bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity and structure assessment of the genetic resources in a germplasm collection from a vanilla breeding programme in Madagascar
Authors: Rasoamanalina Rivo Onisoa Léa , Mirzaei Khaled , El Jaziri Mondher , Ramirez Ramirez Angel Rafael , Bertin Pierre 
Published: December 2023

AbstractA breeding programme of aromatic vanilla, dating back to 1944, was conducted in Ambohitsara, Antalaha, SAVA (Sambava, Antalaha, Vohemara, Andapa) – Madagascar. Imported, local, wild and cultivated vanillas were used as progenitors and thousands of hybrids were generated. However, this germplasm has not undergone any genetic evaluation, and it appears that these valuable genetic resources have been dispersed or lost after the end of the programme (2000). This study aims to investigate the genetic diversity and structure of rescued genotypes currently held in a local collection in Antalaha. Double digest restriction associated-site (RAD)-seq (ddRAD)-seq protocol was applied, providing 865 million read sequences from 56 accessions. The ddRAD sequences have been deposited to the SRA archive of NCBI. From the data, 23,701 filtered concordant common Single Nucleotide Polymorphisms (SNPs) were identified using the three widely used tools (Stacks, BCFtools, Genome Analysis ToolKit - GATK) for short-read library sequencing. These SNPs were used for germplasm evaluation. Clustering analysis segregated samples into five genetic groups: Vanilla planifolia, Vanilla pompona, hybrid Tsitaitra, Vanille Banane and the phenotype Tsivaky. Our analysis revealed distinct subgroups within V. pompona and Tsitaitra, emphasizing the importance of further characterization to accurately reflect the genetic diversity and facilitate better utilization of these accessions in future research and germplasm management. The presence of private alleles in all groups (from 487 to 2866) indicated that populations were diverging and represented a large gene pool that could be useful for future breeding efforts. The genetic data obtained from this study offers valuable insights into the genetic diversity and structure of the vanilla population, with potential applications in breeding and conservation efforts.
Automatic Extraction of Surface Wave Dispersion Curves Using Unsupervised Learning and High‐Resolution Tau‐p Transform
Authors: Yao Hai , Cao Weiping , Huang Xuri , Li Luo , Wu Bin 
Published: December 2023

AbstractDispersion curves for surface wave recordings are required input for many surface wave inversion methods to image subsurface shear wave velocity distribution, while the conventional extraction of dispersion curves requires significant amount of human interaction. This step impedes efficiency enhancement of surface wave analysis and its automation. In this paper, we present an unsupervised learning scheme to achieve efficient automatic picking of dispersion curves of the fundamental mode for surface wave gathers. This scheme is composed of four major steps: computing a frequency velocity(f‐v) spectrum for the surface wave gather using a high‐resolution Tau‐p transform improved by the iteratively shrinkage Thresholding algorithm (ISTA) algorithm, generating clusters points along the dispersion energy in the f‐v spectrum via a weighted Kmeans algorithm, filtering these cluster points by principal component analysis (PCA) and Local Outlier Factor (LOF) algorithms to remove the erroneous clusters, and fitting the remaining clusters to form the dispersion curve. Tests with synthetic and field noisy surface wave recordings demonstrated the effectiveness of this approach and its potential in automatic processing of noisy surface wave data sets.
ITRF2020 Plate Motion Model
Authors: Altamimi Z. , Métivier L. , Rebischung P. , Collilieux X. , Chanard K. , Barnéoud J. 
Published: December 2023

AbstractA tectonic Plate Motion Model (PMM) is essential for geodetic applications, while contributing to the understanding of geodynamic processes affecting the Earth's surface. We introduce a PMM derived from the horizontal velocities of 518 sites extracted from the ITRF2020 solution. These sites were chosen away from plate boundaries, Glacial Isostatic Adjustment regions, and other deforming zones. Unlike the ITRF2014‐PMM, which showed no significant Origin Rate Bias (ORB), velocities used to determine the ITRF2020‐PMM exhibit a statistically significant ORB (0.74 ± 0.09 mm/yr along the Z‐component). Users are advised to add the estimated ORB to the horizontal velocities predicted by the ITRF2020‐PMM rotation poles for full consistency with the ITRF2020. However, the predicted vertical velocities resulting from the addition of the ORB should be discarded. The overall precision with which the ITRF2020 velocity field is represented by the rigid ITRF2020‐PMM is at the level of 0.25 mm/yr WRMS.
Global Observations of Tropospheric Bromine Monoxide (BrO) Columns From TROPOMI
Authors: Chen Yuyang , Liu Song , Zhu Lei , Seo Sora , Richter Andreas , Li Xicheng , Ding Ao , Sun Wenfu , Shu Lei , Wang Xuan , Valks Pieter , Hendrick Francois , Koenig Theodore K. , Volkamer Rainer , Bai Bin , Wang Dakang , Pu Dongchuan , Sun Shuai , Li Juan , Zuo Xiaoxing , Fu Weitao , Li Yali , Zhang Peng , Yang Xin , Fu Tzung‐May 
Published: December 2023

