bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Sagittal and Vertical Changes in Maxillary Dental, Skeletal, and Soft Tissue Following Surgically Assisted Rapid Maxillary Expansion: A Retrospective Longitudinal Study
Authors: Farfel Vivian , Morea Gladys Cristina , Ferreira Lydia Masako , Pereira Max Domingues 
Published: October 2021

Objective:
To evaluate whether the maxillary complex would be sagittally, vertically, or mutually displaced after the transverse maxillary correction by surgically assisted rapid maxillary expansion and how the facial profile would be affected.

Materials and Methods:
The sample comprised 28 adult patients (mean age 25.8 [age range 19–39 years]; 50% women) with transverse maxillary deficiency greater than 7 mm who underwent the surgical rapid maxillary expansion. Cephalometric analysis (n
= 112), intra- and extra-oral registries, and radiographic records were taken before treatment (T1), right after the end of the expansion (T2), 4 months after the expansion (T3), and 10 months after the end of the expansion (T4). Dental and skeletal cephalometric measurements were evaluated at each time-point, whereas soft tissue cephalometric analyses were determined at 2 time points (T1 and T4).

Results:
The results indicated that no sagittal, vertical, skeletal, or soft tissue variation was found after the surgical expansion. However, statistically significant dental changes (P
< 0.05) were observed in dental angles (1.NA/1.SN/1.PoOR/1.PP) throughout the different time-points. The authors found statistically relevant posterior inclination of the incisors from T2 to T3 based on multiple comparisons.

Conclusions:
Surgically assisted rapid maxillary expansion does not promote anterior and vertical displacement of the maxilla. Notwithstanding, the surgical intervention causes upper incisor palatal inclination.
Early intervention with a glycerol throat spray containing cold-adapted cod trypsin after self-diagnosis of the common cold: a randomised prospective, parallel group and single-blind methods trial (Glycerol-cod trypsin spray in common cold)
Authors: Lindberg B. Fredrik , Nelson Ida , Ranstam Jonas , Riker Donald K. 
Published: October 2021

AbstractBackgroundA glycerol throat spray containing cold-adapted cod trypsin (GCTS) deactivates common cold virus in vitro and decreases pharyngeal rhinovirus load after inoculation in humans. We relied on early self-diagnosis and evaluated two different scales to detect a treatment effect in naturally occurring common colds.MethodsAdults were enrolled in this randomised, prospective, parallel group, single-blind study to begin treatment six times daily at first sign of a common cold or were assigned to a non-treated group. Jackson’s symptom scale and the 9-item Wisconsin Upper Respiratory Symptom Survey (WURSS)-21 quality of life (QoL) domain were recorded daily by subjects and area under the curve over 12 days (AUC1-12) calculated.ResultsTreatment resulted in reduced symptoms with an AUC1-12 of 45.1 ± 32.5 for Jackson scores compared to 53.8 ± 35.7 in the controls (p=0.023). AUC1-12 for the 9-item WURSS-21 QoL domain was likewise improved, 113.6 ± 107.7 and 152.7 ± 126.3 (p=0.006), respectively. During the first four days fewer of the treated subjects (35.3%) used rescue medication than did the control group (50.4%, p=0.014).ConclusionsReduction in common cold symptoms was seen with treatment with a glycerol throat spray containing cold-adapted cod trypsin. This effect was best detected with the 9-item WURSS-21 QoL domain.
Effect of SARS-CoV-2 vaccination on symptoms from post-acute COVID syndrome: results from the national VAXILONG survey
Authors: Scherlinger Marc , Pijnenburg Luc , Chatelus Emmanuel , Arnaud Laurent , Gottenberg Jacques-Eric , Sibilia Jean , Felten Renaud 
Published: October 2021

AbstractIntroductionFew data are available concerning the effect of SARS-CoV-2 vaccination on the persistent symptoms associated with COVID-19, also called long-COVID or post-acute COVID-19 syndrome (PACS).Patients and methodsWe conducted a nationwide online survey among adult patients with PACS as defined by symptoms persisting over 4 weeks following a confirmed or probable COVID-19, without any identified alternative diagnosis. Information concerning PACS symptoms, vaccine type and scheme and its effect on PACS symptoms were studied.ResultsSix hundred and twenty surveys were completed and 567 satisfied the inclusion criteria and were analyzed. Respondents were 83.4% of women of median age 44 (IQR 25-75: 37-50). Initial infection was proven in 365 patients (64%) and 5.1% had been hospitalized to receive oxygen. 396 patients had received at least one injection of SARS-CoV-2 vaccine at the time of the survey, after a median of 357 [198-431] days following the initially-reported SARS-CoV-2 infection. Among the 380 patients who reported persistent symptoms at the time of SARS-CoV-2 vaccination, 201 (52.8%) reported variation of symptoms following the injection, without difference based on the type of vaccine used. After a complete vaccination scheme, 93.3% (28/30) of initially seronegative patients reported a positive anti-SARS-CoV-2 IgG.170 PACS patients had not been vaccinated. The most common reasons for postponing SARS-CoV-2 vaccine were a fear of worsening PACS symptoms (55.9%) and the idea that vaccination was contraindicated because of PACS (15.6%).ConclusionOur study suggests that SARS-CoV-2 vaccination is well tolerated in the majority of PACS patients and has good immunogenicity. Disseminating these reassuring data might prove crucial to increase vaccine coverage in patients with PACS.
Dynamic metabolic network modeling of a mammalian cell cycle using time-course multi-omics data
Authors: Lee Ho-Joon , Shen Fangzhou , Eames Alec , Jedrychowski Mark P. , Chandrasekaran Sriram 
Published: October 2021

