bluuebunny/crossref_metadata_2025 huggingface dataset:
Electron cryo-microscopy reveals the structure of the archaeal thread filament
Authors: Gaines Matthew C. , Isupov Michail N. , Sivabalasarma Shamphavi , Haque Risat Ul , McLaren Mathew , Mollat Clara L. , Tripp Patrick , Neuhaus Alexander , Gold Vicki A. M. , Albers Sonja-Verena , Daum Bertram
Published: December 2022

Pili are filamentous surface extensions that play roles in bacterial and archaeal cellular processes such as adhesion, biofilm formation, motility, cell-cell communication, DNA uptake and horizontal gene transfer. The model archaeaon Sulfolobus acidocaldarius assembles three filaments of the type-IV pilus superfamily (archaella, archaeal adhesion pili and UV-inducible pili), as well as a so-far uncharacterised fourth filament, named “thread”. Here, we report on the cryo-EM structure of the archaeal thread. The filament is highly glycosylated and consists of subunits of the protein Saci_0406, arranged in a head-to-tail manner. Saci_0406 displays structural similarity, but low sequence homology, to bacterial type-I pilins. Thread subunits are interconnected via donor strand complementation, a feature reminiscent of bacterial chaperone-usher pili. However, despite these similarities in overall architecture, archaeal threads appear to have evolved independently and are likely assembled by a distinct mechanism.
A unified computational framework for single-cell data integration with optimal transport
Authors: Cao Kai , Gong Qiyu , Hong Yiguang , Wan Lin
Published: December 2022

Single-cell data integration can provide a comprehensive molecular view of cells. However, how to integrate heterogeneous single-cell multi-omics as well as spatially resolved transcriptomic data remains a major challenge. Here we introduce uniPort, a unified single-cell data integration framework that combines a coupled variational autoencoder (coupled-VAE) and minibatch unbalanced optimal transport (Minibatch-UOT). It leverages both highly variable common and dataset-specific genes for integration to handle the heterogeneity across datasets, and it is scalable to large-scale datasets. uniPort jointly embeds heterogeneous single-cell multi-omics datasets into a shared latent space. It can further construct a reference atlas for gene imputation across datasets. Meanwhile, uniPort provides a flexible label transfer framework to deconvolute heterogeneous spatial transcriptomic data using an optimal transport plan, instead of embedding latent space. We demonstrate the capability of uniPort by applying it to integrate a variety of datasets, including single-cell transcriptomics, chromatin accessibility, and spatially resolved transcriptomic data.
A universal all-solid synthesis for high throughput production of halide perovskite
Authors: Zheng Luyao , Nozariasbmarz Amin , Hou Yuchen , Yoon Jungjin , Li Wenjie , Zhang Yu , Wu Haodong , Yang Dong , Ye Tao , Sanghadasa Mohan , Wang Ke , Poudel Bed , Priya Shashank , Wang Kai
Published: December 2022

Halide perovskites show ubiquitous presences in growing fields at both fundamental and applied levels. Discovery, investigation, and application of innovative perovskites are heavily dependent on the synthetic methodology in terms of time-/yield-/effort-/energy- efficiency. Conventional wet chemistry method provides the easiness for growing thin film samples, but represents as an inefficient way for bulk crystal synthesis. To overcome these, here we report a universal solid state-based route for synthesizing high-quality perovskites, by means of simultaneously applying both electric and mechanical stress fields during the synthesis, i.e., the electrical and mechanical field-assisted sintering technique. We employ various perovskite compositions and arbitrary geometric designs for demonstration in this report, and establish such synthetic route with uniqueness of ultrahigh yield, fast processing and solvent-free nature, along with bulk products of exceptional quality approaching to single crystals. We exemplify the applications of the as-synthesized perovskites in photodetection and thermoelectric as well as other potentials to open extra chapters for future technical development.
Azoarene activation for Schmidt-type reaction and mechanistic insights
Authors: Meng Fan-Tao , Wang Ya-Nan , Qin Xiao-Yan , Li Shi-Jun , Li Jing , Hao Wen-Juan , Tu Shu-Jiang , Lan Yu , Jiang Bo
Published: December 2022

The Schmidt rearrangement, a reaction that enables C-C or C-H σ bond cleavage and nitrogen insertion across an aldehyde or ketone substrate, is one of the most important and widely used synthetic tools for the installation of amides and nitriles. However, such a reaction frequently requires volatile, potentially explosive, and highly toxic azide reagents as the nitrogen donor, thus limiting its application to some extent. Here, we show a Schmidt-type reaction where aryldiazonium salts act as the nitrogen precursor and in-situ-generated cyclopenta-1,4-dien-1-yl acetates serve as pronucleophiles from gold-catalyzed Nazarov cyclization of 1,3-enyne acetates. Noteworthy is that cycloketone-derived 1,3-enyne acetates enabled ring-expansion relay to access a series of 2-pyridone-containing fused heterocycles, in which nonsymmetric cycloketone-derived counterparts demonstrated high regioselectivity. Aside from investigating the scope of this Schmidt-type reaction, mechanistic details of this transformation are provided by performing systematic theoretical calculations.
Visual, spectral, and microchemical quantification of crystalline anomalies in otoliths of wild and cultured delta smelt
Authors: Lewis Levi S. , Huang Jonathan L. , Willmes Malte , Fichman Rachel A. , Hung Tien-Chieh , Ellison Luke T. , Stevenson Troy A. , Teh Swee J. , Hammock Bruce G. , Schultz Andrew A. , Grimsich John L. , Huyskens Magdalena H. , Yin Qing-Zhu , Cavole Leticia M. , Botto Nicholas W. , Hobbs James A.
Published: December 2022

Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in otoliths of delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the San Francisco Estuary. Left–right asymmetry and anomalous crystalline polymorphs (i.e., vaterite) were quantified and compared between wild and cultured populations using digital image analysis. Visual estimates of vaterite were validated using X-ray diffraction, Raman spectroscopy, laser ablation ICPMS, and electron probe microanalysis. Results indicated that cultured delta smelt were 80 times more likely to contain a vateritic otolith and 18 times more likely to contain relatively large (≥ 15%) amounts of vaterite. Similarly, cultured fish exhibited 30% greater asymmetry than wild fish. These results indicate that cultured delta smelt exhibit a significantly higher frequency of vestibular abnormalities which are known to reduce fitness and survival. Such hatchery effects on otolith development could have important implications for captive culture practices and the supplementation of wild fish populations with cultured individuals.
Simultaneous bioremediation of Disperse orange-2RL Azo dye and fatty acids production by Scenedesmus obliquus cultured under mixotrophic and heterotrophic conditions
Authors: Hamouda Ragaa A. , El‑Naggar Noura El‑Ahmady , Abou-El-Souod Ghada W.
Published: December 2022

Several types of green photosynthetic microalgae can grow through the process of heterotrophic growth in the dark with the help of a carbon source instead of the usual light energy. Heterotrophic growth overcomes important limitations in the production of valuable products from microalgae, such as the reliance on light, which complicates the process, raises costs, and lowers the yield of potentially useful products. The present study was conducted to explore the potential growth of green microalga Scenedesmus obliquus under mixotrophic and heterotrophic conditions utilizing Disperse orange 2RL Azo dye as a carbon source to produce a high lipid content and the maximum dye removal percentage. After 7 days of algal growth with dye under mixotrophic and heterotrophic conditions with varying pH levels (5, 7, 9, and 11), KNO3 concentrations (1, 1.5, 2, and 3 g/L), and dye concentrations (20, 40, and 60 ppm); dye removal percentage, algal dry weight, and lipid content were determined. The results showed that the highest decolorization of Disperse orange 2RL Azo dye (98.14%) was attained by S. obliquus in heterotrophic medium supplemented with glucose at the optimal pH 11 when the nitrogen concentration was 1 g/L and the dye concentration was 20 ppm. FT-IR spectroscopy of the dye revealed differences in peaks position and intensity before and after algal treatment. S. obliquus has a high concentration of oleic acid, which is enhanced when it is grown with Disperse orange 2RL Azo dye, making it ideal for production of high-quality biodiesel. In general, and in the vast majority of instances, heterotrophic cultivation is substantially less expensive, easier to set up, and requires less maintenance than mixotrophic cultivation. Heterotrophic cultivation allows for large-scale applications such as separate or mixed wastewater treatment along with biofuel production.
Maternal iron status during pregnancy and attention deficit/hyperactivity disorder symptoms in 7-year-old children: a prospective cohort study
Authors: Díaz-López Andrés , Canals-Sans Josefa , Julvez Jordi , Fernandez-Barrés Silvia , Llop Sabrina , Rebagliato Marisa , Lertxundi Nerea , Santa-Marina Loreto , Guxens Mònica , Sunyer Jordi , Arija Victoria
Published: December 2022

Evidence suggests that iron status may be linked to symptoms of childhood attention deficit/hyperactivity disorder (ADHD), but there is little data available on the relationship between iron status in pregnancy and the risk of developing ADHD. And the data that does exist is inconsistent. Our aim here is to assess the effect of maternal serum ferritin (SF) and haemoglobin (Hb) levels during pregnancy on manifestations of ADHD in children at 7 years of age. This prospective study analysed data from 1204 mother–child pairs from three Spanish cohorts participating in the INMA project. Maternal SF and Hb levels during pregnancy and other mother and child characteristics were collected. The children’s ADHD behaviours were reported by their parents using Conners’ Parent Rating Scale-Revised Short Form (CPRS-R:S). In the unadjusted regression analysis, maternal SF was positively associated with children’s T-scores on the subscales Cognitive problems/Inattention (β: 0.63, 95%CI 0.06–1.19; p = 0.029) and ADHD index (β: 0.72, 95%CI 0.20–1.24; p = 0.007). These associations were not present after multivariate adjustment or stratification by first and second trimester of pregnancy. The Hb levels were not related to any of the CPRS-R:S subscales in unadjusted or multivariate-adjusted models. We observed no association between maternal SF or Hb levels and the risk of ADHD symptomatology (T-score ≥ 65 for CPRS-R:S subscales). Our results suggest that neither maternal SF nor Hb levels during pregnancy are related to ADHD symptoms in 7-year-old children.
Integrating multiple information sources for landslide hazard assessment: the case of Italy
Authors: Franceschini Rachele , Rosi Ascanio , del Soldato Matteo , Catani Filippo , Casagli Nicola
Published: December 2022

