patel Manish , Bellucci Giancarlo , Lopez‐Moreno Jose Juan , Vandaele Ann Carine
Published: June 2022

We report vertical profiles of water and D/H for one Martian year as measured with the TGO/NOMAD instrument. The observations were performed via solar occultation, providing water profiles up to ∼100 km and D/H up to ∼60 km, with a vertical resolution of 1–2 km. The measurements reveal dramatic variability of water and D/H over short timescales and with altitude and location on the planet. We investigated the release of seasonal water from the polar caps during southern and northern summer, by mapping water and its D/H near the polar regions. Above the hygropause, the D/H drops substantially below 2 VSMOW, and both seasonal polar caps show a consistent and enriched D/H of 5–7 VSMOW within the hygrosphere.
Simultaneous Measurements of Elastic Wave Velocity and Porosity of Epidosites Collected From the Oman Ophiolite: Implication for Low VP/VS Anomaly in the Oceanic Crust
Authors: Nagase Kumpei , Hatakeyama Kohei , Okazaki Keishi , Akamatsu Yuya , Abe Natsue , Michibayashi Katsuyoshi , Katayama Ikuo
Published: June 2022

Geophysical surveys of the oceanic crust indicate that hydrothermal circulation universally occurs in seismic layer 2, which results in a low seismic velocity and high VP/VS due to the occurrence of cracks. However, the anomalously low VP/VS observed at the layer 2/3 transition cannot be explained by the crack model, because the effective medium theory predicts an increase in VP/VS due to crack development. In this study, we present the first evidence that shows the low VP/VS in the oceanic crust is caused by epidotization due to upward fluid flow in hydrothermal systems. Simultaneous measurements of elastic wave velocity and porosity of epidosites collected by the Oman Drilling Project show that quartz precipitation and spheroidal pores results in low VP/VS, in contrast to diabases that contain thin cracks. The presence of spheroidal pores in epidosites is supported by CT imaging, and is consistent with predictions from the effective medium model.
Marsh Sedimentation Controls Delta Top Morphology, Slope, and Mass Balance
Authors: Sanks K. M. , Zapp S. M. , Silvestre J. R. , Shaw J. B. , Dutt R. , Straub K. M.
Published: June 2022

Rising sea levels, subsidence, and decreased fluvial sediment load threaten river deltas and their wetlands. However, the feedbacks between fluvial and non‐fluvial (marsh) deposition remain weakly constrained. We investigate how non‐riverine, elevation‐controlled deposition typified by marshes impacts sediment partitioning between a delta's topset, coastal zone, and foreset by comparing a delta experiment with proxy marsh accumulation to a control. Marsh accumulation alters fluvial sediment distribution by decreasing the slope in the marsh window by ∼50%, creating a 78% larger marsh zone. Fluvial incursions into the marsh window trap 1.3 times more clastic volume. The volume exported to deep water remains unchanged. Marsh deposition shifts elevation distributions toward sea level, which produces a hypsometry akin to field‐scale deltas. The elevation‐lowering effect of marshes on an equilibrium delta shown here constitutes an unexplored feedback and an important aspect of coastal sustainability.
Record Low Antarctic Sea Ice Cover in February 2022
Authors: Turner John , Holmes Caroline , Caton Harrison Thomas , Phillips Tony , Jena Babula , Reeves‐Francois Tylei , Fogt Ryan , Thomas Elizabeth R. , Bajish C. C.
Published: June 2022

On 25 February 2022 Antarctic sea ice extent dropped to a satellite‐era record low level of 1.92 × 106 km2, 0.92 × 106 km2 below the long‐term mean. The area of sea ice was also at a record low level of 1.24 × 106 km2. Although no individual sector was at a record low, at the minimum there were negative sea ice anomalies in all sectors of the Southern Ocean, with the largest in the Ross (contributing 46%) and Weddell Seas (26%). The Amundsen Sea Low had a record low depth in October/November 2021, with a series of very deep depressions giving strong offshore winds. These accelerated ice loss during the melt season, creating a 1.00 × 106 km2 coastal polynya in the Ross Sea. In the northern Weddell Sea, westerly winds of record strength led to ice export from the region.
Change of neck circumference in relation to visceral fat area: a Chinese community-based longitudinal cohort study
Authors: Cao Weijie , Xu Yiting , Shen Yun , Hu Tingting , Xiao Yunfeng , Wang Yufei , Ma Xiaojing , Bao Yuqian
Published: June 2022

Background/Objectives

Neck circumference (NC) has been positively associated with visceral fat area (VFA) in cross-sectional studies. This study aimed to evaluate the effects of NC changes on VFA in a Chinese community-based longitudinal cohort.

