bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disentangling the effects of past logging and ongoing cryptic anthropogenic disturbance on vegetation structure and composition in Himalayan Foothills, India
Authors: Kaushik Monica , Dutta Sutirtha , Rawat Gopal S. , Singh Pratap , Mohan Dhananjai 
Published: April 2021

AbstractMost tropical forests have undergone commercial logging. Even where logging has ceased, subsistence harvest of forest resources often persists especially in South-East Asia. Understanding of impacts of frequent forest resources extraction in areas recovering from past selective logging would be essential for designing the appropriate management interventions.We studied the impacts of current chronic anthropogenic disturbances (hereafter CAD) and past selective logging on vegetation structure, diversity, and regeneration, and the invasion of a non-native shrub,Lantana camara, in three major forest types in the Himalayan foothills, India. We analyzed field data on intensity of CAD and vegetation variables, collected from 269 stratified random plots, using ordination and generalized linear (mixed) modeling approaches.Our results, based on 2758 adult trees of 54 species, showed that forest types differed in disturbance regimes depending on protection level and availability of fodder tree species. Intensity of CAD depended on proximity to settlements (for livestock related disturbances). Whereas selective logging, including firewood collection, was associated with land protection status. Selective logging reduced the extent of mature forest but facilitated regeneration, thereby promoting secondary forest features such as tree density and canopy cover. In contrast, the interaction between lopping and selective logging was negatively associated with regeneration. Past logging facilitatedL. camarainvasion in Dry and Hill forests but not in Moist forest. Finally, while selective logging marginally enhanced tree diversity, CAD reduced native shrub diversity.Our study demonstrates that selective logging followed by CAD arrest forest recovery, as evident from the suppression of mature forest elements, loss of shrub biomass, reduced regeneration rate, and facilitation of invasive species. To abate these impacts, alternative livelihood/subsistence options that sustain forests and local communities should be explored. Additionally, CAD management should be site-specific as local ecological contexts modify their impacts on forests.
Comparative anatomy and phylogenetic contribution of intracranial osseous canals and cavities in armadillos and glyptodonts (Xenarthra, Cingulata)
Authors: Le Verger Kévin , González Ruiz Laureano R. , Billet Guillaume 
Published: April 2021

ABSTRACTThe evolutionary history of the Cingulata, as for many groups, remains a highly debated topic to this day, particularly for one of their most emblematic representatives: the glyptodonts. There is no consensus among morphological and molecular phylogenies relative to their position within Cingulata. As demonstrated by recent works, the study of the internal anatomy constitutes a promising path for enriching morphological matrices for the phylogenetic study of armadillos. However, internal cranial anatomy remains under-studied in the Cingulata. Here we explored and compared the anatomy of intracranial osseous canals and cavities in a diverse sample of extant and extinct cingulates, including the earliest well-preserved glyptodont crania. The virtual 3D reconstruction (using X-ray microtomography) of selected canals, i.e., the nasolacrimal canal, the palatine canal, the sphenopalatine canal, the canal for the frontal diploic vein, the transverse canal, the orbitotemporal canal, the canal for the capsuloparietal emissary vein and the posttemporal canal, and alveolar cavities related to cranial vascularization, innervation or tooth insertion allowed us to compare the locations, trajectories and shape of these structures and to discuss their potential interest for cingulate systematics. We tentatively reconstructed evolutionary scenarios for eight selected traits on these structures, in which glyptodonts often showed a greater resemblance to pampatheres, to the genusProeutatusand/or to chlamyphorines. This latter pattern was partly congruent with recent molecular hypotheses, but more research is needed on these resemblances and on the potential effects of development and allometry on the observed variations. Overall, these comparisons have enabled us to highlight new anatomical variation that may be of great interest to further explore the evolutionary history of cingulates and the origins of glyptodonts on a morphological basis.
A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines
Authors: Chen Ying , Davidson Nadia M. , Wan Yuk Kei , Patel Harshil , Yao Fei , Low Hwee Meng , Hendra Christopher , Watten Laura , Sim Andre , Sawyer Chelsea , Iakovleva Viktoriia , Lee Puay Leng , Xin Lixia , Ng Hui En Vanessa , Loo Jia Min , Ong Xuewen , Ng Hui Qi Amanda , Wang Jiaxu , Koh Wei Qian Casslynn , Poon Suk Yeah Polly , Stanojevic Dominik , Tran Hoang-Dai , Lim Kok Hao Edwin , Toh Shen Yon , Ewels Philip Andrew , Ng Huck-Hui , Iyer N.Gopalakrishna , Thiery Alexandre , Chng Wee Joo , Chen Leilei , DasGupta Ramanuj , Sikic Mile , Chan Yun-Shen , Tan Boon Ooi Patrick , Wan Yue , Tam Wai Leong , Yu Qiang , Khor Chiea Chuan , Wüstefeld Torsten , Pratanwanich Ploy N. , Love Michael I. , Goh Wee Siong Sho , Ng Sarah B. , Oshlack Alicia , Göke Jonathan ,   SG-NEx consortium
Published: April 2021

