bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climate warming has compounded plant responses to habitat conversion in northern Europe
Authors: Auffret Alistair G. , Svenning Jens-Christian 
Published: December 2022

AbstractSerious concerns exist about potentially reinforcing negative effects of climate change and land conversion on biodiversity. Here, we investigate the tandem and interacting roles of climate warming and land-use change as predictors of shifts in the regional distributions of 1701 plant species in Sweden over 60 years. We show that species associated with warmer climates have increased, while grassland specialists have declined. Our results also support the hypothesis that climate warming and vegetation densification through grazing abandonment have synergistic effects on species distribution change. Local extinctions were related to high levels of warming but were reduced by grassland retention. In contrast, colonisations occurred more often in areas experiencing high levels of both climate and land-use change. Strong temperature increases were experienced by species across their ranges, indicating time lags in expected warming-related local extinctions. Our results highlight that the conservation of threatened species relies on both reduced greenhouse gas emissions and the retention and restoration of valuable habitat.
Self-growing photonic composites with programmable colors and mechanical properties
Authors: Xue Juan , Yin Xuewu , Xue Lulu , Zhang Chenglin , Dong Shihua , Yang Li , Fang Yuanlai , Li Yong , Li Ling , Cui Jiaxi 
Published: December 2022

AbstractMany organisms produce stunning optical displays based on structural color instead of pigmentation. This structural or photonic color is achieved through the interaction of light with intricate micro-/nano-structures, which are “grown” from strong, sustainable biological materials such as chitin, keratin, and cellulose. In contrast, current synthetic structural colored materials are usually brittle, inert, and produced via energy-intensive processes, posing significant challenges to their practical uses. Inspired by the brilliantly colored peacock feathers which selectively grow keratin-based photonic structures with different photonic bandgaps, we develop a self-growing photonic composite system in which the photonic bandgaps and hence the coloration can be easily tuned. This is achieved via the selective growth of the polymer matrix with polymerizable compounds as feeding materials in a silica nanosphere-polymer composite system, thus effectively modulating the photonic bandgaps without compromising nanostructural order. Such strategy not only allows the material system to continuously vary its colors and patterns in an on-demand manner, but also endows it with many appealing properties, including flexibility, toughness, self-healing ability, and reshaping capability. As this innovative self-growing method is simple, inexpensive, versatile, and scalable, we foresee its significant potential in meeting many emerging requirements for various applications of structural color materials.
Passive margins in accreting Archaean archipelagos signal continental stability promoting early atmospheric oxygen rise
Authors: Peng Yaying , Kusky Timothy , Wang Lu , Luan Zhikang , Wang Chuanhai , Liu Xuanyu , Zhong Yating , Evans Noreen J. 
Published: December 2022

AbstractSignificant changes in tectonic style and climate occurred from the late Archaean to early Proterozoic when continental growth and emergence provided opportunities for photosynthetic life to proliferate by the initiation of the Great Oxidation Event (GOE). In this study, we report a Neoarchaean passive-margin-type sequence (2560–2500 million years ago) from the Precambrian basement of China that formed in an accretionary orogen. Tectonostratigraphic and detrital zircon analysis reveal that thermal subsidence on the backside of a recently amalgamated oceanic archipelago created a quiet, shallow water environment, marked by deposition of carbonates, shales, and shallow water sediments, likely hosts to early photosynthetic microbes. Distinct from the traditional understanding of passive margins generated by continental rifting, post-collisional subsidence of archipelago margins represents a novel stable niche, signalling initial continental maturity and foreshadowing great changes at the Archaean-Proterozoic boundary.
Targeting the transcription factor HES1 by L-menthol restores protein phosphatase 6 in keratinocytes in models of psoriasis
Authors: Wang Zhikai , Sun Yang , Lou Fangzhou , Bai Jing , Zhou Hong , Cai Xiaojie , Sun Libo , Yin Qianqian , Tang Sibei , Wu Yue , Fan Li , Xu Zhenyao , Wang Hong , Hu Xiaoyu , Wang Honglin 
Published: December 2022

