bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visualizing the disordered nuclear transport machinery in situ
Authors: Yu Miao , Heidari Maziar , Mikhaleva Sofya , Tan Piau Siong , Mingu Sara , Ruan Hao , Reinkemeier Christopher D. , Obarska-Kosinska Agnieszka , Siggel Marc , Beck Martin , Hummer Gerhard , Lemke Edward A. 
Published: April 2023

AbstractThe approximately 120 MDa mammalian nuclear pore complex (NPC) acts as a gatekeeper for the transport between the nucleus and cytosol1. The central channel of the NPC is filled with hundreds of intrinsically disordered proteins (IDPs) called FG-nucleoporins (FG-NUPs)2,3. Although the structure of the NPC scaffold has been resolved in remarkable detail, the actual transport machinery built up by FG-NUPs—about 50 MDa—is depicted as an approximately 60-nm hole in even highly resolved tomograms and/or structures computed with artificial intelligence4–11. Here we directly probed conformations of the vital FG-NUP98 inside NPCs in live cells and in permeabilized cells with an intact transport machinery by using a synthetic biology-enabled site-specific small-molecule labelling approach paired with highly time-resolved fluorescence microscopy. Single permeabilized cell measurements of the distance distribution of FG-NUP98 segments combined with coarse-grained molecular simulations of the NPC allowed us to map the uncharted molecular environment inside the nanosized transport channel. We determined that the channel provides—in the terminology of the Flory polymer theory12—a ‘good solvent’ environment. This enables the FG domain to adopt expanded conformations and thus control transport between the nucleus and cytoplasm. With more than 30% of the proteome being formed from IDPs, our study opens a window into resolving disorder–function relationships of IDPs in situ, which are important in various processes, such as cellular signalling, phase separation, ageing and viral entry.
A druggable copper-signalling pathway that drives inflammation
Authors: Solier Stéphanie , Müller Sebastian , Cañeque Tatiana , Versini Antoine , Mansart Arnaud , Sindikubwabo Fabien , Baron Leeroy , Emam Laila , Gestraud Pierre , Pantoș G. Dan , Gandon Vincent , Gaillet Christine , Wu Ting-Di , Dingli Florent , Loew Damarys , Baulande Sylvain , Durand Sylvère , Sencio Valentin , Robil Cyril , Trottein François , Péricat David , Näser Emmanuelle , Cougoule Céline , Meunier Etienne , Bègue Anne-Laure , Salmon Hélène , Manel Nicolas , Puisieux Alain , Watson Sarah , Dawson Mark A. , Servant Nicolas , Kroemer Guido , Annane Djillali , Rodriguez Raphaël 
Published: April 2023

AbstractInflammation is a complex physiological process triggered in response to harmful stimuli1. It involves cells of the immune system capable of clearing sources of injury and damaged tissues. Excessive inflammation can occur as a result of infection and is a hallmark of several diseases2–4. The molecular bases underlying inflammatory responses are not fully understood. Here we show that the cell surface glycoprotein CD44, which marks the acquisition of distinct cell phenotypes in the context of development, immunity and cancer progression, mediates the uptake of metals including copper. We identify a pool of chemically reactive copper(ii) in mitochondria of inflammatory macrophages that catalyses NAD(H) redox cycling by activating hydrogen peroxide. Maintenance of NAD+ enables metabolic and epigenetic programming towards the inflammatory state. Targeting mitochondrial copper(ii) with supformin (LCC-12), a rationally designed dimer of metformin, induces a reduction of the NAD(H) pool, leading to metabolic and epigenetic states that oppose macrophage activation. LCC-12 interferes with cell plasticity in other settings and reduces inflammation in mouse models of bacterial and viral infections. Our work highlights the central role of copper as a regulator of cell plasticity and unveils a therapeutic strategy based on metabolic reprogramming and the control of epigenetic cell states.
Reducing brassinosteroid signalling enhances grain yield in semi-dwarf wheat
Authors: Song Long , Liu Jie , Cao Beilu , Liu Bin , Zhang Xiaoping , Chen Zhaoyan , Dong Chaoqun , Liu Xiangqing , Zhang Zhaoheng , Wang Wenxi , Chai Lingling , Liu Jing , Zhu Jun , Cui Shubin , He Fei , Peng Huiru , Hu Zhaorong , Su Zhenqi , Guo Weilong , Xin Mingming , Yao Yingyin , Yan Yong , Song Yinming , Bai Guihua , Sun Qixin , Ni Zhongfu 
Published: April 2023

