bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bottlenose dolphins in the Netherlands come from two sides: across the North Sea and through the English Channel
Authors: Hoekendijk Jeroen P. A. , Leopold Mardik F. , Cheney Barbara J. 
Published: October 2021

AbstractOn 19 July 2019 an estimated 20 bottlenose dolphins (Tursiops truncatus) were observed in the Marsdiep, a tidal inlet connecting the North Sea and the Dutch Wadden Sea, between Den Helder and the island of Texel. Photographs and video recordings were made and nine individuals were matched with known dolphins from the Moray Firth, NE Scotland. These are the first matches of this east coast of Scotland population outside the UK and Ireland. Subsequent observations of individuals from this group show that at least some of the animals have returned to Scottish waters, while others were photographed in Danish waters. Furthermore, we report on a photo identification match of a solitary bottlenose dolphin between France and the Netherlands. These matches suggest that bottlenose dolphins, in the Netherlands, originate from two different genetically distinct populations: ‘Coastal South’ and ‘Coastal North’. This evidence of previously unknown long-range movements may have important implications for the conservation and management of this species in European waters.
New dualities from old: generating geometric, Petrie, and Wilson dualities and trialities of ribbon graphs
Authors: Abrams Lowell , Ellis-Monaghan Joanna A. 
Published: October 2021

AbstractWe define a new ribbon group action on ribbon graphs that uses a semidirect product of a permutation group and the original ribbon group of Ellis-Monaghan and Moffatt to take (partial) twists and duals, or twuals, of ribbon graphs. A ribbon graph is a fixed point of this new ribbon group action if and only if it is isomorphic to one of its (partial) twuals. This extends the original ribbon group action, which only used the canonical identification of edges, to the more natural setting of self-twuality up to isomorphism. We then show that every ribbon graph has in its orbit an orientable embedded bouquet and prove that the (partial) twuality properties of these bouquets propagate through their orbits. Thus, we can determine (partial) twualities via these one vertex graphs, for which checking isomorphism reduces simply to checking dihedral group symmetries. Finally, we apply the new ribbon group action to generateallself-trial ribbon graphs on up to seven edges, in contrast with the few, large, very high-genus, self-trial regular maps found by Wilson, and by Jones and Poultin. We also show how the automorphism group of a ribbon graph yields self-dual, -petrial or –trial graphs in its orbit, and produce an infinite family of self-trial graphs that do not arise as covers or parallel connections of regular maps, thus answering a question of Jones and Poulton.
A Replication Study on Coral δ11B and B/Ca and Their Variation in Modern and Fossil Porites: Implications for Coral Calcifying Fluid Chemistry and Seawater pH Changes Over the Last Millennium
Authors: Chen Xuefei , Deng Wenfeng , Kang Huiling , Zeng Ti , Zhang Le , Zhao Jian‐xin , Wei Gangjian 
Published: October 2021

AbstractBoron systematics offer a unique opportunity to reveal coral calcifying fluid (CF) chemistry and seawater pH (pHsw). Here, we assess the intercolony differences of skeletal δ11B and B/Ca, and examine their variation in modern and fossil Porites spp. collected from the east Hainan Island in the northern South China Sea (SCS), to explore changes in coral CF chemistry and pHsw over the last millennium. This enables us to assess whether ocean acidification (OA) has disturbed the ability of corals to control their CF chemistry, and whether splicing coral δ11B‐pH records can trace long‐term pHsw variability. We demonstrate that coral boron systematics bear remarkable intercolony differences, with mean offset as high as 1.05‰ for δ11B and 183.1 μmol/mol for B/Ca. With this in mind, we show that fossil corals exhibit no significant difference in their CF carbonate chemistry, but all have systematically higher CF pH (pHcf, by an average of 0.12 units) and almost equivalent CF dissolved inorganic carbon (DICcf) concentration, compared to modern corals. This suggests greater OA impacts on coral pHcf but less noticeable effects on DICcf. In addition, the ∼0.12 decline in pHcf translates to about 0.24 reduction in pHsw, similar to another coral‐based estimate (∼0.24) from south Hainan Island, corroborating significant OA in the northern SCS since the industrial era. Nevertheless, we find that pHsw in the east Hainan Island has staged a recovery from 1980 to 2010, slowing down the OA pace, highlighting important roles of other local forcing on pHsw regulation.
Multi-omics driven predictions of response to acute phase combination antidepressant therapy: a machine learning approach with cross-trial replication
Authors: Joyce Jeremiah B. , Grant Caroline W. , Liu Duan , MahmoudianDehkordi Siamak , Kaddurah-Daouk Rima , Skime Michelle , Biernacka Joanna , Frye Mark A. , Mayes Taryn , Carmody Thomas , Croarkin Paul E. , Wang Liewei , Weinshilboum Richard , Bobo William V. , Trivedi Madhukar H. , Athreya Arjun P. 
Published: October 2021