Landslides are the most frequent and diffuse natural hazards in Italy causing the greatest number of fatalities and damage to urban areas. The integration of natural hazard information and social media data could improve warning systems to enhance the awareness of disaster managers and citizens about emergency events. The news about landslide events in newspapers or crowdsourcing platforms allows fast observation, surveying and classification. Currently, few studies have been produced on the combination of social media data and traditional sensors. This gap indicates that it is unclear how their integration can effectively provide emergency managers with appropriate knowledge. In this work, rainfall, human lives, and earmarked fund data sources were correlated to “landslide news”. Analysis was applied to obtain information about temporal (2010–2019) and spatial (regional and warning hydrological zone scale) distribution. The temporal distribution of the data shows a continuous increase from 2015 until 2019 for both landslide and rainfall events. The number of people involved and the amount of earmarked funds do not exhibit any clear trend. The spatial distribution displays good correlation between “landslide news”, traditional sensors (e.g., pluviometers) and possible effects in term of fatalities. In addition, the cost of soil protection, in monetary terms, indicates the effects of events.
Frequency-specific electrogastrography as a non-invasive tool to measure gastrointestinal maturity in preterm infants
Authors: Chaudhari Akhil , Wang Xinlong , Roblyer Lindsay , Sanghavi Rinarani , Liu Hanli , Ortigoza Eric B.
Published: December 2022

Enteral feeding is challenging in preterm infants because of gastrointestinal (GI) immaturity. Electrogastrography (EGG) is a non-invasive technology that measures gastric myoelectrical activity and can be utilized to measure changes that occur with maturation at different gestational ages (GA). Three gastric rhythms (GR) exist between 0.5–9 cycles per minute (cpm), namely, bradygastria (0.5 ≤ GR < 2 cpm), normogastria (2 ≤ GR < 4 cpm), and tachygastria (4 ≤ GR < 9 cpm). We aimed to characterize EGG-derived parameters for different GA by quantifying (1) power spectral density (PSD) and its spectral means at three GR bands (i.e., mPSDGR) and (2) the percent (%) time spent in each band. Data analyzed was from a longitudinal cohort of preterm infants (n = 51) born at early, mid, and term GA of < 29, 29–33, and ≥ 37 weeks, respectively. Weekly EGG monitoring was performed until 40 weeks’ postmenstrual age or discharge. Pre-, during, and post-feed data were analyzed for mPSDGR at each GR band. Also, % bradygastria, % normogastria, and % tachygastria were calculated by continuous wavelet transform analysis. Results showed (1) mPSD values in normogastria and tachygastria during feeding increased with advancing GA, and (2) % normogastria increased with advancing GA regardless of GR ranges, suggesting EGG may measure GI maturity in preterm infants.
Systematic review and meta-analysis of outcome-relevant anemia in patients with subarachnoid hemorrhage
Authors: Said Maryam , Gümüs Meltem , Rodemerk Jan , Rauschenbach Laurèl , Chihi Mehdi , Dinger Thiemo Florin , Darkwah Oppong Marvin , Schmidt Börge , Ahmadipour Yahya , Dammann Philipp , Wrede Karsten Henning , Sure Ulrich , Jabbarli Ramazan
Published: December 2022

Anemia is a common, treatable condition in patients with aneurysmal subarachnoid hemorrhage (SAH) and has been associated with poor outcome. As there are still no guidelines for anemia management after aneurysm rupture, we aimed to identify outcome-relevant severity of anemia in SAH. We systematically searched PubMed, Embase, Scopus, Web of Science, and Cochrane Library for publications before Oct 23rd, 2022, reporting on anemia in SAH patients. The presence and severity of anemia were assessed according to the reported hemoglobin values and/or institutional thresholds for red blood cells transfusion (RBCT). Out of 1863 original records, 40 full-text articles with a total of 14,701 patients treated between 1996 and 2020 were included in the final analysis (mean 445.48 patients per study). A substantial portion of patients developed anemia during SAH (mean pooled prevalence 40.76%, range 28.3–82.6%). RBCT was administered in a third of the cases (mean 32.07%, range 7.8–88.6%), with institutional threshold varying from 7.00 to 10.00 g/dL (mean 8.5 g/dL). Anemia at the onset of SAH showed no impact on SAH outcome. In contrast, even slight anemia (nadir hemoglobin < 11.0–11.5 g/dL) occurring during SAH was associated with the risk of cerebral infarction and poor outcome at discharge and follow-up. The strongest association with SAH outcome was observed for nadir hemoglobin values ranging between 9.0 and 10.0 g/dL. The effect of anemia on SAH mortality was marginal. The development of anemia during SAH is associated with the risk of cerebral infarction and poor outcome at discharge and follow-up. Outcome-relevant severity of post-SAH anemia begins at hemoglobin levels clearly above the thresholds commonly set for RBCT. Our findings underline the need for further studies to define the optimal management of anemia in SAH patients.
Hydroclimate variability in the Caribbean during North Atlantic Heinrich cooling events (H8 and H9)
Authors: Ait Brahim Yassine , Peros Matthew C. , Viau André E. , Liedtke Mercedes , Pajón Jesús M. , Valdes Julio , Li Xianglei , Edwards R. Lawrence , Reinhardt Eduard G. , Oliva Frank
Published: December 2022

We present a speleothem record from western Cuba, spanning the period 98.7–84.9 ka BP. Our record shows two distinctive periods of high δ18O corresponding to dry and/or cold periods during 85–87.6 and 90.2–93.1 ka BP, synchronous with Heinrich events 8 and 9 (H8 and H9). Hence, we provide the first proxy evidence of the local Caribbean climate response to H8 and H9. Interestingly, H8 is more pronounced compared to H9, which may be a local response to lower temperatures in the North Atlantic resulting in a weak AMOC and reduced deep water formation, therefore a stronger south shift of the ITCZ. Our data complement existing speleothem records from western Cuba which, collectively, provide a nearly continuous paleoclimate time-series spanning the last 100 ka BP, indicating a consistent response to millennial-scale events as dry and/or cooler conditions. The comparison with regional paleoclimate records reveals an anti-phased relationship with South America, caused by the southern movements of the ITCZ during millennial-scale events which lead to dry conditions in the Caribbean and a stronger South American Monsoon System.
Arbuscular mycorrhiza can be disadvantageous for weedy annuals in competition with paired perennial plants
Authors: Řezáčová Veronika , Řezáč Milan , Wilson Gail W. T. , Michalová Tereza
Published: December 2022