AbstractModern green revolution varieties of wheat (Triticum aestivum L.) confer semi-dwarf and lodging-resistant plant architecture owing to the Reduced height-B1b (Rht-B1b) and Rht-D1b alleles1. However, both Rht-B1b and Rht-D1b are gain-of-function mutant alleles encoding gibberellin signalling repressors that stably repress plant growth and negatively affect nitrogen-use efficiency and grain filling2–5. Therefore, the green revolution varieties of wheat harbouring Rht-B1b or Rht-D1b usually produce smaller grain and require higher nitrogen fertilizer inputs to maintain their grain yields. Here we describe a strategy to design semi-dwarf wheat varieties without the need for Rht-B1b or Rht-D1b alleles. We discovered that absence of Rht-B1 and ZnF-B (encoding a RING-type E3 ligase) through a natural deletion of a haploblock of about 500 kilobases shaped semi-dwarf plants with more compact plant architecture and substantially improved grain yield (up to 15.2%) in field trials. Further genetic analysis confirmed that the deletion of ZnF-B induced the semi-dwarf trait in the absence of the Rht-B1b and Rht-D1b alleles through attenuating brassinosteroid (BR) perception. ZnF acts as a BR signalling activator to facilitate proteasomal destruction of the BR signalling repressor BRI1 kinase inhibitor 1 (TaBKI1), and loss of ZnF stabilizes TaBKI1 to block BR signalling transduction. Our findings not only identified a pivotal BR signalling modulator but also provided a creative strategy to design high-yield semi-dwarf wheat varieties by manipulating the BR signal pathway to sustain wheat production.
Very High Resolution Projections over Italy under different CMIP5 IPCC scenarios
Authors: Raffa Mario , Adinolfi Marianna , Reder Alfredo , Marras Gian Franco , Mancini Marco , Scipione Gabriella , Santini Monia , Mercogliano Paola 
Published: April 2023

AbstractThis paper introduces VHR-PRO_IT (Very High-Resolution PROjections for ITaly), an open access hourly climate projection with a resolution of ≃2.2 km (i.e., Convection Permitting Scale) up to 2050, covering the Italian peninsula and some neighbouring areas. VHR-PRO_IT is produced within the Highlander project (https://highlanderproject.eu/) by dynamically downscaling the Italy8km-CM climate projection (spatial resolution ≃8 km; output frequency = 6 h; driven CMIP5 GCM = CMCC-CM) with the Regional Climate Model COSMO-CLM under the IPCC RCP4.5 and RCP8.5 scenarios. It covers the 60-year period 1989–2050. VHR-PRO_IT is intended for research purposes in the field of climate studies. For example, it may be included in the ongoing activities to clarify the added value of running climate simulation at the convection-permitting scale.
Insider trading
Authors: Balogh Attila 
Published: April 2023

AbstractThis paper describes a dataset capturing insider trading activity at publicly traded companies. Investors and investment analysts demand this information because executives, directors and large shareholders are expected to have more intimate knowledge of their company’s prospects than outsiders. Insider stock sales and purchases may reveal information about the firm’s business not disclosed in financial statements. They may also convey new information predictive of stock price movements if insiders can better interpret public information about the firm. Since mid-2003, the Securities and Exchange Commission has made these insider trading reports available to the public in a structured format; however, most academic papers use proprietary commercial databases instead of regulatory filings directly. This makes replication challenging as the data manipulation and aggregation processes are opaque and historical records could be altered by the database provider over time. To overcome these limitations, the presented dataset is created from original regulatory filings; it is updated daily and includes all information reported by insiders without alteration.
Pest scenario of Helicoverpa armigera (Hub.) on pigeonpea during future climate change periods under RCP based projections in India
Authors: Srinivasa Rao M. , Rama Rao C. A. , Raju B. M. K. , Subba Rao A. V. M. , Gayatri D. L. A. , Islam Adlul , Prasad T. V. , Navya M. , Srinivas K. , Pratibha G. , Srinivas I. , Prabhakar M. , Yadav S. K. , Bhaskar S. , Singh V. K. , Chaudhari S. K. 
Published: April 2023