Subjects/Methods

Subjects recruited from Shanghai communities were followed up for 1.1–2.9 years. A total of 1421 subjects (men 578, women 843) were included, aged 24–80 years, with an average age of 57.8 ± 7.1 years.

Interventions/Methods

Biochemical and anthropometric measurements, including NC, were obtained from all subjects. VFA was assessed by magnetic resonance imaging. Abdominal obesity was defined as a VFA ≥ 80 cm2.

Results

After a mean follow-up of 2.1 years, the NCs for men and women were 38.1 ± 2.3 cm and 33.8 ± 2.0 cm, respectively, and the average value of VFA was 84.55 (59.83–113.50) cm2. After adjusting for age, sex, body mass index, smoking, history of drinking, glycated hemoglobin, blood pressure and blood lipids, individuals who had gained a NC of more than 5% had 1.26 (95% CI: 1.05–1.49) times more visceral adipose tissue at follow-up than NC maintainers (NC change between –2.5% and 2.5%). In the non-abdominal obesity group at baseline (n = 683), after adjusting for confounding factors, changes in NC were associated with abdominal obesity (odd ratio 1.23, 95% CI: 1.09–1.39).

Conclusions

Changes in NC were positively associated with VFA in a Chinese community-based cohort, suggesting that NC measurement is practical for assessing abdominal obesity.
Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes
Authors: Pilátová Jana , Pánek Tomáš , Oborník Miroslav , Čepička Ivan , Mojzeš Peter
Published: June 2022

Despite the widespread occurrence of intracellular crystalline inclusions in unicellular eukaryotes, scant attention has been paid to their composition, functions, and evolutionary origins. Using Raman microscopy, we examined >200 species from all major eukaryotic supergroups. We detected cellular crystalline inclusions in 77% species out of which 80% is composed of purines, such as anhydrous guanine (62%), guanine monohydrate (2%), uric acid (12%) and xanthine (4%). Our findings shifts the paradigm assuming predominance of calcite and oxalates. Purine crystals emerge in microorganisms in all habitats, e.g., in freshwater algae, endosymbionts of reef-building corals, deadly parasites, anaerobes in termite guts, or slime molds. Hence, purine biocrystallization is a general and ancestral eukaryotic process likely present in the last eukaryotic common ancestor (LECA) and here we propose two proteins omnipresent in eukaryotes that are likely in charge of their metabolism: hypoxanthine-guanine phosphoribosyl transferase and equilibrative nucleoside transporter. Purine crystalline inclusions are multifunctional structures representing high-capacity and rapid-turnover reserves of nitrogen and optically active elements, e.g., used in light sensing. Thus, we anticipate our work to be a starting point for further studies spanning from cell biology to global ecology, with potential applications in biotechnologies, bio-optics, or in human medicine.
High glutamine suppresses osteogenesis through mTORC1-mediated inhibition of the mTORC2/AKT-473/RUNX2 axis
Authors: Gayatri Meher Bolisetti , Gajula Navya Naidu , Chava Suresh , Reddy Aramati B. M.
Published: June 2022