AbstractProtein Phosphatase 6 down-regulation in keratinocytes is a pivotal event that amplifies the inflammatory circuits in psoriasis, indicating that restoration of protein phosphatase 6 can be a rational strategy for psoriasis treatment. Through the phenotypic screen, we here identify L-menthol that ameliorates psoriasis-like skin inflammation by increasing protein phosphatase 6 in keratinocytes. Target identification approaches reveal an indispensable role for the transcription factor hairy and enhancer of split 1 in governing the protein phosphatase 6-upregulating function of L-menthol in keratinocytes. The transcription factor hairy and enhancer of split 1 is diminished in the epidermis of psoriasis patients and imiquimod-induced mouse model, while L-menthol upregulates the transcription factor hairy and enhancer of split 1 by preventing its proteasomal degradation. Mechanistically, the transcription factor hairy and enhancer of split 1 transcriptionally activates the expression of immunoglobulin-binding protein 1 which promotes protein phosphatase 6 expression and inhibits its ubiquitination. Collectively, we discover a therapeutic compound, L-menthol, for psoriasis, and uncover the dysfunctional the transcription factor hairy and enhancer of split 1- immunoglobulin-binding protein 1- protein phosphatase 6 axis that contributes to psoriasis pathology by using L-menthol as a probe.
The Milky Way’s plane of satellites is consistent with ΛCDM
Authors: Sawala Till , Cautun Marius , Frenk Carlos , Helly John , Jasche Jens , Jenkins Adrian , Johansson Peter H. , Lavaux Guilhem , McAlpine Stuart , Schaller Matthieu 
Published: December 2022

AbstractThe Milky Way is surrounded by 11 ‘classical’ satellite galaxies in a remarkable configuration: a thin plane that is possibly rotationally supported. Such a structure is thought to be highly unlikely to arise in the standard (ΛCDM) cosmological model (Λ cold dark matter model, where Λ is the cosmological constant). While other apparent discrepancies between predictions and observations of Milky Way satellite galaxies may be explained either through baryonic effects or by invoking alternative forms of dark matter particles, there is no known mechanism for making rotating satellite planes within the dispersion-supported dark matter haloes predicted to surround galaxies such as the Milky Way. This is the so-called ‘plane of satellites problem’, which challenges not only the ΛCDM model but the entire concept of dark matter. Here we show that the reportedly exceptional anisotropy of the Milky Way satellites is explained, in large part, by their lopsided radial distribution combined with the temporary conjunction of the two most distant satellites, Leo I and Leo II. Using Gaia proper motions, we show that the orbital pole alignment is much more common than previously reported, and reveal the plane of satellites to be transient rather than rotationally supported. Comparing with new simulations, where such short-lived planes are common, we find the Milky Way satellites to be compatible with standard model expectations.
Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing
Authors: Begik Oguzhan , Diensthuber Gregor , Liu Huanle , Delgado-Tejedor Anna , Kontur Cassandra , Niazi Adnan Muhammad , Valen Eivind , Giraldez Antonio J. , Beaudoin Jean-Denis , Mattick John S. , Novoa Eva Maria 
Published: December 2022

AbstractRNA polyadenylation plays a central role in RNA maturation, fate, and stability. In response to developmental cues, polyA tail lengths can vary, affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore 3′ end-capture sequencing (Nano3P-seq), a method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance, tail composition, and tail length dynamics at per-read resolution. By employing a template-switching-based sequencing protocol, Nano3P-seq can sequence RNA molecule from its 3′ end, regardless of its polyadenylation status, without the need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P-seq provides quantitative estimates of RNA abundance and tail lengths, and captures a wide diversity of RNA biotypes. We find that, in addition to mRNA and long non-coding RNA, polyA tails can be identified in 16S mitochondrial ribosomal RNA in both mouse and zebrafish models. Moreover, we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform-specific level, correlating with mRNA decay. Finally, we demonstrate the ability of Nano3P-seq in capturing non-A bases within polyA tails of various lengths, and reveal their distribution during vertebrate embryogenesis. Overall, Nano3P-seq is a simple and robust method for accurately estimating transcript levels, tail lengths, and tail composition heterogeneity in individual reads, with minimal library preparation biases, both in the coding and non-coding transcriptome.
Microglia ferroptosis is regulated by SEC24B and contributes to neurodegeneration
Authors: Ryan Sean K. , Zelic Matija , Han Yingnan , Teeple Erin , Chen Luoman , Sadeghi Mahdiar , Shankara Srinivas , Guo Lilu , Li Cong , Pontarelli Fabrizio , Jensen Elizabeth H. , Comer Ashley L. , Kumar Dinesh , Zhang Mindy , Gans Joseph , Zhang Bailin , Proto Jonathan D. , Saleh Jacqueline , Dodge James C. , Savova Virginia , Rajpal Deepak , Ofengeim Dimitry , Hammond Timothy R. 
Published: December 2022