AbstractGram pod borer, Helicoverpa armigera (Hub.) is the major insect pest of pigeonpea and prediction of number of generations (no. of gen.) and generation time (gen. time) using growing degree days (GDD) approach during three future climate change periods viz., Near (NP), Distant (DP) and Far Distant (FDP) periods at eleven major pigeonpea growing locations of India was attempted. Multi-model ensemble of Maximum (Tmax) and Minimum (Tmin) temperature data of four Representative Concentration Pathways viz., RCP 2.6, 4.5, 6.0 and 8.5 of Coupled Model Inter comparison Project 5 (CMIP5) models was adopted here. The increase in projected Tmax and Tmin are significant during 3 climate change periods (CCPs) viz., the NP, DP and FDP over base line (BL) period under four RCP scenarios at all locations and would be higher (4.7–5.1 °C) in RCP 8.5 and in FDP. More number of annual (10–17) and seasonal (5–8) gens. are expected to occur with greater percent increase in FDP (8 to 38%) over base line followed by DP (7 to 22%) and NP (5to 10%) periods with shortened annual gen. time (4 to 27%) across 4 RCPs. The reduction of crop duration was substantial in short, medium and long duration pigeonpeas at all locations across 4 RCPs and 3 CCPs. The seasonal no.of gen. is expected to increase (5 to 35%) with shortened gen. time (4 to 26%) even with reduced crop duration across DP and FDP climate periods of 6.0 and 8.5 RCPs in LD pigeonpea. More no. of gen. of H. armigera with reduced gen. time are expected to occur at Ludhiana, Coimbatore, Mohanpur, Warangal and Akola locations over BL period in 4 RCPs when normal duration of pigeonpeas is considered. Geographical location (66 to 72%), climate period (11 to 19%), RCPs (5–7%) and their interaction (0.04–1%) is vital and together explained more than 90% of the total variation in future pest scenario. The findings indicate that the incidence of H. armigera would be higher on pigeonpea during ensuing CCPs in India under global warming context.
The effect of claudin-15 deletion on cationic selectivity and transport in paracellular pathways of the cecum and large intestine
Authors: Hempstock Wendy , Nagata Nozomi , Ishizuka Noriko , Hayashi Hisayoshi 
Published: April 2023

AbstractThe large intestine plays a pivotal role in water and electrolyte balance. Paracellular transport may play a role in ion transport mechanisms in the cecum and large intestine; however, these molecular mechanisms and their physiological roles have not been fully studied. Claudin-15 forms a cation channel in tight junctions in the small intestine, but its role in the cecum and large intestine has not been investigated. This study aimed to explore the physiological role of claudin-15 in the cecum and large intestine using claudin-15 (Cldn15) KO mice. Electrical conductance, short-circuit current, Na+ flux, and dilution potential were assessed in isolated tissue preparations mounted in Ussing chambers. The induced short-circuit current of short-chain fatty acids, which are fermentative products in the intestinal tract, was also measured. Compared to wild type mice, the electrical conductance and paracellular Na+ flux was decreased in the cecum, but not the middle large intestine, while in both the cecum and the middle large intestine, paracellular Na+ permeability was decreased in Cldn15 KO mice. These results suggest that claudin-15 is responsible for Na+ permeability in the tight junctions of the cecum and large intestine and decreased Na+ permeability in the cecum may cause impaired absorption function.
Wrist redundancy management during pointing tasks remains stable over time and in presence of a visuomotor perturbation
Authors: Raiano Luigi , Noccaro Alessia , Di Pino Giovanni , Formica Domenico 
Published: April 2023

AbstractPointing at a screen using wrist and forearm movements is a kinematically redundant task, and the Central Nervous System seems to manage this redundancy by using a simplifying strategy, named Donders’ Law for the wrist. In this work we investigated (1) whether this simplifying approach is stable over time and (2) whether a visuomotor perturbation provided in the task space influences the strategy used to solve the redundancy problem. We conducted two experiments asking participants to perform the same pointing task in four different days (first experiment), and providing a visual perturbation, i.e. a visuomotor rotation to the controlled cursor (second experiment), while recording their wrist and forearm rotations. Results showed that the participant-specific wrist redundancy management (described by the Donders’ surfaces) (1) neither changes over time (2) nor varies when a visuomotor perturbation is provided in the task space.
High-precision density mapping of marine debris and floating plastics via satellite imagery
Authors: Booth Henry , Ma Wanli , Karakuş Oktay 
Published: April 2023