AbstractBromine monoxide (BrO) plays an important role in tropospheric chemistry. The state‐of‐the‐science TROPOspheric Monitoring Instrument (TROPOMI) offers the potential to monitor atmospheric composition with a fine spatial resolution of up to 5.5 × 3.5 km2. We present here the retrieval of tropospheric BrO columns from TROPOMI. We implement a stratospheric correction scheme using a climatological approach based on the latest GEOS‐Chem High Performance chemical transport model, and improve the tropospheric air mass factor calculation with TROPOMI surface albedo data accounting for the geometrical dependency. Our product presents a good level of consistency in comparison with measurements from ground‐based zenith‐sky differential optical absorption spectroscopy (r = 0.67), aircrafts (r = 0.46), and satellites (similar spatial distributions of BrO columns). Furthermore, our retrieval captures BrO enhancements in the polar springtime with values up to 7.8 × 1013 molecules cm−2 and identifies small‐scale emission sources such as volcanoes and salt marshes. Based on TROPOMI data, we probe a blowing snow aerosol bromine mechanism in which the snow salinity is reduced to better match simulation and observation. Our TROPOMI tropospheric BrO product contributes high‐resolution global information to studies investigating atmospheric bromine chemistry.
Interindividual variability in appetitive sensations and relationships between appetitive sensations and energy intake
Authors: Cheon Eunjin , Mattes Richard D. 
Published: December 2023

Abstract
Background
Appetitive sensations (AS) are signals that guide eating behaviors. Marked short-term inter-individual variability in AS has been reported but the long-term stability of individual ratings and their dietary implications are not well characterized.

Objectives
This study explored the stability of inter-individual ratings of hunger, fullness and thirst for 17 weeks; determined the relationships between these sensations, eating patterns and energy intake (EI); as well as the associations between ratings and selected individual characteristics (age, gender, BMI).

Methods
A 17-week observational study collected hourly appetitive ratings and dietary intake data from 97 (90 completers, 7 partial completers) healthy adults at weeks 1, 9, and 17.

Results
There were marked and stable inter-individual differences over the 17 weeks for hunger (week 1 vs. week 9, r = 0.72 (p < 0.001); week 1 vs. week 17, r = 0.67 (p < 0.001); week 9 vs. week 17, r = 0.77 (p < 0.001)); fullness (week 1 vs. week 9 r = 0.74 (p < 0.001); week 1 vs. week 17, r = 0.71 (p < 0.001); week 9 vs. week 17, r = 0.81 (p < 0.001)); and thirst (week 1 vs. week 9 r = 0.82 (p < 0.001); week 1 vs. week 17, r = 0.81 (p < 0.001); week 9 vs. week 17, r = 0.88 (p < 0.001)). Cross-correlation functions revealed EI and eating pattern exerted stronger effects on AS than the reverse. However, the absolute effect sizes were small. Path analyses also indicated that there were weak relationships between AS and EI. No robust effects of the studied individual characteristics were observed.

Conclusion
This study found that acute and chronic sensations of hunger, fullness and thirst are relatively stable within individuals but vary markedly between individuals. In addition, the present data indicate AS are poorly associated with dietary patterns or with EI under conditions of relatively stable energy balance.
SPHK1 potentiates colorectal cancer progression and metastasis via regulating autophagy mediated by TRAF6-induced ULK1 ubiquitination
Authors: Chen Da , Wu Jiangni , Qiu Xinze , Luo Shibo , Huang Shanpei , Wei Erdan , Qin Mengbin , Huang Jiean , Liu Shiquan 
Published: December 2023