Activation of the key nutrient cellular sensors mTORC1 and mTORC2 directs the fate of mesenchymal stromal cells (MSCs). Here, we report that glutamine regulates crosstalk between mTOR complexes and lineage commitment of MSCs independent of glucose concentration. High glutamine-induced mTORC1 hyperactivation resulted in the suppression of mTORC2, which otherwise stabilizes RUNX2 via GSK3β inhibition through pAKT-473. Activation of GSK3β resulted in the ubiquitination of RUNX2, a key transcription factor for the osteogenic commitment of MSCs. However, low glutamine conditions inhibit mTORC1 hyperactivation followed by increased mTORC2 activation and RUNX2 stabilization. Under diabetic/high-glucose conditions, glutamine-triggered hyperactivation of mTORC1 resulted in mTORC2 suppression, and active GSK3β led to suppression of RUNX2. Activation of p-AMPK by metformin inhibits high glutamine-induced mTORC1 hyperactivation and rescues RUNX2 through the mTORC2/AKT-473 axis. Collectively, our study indicates the role of glutamine in modulating MSC fate through cross-talk between mTOR complexes by identifying a critical switch in signaling. It also shows the importance of glutamine in modulating molecular cues (mTORC1/p-70S6K/mTORC2/RUNX2) that are involved in driving diabetes-induced bone adipogenesis and other secondary complications.
Assembling covalent organic framework membranes via phase switching for ultrafast molecular transport
Authors: Khan Niaz Ali , Zhang Runnan , Wang Xiaoyao , Cao Li , Azad Chandra S. , Fan Chunyang , Yuan Jinqiu , Long Mengying , Wu Hong , Olson Mark. A. , Jiang Zhongyi
Published: June 2022

Fabrication of covalent organic framework (COF) membranes for molecular transport has excited highly pragmatic interest as a low energy and cost-effective route for molecular separations. However, currently, most COF membranes are assembled via a one-step procedure in liquid phase(s) by concurrent polymerization and crystallization, which are often accompanied by a loosely packed and less ordered structure. Herein, we propose a two-step procedure via a phase switching strategy, which decouples the polymerization process and the crystallization process to assemble compact and highly crystalline COF membranes. In the pre-assembly step, the mixed monomer solution is casted into a pristine membrane in the liquid phase, along with the completion of polymerization process. In the assembly step, the pristine membrane is transformed into a COF membrane in the vapour phase of solvent and catalyst, along with the completion of crystallization process. Owing to the compact and highly crystalline structure, the resultant COF membranes exhibit an unprecedented permeance (water ≈ 403 L m−2 bar−1 h−1 and acetonitrile ≈ 519 L m−2 bar−1 h−1). Our two-step procedure via phase switching strategy can open up a new avenue to the fabrication of advanced organic crystalline microporous membranes.
Steering surface reconstruction of copper with electrolyte additives for CO2 electroreduction
Authors: Han Zishan , Han Daliang , Chen Zhe , Gao Jiachen , Jiang Guangyi , Wang Xinyu , Lyu Shuaishuai , Guo Yong , Geng Chuannan , Yin Lichang , Weng Zhe , Yang Quan-Hong
Published: June 2022

Electrocatalytic CO2 reduction to value-added hydrocarbon products using metallic copper (Cu) catalysts is a potentially sustainable approach to facilitate carbon neutrality. However, Cu metal suffers from unavoidable and uncontrollable surface reconstruction during electrocatalysis, which can have either adverse or beneficial effects on its electrocatalytic performance. In a break from the current catalyst design path, we propose a strategy guiding the reconstruction process in a favorable direction to improve the performance. Typically, the controlled surface reconstruction is facilely realized using an electrolyte additive, ethylenediamine tetramethylenephosphonic acid, to substantially promote CO2 electroreduction to CH4 for commercial polycrystalline Cu. As a result, a stable CH4 Faradaic efficiency of 64% with a partial current density of 192 mA cm−2, thus enabling an impressive CO2-to-CH4 conversion rate of 0.25 µmol cm−2 s−1, is achieved in an alkaline flow cell. We believe our study will promote the exploration of electrochemical reconstruction and provide a promising route for the discovery of high-performance electrocatalysts.
Neonatal gene therapy achieves sustained disease rescue of maple syrup urine disease in mice
Authors: Pontoizeau Clément , Simon-Sola Marcelo , Gaborit Clovis , Nguyen Vincent , Rotaru Irina , Tual Nolan , Colella Pasqualina , Girard Muriel , Biferi Maria-Grazia , Arnoux Jean-Baptiste , Rötig Agnès , Ottolenghi Chris , de Lonlay Pascale , Mingozzi Federico , Cavazzana Marina , Schiff Manuel
Published: June 2022