AbstractThe human genome contains more than 200,000 gene isoforms. However, different isoforms can be highly similar, and with an average length of 1.5kb remain difficult to study with short read sequencing. To systematically evaluate the ability to study the transcriptome at a resolution of individual isoforms we profiled 5 human cell lines with short read cDNA sequencing and Nanopore long read direct RNA, amplification-free direct cDNA, PCR-cDNA sequencing. The long read protocols showed a high level of consistency, with amplification-free RNA and cDNA sequencing being most similar. While short and long reads generated comparable gene expression estimates, they differed substantially for individual isoforms. We find that increased read length improves read-to-transcript assignment, identifies interactions between alternative promoters and splicing, enables the discovery of novel transcripts from repetitive regions, facilitates the quantification of full-length fusion isoforms and enables the simultaneous profiling of m6A RNA modifications when RNA is sequenced directly. Our study demonstrates the advantage of long read RNA sequencing and provides a comprehensive resource that will enable the development and benchmarking of computational methods for profiling complex transcriptional events at isoform-level resolution.
Relationship between Deceleration Morphology and Phase Rectified Signal Averaging-based Parameters during Labor
Authors: Rivolta Massimo W. , Barbieri Moira , Stampalija Tamara , Sassi Roberto , Frasch Martin G. 
Published: April 2021

AbstractDuring labor, uterine contractions trigger the response of the autonomic nervous system (ANS) of the fetus, producing sawtooth-like decelerations in the fetal heart rate (FHR) series. Under chronic hypoxia, ANS is known to regulate FHR differently with respect to healthy fetuses. In this study, we hypothesized that such different ANS regulation might also lead to a change in the FHR deceleration morphology. The hypothesis was tested in an animal model comprising 7 normoxic and 5 chronically hypoxic fetuses that underwent a protocol of umbilical cord occlusions (UCOs). Deceleration morphologies in the fetal inter-beat time interval (FRR) series were modeled using a trapezoid with four parameters, i.e., baselineb, deceleration deptha, UCO response timeτuand recovery timeτr. Comparing normoxic and hypoxic sheep, we found a clear difference forτu(24.8 ± 9.4 vs 39.8 ± 9.7 s;p <0.05),a(268.1 ± 109.5 vs 373.0 ± 46.0 ms;p <0.1) and Δτ=τu−τr(13.2 ± 6.9 vs 23.9 ± 7.5 s;p <0.05). Therefore, the animal model supported the hypothesis that hypoxic fetuses have a longer response timeτuand larger asymmetry Δτas a response to UCOs. Assessing these morphological parameters during labor is challenging due to non-stationarity, phase desynchronization and noise. For this reason, in the second part of the study, we quantified whether acceleration capacity (AC), deceleration capacity (DC), and deceleration reserve (DR), computed through Phase-Rectified Signal Averaging (PRSA, known to be robust to noise), were correlated with the morphological parameters. DR and DC correlated with Δτandτufor a wide range of the PRSA parameterT(max Pearson’s correlationρ= 0.9,p <0.05, andρ= 0.6,p <0.1, respectively). In conclusion, deceleration morphologies have been found to differ between normoxic and hypoxic sheep fetuses during UCOs. The same difference can be assessed through PRSA based parameters, further motivating future investigations on the translational potential of this methodology on human data.
Assessment of the pollution incident performance of water and sewerage companies in England
Authors: Purnell Sarah , Mills Nick , Davis Keith , Joyce Christopher 
Published: April 2021