AbstractA sphingolipid metabolite regulator, sphingosine kinase 1 (SPHK1), plays a critical role in the development of colorectal cancer (CRC). Studies have demonstrated that invasion and metastasis of CRC are promoted by SPHK1-driven autophagy. However, the exact mechanism of SPHK1 drives autophagy to promote tumor progression remains unclear. Here, immunohistochemical detection showed the expression of SPHK1 and tumor necrosis factor receptor-associated factor-6 (TRAF6) in human CRC tissues was stronger than in adjacent normal tissues, they were both associated with distance metastasis. It was discovered that knockdown of SPHK1 reduced the expression of TRAF6, inhibited autophagy, and inhibited the growth and metastasis of CRC cells in vitro. Moreover, the effects of SPHK1-downregulating were reversed by overexpression of TRAF6 in CRC cells transfected by double-gene. Overexpression of SPHK1 and TRAF6 promoted the expression of autophagy protein LC3 and Vimentin, while downregulated the expression of autophagy protein P62 and E-cadherin. The expression of autophagy-related ubiquitination protein ULK1 and Ubiquitin protein were significantly upregulated in TRAF6-overexpressed CRC cells. In addition, autophagy inhibitor 3-methyladenine (3MA) significantly inhibited the metastasis-promoting effect of SPHK1 and TRAF6, suppressed the expression of LC3 and Vimentin, and promoted the expression of P62 and E-cadherin, in CRC cells. Immunofluorescence staining showed SPHK1 and TRAF6 were co-localized in HT29 CRC cell membrane and cytoplasm. Immunoprecipitation detection showed SPHK1 was efficiently combined with the endogenous TRAF6, and the interaction was also detected reciprocally. Additionally, proteasome inhibitor MG132 treatment upregulated the expression of TRAF6 and the level of Ubiquitin protein, in SPHK1-downregulating CRC cells. These results reveal that SPHK1 potentiates CRC progression and metastasis via regulating autophagy mediated by TRAF6-induced ULK1 ubiquitination. SPHK1-TRAF6-ULK1 signaling axis is critical to the progression of CRC and provides a new strategy for the therapeutic control of CRC.
A small molecule iCDM-34 identified by in silico screening suppresses HBV DNA through activation of aryl hydrocarbon receptor
Authors: Furutani Yutaka , Hirano Yoshinori , Toguchi Mariko , Higuchi Shoko , Qin Xian-Yang , Yanaka Kaori , Sato-Shiozaki Yumi , Takahashi Nobuaki , Sakai Marina , Kongpracha Pornparn , Suzuki Takehiro , Dohmae Naoshi , Kukimoto-Niino Mutsuko , Shirouzu Mikako , Nagamori Shushi , Suzuki Harukazu , Kobayashi Kaoru , Masaki Takahiro , Koyama Hiroo , Sekiba Kazuma , Otsuka Motoyuki , Koike Kazuhiko , Kohara Michinori , Kojima Soichi , Kakeya Hideaki , Matsuura Tomokazu 
Published: December 2023

AbstractIFN-alpha have been reported to suppress hepatitis B virus (HBV) cccDNA via APOBEC3 cytidine deaminase activity through interferon signaling. To develop a novel anti-HBV drug for a functional cure, we performed in silico screening of the binding compounds fitting the steric structure of the IFN-alpha-binding pocket in IFNAR2. We identified 37 compounds and named them in silico cccDNA modulator (iCDM)-1–37. We found that iCDM-34, a new small molecule with a pyrazole moiety, showed anti-HCV and anti-HBV activities. We measured the anti-HBV activity of iCDM-34 dependent on or independent of entecavir (ETV). iCDM-34 suppressed HBV DNA, pgRNA, HBsAg, and HBeAg, and also clearly exhibited additive inhibitory effects on the suppression of HBV DNA with ETV. We confirmed metabolic stability of iCDM-34 was stable in human liver microsomal fraction. Furthermore, anti-HBV activity in human hepatocyte-chimeric mice revealed that iCDM-34 was not effective as a single reagent, but when combined with ETV, it suppressed HBV DNA compared to ETV alone. Phosphoproteome and Western blotting analysis showed that iCDM-34 did not activate IFN-signaling. The transcriptome analysis of interferon-stimulated genes revealed no increase in expression, whereas downstream factors of aryl hydrocarbon receptor (AhR) showed increased levels of the expression. CDK1/2 and phospho-SAMHD1 levels decreased under iCDM-34 treatment. In addition, AhR knockdown inhibited anti-HCV activity of iCDM-34 in HCV replicon cells. These results suggest that iCDM-34 decreases the phosphorylation of SAMHD1 through CDK1/2, and suppresses HCV replicon RNA, HBV DNA, and pgRNA formation.
Hemozoin in malaria eradication—from material science, technology to field test
Authors: Rathi Ashutosh , Chowdhry Z. , Patel Anand , Zuo Siming , Veettil Thulya Chakkumpulakkal Puthan , Adegoke John A. , Heidari Hadi , Wood Bayden R. , Bhallamudi Vidya Praveen , Peng Weng Kung 
Published: December 2023