Maple syrup urine disease (MSUD) is a rare recessively inherited metabolic disorder causing accumulation of branched chain amino acids leading to neonatal death, if untreated. Treatment for MSUD represents an unmet need because the current treatment with life-long low-protein diet is challenging to maintain, and despite treatment the risk of acute decompensations and neuropsychiatric symptoms remains. Here, based on significant liver contribution to the catabolism of the branched chain amino acid leucine, we develop a liver-directed adeno-associated virus (AAV8) gene therapy for MSUD. We establish and characterize the Bckdha (branched chain keto acid dehydrogenase a)−/− mouse that exhibits a lethal neonatal phenotype mimicking human MSUD. Animals were treated at P0 with intravenous human BCKDHA AAV8 vectors under the control of either a ubiquitous or a liver-specific promoter. BCKDHA gene transfer rescued the lethal phenotype. While the use of a ubiquitous promoter fully and sustainably rescued the disease (long-term survival, normal phenotype and correction of biochemical abnormalities), liver-specific expression of BCKDHA led to partial, though sustained rescue. Here we show efficacy of gene therapy for MSUD demonstrating its potential for clinical translation.
Dietary restriction and the transcription factor clock delay eye aging to extend lifespan in Drosophila Melanogaster
Authors: Hodge Brian A. , Meyerhof Geoffrey T. , Katewa Subhash D. , Lian Ting , Lau Charles , Bar Sudipta , Leung Nicole Y. , Li Menglin , Li-Kroeger David , Melov Simon , Schilling Birgit , Montell Craig , Kapahi Pankaj
Published: June 2022

Many vital processes in the eye are under circadian regulation, and circadian dysfunction has emerged as a potential driver of eye aging. Dietary restriction is one of the most robust lifespan-extending therapies and amplifies circadian rhythms with age. Herein, we demonstrate that dietary restriction extends lifespan in Drosophila melanogaster by promoting circadian homeostatic processes that protect the visual system from age- and light-associated damage. Altering the positive limb core molecular clock transcription factor, CLOCK, or CLOCK-output genes, accelerates visual senescence, induces a systemic immune response, and shortens lifespan. Flies subjected to dietary restriction are protected from the lifespan-shortening effects of photoreceptor activation. Inversely, photoreceptor inactivation, achieved via mutating rhodopsin or housing flies in constant darkness, primarily extends the lifespan of flies reared on a high-nutrient diet. Our findings establish the eye as a diet-sensitive modulator of lifespan and indicates that vision is an antagonistically pleiotropic process that contributes to organismal aging.
Low-dose self-amplifying mRNA COVID-19 vaccine drives strong protective immunity in non-human primates against SARS-CoV-2 infection
Authors: Rappaport Amy R. , Hong Sue-Jean , Scallan Ciaran D. , Gitlin Leonid , Akoopie Arvin , Boucher Gregory R. , Egorova Milana , Espinosa J. Aaron , Fidanza Mario , Kachura Melissa A. , Shen Annie , Sivko Gloria , Van Abbema Anne , Veres Robert L. , Jooss Karin
Published: June 2022

The coronavirus disease 2019 (COVID-19) pandemic continues to spread globally, highlighting the urgent need for safe and effective vaccines that could be rapidly mobilized to immunize large populations. We report the preclinical development of a self-amplifying mRNA (SAM) vaccine encoding a prefusion stabilized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein and demonstrate strong cellular and humoral immune responses at low doses in mice and rhesus macaques. The homologous prime-boost vaccination regimen of SAM at 3, 10 and 30 μg induced potent neutralizing antibody (nAb) titers in rhesus macaques following two SAM vaccinations at all dose levels, with the 10 μg dose generating geometric mean titers (GMT) 48-fold greater than the GMT of a panel of SARS-CoV-2 convalescent human sera. Spike-specific T cell responses were observed with all tested vaccine regimens. SAM vaccination provided protective efficacy against SARS-CoV-2 challenge as both a homologous prime-boost and as a single boost following ChAd prime, demonstrating reduction of viral replication in both the upper and lower airways. The SAM vaccine is currently being evaluated in clinical trials as both a homologous prime-boost regimen at low doses and as a boost following heterologous prime.
Structural basis for MTA1c-mediated DNA N6-adenine methylation
Authors: Chen Jiyun , Hu Rong , Chen Ying , Lin Xiaofeng , Xiang Wenwen , Chen Hong , Yao Canglin , Liu Liang
Published: June 2022