Arbuscular mycorrhizal (AM) fungi can support the establishment of mycotrophic plants in new environments. However, the role of mycorrhizal symbiosis in interactions between perennial and weedy annual plants is not well understood. In our current study, we examine how widespread generalist AM fungi and soil disturbance, including disturbance of AM fungal networks (CMNs), affect the performance of two late-successional perennial plants of Central Europe, Senecio jacobaea and Crepis biennis, co-occurring with weedy annual forbs, Conyza canadensis and Erigeron annuus. Although presence of weedy annual E. annuus or C. canadensis did not affect the performance of the paired perennials, AM fungi supported perennial C. biennis in competition with weedy annual E. annuus. However, this AM-aided underpinning was independent of disturbance of CMNs. Conversely, although AM fungi benefited perennial S. jacobaea, this did not affect its competitive abilities when grown with weedy annual C. canadensis. Similarly, soil disturbance, independent of AM fungal presence, improved plant tissue P and biomass production of S. jacobaea, but not its competitive abilities. Our results show AM fungi may be advantageous for perennial plants growing in competition with weedy annual plants. Therefore, maintaining healthy soils containing an abundance of AM fungi, may encourage late successional perennial plants, potentially limiting establishment of weedy annual plant species.
Interrelations of vegetation growth and water scarcity in Iran revealed by satellite time series
Authors: Behling Robert , Roessner Sigrid , Foerster Saskia , Saemian Peyman , Tourian Mohammad J. , Portele Tanja C. , Lorenz Christof
Published: December 2022

Iran has experienced a drastic increase in water scarcity in the last decades. The main driver has been the substantial unsustainable water consumption of the agricultural sector. This study quantifies the spatiotemporal dynamics of Iran’s hydrometeorological water availability, land cover, and vegetation growth and evaluates their interrelations with a special focus on agricultural vegetation developments. It analyzes globally available reanalysis climate data and satellite time series data and products, allowing a country-wide investigation of recent 20+ years at detailed spatial and temporal scales. The results reveal a wide-spread agricultural expansion (27,000 km$$^2$$

2

) and a significant cultivation intensification (48,000 km$$^2$$

2

). At the same time, we observe a substantial decline in total water storage that is not represented by a decrease of meteorological water input, confirming an unsustainable use of groundwater mainly for agricultural irrigation. As consequence of water scarcity, we identify agricultural areas with a loss or reduction of vegetation growth (10,000 km$$^2$$

2

), especially in irrigated agricultural areas under (hyper-)arid conditions. In Iran’s natural biomes, the results show declining trends in vegetation growth and land cover degradation from sparse vegetation to barren land in 40,000 km$$^2$$

2

, mainly along the western plains and foothills of the Zagros Mountains, and at the same time wide-spread greening trends, particularly in regions of higher altitudes. Overall, the findings provide detailed insights in vegetation-related causes and consequences of Iran’s anthropogenic drought and can support sustainable management plans for Iran or other semi-arid regions worldwide, often facing similar conditions.
Evaluation of roadside air quality using deep learning models after the application of the diesel vehicle policy (Euro 6)
Authors: Hwang Hyemin , Choi Sung Rak , Lee Jae Young
Published: December 2022

Euro 6 is the latest vehicle emission standards for pollutants such as CO, NO2 and PM, that all new vehicles must comply, and it was introduced in September 2015 in South Korea. This study examined the effect of Euro 6 by comparing the measured pollutant concentrations after 2016 (Euro 6–era) to the estimated concentrations without Euro 6. The concentration without Euro 6 was estimated by first modeling the air quality using various environmental factors related to diesel vehicles, meteorological conditions, temporal information such as date and precursors in 2002–2015 (pre–Euro 6–era), and then applying the model to predict the concentration after 2016. In this study, we used both recurrent neural network (RNN) and random forest (RF) algorithms to model the air quality and showed that RNN can achieve higher R2 (0.634 ~ 0.759 depending on pollutants) than RF, making it more suitable for air quality modeling. According to our results, the measured concentrations during 2016–2019 were lower than the concentrations predicted using RNN by − 1.2%, − 3.4%, and − 4.8% for CO, NO2 and PM10. Such reduction can be attributed to the result of Euro 6.
Brain computer interface to distinguish between self and other related errors in human agent collaboration
Authors: Dimova-Edeleva Viktorija , Ehrlich Stefan K. , Cheng Gordon
Published: December 2022

When a human and machine collaborate on a shared task, ambiguous events might occur that could be perceived as an error by the human partner. In such events, spontaneous error-related potentials (ErrPs) are evoked in the human brain. Knowing whom the human perceived as responsible for the error would help a machine in co-adaptation and shared control paradigms to better adapt to human preferences. Therefore, we ask whether self- and agent-related errors evoke different ErrPs. Eleven subjects participated in an electroencephalography human-agent collaboration experiment with a collaborative trajectory-following task on two collaboration levels, where movement errors occurred as trajectory deviations. Independently of the collaboration level, we observed a higher amplitude of the responses on the midline central Cz electrode for self-related errors compared to observed errors made by the agent. On average, Support Vector Machines classified self- and agent-related errors with 72.64% accuracy using subject-specific features. These results demonstrate that ErrPs can tell if a person relates an error to themselves or an external autonomous agent during collaboration. Thus, the collaborative machine will receive more informed feedback for the error attribution that allows appropriate error identification, a possibility for correction, and avoidance in future actions.
Moral suasion and charitable giving
Authors: Balafoutas Loukas , Rezaei Sarah
Published: December 2022