AbstractMalaria continues to be among the most lethal infectious diseases. Immediate barriers include the detection of low-parasitemia levels in asymptomatic individuals, which act as a reservoir for future infections, and the emergence of multidrug-resistant strains in malaria-endemic, under-resourced regions. The development of technologies for field-deployable devices for early detection and targeted drugs/vaccines is an ongoing challenge. In this respect, the identification of hemozoin during the Plasmodium growth cycle presents a unique opportunity as a biomarker for malaria infection. The last decade has witnessed the development of numerous opto-/magnetic- based ultrasensitive hemozoin sensing technologies with tremendous potential of rapid and accurate malaria diagnosis and drug testing. The unique information in hemozoin formation can also shed light on the development of targeted drugs. Here, we present a comprehensive perspective on state-of-the-art hemozoin-based methodologies for detecting and studying malaria. We discuss the challenges (and opportunities) to expedite the translation of the technology as a point-of-site tool to assist in the global eradication of malaria infection.
The role of ion migration, octahedral tilt, and the A-site cation on the instability of Cs1-xFAxPbI3
Authors: Li Weilun , Hao Mengmeng , Baktash Ardeshir , Wang Lianzhou , Etheridge Joanne 
Published: December 2023

AbstractOrganic-inorganic hybrid perovskites are promising materials for the next generation photovoltaics and optoelectronics; however, their practical application has been hindered by poor structural stability mainly caused by ion migration and external stimuli. Understanding the mechanism(s) of ion migration and structure decomposition is thus critical. Here we observe the sequence of structural changes at the atomic level that precede structural decomposition in the technologically important Cs1-xFAxPbI3 using ultralow dose transmission electron microscopy. We find that these changes differ, depending upon the A-site composition. Initially, there is a random loss of FA+, complemented by the loss of I-. The remaining FA+ and I- ions then migrate, unit cell by unit cell, into an ordered and more stable phase with a √2 x √2 superstructure. Further ion loss is accompanied by A-site dependent octahedral tilt modes and associated tetragonal phases with different stabilities. These observations of the loss of FA+/I- ion pairs, ion migration, octahedral tilt modes, and the role of the A-cation, provide insights into the atomic-scale structural mechanisms that drive and block ion loss and ion migration, opening pathways to inhibit ion loss, migration and improve structural stability.
Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults
Authors: Li Xuanji , Brejnrod Asker , Thorsen Jonathan , Zachariasen Trine , Trivedi Urvish , Russel Jakob , Vestergaard Gisle Alberg , Stokholm Jakob , Rasmussen Morten Arendt , Sørensen Søren Johannes 
Published: December 2023

AbstractDespite their crucial importance for human health, there is still relatively limited knowledge on how the gut resistome changes or responds to antibiotic treatment across ages, especially in the latter case. Here, we use fecal metagenomic data from 662 Danish infants and 217 young adults to fill this gap. The gut resistomes are characterized by a bimodal distribution driven by E. coli composition. The typical profile of the gut resistome differs significantly between adults and infants, with the latter distinguished by higher gene and plasmid abundances. However, the predominant antibiotic resistance genes (ARGs) are the same. Antibiotic treatment reduces bacterial diversity and increased ARG and plasmid abundances in both cohorts, especially core ARGs. The effects of antibiotic treatments on the gut microbiome last longer in adults than in infants, and different antibiotics are associated with distinct impacts. Overall, this study broadens our current understanding of gut resistome dynamics and the impact of antibiotic treatment across age groups.
Co-adjuvanting DDA/TDB liposomes with a TLR7 agonist allows for IgG2a/c class-switching in the absence of Th1 cells
Authors: Zimmermann Julie , van Haren Simon D. , Diray-Arce Joann , Adriawan Ignatius Ryan , Wørzner Katharina , Krog Ricki T. , Guleed Safia , Hu Tu , Mortensen Rasmus , Dietrich Jes , Solbak Sara M. Ø. , Levy Ofer , Christensen Dennis , Pedersen Gabriel K. 
Published: December 2023