AbstractThe last couple of years has been ground-breaking for marine pollution monitoring purposes. It has been suggested that combining multi-spectral satellite information and machine learning approaches are effective to monitor plastic pollutants in the ocean environment. Recent research has made theoretical progress in identifying marine debris and suspected plastic (MD&SP) through machine learning whereas no study has fully explored the application of these methods for mapping and monitoring marine debris density. Therefore, this article consists of three main components: (1) the development and validation of a supervised machine learning marine debris detection model, (2) to map the MD&SP density into an automated tool called MAP-Mapper and finally (3) evaluation of the entire system for out-of-distribution (OOD) test locations. Developed MAP-Mapper architectures provide users with options to achieve high precision (abbv. -HP) or optimum precision-recall (abbv. -Opt) values in terms of training/test dataset. Our MAP-Mapper-HP model greatly increases the MD&SP detection precision to 95%, while the MAP-Mapper-Opt achieves 87–88% precision–recall pair. To efficiently measure density mapping findings at OOD test locations, we propose the Marine Debris Map (MDM) index, which combines the average probability of a pixel belonging to the MD&SP class and the number of detections in a given time frame. The high MDM findings of the proposed approach are found to be consistent with existing marine litter and plastic pollution areas, and these are presented with available evidence citing literature and field studies.
Trends in semen parameters of infertile men in South Africa and Nigeria
Authors: Akang Edidiong Nnamso , Opuwari Chinyerum Sylvia , Enyioma-Alozie Swesme , Moungala Lionel Wildy , Amatu Tamarapreye Emmanuel , Wada Ibrahim , Ogbeche Rose Ogeyi , Ajayi Oluwatoyin Omolayo , Aderonmu Mojisola Modupe , Shote Olaitan Boluwatife , Akinola Lateef Adekunle , Ashiru Oladapo Adenrele , Henkel Ralf 
Published: April 2023

AbstractThere are conflicting reports on trends of semen parameters from different parts of the globe. However, in recent times there is dearth of information on the trend in Sub-Saharan countries. Therefore, in this study we aimed at determining the trends in semen parameters in Nigeria and South Africa between 2010 and 2019. A retrospective study of semen analyses of 17,292 men attending fertility hospitals in Nigeria and South Africa in 2010, 2015 and 2019. Patients who had undergone vasectomy and those who had a pH less than 5 or greater than 10 were excluded from this study. The following variables were assessed: ejaculate volume, sperm concentration, progressive motility, total progressively motile sperm count (TPMSC), total sperm count, and normal sperm morphology. Between 2010 and 2019, significant trends of decreasing values were observed in normal sperm morphology (− 50%), and the ejaculatory volume (− 7.4%), indicating a progressive deterioration of the values in both countries. In Nigeria, there were significant decreases in progressive motility (− 87%), TPMSC (− 78%), and sperm morphology (− 55%) between 2010 and 2019 (P < 0.001). Spearman`s rank correlation revealed significant negative associations between age and morphology (ρ =  − 0.24, P < 0.001), progressive motility (ρ =  − 0.31. P < 0.001), and TPMSC (ρ =  − 0.32, P < 0.001). Patients in South Africa were younger than those from Nigeria, with also a significantly higher sperm morphology, sperm concentration, progressive motility, total sperm count and TPMSC. Our findings provide a quantitative evidence of an alarming decreasing trend in semen parameters in Nigeria and South Africa from 2010 to 2019. It also proves that astheno- and teratozoospermia are the leading causes of male infertility in these regions. In addition to this, it also shows empirically that semen parameters decrease with advancement in age. These findings are the first report of temporal trends in semen parameters in Sub-Saharan countries, necessitating a thorough investigation on the underlying factors promoting this worrisome decline.
Simultaneous multi-crop land suitability prediction from remote sensing data using semi-supervised learning
Authors: Bhullar Amanjot , Nadeem Khurram , Ali R. Ayesha 
Published: April 2023

