bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chlorophyll fluorescence-based high-throughput phenotyping facilitates the genetic dissection of photosynthetic heat tolerance in African (Oryza glaberrima) and Asian (Oryza sativa) rice
Authors: Robson Jordan K , Ferguson John N , McAusland Lorna , Atkinson Jonathan A , Tranchant-Dubreuil Christine , Cubry Phillipe , Sabot François , Wells Darren M , Price Adam H , Wilson Zoe A , Murchie Erik H 
Published: June 2023

Abstract
Rising temperatures and extreme heat events threaten rice production. Half of the global population relies on rice for basic nutrition, and therefore developing heat-tolerant rice is essential. During vegetative development, reduced photosynthetic rates can limit growth and the capacity to store soluble carbohydrates. The photosystem II (PSII) complex is a particularly heat-labile component of photosynthesis. We have developed a high-throughput chlorophyll fluorescence-based screen for photosynthetic heat tolerance capable of screening hundreds of plants daily. Through measuring the response of maximum PSII efficiency to increasing temperature, this platform generates data for modelling the PSII–temperature relationship in large populations in a small amount of time. Coefficients from these models (photosynthetic heat tolerance traits) demonstrated high heritabilities across African (Oryza glaberrima) and Asian (Oryza sativa, Bengal Assam Aus Panel) rice diversity sets, highlighting valuable genetic variation accessible for breeding. Genome-wide association studies were performed across both species for these traits, representing the first documented attempt to characterize the genetic basis of photosynthetic heat tolerance in any species to date. A total of 133 candidate genes were highlighted. These were significantly enriched with genes whose predicted roles suggested influence on PSII activity and the response to stress. We discuss the most promising candidates for improving photosynthetic heat tolerance in rice.
Developing an Integrated Petrogenetic Model for Understanding REE Deportment of the Ampasibitika Intrusion and Associated Ion Adsorption Deposits
Authors: Marquis E , Goodenough K M , Smith M P , Estrade G , Rasolonirina F , Rakotoson R L 
Published: June 2023

Abstract
Alkaline–peralkaline igneous systems are promising sources of rare earth elements (REEs). Preservation bias has resulted in a gap in the geological record for alkaline–peralkaline magmatic systems, with the hypabyssal plumbing system linking magma chambers to extrusive volcanic rocks poorly represented. Large plutonic varieties of these systems are often proposed to have fed (now eroded) volcanoes, and current peralkaline volcanic systems obscure the plutonic system at depth. The alkaline to peralkaline Ampasibitika Intrusion in Madagascar is a rare example where the magmatic–volcanic interface between a deeper level magma reservoir and its genetically related caldera volcano is exposed. This c. 24 Ma sub-volcanic intrusive system comprises silica-undersaturated to silica-oversaturated units, of peralkaline to metaluminous and peraluminous characters, with varying styles of REE mineralisation, including supergene ion adsorption-style REE occurrences in the overlying weather profiles. There are two main intrusive suites: (1) the concentric Marginal Dyke Swarm (MDS) formed of quartz–microsyenite and peralkaline granite dykes (PGDs), and (2) the Ampasibitika Ring Dyke (ARD) comprising alkali feldspar syenites and subordinate nepheline syenites, trachytes and phonolites. We present new field observations and geochemical data to indicate that the MDS was emplaced as a series of low-viscosity, volatile-rich melt batches, which coalesced in the magma reservoir roof zone and intruded prior to caldera collapse, whereas the ARD was emplaced into the ring fault as a heterogeneous mix of variably evolved syenitic crystal mushes and phonolitic to trachytic-melt batches. As such, we suggest the MDS represents the residual melt fraction of the magma reservoir, whereas the ARD contains portions of the fractionating, silica-neutral to silica-undersaturated syenite, cumulate assemblage. In this revised framework, we assess the major and trace element geochemistry of amphibole- and clinopyroxene-group minerals to gain insight into the magmatic evolution of the Ampasibitika Intrusion and partitioning of REE between early cumulate and residual melt phases. Ultimately, the most REE-enriched units, the PGDs of the MDS, are identified as the product of the most volatile-rich, highly evolved melts from the roof zone of the magma reservoir. However, although REE enriched, the mineralogy does not always enable efficient release of REE for ion adsorption-style mineralisation; instead, lower REE-content protoliths with REE-host phases more amenable to decomposition release a greater proportion of REE.
SPOTTED-LEAF7 targets the gene encoding β-galactosidase9, which functions in rice growth and stress responses
Authors: Hoang Trung Viet , Vo Kieu Thi Xuan , Rahman Md Mizanor , Zhong Ruiqin , Lee Chanhui , Ketudat Cairns James R , Ye Zheng-Hua , Jeon Jong-Seong 
Published: June 2023