AbstractCombination antidepressant pharmacotherapies are frequently used to treat major depressive disorder (MDD). However, there is no evidence that machine learning approaches combining multi-omics measures (e.g., genomics and plasma metabolomics) can achieve clinically meaningful predictions of outcomes to combination pharmacotherapy. This study examined data from 264 MDD outpatients treated with citalopram or escitalopram in the Mayo Clinic Pharmacogenomics Research Network Antidepressant Medication Pharmacogenomic Study (PGRN-AMPS) and 111 MDD outpatients treated with combination pharmacotherapies in the Combined Medications to Enhance Outcomes of Antidepressant Therapy (CO-MED) study to predict response to combination antidepressant therapies. To assess whether metabolomics with functionally validated single-nucleotide polymorphisms (SNPs) improves predictability over metabolomics alone, models were trained/tested with and without SNPs. Models trained with PGRN-AMPS’ and CO-MED’s escitalopram/citalopram patients predicted response in CO-MED’s combination pharmacotherapy patients with accuracies of 76.6% (p < 0.01; AUC: 0.85) without and 77.5% (p < 0.01; AUC: 0.86) with SNPs. Then, models trained solely with PGRN-AMPS’ escitalopram/citalopram patients predicted response in CO-MED’s combination pharmacotherapy patients with accuracies of 75.3% (p < 0.05; AUC: 0.84) without and 77.5% (p < 0.01; AUC: 0.86) with SNPs, demonstrating cross-trial replication of predictions. Plasma hydroxylated sphingomyelins were prominent predictors of treatment outcomes. To explore the relationship between SNPs and hydroxylated sphingomyelins, we conducted multi-omics integration network analysis. Sphingomyelins clustered with SNPs and metabolites related to monoamine neurotransmission, suggesting a potential functional relationship. These results suggest that integrating specific metabolites and SNPs achieves accurate predictions of treatment response across classes of antidepressants. Finally, these results motivate functional investigation into how sphingomyelins might influence MDD pathophysiology, antidepressant response, or both.
ATP-citrate lyase promotes axonal transport across species
Authors: Even Aviel , Morelli Giovanni , Turchetto Silvia , Shilian Michal , Bail Romain Le , Laguesse Sophie , Krusy Nathalie , Brisker Ariel , Brandis Alexander , Inbar Shani , Chariot Alain , Saudou Frédéric , Dietrich Paula , Dragatsis Ioannis , Brone Bert , Broix Loïc , Rigo Jean-Michel , Weil Miguel , Nguyen Laurent 
Published: October 2021

AbstractMicrotubule (MT)-based transport is an evolutionary conserved process finely tuned by posttranslational modifications. Among them, α-tubulin acetylation, primarily catalyzed by a vesicular pool of α-tubulin N-acetyltransferase 1 (Atat1), promotes the recruitment and processivity of molecular motors along MT tracks. However, the mechanism that controls Atat1 activity remains poorly understood. Here, we show that ATP-citrate lyase (Acly) is enriched in vesicles and provide Acetyl-Coenzyme-A (Acetyl-CoA) to Atat1. In addition, we showed that Acly expression is reduced upon loss of Elongator activity, further connecting Elongator to Atat1 in a pathway regulating α-tubulin acetylation and MT-dependent transport in projection neurons, across species. Remarkably, comparable defects occur in fibroblasts from Familial Dysautonomia (FD) patients bearing an autosomal recessive mutation in the gene coding for the Elongator subunit ELP1. Our data may thus shine light on the pathophysiological mechanisms underlying FD.
Epigenetic modifications affect the rate of spontaneous mutations in a pathogenic fungus
Authors: Habig Michael , Lorrain Cecile , Feurtey Alice , Komluski Jovan , Stukenbrock Eva H. 
Published: October 2021