DNA N6-adenine methylation (6 mA) has recently been found to play a crucial role in epigenetic regulation in eukaryotes. MTA1c, a newly discovered 6 mA methyltransferase complex in ciliates, is composed of MTA1, MTA9, p1 and p2 subunits and specifically methylates ApT dinucleotides, yet its mechanism of action remains unknown. Here, we report the structures of Tetrahymena thermophila MTA1 (TthMTA1), Paramecium tetraurelia MTA9 (PteMTA9)-TthMTA1 binary complex, as well as the structures of TthMTA1-p1-p2 and TthMTA1-p2 complexes in apo, S-adenosyl methionine-bound and S-adenosyl homocysteine-bound states. We show that MTA1 is the catalytically active subunit, p1 and p2 are involved in the formation of substrate DNA-binding channel, and MTA9 plays a structural role in the stabilization of substrate binding. We identify that MTA1 is a cofactor-dependent catalytically active subunit, which exhibits stable SAM-binding activity only after assembly with p2. Our structures and corresponding functional studies provide a more detailed mechanistic understanding of 6 mA methylation.
α-Synuclein induced cholesterol lowering increases tonic and reduces depolarization-evoked synaptic vesicle recycling and glutamate release
Authors: Lazarevic Vesna , Yang Yunting , Paslawski Wojciech , Svenningsson Per
Published: June 2022

α-Synuclein (α-syn) is a key molecule linked to Parkinson’s disease pathology. Physiologically, the monomeric α-syn in the presynaptic termini is involved in regulation of neurotransmission, but the pathophysiology of extracellular monomeric α-syn is still unknown. Utilizing both in vivo and in vitro approaches, we investigated how extracellular α-syn impact presynaptic structure and function. Our data revealed that treatment with exogenous α-syn leads to increased tonic and decreased depolarization-evoked synaptic vesicle (SV) recycling and glutamate release. This was associated with mobilization of molecularly distinct SV pools and reorganization of active zone components. Our study also showed that exogenous α-syn impaired neuronal cholesterol level and that the cholesterol binding domain of α-syn was sufficient to exert the same presynaptic phenotype as the full-length protein. The present study sheds new light on physiological functions of extracellular α-syn in overall maintenance of presynaptic activity that involves the reorganization of both presynaptic compartment and cholesterol-rich plasma membrane domains.
A dataset of distribution of antibiotic occurrence in solid environmental matrices in China
Authors: Zhang Qi , Zhang Guanshi , Liu Dongsheng , Zhang Xiu , Fang Ruying , Wang Luqi , Chen Yunxiang , Lin Lingling , Wu Hongjuan , Li Sen
Published: June 2022

While there is growing global concern about the impact of antibiotic residues on emergence and enhancement bacteria’s resistance, toxicity to natural organisms, and, ultimately, public health, a concise picture of measured environmental concentrations of antibiotic occurrence in multiple environmental matrices, particularly in solid matrices (e.g., sludge, soil, and sediments) is still elusive, especially for China. In this paper, we present an up-to-date dataset of the distribution of antibiotic occurrence in solid environmental matrices in China, derived from 210 peer-reviewed literature published between 2000 and 2020. We extracted geographical sampling locations and measured concentration associated with antibiotic occurrence reported in English and Chinese original publications, and applied quality-control procedures to remove duplicates and ensure accuracy. The dataset contains 6929 records of geo-referenced occurrences for 135 antibiotics distributed over 391 locations distinguished at four levels of scale i.e., provincial, prefectural, county, and township or finer. The geographical dataset provides an updated map of antibiotic occurrence in solid environmental matrices in China and can be used for further environmental health risk assessment.
BIRAFFE2, a multimodal dataset for emotion-based personalization in rich affective game environments
Authors: Kutt Krzysztof , Drążyk Dominika , Żuchowska Laura , Szelążek Maciej , Bobek Szymon , Nalepa Grzegorz J.
Published: June 2022