Abstract
β-Galactosidases (Bgals) remove terminal β-D-galactosyl residues from the nonreducing ends of β-D-galactosidases and oligosaccharides. Bgals are present in bacteria, fungi, animals, and plants and have various functions. Despite the many studies on the evolution of BGALs in plants, their functions remain obscure. Here, we identified rice (Oryza sativa) β-galactosidase9 (OsBGAL9) as a direct target of the heat stress-induced transcription factor SPOTTED-LEAF7 (OsSPL7), as demonstrated by protoplast transactivation analysis and yeast 1-hybrid and electrophoretic mobility shift assays. Knockout plants for OsBGAL9 (Osbgal9) showed short stature and growth retardation. Histochemical β-glucuronidase (GUS) analysis of transgenic lines harboring an OsBGAL9pro:GUS reporter construct revealed that OsBGAL9 is mainly expressed in internodes at the mature stage. OsBGAL9 expression was barely detectable in seedlings under normal conditions but increased in response to biotic and abiotic stresses. Ectopic expression of OsBGAL9 enhanced resistance to the rice pathogens Magnaporthe oryzae and Xanthomonas oryzae pv. oryzae, as well as tolerance to cold and heat stress, while Osbgal9 mutant plants showed the opposite phenotypes. OsBGAL9 localized to the cell wall, suggesting that OsBGAL9 and its plant putative orthologs likely evolved functions distinct from those of its closely related animal enzymes. Enzyme activity assays and analysis of the cell wall composition of OsBGAL9 overexpression and mutant plants indicated that OsBGAL9 has activity toward galactose residues of arabinogalactan proteins (AGPs). Our study clearly demonstrates a role for a member of the BGAL family in AGP processing during plant development and stress responses.
A multisociety Delphi consensus statement on new fatty liver disease nomenclature
Authors: Rinella Mary E. , Lazarus Jeffrey V. , Ratziu Vlad , Francque Sven M. , Sanyal Arun J. , Kanwal Fasiha , Romero Diana , Abdelmalek Manal F. , Anstee Quentin M. , Arab Juan Pablo , Arrese Marco , Bataller Ramon , Beuers Ulrich , Boursier Jerome , Bugianesi Elisabetta , Byrne Christopher D. , Castro Narro Graciela E. , Chowdhury Abhijit , Cortez-Pinto Helena , Cryer Donna R. , Cusi Kenneth , El-Kassas Mohamed , Klein Samuel , Eskridge Wayne , Fan Jiangao , Gawrieh Samer , Guy Cynthia D. , Harrison Stephen A. , Kim Seung Up , Koot Bart G. , Korenjak Marko , Kowdley Kris V. , Lacaille Florence , Loomba Rohit , Mitchell-Thain Robert , Morgan Timothy R. , Powell Elisabeth E. , Roden Michael , Romero-Gómez Manuel , Silva Marcelo , Singh Shivaram Prasad , Sookoian Silvia C. , Spearman C. Wendy , Tiniakos Dina , Valenti Luca , Vos Miriam B. , Wong Vincent Wai-Sun , Xanthakos Stavra , Yilmaz Yusuf , Younossi Zobair , Hobbs Ansley , Villota-Rivas Marcela , Newsome Philip N. ,   on behalf of the NAFLD Nomenclature consensus group
Published: June 2023