We investigate the effect of moral suasion on charitable giving. Participants in an online experiment choose between two allocations, one of which includes a donation to a well-known charity organization. Before making this choice, they receive one of several messages potentially involving a moral argument from another participant. We find that the use of consequentialist and deontological arguments has a positive impact on the donation rate. Men respond strongly to consequentialist arguments, while women are less responsive to moral suasion altogether. Messages based on virtue ethics, ethical egoism, and a simple donation imperative are ineffective.
Boost piezocatalytic activity of BaSO4 by coupling it with BaTiO3, Cu:BaTiO3, Fe:BaTiO3, S:BaTiO3 and modify them by sucrose for water purification
Authors: Amiri Omid , Abdulla Gashaw L. , Burhan Chnar M. , Hussein Hawnaz H. , Azhdarpour Amir Mahyar , Saadat Mohsen , Joshaghani Mohammad , Mahmood Peshawa H.
Published: December 2022

The purpose of this study is to improve the efficiency of decontamination using BaSO4as a piezocatalyst. Three techniques are employed in this study to enhance the piezocatalytic activity of BaSO4. The first method involves coupling BaSO4with BaTiO3. The acid red 151 and acid blue 113 decontamination rates improved from 56.7% and 60.9% to 61.3% and 64.4%, respectively, as a result of this strategy. Additionally, the composite of BaSO4and BaTiO3was doped with copper, iron, sulfur, and nitrogen. By doping BaTiO3, acid red 151 and acid blue 113 achieved 86.7% and 89.2% efficiency, respectively. Finally, the nanostructures were modified with sucrose. These strategies improved degradation efficiency for acid red 151 and acid blue 113 to 92.9% and 93.3%, respectively. The reusability results showed that the piezo-catalytic activity of the m-S–BaSO4–BaTiO3catalyst did not show a significant loss after five recycles for the degradation of AB113.
Context-independent expression of spatial code in hippocampus
Authors: Kapl S. , Tichanek F. , Zitricky F. , Jezek K.
Published: December 2022

The hippocampus plays a crucial role in the formation and retrieval of spatial memory across mammals and episodic memory in humans. Episodic and spatial memories can be retrieved irrespective of the subject’s awake behavioral state and independently of its actual spatial context. However, the nature of hippocampal network activity during such out-context retrieval has not been described so far. Theoretically, context-independent spatial memory retrieval suggests a shift of the hippocampal spatial representations from coding the current spatial context to coding the remembered environment. In this study we show in rats that the CA3 neuronal population can switch spontaneously across representations and transiently activate another stored familiar spatial pattern without direct external sensory cuing. This phenomenon qualitatively differs from the well-described sharp wave-related pattern reactivations during immobility. Here, it occurs under the theta oscillatory state during active exploration and reflects the preceding experience of sudden environmental change. The respective out-context coding spikes appeared later in the theta cycle than the in-context ones. Finally, the experience also induced the emergence of population vectors with a co-expression of both codes segregated into different phases of the theta cycle.
Integrin beta1 (ITGB1) as a prognostic marker in esophageal adenocarcinoma
Authors: Damanakis Alexander I. , Wahler Isabell , Fuchs Hans , Löser Heike , Schröder Wolfgang , Zander Thomas , Chon Seung-Hun , Bruns Christiane , Quaas Alexander , Gebauer Florian
Published: December 2022

Today, individual prognosis in patients with adenocarcinoma of the esophagus (EAC) is based on post-surgical TNM staging and valid biomarkers are still not implemented. Integrin beta1 (ITGB1) is widely expressed in epithelial cells and promotes cell adhesion and growth. Its impact on tumor progression was described for different tumor entities before, data on its function as a potential biomarker in EAC is not available. Aim of the study is to evaluate the expression level of ITGB1 in a large collective of EAC and its impact on patients´ prognosis. 640 patients with esophageal adenocarcinoma were analyzed immunohistochemically for ITGB1. The data was correlated with long term outcome, clinical, pathological and molecular data (TP53, HER2/neu, c-myc, GATA6, PIK3CA and KRAS). Of 640 patients to be analyzed, 127 (19.8%) showed expression of ITGB1. ITGB1 expression was associated with lymph node metastasis, expression of integrin alphaV and KRAS mutation status. Patients with high ITGB1 expression showed impaired overall survival (22.5 months (95% CI 15.3–29.7 months), vs. 34.1 months (95% CI 25.3–42.4 months), P = 0.024). This effect was particularly evident in the group of patients undergoing primary surgery without prior neoadjuvant therapy (10.2 months (95% CI 1.9–41.7 months) vs. 31.4 months (95% CI 21.1–144.2 months, P = 0.008). ITGB1 was also an independent prognostic marker in multivariable analysis (HR 1.696 (95% CI 1.084–2.653, P = 0.021) in patients that underwent primary surgery. We demonstrate for the first time the prognostic significance of ITGB1 expression in a large EAC patient population.
Moisture content monitoring in withering leaves during black tea processing based on electronic eye and near infrared spectroscopy
Authors: Chen Jiayou , Yang Chongshan , Yuan Changbo , Li Yang , An Ting , Dong Chunwang
Published: December 2022