AbstractIron dysregulation has been implicated in multiple neurodegenerative diseases, including Parkinson’s disease (PD). Iron-loaded microglia are frequently found in affected brain regions, but how iron accumulation influences microglia physiology and contributes to neurodegeneration is poorly understood. Here we show that human induced pluripotent stem cell-derived microglia grown in a tri-culture system are highly responsive to iron and susceptible to ferroptosis, an iron-dependent form of cell death. Furthermore, iron overload causes a marked shift in the microglial transcriptional state that overlaps with a transcriptomic signature found in PD postmortem brain microglia. Our data also show that this microglial response contributes to neurodegeneration, as removal of microglia from the tri-culture system substantially delayed iron-induced neurotoxicity. To elucidate the mechanisms regulating iron response in microglia, we performed a genome-wide CRISPR screen and identified novel regulators of ferroptosis, including the vesicle trafficking gene SEC24B. These data suggest a critical role for microglia iron overload and ferroptosis in neurodegeneration.
Pseudogene SNRPFP1 derived long non-coding RNA facilitates hepatocellular carcinoma progress in vitro by sponging tumor-suppressive miR-126-5p
Authors: Wang Nan , Guo Simin , Hao Fengjie , Zhang Yifan , Chen Yongjun , Fei Xiaochun , Wang Junqing 
Published: December 2022

AbstractPseudogene-derived transcripts, especially those barely transcribed in normal tissues, have been regarded as a kind of non-coding RNAs, and present potential functions in tumorigenicity and tumor development in human beings. However, their exact effects on hepatocellular carcinoma (HCC) remain largely unknown. On basis of our previous research and the constructed online database for the non-coding RNAs related to HCC, a series of pseudogene transcripts have been discovered, and SNRPFP1, the homologous pseudogene of SNRPF, was found to produce an anomalously high expression long non-coding RNA in HCC. In this study, we validated the expression of the SNRPFP1 transcript in both HCC tissues and cell lines. The adverse correlation between SNRPFP1 expression and patients’ outcomes was observed. And depletion of SNRPF1 in HCC cells significantly suppressed cell proliferation and apoptosis resistance. Meanwhile, the motility of HCC cells was potently impaired. Interestingly, miR-126-5p, one of the tumor-suppressive genes commonly decreased in HCC, was found negatively expressed and correlated with SNRPF1, and a specific region of SNRPF1 transcript is directly binding to miR-126-5p in a molecular sponge way. The rescue experiment by knock-out miR-126-5p significantly reversed the cell growth suppression and a higher ratio of cell apoptosis induced by SNRPF1 depletion. Lastly, we concluded that SNRPF1 is a pseudogene active in HCC, and its abnormally over-expressed transcript is a strong promoter of HCC cell progress in vitro by sponging miR-126-5p. We believe that the findings in this study provide new strategies for HCC prevention and therapeutic treatment.
The experienced positive and negative influence of HIV on quality of life of people with HIV and vulnerable to HIV in the Netherlands
Authors: Romijnders Kim A. G. J. , de Groot Laura , Vervoort Sigrid C. J. M. , Basten Maartje , van Welzen Berend J. , Kretzschmar Mirjam E. , Reiss Peter , Davidovich Udi , van der Loeff Maarten F. Schim , Rozhnova Ganna 
Published: December 2022