The principal limitations of the terms NAFLD and NASH are the reliance on exclusionary confounder terms and the use of potentially stigmatising language. This study set out to determine if content experts and patient advocates were in favor of a change in nomenclature and/or definition. A modified Delphi process was led by three large pan-national liver associations. The consensus was defineda priorias a supermajority (67%) vote. An independent committee of experts external to the nomenclature process made the final recommendation on the acronym and its diagnostic criteria. A total of 236 panelists from 56 countries participated in 4 online surveys and 2 hybrid meetings. Response rates across the 4 survey rounds were 87%, 83%, 83%, and 78%, respectively. Seventy-four percent of respondents felt that the current nomenclature was sufficiently flawed to consider a name change. The terms “nonalcoholic” and “fatty” were felt to be stigmatising by 61% and 66% of respondents, respectively. Steatotic liver disease was chosen as an overarching term to encompass the various aetiologies of steatosis. The term steatohepatitis was felt to be an important pathophysiological concept that should be retained. The name chosen to replace NAFLD was metabolic dysfunction–associated steatotic liver disease. There was consensus to change the definition to include the presence of at least 1 of 5 cardiometabolic risk factors. Those with no metabolic parameters and no known cause were deemed to have cryptogenic steatotic liver disease. A new category, outside pure metabolic dysfunction–associated steatotic liver disease, termed metabolic and alcohol related/associated liver disease (MetALD), was selected to describe those with metabolic dysfunction–associated steatotic liver disease, who consume greater amounts of alcohol per week (140–350 g/wk and 210–420 g/wk for females and males, respectively). The new nomenclature and diagnostic criteria are widely supported and nonstigmatising, and can improve awareness and patient identification.
Multiple interspecies recombination events documented by whole genome sequencing in multidrug resistant Haemophilus influenzae clinical isolates.
Authors: Michel Charlotte , Argudín Maria A. , Wautier Magali , Echahidi F. , Prevost Benoit , Vandenberg Olivier , Martiny Delphine , Hallin Marie 
Published: June 2023

Introduction: Haemophilus influenzae (Hi) was long known as an easy-to-treat bacterium but the rise of resistance against beta-lactams and other critically important antibiotics is now an increasing concern. We describe here the whole genome sequencing (WGS) analysis of three non-typeable Hi isolates received in 2018 – 2019 by the Belgian National Reference Centre (NRC) for Hi as they presented an unusual multi-resistant profile.
The three isolates were resistant to ampicillin, cefuroxime, cefotaxime, ceftriaxone, ciprofloxacin, macrolides and trimethoprim-sulfamethoxazole. Two of them were also resistant to amoxicilline-clavulanic acid and showed a reduced susceptibility to meropenem. All three isolates belonged to the MLST Clonal Complex (CC) 422, and WGS revealed that the three were very similar. Their Antimicrobial Resistance (AMR) genotype was studied. They harbored mobile genetic elements (plasmids and transposons carrying blaTEM-1B, mefA and msrD genes associated with resistance), mutations in gyrA and parC linked to fluoroquinolone resistance as well as remodeling events in ompP2 that might be related to lower penems susceptibility or heteroresistance profile. The isolates also harbored interspecies recombination patterns in the murF-murE-ftsI region involved in cell wall synthesis.
Conclusion: The Hi evolution towards AMR is a complex and poorly understood phenomenon. To better understand the respective roles of clonal expansion, horizontal gene transfers, spontaneous mutations and interspecies genetic rearrangements in shaping AMR in Hi, both analysis of Hi communities over time within individuals and worldwide monitoring of non-typeable Hi causing infections should be conducted.
Distinguished biological adaptation architecture aggravated population differentiation of Tibeto-Burman-speaking people inferred from 500 whole-genome data from 39 populations
Authors: Sun Yuntao , Wang Mengge , Sun Qiuxia , Liu Yan , Duan Shuhan , Wang Zhiyong , Zhou Yunyu , Zhong Jun , Huang Yuguo , Huang Xinyu , Li Xiangping , Su Haoran , Cai Yan , Jiang Xiucheng , Chen Jing , Yan Jiangwei , Nie Shengjie , Hu Liping , Yang Junbao , Tang Renkuan , Wang Chuan-Chao , Liu Chao , Deng Xiaohui , He Guanglin , Yun Libing 
Published: June 2023