Monitoring the moisture content of withering leaves in black tea manufacturing remains a difficult task because the external and internal information of withering leaves cannot be simultaneously obtained. In this study, the spectral data and the color/texture information of withering leaves were obtained using near infrared spectroscopy (NIRS) and electronic eye (E-eye), respectively, and then fused to predict the moisture content. Subsequently, the low- and middle-level fusion strategy combined with support vector regression (SVR) was applied to detect the moisture level of withering leaves. In the middle-level fusion strategy, the principal component analysis (PCA) and random frog (RF) were employed to compress the variables and select effective information, respectively. The middle-level-RF (cutoff line = 0.8) displayed the best performance because this model used fewer variables and still achieved a satisfactory result, with 0.9883 and 5.5596 for the correlation coefficient of the prediction set (Rp) and relative percent deviation (RPD), respectively. Hence, our study demonstrated that the proposed data fusion strategy could accurately predict the moisture content during the withering process.
Comparative transcriptomics reveals commonalities and differences in the genetic underpinnings of a floral dimorphism
Authors: Potente Giacomo , Stubbs Rebecca L. , Yousefi Narjes , Pirovano Walter , Szövényi Péter , Conti Elena
Published: December 2022

Distyly, a floral dimorphism associated with heteromorphic self-incompatibility and controlled by the S-locus supergene, evolved independently multiple times. Comparative analyses of the first transcriptome atlas for the main distyly model, Primula veris, with other distylous species produced the following findings. A set of 53 constitutively expressed genes in P. veris did not include any of the housekeeping genes commonly used to normalize gene expression in qPCR experiments. The S-locus gene CYPT acquired its role in controlling style elongation via a change in expression profile. Comparison of genes differentially expressed between floral morphs revealed that brassinosteroids and auxin are the main hormones controlling style elongation in P. veris and Fagopyrum esculentum, respectively. Furthermore, shared biochemical pathways might underlie the expression of distyly in the distantly related P. veris, F. esculentum and Turnera subulata, suggesting a degree of correspondence between evolutionary convergence at phenotypic and molecular levels. Finally, we provide the first evidence supporting the previously proposed hypothesis that distyly supergenes of distantly related species evolved via the recruitment of genes related to the phytochrome-interacting factor (PIF) signaling network. To conclude, this is the first study that discovered homologous genes involved in the control of distyly in distantly related taxa.
Mitigation of tobacco bacteria wilt with microbial degradation of phenolic allelochemicals
Authors: Chang Xiaohan , Wang Yi , Sun Jingguo , Xiang Haibo , Yang Yong , Chen Shouwen , Yu Jun , Yang Chunlei
Published: December 2022

Long-term continuous monoculture cropping of tobacco leads to high incidence of tobacco bacterial wilt (TBW) caused by Ralstonia solanacearum, which threatening world tobacco production and causing great economy loss. In this study, a safe and effective way to control TBW by microbial degradation of phenolic allelochemicals (PAs) was explored. Eleven kinds of PAs were identified from continuous tobacco cropping soil. These PAs exhibited various effects on the growth, chemotaxis and biofilm formation of R. solanacearum. Then we isolated eight strains of Bacillus, one strain of Brucella, one strain of Enterobacter and one strain of Stenotrophomonas capable of degrading these PAs. The results of degradation assay showed that these isolated strains could degrade PAs both in culture solutions and soil. Besides, the incidence of TBW caused by R. solanacearum and deteriorated by PAs were significantly decreased by treating with these degrading strains. Furthermore, six out of eleven isolated strains were combined to degrade all the identified PAs and ultimately sharply reduced the incidence of TBW by 61.44% in pot experiment. In addition, the combined degrading bacteria could promote the plant growth and defense response. This study will provide a promising strategy for TBW control in tobacco production.
Hybrid the long short-term memory with whale optimization algorithm and variational mode decomposition for monthly evapotranspiration estimation
Authors: Fu Tonglin , Li Xinrong
Published: December 2022

The sustainability of artificial sand-binding vegetation is determined by the water balance between evapotranspiration (ET) and precipitation in desert regions. Consequently, accurately estimating ET is a critical prerequisite for determing the types and spatial distribution of artificial vegetation in different sandy areas. For this purpose, a novel hybrid estimation model was proposed to estimate monthly ET by coupling the deep learning long short term memory (LSTM) with variational mode decomposition (VMD) and whale optimization algorithm (WOA) (i.e., VMD-WOA-LSTM) to estimate the monthly ET in the southeast margins of Tengger Desert. The superiority of LSTM was selected due to its capability of automatically extracting the nonlinear and nonstationary features from sequential data, WOA was employed to optimize the hyperparameters of LSTM, and VMD was used to extract the intrinsic traits of ET time series. The estimating results of VMD-WOA-LSTM has been compared with actual ET and estimation of other hybrid models in terms of standard performance metrics. The results reveale that VMD-WOA-LSTM provide more accurate and reliable estimating results than that of LSTM, the support vector machine (SVM), and the variants of those models. Therefore, VMD-WOA-LSTM could be recommended as an essential auxiliary method to estimate ET in desert regions.
Unsupervised real-world knowledge extraction via disentangled variational autoencoders for photon diagnostics
Authors: Hartmann Gregor , Goetzke Gesa , Düsterer Stefan , Feuer-Forson Peter , Lever Fabiano , Meier David , Möller Felix , Vera Ramirez Luis , Guehr Markus , Tiedtke Kai , Viefhaus Jens , Braune Markus
Published: December 2022