ABSTRACTCell cycle is a fundamental process for cell growth and proliferation, and its dysregulation leads to many diseases. How metabolic networks are regulated and rewired during the cell cycle is unknown. Here we apply a dynamic genome-scale metabolic modeling framework (DFA) to simulate a cell cycle of cytokine-activated murine pro-B cells. Phase-specific reaction activity predicted by DFA using time-course metabolomics were validated using matched time-course proteomics and phospho-proteomics data. Our model correctly predicted changes in methionine metabolism at the G1/S transition and the activation of lysine metabolism, nucleotides synthesis, fatty acid elongation and heme biosynthesis at the critical G0/G1 transition into cell growth and proliferation. Metabolic fluxes predicted from proteomics and phosphoproteomics constrained metabolic models were highly consistent with DFA fluxes and revealed that most reaction fluxes are regulated indirectly. Our model can help predict the impact of changes in nutrients, enzymes, or regulators on this critical cellular process.
Codiversification of gut microbiota with humans
Authors: Suzuki Taichi A. , Fitzstevens Liam , Schmidt Victor T. , Enav Hagay , Huus Kelsey , Mbong Mirabeau , Adegbite Bayode R. , Zinsou Jeannot F. , Esen Meral , Velavan Thirumalaisamy P. , Adegnika Ayola A. , Song Le Huu , Spector Timothy D. , Muehlbauer Amanda L. , Marchi Nina , Blekhman Ran , Ségurel Laure , Youngblut Nicholas D. , Kremsner Peter , Ley Ruth E. 
Published: October 2021

AbstractSome gut microbes have cospeciated with hominids, but whether they further codiversified with human populations is unclear. Here, we identify predominant gut microbial species sharing a parallel evolutionary history with human populations. Patterns of strain transfer between populations are generally consistent with an African origin, and suggest long-term vertical transmission over thousands of generations. We show the same strains also faithfully transmit between mothers and their children. Consistent with the development of intimate symbiosis, species with strongest patterns of codiversification have the smallest genomes. This study reveals long-term fidelity of gut microbiota with human populations through transmission among individuals living in close proximity. Dominance of specific strains in different populations is based in part on vertical transmission and they may provide population-specific health benefits.One-sentence summaryIdentification of gut microbes that codiversified with human populations.
A multifaceted ecological assessment reveals the invasion of the freshwater red macroalga Montagnia macrospora (Batrachospermales, Rhodophyta) in Taiwan
Authors: Fontana Silvia , Yeh Lan-Wei , Zhan Shing Hei , Liu Shao-Lun 
Published: October 2021

ABSTRACTInvasive freshwater macroalgae are rarely described. Recently, a freshwater red alga, Montagnia macrospora, was introduced from South America to East Asia via the global aquarium trade. The earliest occurrence record of this alga in Taiwan is dated 2005. To determine whether M. macrospora has become an invasive species in Taiwan and to understand its traits that facilitated its invasion, we took a total-evidence approach that combines examination of ecological background and population genetic analysis. Our island-wide survey showed that M. macrospora alga was widespread in the field across Taiwan, where the climate greatly differs from that of South America. Our population genetic analysis revealed that the cox2-3 sequences of all the specimens of M. macrospora from Taiwan were identical, consistent with the hypothesis that the alga expanded through asexual reproduction. Moreover, during our long-term ecological assessments and field surveys, we observed that M. macrospora is an ecological generalist that can self-sustain for a decade and bloom. Taken together, our data suggest that M. macrospora has successfully invaded the freshwater ecosystems in Taiwan due to its ability to disperse asexually and to grow under broad environmental conditions. We hope that our study brings attention to invasive freshwater algae, which have been overlooked in conservation planning and management.
Neural dynamics of illusory tactile pulling sensations
Authors: De Havas Jack , Ito Sho , Bestmann Sven , Gomi Hiroaki 
Published: October 2021