AbstractComparison of water and sewerage company pollution performance in relation to severity, frequency and self-reporting of pollution incidents is made difficult by differences in environmental and operational conditions. In England, the deterioration in pollution incident performance across the water industry, makes it important to investigate common trends that could be addressed at national and regional levels. Yet, to date there has been no external peer-reviewed analysis of national pollution incident data in England. This project aimed to analyse available pollution incident data to assess and compare the performance of water and sewerage companies in England. Results indicated that there was significant variation in pollution incident numbers and the severity of the impact on the water environment for different asset types (operational property of the water and sewerage company such as a sewage treatment works). Increasing numbers of pollution incidents from pumping stations and sewage treatment works, were largely responsible for overall increases in pollution incidents. The highest increase in pollution incidents in 2019, was observed from pumping stations. Variation was evident in company self-reporting percentages across asset types. There were significant positive relationships between the self-reporting percentages of pollution incidents and total numbers of reported pollution incidents per 10,000 km sewer length for pumping stations and sewage treatment works. These results indicate that in at least these asset types, an estimated 5% of pollution incidents could go unreported, if not self-reported by the company. Pollution events not reported quickly by companies, can lead to more severe impacts to the water environment so rapid and consistent reporting of incidents is crucial for limiting damage. The results have significance for the water industry internationally, because the issues presented here are not restricted to England. Whilst this research highlighted a number of key areas for more detailed analysis, in the short-term, research should focus on investigating best practice for reporting pollution incidents. It is important to get an accurate baseline of the number of pollution incidents and whether a proportion are currently going unreported. This research should seek to aid the standardisation of reporting practice across the water industry.
Isolation and characterization of novel temperate virusAeropyrumglobular virus 1 infecting hyperthermophilic archaeonAeropyrum
Authors: Yumiya Maho , Fukuyama Yuto , Sako Yoshihiko , Yoshida Takashi 
Published: April 2021

ABSTRACTWe isolate a novel archaeal temperate virus namedAeropyrumglobular virus 1 (AGV1) from the hostAeropyrumculture. Reproduction of AGV1 was induced by adding 20 mM tris-acetate buffer to exponentially growing host cells. Negatively stained virions showed spherical morphology (60 ±2 nm in diameter) similar toGlobuloviridaeviruses. The double-stranded circular DNA genome of AGV1 contains 18,222 bp encoding 34 open-reading frames. No ORFs showed significant similarity withGlobuloviridaeviruses. AGV1 shares three genes, including an integrase gene, with reported spindle-shaped temperate viruses. However we couldn’t detect its integration site in the host genome. Moreover AGV1 seemed not to replicate autonomously because there are no origin recognition boxes in the genome. qPCR results showed that the genome copy number of AGV1 was lower than that of the host genome (10−3copies per host genome). Upon the addition of tris-acetate buffer, a steep increase in the AGV1 genome copy number (9.5–26 copies per host genome at 2 days post-treatment) was observed although clustered regularly interspaced short palindromic repeat (CRISPR) elements of the host genome showed significant matches with AGV1 protospacers. Our findings suggest that AGV1 is a novel globular virus exhibiting an unstable carrier state in the growing host and in that way AGV1 can escape from the host defense system and propagate under stressful host conditions.ImportanceStudying archaeal viruses yields novel insights into the roles of virospheres and viruses in the evolutionary process of their hosts. Here, we isolated a novel spherical virus namedAeropyrumglobular virus 1. AGV1 has integrase gene but its genome is not integrated into the host genome. AGV1 could not replicate autonomously due to the lack of origin recognition boxes and thus its copy number was too low (10−3copies per host genome) without any inducing stimulus. However, upon the addition of tris-acetate buffer, the AGV1 genome copy number steeply increased instead of a perfect sequence match between the spacer of the host CRISPR/Cas system and the protospacer. Our findings suggest that AGV1 can escape from the host defense system and propagate under stressful conditions for the host by establishing an unstable carrier state. These results reveals a novel aspect of host–virus interactions in extreme environments.
Hydrogen sulfide blocks HIV rebound by maintaining mitochondrial bioenergetics and redox homeostasis
Authors: Pal Virender Kumar , Agrawal Ragini , Rakshit Srabanti , Shekar Pooja , Narasimha Murthy Diwakar Tumkur , Vyakarnam Annapurna , Singh Amit 
Published: April 2021