We present real-world data processing on measured electron time-of-flight data via neural networks. Specifically, the use of disentangled variational autoencoders on data from a diagnostic instrument for online wavelength monitoring at the free electron laser FLASH in Hamburg. Without a-priori knowledge the network is able to find representations of single-shot FEL spectra, which have a low signal-to-noise ratio. This reveals, in a directly human-interpretable way, crucial information about the photon properties. The central photon energy and the intensity as well as very detector-specific features are identified. The network is also capable of data cleaning, i.e. denoising, as well as the removal of artefacts. In the reconstruction, this allows for identification of signatures with very low intensity which are hardly recognisable in the raw data. In this particular case, the network enhances the quality of the diagnostic analysis at FLASH. However, this unsupervised method also has the potential to improve the analysis of other similar types of spectroscopy data.
Impact of high Fe-concentrations on microbial community structure and dissolved organics in hydrothermal plumes: an experimental study
Authors: Hansen Christian T. , Kleint Charlotte , Böhnke Stefanie , Klose Lukas , Adam-Beyer Nicole , Sass Katharina , Zitoun Rebecca , Sander Sylvia G. , Indenbirken Daniela , Dittmar Thorsten , Koschinsky Andrea , Perner Mirjam
Published: December 2022

Iron (Fe) is an essential trace element for life. In the ocean, Fe can be exceptionally scarce and thus biolimiting or extremely enriched causing microbial stress. The ability of hydrothermal plume microbes to counteract unfavorable Fe-concentrations up to 10 mM is investigated through experiments. While Campylobacterota (Sulfurimonas) are prominent in a diverse community at low to intermediate Fe-concentrations, the highest 10 mM Fe-level is phylogenetically less diverse and dominated by the SUP05 clade (Gammaproteobacteria), a species known to be genetically well equipped to strive in high-Fe environments. In all incubations, Fe-binding ligands were produced in excess of the corresponding Fe-concentration level, possibly facilitating biological Fe-uptake in low-Fe incubations and detoxification in high-Fe incubations. The diversity of Fe-containing formulae among dissolved organics (SPE-DOM) decreased with increasing Fe-concentration, which may reflect toxic conditions of the high-Fe treatments. A DOM-derived degradation index (IDEG) points to a degradation magnitude (microbial activity) that decreases with Fe and/or selective Fe-DOM coagulation. Our results show that some hydrothermal microbes (especially Gammaproteobacteria) have the capacity to thrive even at unfavorably high Fe-concentrations. These ligand-producing microbes could hence play a key role in keeping Fe in solution, particularly in environments, where Fe precipitation dominates and toxic conditions prevail.
Dialysis based-culture medium conditioning improved the generation of human induced pluripotent stem cell derived-liver organoid in a high cell density
Authors: Torizal Fuad Gandhi , Utami Tia , Lau Qiao You , Inamura Kousuke , Nishikawa Masaki , Sakai Yasuyuki
Published: December 2022

Human pluripotent stem cell-derived liver organoids (HLOs) have recently become a promising alternative for liver regenerative therapy. To realize this application, a large amount of human-induced pluripotent stem cells (hiPSCs) derived-liver cells are required for partial liver replacement during transplantation. This method requires stepwise induction using costly growth factors to direct the hiPSCs into the hepatic lineage. Therefore, we developed a simple dialysis-based medium conditioning that fully utilized growth factors accumulation to improve hepatic differentiation of hiPSCs at a high cell density. The results demonstrated that the dialysis culture system could accumulate the four essential growth factors required in each differentiation stage: activin A, bone morphogenetic protein 4 (BMP4), hepatocyte growth factor (HGF), and oncostatin M (OSM). As a result, this low lactate culture environment allowed high-density bipotential hepatic differentiation of up to 4.5 × 107 cells/mL of human liver organoids (HLOs), consisting of hiPSC derived-hepatocyte like cells (HLCs) and cholangiocyte like-cells (CLCs). The differentiated HLOs presented a better or comparable hepatic marker and hepatobiliary physiology to the one that differentiated in suspension culture with routine daily medium replacement at a lower cell density. This simple miniaturized dialysis culture system demonstrated the feasibility of cost-effective high-density hepatic differentiation with minimum growth factor usage.
Anatomical study for elucidating the stabilization mechanism in the trapeziometacarpal joint
Authors: Norose Mio , Nimura Akimoto , Tsutsumi Masahiro , Fujita Koji , Okawa Atsushi , Akita Keiichi
Published: December 2022

To determine the pathogenesis of trapeziometacarpal (TMC) joint instability, which leads to osteoarthritis, we investigated the anatomical relationships among the surrounding ligaments, muscles (first dorsal interosseous [FDI] and opponens pollicis [OPP]), and joint capsule. We examined the bone morphology and cortical bone thickening in 25 cadaveric thumbs using micro-computed tomography and performed macroscopic and histological analyses. The dorsal trapezium had a tubercle with cortical bone thickening, corresponding to the attachment of the FDI aponeurosis intermingled with the joint capsule. Radially, the thin joint capsule was observed to underlie the muscular part of the OPP. Therefore, the dorsal ligaments, which have been previously considered static stabilizers, could be interpreted as parts of the capsuloaponeurotic complex consisting of the FDI aponeurosis and joint capsule. In the radial aspect, muscular OPP activation may be essential for TMC joint stabilization. Our findings may contribute to the appropriate management of TMC osteoarthritis.
Arg/Lys-containing IDRs are cryptic binding domains for ATP and nucleic acids that interplay to modulate LLPS
Authors: Dang Mei , Li Tongyang , Zhou Shibo , Song Jianxing
Published: December 2022