AbstractMutations are the source of genetic variation and the substrate for evolution. Genome-wide mutation rates appear to be affected by selection and are probably adaptive. Mutation rates are also known to vary along genomes, possibly in response to epigenetic modifications, but causality is only assumed. In this study we determine the direct impact of epigenetic modifications and temperature stress on mitotic mutation rates in a fungal pathogen using a mutation accumulation approach. Deletion mutants lacking epigenetic modifications confirm that histone mark H3K27me3 increases whereas H3K9me3 decreases the mutation rate. Furthermore, cytosine methylation in transposable elements (TE) increases the mutation rate 15-fold resulting in significantly less TE mobilization. Also accessory chromosomes have significantly higher mutation rates. Finally, we find that temperature stress substantially elevates the mutation rate. Taken together, we find that epigenetic modifications and environmental conditions modify the rate and the location of spontaneous mutations in the genome and alter its evolutionary trajectory.
Next generation of tumor-activating type I IFN enhances anti-tumor immune responses to overcome therapy resistance
Authors: Cao Xuezhi , Liang Yong , Hu Zhenxiang , Li Huiyu , Yang Jiaming , Hsu Eric J. , Zhu Jiankun , Zhou Jin , Fu Yang-Xin 
Published: October 2021

AbstractType I interferon is promising in treating different kinds of tumors, but has been limited by its toxicity, lack of tumor targeting, and very short half-life. To target tumors, reduce systemic toxicity, and increase half-life, here we engineer a masked type I IFN-Fc (ProIFN) with its natural receptor connected by a cleavable linker that can be targeted by tumor-associated proteases. ProIFN has a prolonged serum half-life and shows an improved tumor-targeting effect. Interestingly, ProIFN-treated mice show enhanced DC cross-priming and significant increased CD8+ infiltration and effector function in the tumor microenvironment. ProIFN is able to improve checkpoint blockade efficacy in established tumors, as well as radiation efficacy for both primary and metastatic tumors. ProIFN exhibits superior long-term pharmacokinetics with minimal toxicity in monkeys. Therefore, this study demonstrates an effective tumor-activating IFN that can increase targeted immunity against primary tumor or metastasis and reduce periphery toxicity to the host.
Structure-controllable growth of nitrogenated graphene quantum dots via solvent catalysis for selective C-N bond activation
Authors: Moon Byung Joon , Kim Sang Jin , Lee Aram , Oh Yelin , Lee Seoung-Ki , Lee Sang Hyun , Kim Tae-Wook , Hong Byung Hee , Bae Sukang 
Published: October 2021

AbstractPhotophysical and photochemical properties of graphene quantum dots (GQDs) strongly depend on their morphological and chemical features. However, systematic and uniform manipulation of the chemical structures of GQDs remains challenging due to the difficulty in simultaneous control of competitive reactions, i.e., growth and doping, and the complicated post-purification processes. Here, we report an efficient and scalable production of chemically tailored N-doped GQDs (NGs) with high uniformity and crystallinity via a simple one-step solvent catalytic reaction for the thermolytic self-assembly of molecular precursors. We find that the graphitization of N-containing precursors during the formation of NGs can be modulated by intermolecular interaction with solvent molecules, the mechanism of wh	ich is evidenced by theoretical calculations and various spectroscopic analyses. Given with the excellent visible-light photoresponse and photocatalytic activity of NGs, it is expected that the proposed approach will promote the practical utilization of GQDs for various applications in the near future.
Method for assessing atomic sources of flicker noise in superconducting qubits
Authors: Reshef Almog , Caspary Toroker Maytal 
Published: October 2021

AbstractFlicker noise causes decoherence in Josephson junction-based superconducting qubits, thus limiting their practical potential as building blocks for quantum computers. This is due to limited length and complexity of executable algorithms, and increased dependency on error-correcting measures. Therefore, identifying and subsiding the atomic sources of flicker noise are of great importance to the development of this technology. We developed a method that combines ab initio DFT calculations and quantum dynamics to model charge transport across a Josephson junction, by which it is possible to more accurately assess different defects as sources of flicker noise. We demonstrate the use of our method in an investigation of various atomic defects, including vacancies, trapping, and substitutions, in an Al|Al2O3|Al Josephson junction. This demonstration both reveals weaknesses in previous attempts to pinpoint the atomic sources of flicker noise and highlights new candidates.
Effect of an anti-adhesion agent on vision-based assessment of cervical adhesions after thyroid surgery: randomized, placebo-controlled trial
Authors: Yu Hyeong Won , Lee Dongheon , Lee Keunchul , Kim Su-jin , Chai Young Jun , Kim Hee Chan , Choi June Young , Lee Kyu Eun 
Published: October 2021