AbstractClass-switching to IgG2a/c in mice is a hallmark response to intracellular pathogens. T cells can promote class-switching and the predominant pathway for induction of IgG2a/c antibody responses has been suggested to be via stimulation from Th1 cells. We previously formulated CAF®01 (cationic liposomes containing dimethyldioctadecylammonium bromide (DDA) and Trehalose-6,6-dibehenate (TDB)) with the lipidated TLR7/8 agonist 3M-052 (DDA/TDB/3M-052), which promoted robust Th1 immunity in newborn mice. When testing this adjuvant in adult mice using the recombinant Chlamydia trachomatis (C.t.) vaccine antigen CTH522, it similarly enhanced IgG2a/c responses compared to DDA/TDB, but surprisingly reduced the magnitude of the IFN-γ+Th1 response in a TLR7 agonist dose-dependent manner. Single-cell RNA-sequencing revealed that DDA/TDB/3M-052 liposomes initiated early transcription of class-switch regulating genes directly in pre-germinal center B cells. Mixed bone marrow chimeras further demonstrated that this adjuvant did not require Th1 cells for IgG2a/c switching, but rather facilitated TLR7-dependent T-bet programming directly in B cells. This study underlines that adjuvant-directed IgG2a/c class-switching in vivo can occur in the absence of T-cell help, via direct activation of TLR7 on B cells and positions DDA/TDB/3M-052 as a powerful adjuvant capable of eliciting type I-like immunity in B cells without strong induction of Th1 responses.
Effects of calibrated blue–yellow changes in light on the human circadian clock
Authors: Blume Christine , Cajochen Christian , Schöllhorn Isabel , Slawik Helen C. , Spitschan Manuel 
Published: December 2023

AbstractEvening exposure to short-wavelength light can affect the circadian clock, sleep and alertness. Intrinsically photosensitive retinal ganglion cells expressing melanopsin are thought to be the primary drivers of these effects. Whether colour-sensitive cones also contribute is unclear. Here, using calibrated silent-substitution changes in light colour along the blue–yellow axis, we investigated whether mechanisms of colour vision affect the human circadian system and sleep. In a 32.5-h repeated within-subjects protocol, 16 healthy participants were exposed to three different light scenarios for 1 h starting 30 min after habitual bedtime: baseline control condition (93.5 photopic lux), intermittently flickering (1 Hz, 30 s on–off) yellow-bright light (123.5 photopic lux) and intermittently flickering blue-dim light (67.0 photopic lux), all calibrated to have equal melanopsin excitation. We did not find conclusive evidence for differences between the three lighting conditions regarding circadian melatonin phase delays, melatonin suppression, subjective sleepiness, psychomotor vigilance or sleep.The Stage 1 protocol for this Registered Report was accepted in principle on 9 September 2020. The protocol, as accepted by the journal, can be found at https://doi.org/10.6084/m9.figshare.13050215.v1.
Unsupervised machine learning to investigate trajectory patterns of COVID-19 symptoms and physical activity measured via the MyHeart Counts App and smart devices
Authors: Gupta Varsha , Kariotis Sokratis , Rajab Mohammed D. , Errington Niamh , Alhathli Elham , Jammeh Emmanuel , Brook Martin , Meardon Naomi , Collini Paul , Cole Joby , Wild Jim M. , Hershman Steven , Javed Ali , Thompson A. A. Roger , de Silva Thushan , Ashley Euan A. , Wang Dennis , Lawrie Allan 
Published: December 2023

AbstractPrevious studies have associated COVID-19 symptoms severity with levels of physical activity. We therefore investigated longitudinal trajectories of COVID-19 symptoms in a cohort of healthcare workers (HCWs) with non-hospitalised COVID-19 and their real-world physical activity. 121 HCWs with a history of COVID-19 infection who had symptoms monitored through at least two research clinic visits, and via smartphone were examined. HCWs with a compatible smartphone were provided with an Apple Watch Series 4 and were asked to install the MyHeart Counts Study App to collect COVID-19 symptom data and multiple physical activity parameters. Unsupervised classification analysis of symptoms identified two trajectory patterns of long and short symptom duration. The prevalence for longitudinal persistence of any COVID-19 symptom was 36% with fatigue and loss of smell being the two most prevalent individual symptom trajectories (24.8% and 21.5%, respectively). 8 physical activity features obtained via the MyHeart Counts App identified two groups of trajectories for high and low activity. Of these 8 parameters only ‘distance moved walking or running’ was associated with COVID-19 symptom trajectories. We report a high prevalence of long-term symptoms of COVID-19 in a non-hospitalised cohort of HCWs, a method to identify physical activity trends, and investigate their association. These data highlight the importance of tracking symptoms from onset to recovery even in non-hospitalised COVID-19 individuals. The increasing ease in collecting real-world physical activity data non-invasively from wearable devices provides opportunity to investigate the association of physical activity to symptoms of COVID-19 and other cardio-respiratory diseases.