AbstractThis qualitative study aimed to explore the experienced influence of HIV on the quality of life (QoL) of people with HIV (PHIV) and key populations without but are vulnerable to HIV in the Netherlands. We conducted and thematically analyzed interviews with 29 PHIV and 13 participants from key populations without HIV (i.e., men who have sex with men). PHIV and key populations shared positive meaningful experiences regarding HIV, i.e., feeling grateful for ART, life, and the availability of PrEP, being loved and supported in the light of HIV, and providing support to the community. Negative predominant experiences regarding HIV were described by both PHIV and key populations as the negative effects of ART, challenges with regards to disclosing HIV, social stigmatization, and self-stigma. It remains important to support HIV community organizations in their efforts to reduce social stigmatization and to continue improving biomedical interventions for HIV.
Epidemiology and renal injury following 2-methyl-4-chlorophenoxyacetic acid (MCPA) poisoning
Authors: Wijerathna Thilini M. , Buckley Nicholas A. , Gawarammana Indika B. , Raubenheimer Jacques , Shahmy Seyed , Chathuranga Umesh , Palangasinghe Chathura , Shihana Fathima , Mohamed Fahim 
Published: December 2022

Abstract2-Methyl-4-chlorophenoxyacetic acid (MCPA) is a widely used chlorophenoxy herbicide. MCPA poisoning causes mitochondrial dysfunction, which can lead to kidney injury and death. The objective of this study is to describe the epidemiology, case fatality and extent of renal injury in a large cohort of MCPA self-poisonings. The study consists of two parts: (1) A report of epidemiological data and clinical outcomes in MCPA poisoned patients in Sri Lanka between 2002 and 2019; (2) Evaluation of acute kidney injury (AKI) using renal biomarkers in a subset from this cohort. Serum creatinine (sCr) and biomarkers were measured soon after hospitalization (2 [IQR 1–3] h) and at different time intervals. We measured serum biomarkers: sCr, cystatin C (sCysC), creatine kinase (CK), and urinary biomarkers: creatinine, kidney injury molecule-1 (KIM-1), clusterin, albumin, beta-2-microglobulin (β2M), cystatin C, neutrophil gelatinase-associated lipocalin (NGAL), osteopontin (OPN), trefoil factor 3 (TFF3) and cytochrome C (CytoC). Kidney Disease Improving Global Outcomes (KDIGO) criteria was used to define acute kidney injury (AKI). There were 1653 patients; 65% were male. The median time from ingestion to examination was 3:54 (IQR 2:19–6:57) h. The overall case-fatality rate was 5.3%. Patients who died were older (42 [IQR 33.5–54] vs 27 [IQR 20–37] for survivors). The median estimated amount of MCPA ingested by patients who died was also greater (88 [IQR 34–200] vs. 30 [IQR 15–63] ml in survivors). Moderate to severe AKI (AKI2/3) was uncommon (6/59 patients in the biomarker study had KDIGO stage 2 or 3). Most patients in AKI2/3 group with increased sCr were older (median age 35 years [IQR 27–41]) compared to No AKI (23 years (19–29) years) or AKI1 (26 years (21–40) years) group who had no or mild increase in sCr. These patients had no pre-existing kidney diseases. In these patients, serum creatinine (maximum medium concentration; 1.12 [IQR 0.93–1.67] mg/dl) and CK (maximum medium concentration; 284 [IQR 94–428] U/l) were increased but sCysC (maximum medium concentration; 0.79 [IQR 0.68–0.81] mg/l) remained in the normal range within 72 h. All urinary biomarkers performed poorly in diagnosing AKI (area under the receiver operating characteristic curve < 0.68). The higher numbers of men with MCPA poisoning likely reflects greater occupational access to pesticides. Fatal outcome and higher ingested dose were more common in the elderly. Significant AKI with tubular injury biomarkers was uncommon. Most people with raised sCr were older and appeared to have no pre-existing kidney disease.
Diagnostic comparison of vibration-controlled transient elastography and MRI techniques in overweight and obese patients with NAFLD
Authors: Nogami Asako , Yoneda Masato , Iwaki Michihiro , Kobayashi Takashi , Kessoku Takaomi , Honda Yasushi , Ogawa Yuji , Imajo Kento , Higurashi Takuma , Hosono Kunihiro , Kirikoshi Hiroyuki , Saito Satoru , Nakajima Atsushi 
Published: December 2022