SUMMARYTibeto-Burman (TB) people have tried to adapt to the hypoxic, cold and high-UV high-altitude Tibetan Plateau and complex disease exposure in the lowland wet and hot rainforest since the late Paleolithic period. However, the full landscape of genetic history and biological adaptation of geographically diverse TB people and their interaction mechanism remained unknown. We generated a whole-genome-based meta-database of 500 individuals from 39 TB populations from East Asia and Southeast Asia and presented a comprehensive landscape of genetic diversity, admixture history and differentiated adaptative features of geographically different TB people. We identified geography/language-related genetic differentiation among Tibetan Plateau, Tibetan-Yi-Corridor (TYC) and Southeast Asian TB people, consistent with their differentiated admixture process with incoming or indigenous ancestral source populations. A robust genetic connection between TYC people and ancient YR people supported the Northern origin hypothesis of TB people. We reported population substructure-related differentiated biological adaptative signatures between highland Tibetans and lowland TB people and between geographically different Lolo speakers. Highland adaptativeEPAS1andEGLNvariants riched in Tibetans but lacked in TYC people whose adaptation is associated with the physical features and skin pigmentation (EDARandSLC24A5), hepatic alcohol metabolism (ALDH9A1), regulation of cell-cell adhesion of muscle cells (CTNNA3)and immune/fat metabolism-related adaptative signature. TB-related genomic resources provided new insights into the genetic basis of phenotype differences and better reference for the anthropologically-informed sampling design in biomedical and genomic cohort research.
(Micro)saccade-related potentials during face recognition: A study combining EEG, eye-tracking, and deconvolution modeling
Authors: Spiering Lisa , Dimigen Olaf 
Published: June 2023

ABSTRACTUnder natural viewing conditions, complex stimuli such as human faces are typically looked at several times in succession, implying that their recognition may unfold across multiple eye fixations. Although electrophysiological (EEG) experiments on face recognition typically prohibit eye movements, participants still execute frequent (micro)saccades on the face, each of which generates its own visuocortical response. This finding raises the question of whether the fixation-related potentials (FRPs) evoked by these tiny gaze shifts also contain psychologically valuable information about face processing. Here we investigated this question by co-recording EEG and eye movements in an experiment with emotional faces (happy, angry, neutral). Deconvolution modeling was used to separate the stimulus-ERPs to face onset from the FRPs generated by subsequent microsaccades-induced refixations on the face. As expected, stimulus-ERPs exhibited typical emotion effects, with a larger early posterior negativity (EPN) for happy/angry compared to neutral faces. Eye-tracking confirmed that participants made small saccades within the face in 98% of the trials. However, while each saccade produced a strong response over visual areas, this response was unaffected by the face’s emotional expression, both for the first and for subsequent (micro)saccades. This finding suggests that the face’s affective content is rapidly evaluated after stimulus onset, leading to only a short-lived sensory enhancement by arousing stimuli that does not repeat itself during immediate refixations. Methodologically, our work demonstrates how eye-tracking and deconvolution modeling can be used to extract several brain responses from each EEG trial, providing insights into neural processing at different latencies after stimulus onset.
Task-evoked pulse wave amplitude tracks cognitive load
Authors: Pavlov Yuri G. , Gashkova Anastasia S. , Kasanov Dauren , Kosachenko Alexandra I. , Kotyusov Alexander I. , Kotchoubey Boris 
Published: June 2023

AbstractCognitive load is a crucial factor in mentally demanding activities and holds significance across various research fields. This study aimed to investigate the effectiveness of pulse wave amplitude (PWA) as a measure for tracking cognitive load and associated mental effort in comparison to heart rate (HR) during a digit span task. The data from 78 participants were included in the analyses. Participants performed a memory task in which they were asked to memorize sequences of 5, 9, or 13 digits, and a control task where they passively listened to the sequences. PWA and HR were quantified from photoplethysmography (PPG) and electrocardiography (ECG), respectively. Pupil dilation was also assessed as a measure of cognitive load. We found that PWA showed a strong suppression with increasing memory load, indicating sensitivity to cognitive load. In contrast, HR did not show significant changes with task difficulty. Moreover, when memory load exceeded the capacity of working memory, a reversal of the PWA pattern was observed, indicating cognitive overload. In this respect, changes in PWA in response to cognitive load correlated with the dynamics of pupil dilation, suggesting a potential shared underlying mechanism. Additionally, both HR and PWA demonstrated a relationship with behavioral performance, with higher task-evoked HR and lower PWA associated with better memory performance. Our findings suggest that PWA is a more sensitive measure than HR for tracking cognitive load and overload. PWA, measured through PPG, holds significant potential for practical applications in assessing cognitive load due to its ease of use and sensitivity to cognitive overload. The findings contribute to the understanding of psychophysiological indicators of cognitive load and offer insights into the use of PWA as a non-invasive measure in various contexts.
Unexpectedly high coral heat tolerance at thermal refugia
Authors: Lachs Liam , Humanes Adriana , Mumby Peter J , Donner Simon D. , Bythell John , Beauchamp Elizabeth , Bukurou Leah , Buzzoni Daisy , de la Torre Cerro Ruben , East Holly K. , Edwards Alasdair J. , Golbuu Yimnang , Martinez Helios M. , van der Steeg Eveline , Ward Alex , Guest James R. 
Published: June 2023