Most membrane-less organelles (MLOs) formed by LLPS contain both nucleic acids and IDR-rich proteins. Currently while IDRs are well-recognized to drive LLPS, nucleic acids are thought to exert non-specific electrostatic/salt effects. TDP-43 functions by binding RNA/ssDNA and its LLPS was characterized without nucleic acids to be driven mainly by PLD-oligomerization, which may further transit into aggregation characteristic of various neurodegenerative diseases. Here by NMR, we discovered unexpectedly for TDP-43 PLD: 1) ssDNAs drive and then dissolve LLPS by multivalently and specifically binding Arg/Lys. 2) LLPS is driven by nucleic-acid-binding coupled with PLD-oligomerization. 3) ATP and nucleic acids universally interplay in modulating LLPS by competing for binding Arg/Lys. However, the unique hydrophobic region within PLD renders LLPS to exaggerate into aggregation. The study not only unveils the first residue-resolution mechanism of the nucleic-acid-driven LLPS of TDP-43 PLD, but also decodes a general principle that not just TDP-43 PLD, all Arg/Lys-containing IDRs are cryptic nucleic-acid-binding domains that may phase separate upon binding nucleic acids. Strikingly, ATP shares a common mechanism with nucleic acids in binding IDRs, thus emerging as a universal mediator for interactions between IDRs and nucleic acids, which may underlie previously-unrecognized roles of ATP at mM in physiology and pathology.
Synthesis of graphdiyne on a copper substrateviaa self-coupling reaction
Authors: Wu Jiasheng , Liu Jie , Liang Jizhe , Zhang Yijie , Zhao Xiaoli , Yuan Chunxue
Published: December 2022

The preparation of graphdiyneviathe self-coupling reaction of hexakis(bromoethynyl)benzene (hBEP) with alkynyl bromide groups is reported, where the reaction can proceed moderately in 12 h at room temperature.
Performance of a multi-tubular Fischer–Tropsch reactor with two catalytic zones of different intrinsic chemical activity
Authors: Kern Christoph , Jess Andreas
Published: December 2022

The effect of axial distribution of the intrinsic catalytic activity on the performance of a multi-tubular fixed bed Fischer–Tropsch reactor was investigated.
Insights into an air-stable methylene blue catholyte towards kW-scale practical aqueous organic flow batteries
Authors: Zhang Yonghui , Li Fan , Li Tianyu , Zhang Mengqi , Yuan Zhizhang , Hou Guangjin , Fu Jie , Zhang Changkun , Li Xianfeng
Published: December 2022

A kW-scale AOFB stack with a long and stable lifespan was achieved based on the air-stable MB catholyte for the first time.
Inter-individual characteristics on basic taste recognition thresholds in a college-aged cohort: potential predictive factors
Authors: Trius-Soler Marta , Laveriano-Santos Emily P. , Góngora Clara , Moreno Juan J.
Published: December 2022

Studying nutritional status from the perspective of taste sensitivity, rather than only dietary patterns, may provide new insights into the physiological implications of the gustatory function and predictors of taste sensitivity.
Platycodin D ameliorates hyperglycaemia and liver metabolic disturbance in HFD/STZ-induced type 2 diabetic mice
Authors: Shen Qiong , Zhong Yu-te , Liu Xiang-xiang , Hu Jun-nan , Qi Si-min , Li Ke , Wang Zi , Zhu Hong-yan , Li Xin-dian , Wang Ying-ping , Li Wei
Published: December 2022

PD can regulate HFD/STZ-induced disorders of glycolipid metabolism in mice through gluconeogenesis and fatty acid metabolism pathways and restore liver function.
Size driven barrier to chirality reversal in electric control of magnetic vortices in ferromagnetic nanodiscs
Authors: Aldulaimi W. A. S. , Okatan M. B. , Sendur K. , Onbasli M. C. , Misirlioglu I. B.
Published: December 2022

We study the response of nanoscale ferromagnetic permalloy discs stabilized in vortex state to pulsed electric fields and analyze the energy barrier to the chirality reversal process using a micromagnetic simulation.
Frictionless nanohighways on crystalline surfaces
Authors: Panizon Emanuele , Silva Andrea , Cao Xin , Wang Jin , Bechinger Clemens , Vanossi Andrea , Tosatti Erio , Manini Nicola
Published: December 2022

A novel kind of geometry of nanoscale contacts realizes stable directional locking, with one structurally lubric sliding direction - the frictionless nanohighway, and large friction perpendicular to it.
Molecularly “clicking” active moieties to germanium-based inorganic 2D materials
Authors: Palacios-Corella Mario , Muñoz Jose , Pumera Martin
Published: December 2022

Thiol–ene click chemistry is presented as a “one-pot” synthetic strategy to implant molecular features upon commercially available allyl germanane 2D-Ge–CH2CHCH2 by covalently grafting thiol-rich active molecular components (R′–SH).
Natural products as antivibrio agents: insight into the chemistry and biological activity
Authors: Kasanah Noer , Ulfah Maria , Rowley David C.
Published: December 2022

Natural products provide chemical diversity of antivibrio compounds.
Preparation of immobilized pepsin for extraction of collagen from bovine hide
Authors: Duan Youdan , Cheng Haiming
Published: December 2022

In the extraction of collagens from mammalian tissues, the free pepsin used in the acid–pepsin extraction system is hard to recycle, and there is a risk of enzyme protein contamination in the extracted collagen products, which limits their applications.
Retraction: Droplet microfluidics: fundamentals and its advanced applications
Authors: Sohrabi Somayeh , kassir Nour , Keshavarz Moraveji Mostafa
Published: December 2022

Retraction of ‘Droplet microfluidics: fundamentals and its advanced applications’ by Somayeh Sohrabi et al., RSC Adv., 2020, 10, 27560–27574, https://doi.org/10.1039/D0RA04566G.