AbstractNon-invasive imaging techniques have greatly advanced the assessment of liver fibrosis and steatosis but are not fully evaluated in overweight patients. We evaluated the diagnostic performance of vibration-controlled transient elastography (VCTE) and magnetic resonance elastography (MRE) to assess fibrosis and controlled attenuation parameter (CAP) and MR imaging (MRI)-proton density fat fraction (MRI-PDFF) to assess steatosis in overweight and obese patients with non-alcoholic fatty liver disease (NAFLD). We included 163 biopsy-proven patients with NAFLD who underwent VCTE, MRE/MRI-PDFF, and liver biopsy (years 2014–2020) who were classified according to their body mass index (BMI) as normal (BMI < 25 kg/m2, n = 38), overweight (25 ≤ BMI < 30 kg/m2, n = 68), and obese (BMI ≥ 30 kg/m2, n = 57). VCTE and MRE detected fibrosis of stages ≥ 2, ≥ 3, and 4 with an area under the receiver operating curve (AUROC) of 0.83–0.94 (VCTE) and 0.85–0.95 (MRE) in all groups, without considerable differences. MRI-PDFF detected steatosis of grades ≥ 2 and 3 with high AUROC in all groups (0.81–1.00). CAP’s diagnostic ability (0.63–0.95) was lower than that of MRI-PDFF and decreased with increasing BMI compared to MRI-PDFF. VCTE and MRE similarly accurately assess fibrosis, although MRI-PDFF is more accurate than CAP in detecting steatosis in overweight and obese patients with NAFLD.
Localization and classification of space objects using EfficientDet detector for space situational awareness
Authors: AlDahoul Nouar , Karim Hezerul Abdul , De Castro Angelo , Tan Myles Joshua Toledo 
Published: December 2022

AbstractSpace situational awareness (SSA) systems play a significant role in space navigation missions. One of the most essential tasks of this system is to recognize space objects such as spacecrafts and debris for various purposes including active debris removal, on-orbit servicing, and satellite formation. The complexity of object recognition in space is due to several sensing conditions, including the variety of object sizes with high contrast, low signal-to-noise ratio, noisy backgrounds, and several orbital scenarios. Existing methods have targeted the classification of images containing space objects with complex backgrounds using various convolutional neural networks. These methods sometimes lose attention on the objects in these images, which leads to misclassification and low accuracy. This paper proposes a decision fusion method that involves training an EfficientDet model with an EfficientNet-v2 backbone to detect space objects. Furthermore, the detected objects were augmented by blurring and by adding noise, and were then passed into the EfficientNet-B4 model for training. The decisions from both models were fused to find the final category among 11 categories. The experiments were conducted by utilizing a recently developed space object dataset (SPARK) generated from realistic space simulation environments. The dataset consists of 11 categories of objects with 150,000 RGB images and 150,000 depth images. The proposed object detection solution yielded superior performance and its feasibility for use in real-world SSA systems was demonstrated. Results show significant improvement in accuracy (94%), and performance metric (1.9223%) for object classification and in mean precision (78.45%) and mean recall (92.00%) for object detection.
Effects of application of rice husk biochar and limestone on cadmium accumulation in wheat under glasshouse and field conditions
Authors: Niu Zehui , Ma Jiayan , Fang Xianzhi , Xue Zhaokun , Ye Zhengqian 
Published: December 2022

AbstractCadmium (Cd) has seriously threatened the safe production of food crops. Passivator amendments are commonly used to control the soil Cd availability. Yet, few studies are tested to explore the effect of the combination of various amendments. Here, we investigated the effects of different amendments (2% rice husk biochar, 2% limestone, and 1% rice husk biochar + 1% limestone) on the growth and Cd accumulation of wheat in pot and field experiments. The results showed that under the low soil Cd condition, the maximum increase of soil pH (1.83) was found in the limestone treatment compared to CK in pot experiment. Compared with the CK, the treatment of rice husk biochar decreased soil Cd availability and grain Cd content by about 25% and 31.2%, respectively. In contrast, under high soil Cd condition, the highest soil pH was observed in limestone, while the lowest soil Cd availability and grain Cd concentrations were found in rice husk biochar treatment. In the field experiment, the treatment of 1% rice husk biochar + 1% limestone caused a significant increase of soil pH by about 28.2%, whereas the treatment of 2% rice husk biochar reduced soil Cd availability and grain Cd content by about 38.9% and 38.5% compared to the CK. Therefore, rice husk biochar showed great potential to reduce Cd availability and ensure safe food production.