AbstractThe sensation of directional forces and their associated sensorimotor commands are inextricably intertwined, complicating the identification of brain circuits responsible for tactile pulling sensations. One hypothesis is that, like tactile frequency discrimination, pulling sensations are generated by early sensory-frontal activity. Alternatively, they may be generated later in the somatosensory association cortex. To dissociate these accounts and uncouple the pulling sensation from unrelated but correlated sensory and motor processing, we combined high-density EEG with an oddball paradigm and asymmetric vibration, which creates an illusory sensation of the hand being directionally pulled. Oddballs that created a pulling sensation in the opposite direction to common stimuli were compared to the same oddballs in the context of neutral common stimuli (symmetric vibration) and to neutral oddballs. Brain responses to having directional pulling expectations violated by directional stimuli were therefore isolated. Contrary to the sensory-frontal account, frontal N140 brain activity was actually larger for neutral than pulling oddballs. Instead, pulling sensations were associated with amplitude and latency modulations of midline P200 and P3b potentials, and specifically, to contralateral parietal lobe activity 280ms post-stimulus. The timing of this activity suggested pulling sensations involve spatial processing, such as tactile remapping between coordinate frames. Source localization showed this activity to be centered on the postcentral sulcus, superior parietal lobule and intraparietal sulcus, suggesting that pulling sensations arise via the processing of body position, tactile orientation and peripersonal space. Our results demonstrate how tactile illusions can uniquely disambiguate parietal contributions to somatosensation by removing unrelated sensory processing.Significance statementThe neural mechanisms of tactile pulling sensations are poorly understood. Competing early sensory-frontal and later somatosensory association cortex accounts are hard to dissociate due to confounding sensory and motor signals present when forces are applied to the skin. Here, we used EEG and a novel asymmetric vibration approach to induce an illusory pulling sensation, which circumvents these issues. We found that pulling sensations were associated with parietal lobe activity 280ms post-stimulus and modulations of the P200. The timing and location of this activity suggested that pulling sensations necessitate spatial processing and supported a somatosensory association cortex account of the pulling sensation.
PoSTcode: Probabilistic image-based spatial transcriptomics decoder
Authors: Gataric Milana , Park Jun Sung , Li Tong , Vaskivskyi Vasyl , Svedlund Jessica , Strell Carina , Roberts Kenny , Nilsson Mats , Yates Lucy R. , Bayraktar Omer , Gerstung Moritz 
Published: October 2021

AbstractRealising the full potential of novel image-based spatial transcriptomic (IST) technologies requires robust and accurate algorithms for decoding the hundreds of thousand fluorescent signals each derived from single molecules of mRNA. In this paper, we introduce PoSTcode, a probabilistic method for transcript decoding from cyclic multi-channel images, whose effectiveness is demonstrated on multiple large-scale datasets generated using different versions of the in situ sequencing protocols. PoSTcode is based on a re-parametrised matrix-variate Gaussian mixture model designed to account for correlated noise across fluorescence channels and imaging cycles. PoSTcode is shown to recover up to 50% more confidently decoded molecules while simultaneously decreasing transcript mislabeling when compared to existing decoding techniques. In addition, we demonstrate its increased stability to various types of noise and tuning parameters, which makes this new approach reliable and easy to use in practice. Lastly, we show that PoSTcode produces fewer doublet signals compared to a pixel-based decoding algorithm.
FAIRly big: A framework for computationally reproducible processing of large-scale data
Authors: Wagner Adina S. , Waite Laura K. , Wierzba Małgorzata , Hoffstaedter Felix , Waite Alexander Q. , Poldrack Benjamin , Eickhoff Simon B. , Hanke Michael 
Published: October 2021

AbstractLarge-scale datasets present unique opportunities to perform scientific investigations with un-precedented breadth. However, they also pose considerable challenges for the findability, accessibility, interoperability, and reusability (FAIR) of research outcomes due to infrastructure limitations, data usage constraints, or software license restrictions. Here we introduce a DataLad-based, domain-agnostic framework suitable for reproducible data processing in compliance with open science mandates. The framework attempts to minimize platform idiosyncrasies and performance-related complexities. It affords the capture of machine-actionable computational provenance records that can be used to retrace and verify the origins of research outcomes, as well as be re-executed independent of the original computing infrastructure. We demonstrate the framework’s performance using two showcases: one highlighting data sharing and transparency (using the studyforrest.org dataset) and another highlighting scalability (using the largest public brain imaging dataset available: the UK Biobank dataset).
Diversity of reptile sex chromosome evolution revealed by cytogenetic and linked-read sequencing
Authors: Zhu Zexian , Matsubara Kazumi , Shams Foyez , Dobry Jason , Wapstra Erik , Gamble Tony , Sarre Stephen D. , Georges Arthur , Marshall Graves Jennifer A. , Zhou Qi , Ezaz Tariq 
Published: October 2021