AbstractMany patients experience cervical adhesions after thyroid surgery. To date, however, no studies have objectively measured the effects of anti-adhesion agents on cervical adhesion symptoms. This study evaluated the effects of an anti-adhesion agent on cervical adhesions after thyroid surgery, as determined using a system that measures the extent of marker movement objectively. One hundred patients were randomized in a 1:1 ratio to undergo thyroid surgery with or without the anti-adhesion agent Collabarrier. Using specially manufactured recording equipment, the position of the marker on neck skin was measured before surgery, and 2 weeks, 3 months, and 9 months after surgery. Relative change in marker distance, calculated by subtracting the marker position before surgery from the marker positions 2 weeks, 3 months, and 9 months after surgery, differed significantly in the groups of patients who underwent thyroid surgery with and without the anti-adhesion agent (P < 0.05). A novel measuring system can objectively evaluate the effectiveness of a thyroid anti-adhesion agent. The anti-adhesion agent used significantly reduced adhesions compared with the control group. The trial is registered at www.cris.nih.go.kr (KCT0005745; date of registration, 08/01/2021).
The effect of age on the association between daily gait speed and abdominal obesity in Japanese adults
Authors: Kinoshita Keita , Ozato Naoki , Yamaguchi Tohru , Sudo Motoki , Yamashiro Yukari , Mori Kenta , Kumagai Mika , Sawada Kaori , Katsuragi Yoshihisa , Imoto Seiya , Ihara Kazushige , Nakaji Shigeyuki 
Published: October 2021

AbstractThe aim of this work was to investigate the effect of age on the association between daily gait speed (DGS) and abdominal obesity defined by visceral fat area (VFA). A cross-sectional study was performed using data from an annual community-based health check-up. A total of 699 participants aged 20–88 years were enrolled in this analysis. DGS was assessed using tri-axial accelerometers worn for ≥ 7 days with at least 10 measuring hours each day. VFA was measured using a visceral fat meter. Since DGS differed significantly with age, the participants were divided into two groups: younger adults (YA), aged 20–49 years, and older adults (OA), aged 50–88 years. The association between DGS and VFA differed significantly with age (r = 0.099 for YA and r =  − 0.080 for OA; test for difference between correlation coefficients, P = 0.023). In OA, the adjusted odds ratio of abdominal obesity (VFA ≥ 100 cm2) was 0.40 (95% confidence interval 0.18, 0.88, P = 0.022) for the highest DGS quartile (DGS ≥ 1.37 m/s) compared to that for the lowest quartile (DGS < 1.11 m/s), whereas no significant association was found in YA. These data could aid in raising awareness of the self-management of obesity via DGS monitoring, especially in OA.
Cardiovascular risk moderates the effect of aerobic exercise on executive functions in older adults with subcortical ischemic vascular cognitive impairment
Authors: Barha Cindy K. , Dao Elizabeth , Marcotte Lauren , Hsiung Ging-Yuek Robin , Tam Roger , Liu-Ambrose Teresa 
Published: October 2021

AbstractAerobic training (AT) can promote cognitive function in adults with Subcortical Ischemic Vascular Cognitive Impairment (SIVCI) by modifying cardiovascular risk factors. However, pre-existing cardiovascular health may attenuate the benefits of AT on cognitive outcomes in SIVCI. We examined whether baseline cardiovascular risk moderates the effect of a 6-month progressive AT program on executive functions with a secondary analysis of a randomized controlled trial in 71 adults, who were randomized to either: (1) 3×/week progressive AT; or (2) education program (CON). Three executive processes were measured: (1) response inhibition by Stroop Test; (2) working memory by digits backward test; and (3) set shifting by the Trail Making Test. Baseline cardiovascular risk was calculated using the Framingham cardiovascular disease (CVD) Risk Score (FCRS), and participants were classified as either low risk (< 20% FCRS score; LCVR) or high risk (≥ 20% FCRS score; HCVR). A complete case analysis (n = 58) was conducted using an analysis of covariance (ANCOVA) to evaluate between-group differences in the three executive processes. A significant interaction was found between cardiovascular risk group and intervention group (AT or CON) for the digit span backward and the Trail Making Test. AT improved performance compared with CON in those with LCVR, while in those with HCVR, AT did not improve performance compared with CON. Baseline cardiovascular risk significantly moderates the efficacy of AT on cognition. Our findings highlight the importance of intervening early in the disease course of SIVCI, when cardiovascular risk may be lower, to reap maximum benefits of aerobic exercise.
Oxytocinergic cells of the posterior hypothalamic paraventricular nucleus participate in the food entrained clock
Authors: Caba Mario , Meza Enrique , Escobar Carolina , Jiménez Angeles , Caba-Flores Mario Daniel , Moreno-Cortés María Luisa , Melo Angel I. 
Published: October 2021