AbstractA fundamental challenge in HIV eradication is to understand how the virus establishes latency, maintains stable cellular reservoirs, and promotes rebound upon interruption of antiretroviral treatment (ART). Here, we discovered an unexpected role of the ubiquitous gasotransmitter hydrogen sulfide (H2S) in HIV latency and reactivation. We show that reactivation of HIV-1 is associated with down-regulation of the key H2S producing enzyme cystathionine-γ-lyase (CTH) and reduction in endogenous H2S. Genetic silencing of CTH disrupts redox homeostasis, impairs mitochondrial function, and remodels the transcriptome of latent cells to trigger HIV reactivation. Chemical complementation of CTH activity using a slow-releasing H2S donor, GYY4137, suppressed HIV reactivation and diminished virus replication. Mechanistically, GYY4137 blocked HIV reactivation by inducing the Keap1-Nrf2 pathway, inhibiting NF-κB, and recruiting the epigenetic silencer, YY1, to the HIV promoter. In latently infected CD4+T cells from ART-suppressed human subjects, GYY4137 in combination with ART prevented viral rebound and improved mitochondrial bioenergetics. Moreover, prolonged exposure to GYY4137 exhibited no adverse influence on proviral content or CD4+T cell subsets, indicating that diminished viral rebound is due to a loss of transcription rather than a selective loss of infected cells. In summary, this work provides mechanistic insight into H2S-mediated suppression of viral rebound and suggests the inclusion of an H2S donor in the current ART regimen to achieve a functional HIV-1 cure.
General object-based features account for letter perception
Authors: Janini Daniel , Hamblin Chris , Deza Arturo , Konkle Talia 
Published: April 2021

ABSTRACTAfter years of experience, humans become experts at perceiving letters. Is this visual capacity attained by learning specialized letter features, or by reusing general visual features previously learned in service of object categorization? To explore this question, we first measured the perceptual similarity of letters in two behavioral tasks, visual search and letter categorization. Then, we trained deep convolutional neural networks on either 26-way letter categorization or 1000-way object categorization, as a way to operationalize possible specialized letter features and general object-based features, respectively. We found that the general object-based features more robustly correlated with the perceptual similarity of letters. We then operationalized additional forms of experience-dependent letter specialization by altering object-trained networks with varied forms of letter training; however, none of these forms of letter specialization improved the match to human behavior. Thus, our findings reveal that it is not necessary to appeal to specialized letter representations to account for perceptual similarity of letters. Instead, we argue that it is more likely that the perception of letters depends on domain-general visual features.AUTHOR SUMMARYFor over a century, scientists have conducted behavioral experiments to investigate how the visual system recognizes letters, but it has proven difficult to propose a model of the feature space underlying this capacity. Here we leveraged recent advances in machine learning to model a wide variety of features ranging from specialized letter features to general object-based features. Across two large-scale behavioral experiments we find that general object-based features account well for letter perception, and that adding letter specialization did not improve the correspondence to human behavior. It is plausible that the ability to recognize letters largely relies on general visual features unaltered by letter learning.
Leveraging probability concepts for genotype by environment recommendation
Authors: Dias Kaio O.G. , dos Santos Jhonathan P.R. , Krause Matheus D. , Piepho Hans-Peter , Guimarães Lauro J.M. , Pastina Maria M. , Garcia Antonio A.F. 
Published: April 2021

AbstractStatistical models that capture the phenotypic plasticity of a genotype across environments are crucial in plant breeding programs to potentially identify parents, generate offspring, and obtain highly productive genotypes for distinct environments. In this study, our aim is to leverage concepts of Bayesian models and probability methods of stability analysis to untangle genotype-by-environment interaction (GEI). The proposed method employs the posterior distribution obtained with the No-U-Turn sampler algorithm to get Monte Carlo estimates of adaptation and stability probabilities. We applied the proposed models in two empirical tropical datasets. Our findings provide a basis to enhance our ability to consider the uncertainty of cultivar recommendation for global or specific adaptation. We further demonstrate that probability methods of stability analysis in a Bayesian framework are a powerful tool for unraveling GEI given a defined intensity of selection that results in a more informed decision-making process towards cultivar recommendation in multi-environment trials.
NAC transcription factor RD26 is a regulator of root hair morphogenic plasticity
Authors: Kamranfar Iman , Balazadeh Salma , Mueller-Roeber Bernd 
Published: April 2021