AbstractLand suitability models for Canada are currently based on single-crop inventories and expert opinion. We present a data-driven multi-layer perceptron that simultaneously predicts the land suitability of several crops in Canada, including barley, peas, spring wheat, canola, oats, and soy. Available crop yields from 2013–2020 are downscaled to the farm level by masking the district level crop yield data to focus only on areas where crops are cultivated and leveraging soil-climate-landscape variables obtained from Google Earth Engine for crop yield prediction. This new semi-supervised learning approach can accommodate data from different spatial resolutions and enables training with unlabelled data. The incorporation of a crop indicator function further allows for the training of a multi-crop model that can capture the interdependences and correlations between various crops, thereby leading to more accurate predictions. Through k-fold cross-validation, we show that compared to the single crop models, our multi-crop model could produce up to a 2.82 fold reduction in mean absolute error for any particular crop. We found that barley, oats, and mixed grains were more tolerant to soil-climate-landscape variations and could be grown in many regions of Canada, while non-grain crops were more sensitive to environmental factors. Predicted crop suitability was associated with a region’s growing season length, which supports climate change projections that regions of northern Canada will become more suitable for agricultural use. The proposed multi-crop model could facilitate assessment of the suitability of northern lands for crop cultivation and be incorporated into cost-benefit analyses.
Intravitreal injection of fibrillin 2 (Fbn2) recombinant protein for therapy of retinopathy in a retina-specific Fbn2 knock-down mouse model
Authors: Zhang Rui Xue , Wen Ying , Guo Da Dong , Xu Fu Ru , Wang Gui Min , Wang Xing Rong , Shi Yong Wei , Ding Jie , Jiang Qian , Jiang Wen Jun , Jonas Jost B. , Bi Hong Sheng 
Published: April 2023

AbstractMutations in the extracellular matrix gene Fibrillin-2 (FBN2) are related to genetic macular degenerative disorders including age-related macular degeneration (AMD) and early-onset macular degeneration (EOMD). It was reported that the retinal protein expression of FBN2 was reduced in patients with AMD and EOMD. The effect of exogenously supplied fbn2 recombinant protein on fbn2-deficiency-related retinopathy was not known. Here we investigated the efficacy and molecular mechanism of intravitreally applied fibrin-2 recombinant protein in mice with fbn2-deficient retinopathy. The experimental study included groups (all n = 9) of adult C57BL/6J male mice which underwent no intervention, intravitreal injection of adeno-associated virus (AAV) empty vector or intravitreal injection of AAV-sh-fbn2 (adeno-associated virus for expressing short hairpin RNA for fibrillin-2) followed by three intravitreal injections of fbn2 recombinant protein, given in intervals of 8 days in doses of 0.30 μg, 0.75 μg, 1.50 μg, and 3.00 μg, respectively. Eyes with intravitreally applied AAV-sh-fbn2 as compared to eyes with injection of AAV-empty vector or developed an exudative retinopathy with involvement of the deep retinal layers, reduction in axial length and reduction in ERG amplitudes. After additional and repeated application of fbn2 recombinant protein, the retinopathy improved with an increase in retinal thickness and ERG amplitude, the mRNA and protein expression of transforming growth factor-beta (TGF-β1) and TGF-β binding protein (LTBP-1) increased, and axial length elongated, with the difference most marked for the dose of 0.75 μg of fbn2 recombinant protein. The observations suggest that intravitreally applied fbn2 recombinant protein reversed the retinopathy caused by an fbn2 knockdown.
Cold atmospheric plasma treatment enhances recombinant model protein production in yeast Pichia pastoris
Authors: Kabarkouhi Zeinab , Arjmand Sareh , Ranaei Siadat Seyed Omid , Shokri Babak 
Published: April 2023

AbstractCold atmospheric pressure plasma (CAP) has been described as a novel technology with expanding applications in biomedicine and biotechnology. In the present study, we provide a mildly stressful condition using non-lethal doses of CAP (120, 180, and 240 s) and evaluate its potential benefits on the recombinant production of a model protein (enhanced green fluorescent protein (eGFP)) in yeast Pichia pastoris. The measured eGFP fluorescence augmented proportional to CAP exposure time. After 240 s treatment with CAP, the measured fluorescent intensity of culture supernatant (after 72 h) and results of real-time PCR (after 24 h) indicated an 84% and 76% increase in activity and related RNA concentration, respectively. Real-time analysis of a list of genes involved in oxidative stress response revealed a significant and durable improvement in their expression at five h and 24 h following CAP exposure. The improvement of the recombinant model protein production may be partly explained by the impact of the RONS on cellular constituents and altering the expression of specific stress genes. In conclusion, using CAP strategy may be considered a valuable strategy to improve recombinant protein production, and deciphering the molecular background mechanism could be inspiring in the reverse metabolic engineering of host cells.