AbstractMarine heatwaves and mass bleaching have led to global declines in coral reefs. Corals can adapt, yet, to what extent local variations in thermal stress regimes influence heat tolerance and adaptive potential remains uncertain. Here we identify persistent local-scale thermal refugia and hotspots among the reefs of a remote Pacific archipelago, based on 36 years of satellite-sensed temperatures. Theory suggests that hotspots should promote coral heat tolerance through acclimatisation and directional selection. While historic patterns of mass bleaching and marine heatwaves align with this expectation, we find a contrasting pattern for a single species,Acropora digitifera, exposed to a marine heatwave experiment. Higher heat tolerance at thermal refugia (+0.7 °C-weeks) and correlations with other traits suggest that non-thermal selective pressures may also influence heat tolerance. We also uncover widespread heat tolerance variability, indicating climate adaptation potential. Compared to the least-tolerant 10% of theA. digitiferapopulation, the most-tolerant 10% could withstand an additional heat stress of 5.2 and 4.1 °C-weeks for thermal refugia and hotspots, respectively. Despite expectations, local-scale thermal refugia can harbour higher heat tolerance, and mass bleaching patterns do not necessarily predict species responses. This has important implications for designing climate-smart initiatives to tackle global-scale adaptive management problems.
New distance measure for comparing protein using cellular automata image
Authors: Souza Luryane F. , de B. Pereira Hernane B. , da Rocha Filho Tarcisio M. , Machado Bruna A. S. , Moret Marcelo A. 
Published: June 2023

AbstractOne of the first steps in protein sequence analysis is comparing sequences to look for similarities. We propose an information theoretical distance to compare cellular automata representing protein sequences, and determine similarities. Our approach relies in a stationary Hamming distance for the evolution of the automata according to a properly chosen rule, and to build a pairwise similarity matrix and determine common ancestors among different species in a simpler and less computationally demanding computer codes when compared to other methods.
Does the seed fall far from the tree? Weak fine-scale genetic structure in a continuous Scots pine population
Authors: Niskanen Alina K. , Kujala Sonja T. , Kärkkäinen Katri , Savolainen Outi , Pyhäjärvi Tanja 
Published: June 2023

AbstractKnowledge of fine-scale spatial genetic structure,i.e., the distribution of genetic diversity at short distances, is important in evolutionary research and in practical applications such as conservation and breeding programs. In trees, related individuals often grow close to each other due to limited seed and/or pollen dispersal. The extent of seed dispersal also limits the speed at which a tree species can spread to new areas.We studied the fine-scale spatial genetic structure of Scots pine (Pinus sylvestris) in two naturally regenerated sites located 20 km from each other in continuous south-eastern Finnish forest. We genotyped almost 500 adult trees for 150k SNPs using a custom made Affymetrix array. We detected some pairwise relatedness at short distances, but the average relatedness was low and decreased with increasing distance, as expected.Despite the clustering of related individuals, the sampling sites were not differentiated (FST= 0.0005). According to our results, Scots pine has a large neighborhood size (Nb= 1680– 3210), but a relatively short gene dispersal distance (σg= 36.5–71.3 m). Knowledge of Scots pine fine-scale spatial genetic structure can be used to define suitable sampling distances for evolutionary studies and practical applications. Detailed empirical estimates of dispersal are necessary both in studying post-glacial recolonization and predicting the response of forest trees to climate change.