Generic emotion prediction models based on physiological data developed in the field of affective computing apparently are not robust enough. To improve their effectiveness, one needs to personalize them to specific individuals and incorporate broader contextual information. To address the lack of relevant datasets, we propose the 2nd Study in Bio-Reactions and Faces for Emotion-based Personalization for AI Systems (BIRAFFE2) dataset. In addition to the classical procedure in the stimulus-appraisal paradigm, it also contains data from an affective gaming session in which a range of contextual data was collected from the game environment. This is complemented by accelerometer, ECG and EDA signals, participants’ facial expression data, together with personality and game engagement questionnaires. The dataset was collected on 102 participants. Its potential usefulness is presented by validating the correctness of the contextual data and indicating the relationships between personality and participants’ emotions and between personality and physiological signals.
Direct production of polyhydroxybutyrate and alginate from crude glycerol by Azotobacter vinelandii using atmospheric nitrogen
Authors: Yoshida Nobuhiro , Takase Ryuichi , Sugahara Yoshimi , Nambu Yuko , Hashimoto Wataru
Published: June 2022

While biodiesel is drawing attention as an eco-friendly fuel, the use of crude glycerol, a byproduct of the fuel production process, has increasingly become a concern to be addressed. Here we show the development of a low-cost fermentation technology using an atmospheric nitrogen-fixing bacterium to recycle crude glycerol into functional biopolymers. Azotobacter vinelandii showed substantial growth on tap water-diluted crude glycerol without any pretreatment. The number of viable A. vinelandii cells increased over 1000-fold under optimal growth conditions. Most of the glycerol content (~ 0.2%) in the crude glycerol medium was completely depleted within 48 h of culture. Useful polymers, such as polyhydroxybutyrate and alginate, were also produced. Polyhydroxybutyrate productivity was increased ten-fold by blocking the alginate synthesis pathway. Although there are few examples of using crude glycerol directly as a carbon source for microbial fermentation, there are no reports on the use of crude glycerol without the addition of a nitrogen source. This study demonstrated that it is possible to develop a technology to produce industrially useful polymers from crude glycerol through energy-saving and energy-efficient fermentation using the atmospheric nitrogen-fixing microorganism A. vinelandii.
Effect of weightbearing and foot positioning on 3D distal tibiofibular joint parameters
Authors: Souleiman Firas , Heilemann Martin , Hennings Robert , Hepp Pierre , Gueorguiev Boyko , Richards Geoff , Osterhoff Georg , Gehweiler Dominic
Published: June 2022

The aim of this study was to investigate the effect of different loading scenarios and foot positions on the configuration of the distal tibiofibular joint (DTFJ). Fourteen paired human cadaveric lower legs were mounted in a loading frame. Computed tomography scans were obtained in unloaded state (75 N) and single-leg loaded stand (700 N) of each specimen in five foot positions: neutral, 15° external rotation, 15° internal rotation, 20° dorsiflexion, and 20° plantarflexion. An automated three-dimensional measurement protocol was used to assess clear space (diastasis), translational angle (rotation), and vertical offset (fibular shortening) in each foot position and loading condition. Foot positioning had a significant effect on DTFJ configuration. Largest effects were related to clear space increase by 0.46 mm (SD 0.21 mm) in loaded dorsal flexion and translation angle of 2.36° (SD 1.03°) in loaded external rotation, both versus loaded neutral position. Loading had no effect on clear space and vertical offset in any position. Translation angle was significantly influenced under loading by − 0.81° (SD 0.69°) in internal rotation only. Foot positioning noticeably influences the measurements when evaluating DTFJ configuration. Loading seems to have no relevant effect on native ankles in neutral position.
Evaluation and comparison of antibiotic susceptibility profiles of Streptomyces spp. from clinical specimens revealed common and region-dependent resistance patterns
Authors: Kotrbová Lucie , Lara Ana Catalina , Corretto Erika , Scharfen Josef , Ulmann Vít , Petříčková Kateřina , Chroňáková Alica
Published: June 2022