AbstractRoot hairs are outgrowths of epidermal cells central for water and nutrient acquisition. Root hair growth is plastically modified by environmental cues. A frequent response to water limitation is active shortening of root hairs, involving largely unknown molecular mechanisms. A root hair-specificcis-regulatory element (RHE) integrates developmental cues with downstream signalling of root hair morphogenesis. Here, we demonstrate NAC transcription factor RD26 to be a key expressional regulator of this drought stress-triggered developmental response inArabidopsis thaliana. RD26 directly repressesRSL4andRSL1, two master transcription regulators of root hair morphogenesis, by binding RHE. RD26 further represses core cell wall modification genes including expansins (EXPA7,EXPA18), hydroxyproline-rich glycoproteins (LRX1), xyloglucan endotransglucosylases/hydrolases (XTH12,13,14,26), class III peroxidases (PRX44) and plasma membrane H+-ATPase (AHA7) through RHE. Of note, several RD26-repressed genes are activated by RSL4. Thus, by repressing RSL4 and numerous cell wall-related genes, RD26 governs a robust gene regulatory network for restricting root hair growth under drought. A similar regulatory network exists in tomato, indicating evolutionary conservation across species.Significance statementIn plants, root hairs play a vital role for water and nutrient acquisition, soil anchorage, and microbial interactions. During drought stress, root hair growth is suppressed as an adaptive strategy to save cellular energy. We identified NAC transcription factor RD26 as a key regulator of this developmental plasticity in the model plantArabidopsis thaliana. RD26 directly and negatively controls the transcriptional activity of key root hair developmental genes,RSL1andRSL4. Furthermore, RD26 suppresses the expression of several functional genes underlying root hair development including numerous cell wall-related genes. RD26 thus governs a robust gene regulatory network underlying the developmental response to drought stress. A similar regulatory network exists in tomato indicating evolutionary conservation of this mechanism across species.
FACT subunit SUPT16H associates with BRD4 and contributes to silencing of antiviral interferon signaling
Authors: Zhou Dawei , Park Jun-Gyu , Wu Zhenyu , Huang Huachao , Fiches Guillaume N. , Biswas Ayan , Li Tai-Wei , Ma Qin , Martinez-Sobrido Luis , Santoso Netty , Zhu Jian 
Published: April 2021

Summary/AbstractFACT (FAcilitatesChromatinTranscription) is a heterodimeric protein complex composed of SUPT16H and SSRP1, and a histone chaperone participating in chromatin remodeling during gene transcription. FACT complex is profoundly regulated, and contributes to both gene activation and suppression. Here we reported that SUPT16H, a subunit of FACT, is acetylated at lysine 674 (K674) of middle domain (MD), which involves TIP60 histone acetyltransferase. Such acetylation of SUPT16H is recognized by bromodomain protein BRD4, which promotes protein stability of SUPT16H. We further demonstrated that SUPT16H-BRD4 associates with histone modification enzymes (EZH2, HDAC1) and affects histone marks (H3K9me3, H3K27me3 and H3ac). BRD4 is known to profoundly regulate interferon (IFN) signaling, while such function of SUPT16H has never been explored. Surprisingly, our results revealed that SUPT16H genetic knockdown via RNAi or pharmacological inhibition by using its inhibitor, curaxin 137 (CBL0137), results in the induction of IFNs and interferon-stimulated genes (ISGs). Through this mechanism, CBL0137 is shown to efficiently inhibit infection of multiple viruses, including Zika, influenza, and SARS-CoV-2. Furthermore, we demonstrated that CBL0137 also causes the remarkable activation of IFN signaling in natural killer (NK) cells, which promotes the NK-mediated killing of virus-infected cells in a co-culture system using human primary NK cells. Overall, our studies unraveled the previously un-appreciated role of FACT complex in regulating IFN signaling in both epithelial and NK cells, and also proposed the novel application of CBL0137 to treat viral infections.