AbstractThe mechanisms underlying food anticipatory activity are still poorly understood. Here we explored the role of oxytocin (OT) and the protein c-Fos in the supraoptic nucleus (SON), medial (PVNm) and posterior (PVNp) regions of the paraventricular hypothalamic nucleus. Adult rats were assigned to one of four groups: scheduled restricted feeding (RF), ad libitum (AL), fasting after restricted feeding (RF-F), to explore the possible persistence of oscillations, or ad libitum fasted (AL-F). In the SON and in the PVNm, OT cells were c-Fos positive after food intake; in contrast, OT cells in the PVNp showed c-Fos activationin anticipation tofood access, which persisted in RF-F subjects. We conclude that OT and non-OT cells of the SON and PVNm may play a role as recipients of the entraining signal provided by food intake, whereas those of the PVNp which contain motor preautonomic cells that project to peripheral organs, may be involved in the hormonal and metabolic anticipatory changes in preparation for food presentation and thus, may be part of a link between central and peripheral oscillators. In addition, due to their persistent activation they may participate in the neuronal network for the clock mechanism that leads to food entrainment.
A high diversity of mechanisms endows ALS-inhibiting herbicide resistance in the invasive common ragweed (Ambrosia artemisiifolia L.)
Authors: Loubet Ingvild , Caddoux Laëtitia , Fontaine Séverine , Michel Séverine , Pernin Fanny , Barrès Benoit , Le Corre Valérie , Délye Christophe 
Published: October 2021

AbstractAmbrosia artemisiifolia L. (common ragweed) is a globally invasive, allergenic, troublesome arable weed. ALS-inhibiting herbicides are broadly used in Europe to control ragweed in agricultural fields. Recently, ineffective treatments were reported in France. Target site resistance (TSR), the only resistance mechanism described so far for ragweed, was sought using high-throughput genotyping-by-sequencing in 213 field populations randomly sampled based on ragweed presence. Additionally, non-target site resistance (NTSR) was sought and its prevalence compared with that of TSR in 43 additional field populations where ALS inhibitor failure was reported, using herbicide sensitivity bioassay coupled with ALS gene Sanger sequencing. Resistance was identified in 46 populations and multiple, independent resistance evolution demonstrated across France. We revealed an unsuspected diversity of ALS alleles underlying resistance (9 amino-acid substitutions involved in TSR detected across 24 populations). Remarkably, NTSR was ragweed major type of resistance to ALS inhibitors. NTSR was present in 70.5% of the resistant plants and 74.1% of the fields harbouring resistance. A variety of NTSR mechanisms endowing different resistance patterns evolved across populations. Our study provides novel data on ragweed resistance to herbicides, and emphasises that local resistance management is as important as mitigating gene flow from populations where resistance has arisen.
Inverse problems for structured datasets using parallel TAP equations and restricted Boltzmann machines
Authors: Decelle Aurelien , Hwang Sungmin , Rocchi Jacopo , Tantari Daniele 
Published: October 2021

AbstractWe propose an efficient algorithm to solve inverse problems in the presence of binary clustered datasets. We consider the paradigmatic Hopfield model in a teacher student scenario, where this situation is found in the retrieval phase. This problem has been widely analyzed through various methods such as mean-field approaches or the pseudo-likelihood optimization. Our approach is based on the estimation of the posterior using the Thouless–Anderson–Palmer (TAP) equations in a parallel updating scheme. Unlike other methods, it allows to retrieve the original patterns of the teacher dataset and thanks to the parallel update it can be applied to large system sizes. We tackle the same problem using a restricted Boltzmann machine (RBM) and discuss analogies and differences between our algorithm and RBM learning.