Notwithstanding the fact that streptomycetes are overlooked in clinical laboratories, studies describing their occurrence in disease and potential pathogenicity are emerging. Information on their species diversity in clinical specimens, aetiology and appropriate therapeutic treatment is scarce. We identified and evaluated the antibiotic susceptibility profile of 84 Streptomyces clinical isolates from the Czech Republic. In the absence of appropriate disk diffusion (DD) breakpoints for antibiotic susceptibility testing (AST) of Streptomyces spp., we determined DD breakpoints by correlation with the broth microdilution method and by the distribution of zone diameters among isolates. Correlation accuracy was high for 9 antibiotics, leading to the establishment of the most valid DD breakpoints for Streptomyces antibiotic susceptibility evaluation so far. Clinical strains belonged to 17 different phylotypes dominated by a cluster of strains sharing the same percentage of 16S rRNA gene sequence identity with more than one species (S. albidoflavus group, S. hydrogenans, S. resistomycificus, S. griseochromogenes; 70% of isolates). AST results showed that Streptomyces exhibited intrinsic resistance to penicillin, general susceptibility to amikacin, gentamycin, vancomycin and linezolid, and high percentage of susceptibility to tetracyclines and clarithromycin. For the remaining antibiotics, AST showed inter- and intra-species variations when compared to available literature (erythromycin, trimethoprim-sulfamethoxazole), indicating a region-dependent rather than species-specific patterns.
Dynamic insights into the effects of nonsynonymous polymorphisms (nsSNPs) on loss of TREM2 function
Authors: Dash Raju , Munni Yeasmin Akter , Mitra Sarmistha , Choi Ho Jin , Jahan Sultana Israt , Chowdhury Apusi , Jang Tae Jung , Moon Il Soo
Published: June 2022

Single nucleotide variations in Triggering Receptor Expressed on Myeloid Cells 2 (TREM2) are associated with many neurodegenerative diseases, including Nasu-Hakola disease (NHD), frontotemporal dementia (FTD), and late-onset Alzheimer's disease because they disrupt ligand binding to the extracellular domain of TREM2. However, the effects of nonsynonymous single nucleotide polymorphisms (nsSNPs) in TREM2 on disease progression remain unknown. In this study, we identified several high-risk nsSNPs in the TREM2 gene using various deleterious SNP predicting algorithms and analyzed their destabilizing effects on the ligand recognizing region of the TREM2 immunoglobulin (Ig) domain by molecular dynamics (MD) simulation. Cumulative prediction by all tools employed suggested the three most deleterious nsSNPs involved in loss of TREM2 function are rs549402254 (W50S), rs749358844 (R52C), and rs1409131974 (D104G). MD simulation showed that these three variants cause substantial structural alterations and conformational remodeling of the apical loops of the TREM2 Ig domain, which is responsible for ligand recognition. Detailed analysis revealed that these variants substantially increased distances between apical loops and induced conformation remodeling by changing inter-loop nonbonded contacts. Moreover, all nsSNPs changed the electrostatic potentials near the putative ligand-interacting region (PLIR), which suggested they might reduce specificity or loss of binding affinity for TREM2 ligands. Overall, this study identifies three potential high-risk nsSNPs in the TREM2 gene. We propose further studies on the molecular mechanisms responsible for loss of TREM2 function and the associations between TREM2 nsSNPs and neurodegenerative diseases.
CFD simulation of updrafts initiated by a vertically directed jet fed by the heat of water vapor condensation
Authors: Abshaev Magomet T. , Abshaev Ali M. , Aksenov Andrey A. , Fisher Iuliia V. , Shchelyaev Alexander E. , Al Mandous Abdulla , Wehbe Youssef , El-Khazali Reyad
Published: June 2022

This paper presents the results of the development of a mathematical model and numerical simulation of the ascent in the atmosphere of a vertically directed jet fed by the heat of condensation of water vapor on a hygroscopic aerosol introduced into the jet at the start. The possibility of creating artificial convective clouds depending on jet parameters, condensation heat value and vertical profiles of wind speed, air temperature and humidity has been evaluated. Numerical experiments showed that the motion of a high-speed and high-temperature jet in the atmosphere has a complex turbulent nature. As the jet ascends, it expands, losing superheat and velocity. The temperature of the jet decreases faster than the velocity, so the jet rises slightly above the level at which its superheat disappears. The jet's ascent height increases as the humidity of the air and the vertical temperature gradient increase. Wind causes the jet to deform, bend, and decrease the height of ascent. Feed the jet with condensation heat results in a significant increase in jet lift height. This is particularly effective in the case of introducing into the jet two-layer NaCl/TiO2 nanoaerosol, which is capable of absorbing water vapor in an amount significantly greater than its mass. The simulation results are encouraging in the possibility of creating artificial updrafts that can lead to the formation of convective clouds and precipitation on days with favorable atmospheric conditions, when wind speed in the sub-cloud layer is < 6 m/s, air humidity is > 65%, and the temperature lapse rate is > 7.5 °C/km.