AbstractReptile sex determination is attracting much attention because the great diversity of sex-determination and dosage compensation mechanisms permits us to approach fundamental questions about sex chromosome turnover and evolution. However, reptile sex chromosome variation remains largely uncharacterized and no reptile master sex determination genes have yet been identified. Here we describe a powerful and cost-effective “chromosomics” approach, combining probes generated from the microdissected sex chromosomes with transcriptome sequencing to explore this diversity in non-model Australian reptiles with heteromorphic or cryptic sex chromosomes. We tested the pipeline on a turtle, a gecko, and a worm-lizard, and we also identified sequences located on sex chromosomes in a monitor lizard using linked-read sequencing. Genes identified on sex chromosomes were compared to the chicken genome to identify homologous regions among the four species. We identified candidate sex determining genes within these regions, including conserved vertebrate sex-determining genes pdgfa, pdgfra amh and wt1, and demonstrated their testis or ovary-specific expression. All four species showed gene-by-gene rather than chromosome-wide dosage compensation. Our results imply that reptile sex chromosomes originated by independent acquisition of sex-determining genes on different autosomes, as well as translocations between different ancestral macro- and micro-chromosomes. We discuss the evolutionary drivers of the slow differentiation, but rapid turnover, of reptile sex chromosomes.
Thecnf1gene is associated to an expandingEscherichia coliST131H30Rx/C2 sublineage and confers a competitive advantage for host colonization
Authors: Tsoumtsa Meda Landry Laure , Landraud Luce , Petracchini Serena , Descorps-Declere Stéphane , Perthame Emeline , Nahori Marie-Anne , Finn Laura Ramirez , Ingersoll Molly A. , Patiño-Navarrete Rafael , Glaser Philippe , Dussurget Olivier , Denamur Erick , Mettouchi Amel , Lemichez Emmanuel 
Published: October 2021

SUMMARYEpidemiological projections point to acquisition of ever-expanding multidrug resistance (MDR) byEscherichia coli, a commensal of the digestive tract acting as a source of urinary tract pathogens. We performed a high-throughput genetic screening of predominantly clinicalE. coliisolates from wide geographical origins. This revealed a preferential distribution of the Cytotoxic Necrotizing Factor 1 (CNF1)-toxin encoding gene,cnf1, in four sequence types encompassing the pandemicE. coliMDR lineage ST131. This lineage is responsible for a majority of extraintestinal infections that escape first-line antibiotic treatment and has known enhanced capacities to colonize the gastrointestinal tract (GIT). Statistical modeling uncovered a dominant global expansion ofcnf1-positive strains within multidrug-resistant ST131 subcladeH30Rx/C2. Despite the absence of phylogeographical signals,cnf1-positive isolates adopted a clonal distribution into clusters on the ST131-H30Rx/C2 phylogeny, sharing a similar profile of virulence factors and the samecnf1allele. Functional analysis of thecnf1-positive clinical strain EC131GY ST131-H30Rx/C2, established that acnf1-deleted EC131GY is outcompeted by the wildtype strain in a mouse model of competitive infection of the bladder while both strains behave similarly during monoinfections. This points for positive selection ofcnf1during UTI rather than urovirulence. Wildtype EC131GY also outcompeted the mutant when concurrently inoculated into the gastrointestinal tract, arguing for selection within the gut. Whatever the site of selection, these findings support that the benefit ofcnf1enhancing host colonization by ST131-H30Rx/C2 in turn drives a worldwide dissemination of thecnf1gene together with extended spectrum of antibiotic resistance genes.
A weighted constraint satisfaction approach to human goal-directed decision making
Authors: Li Yuxuan , McClelland James L. 
Published: October 2021

AbstractWhen we plan for long-range goals, proximal information cannot be exploited in a blindly myopic way, as relevant future information must also be considered. But when a subgoal must be resolved first, irrelevant future information should not interfere with the processing of more proximal, subgoal-relevant information. We explore the idea that decision making in both situations relies on the flexible modulation of the degree to which different pieces of information under consideration are weighted, rather than explicitly decomposing a problem into smaller parts and solving each part independently. We asked participants to find the shortest goal-reaching paths in mazes and modeled their initial path choices as a noisy, weighted information integration process. In a base task where choosing the optimal initial path required weighting starting-point and goal-proximal factors equally, participants did take both constraints into account, with participants who made more accurate choices tending to exhibit more balanced weighting. The base task was then embedded as an initial subtask in a larger maze, where the same two factors constrained the optimal path to a subgoal, and the final goal position was irrelevant to the initial path choice. In this more complex task, participants’ choices reflected predominant consideration of the subgoal-relevant constraints, but also some influence of the initially-irrelevant final goal. More accurate participants placed much less weight on the optimality-irrelevant goal and again tended to weight the two initially-relevant constraints more equally. These findings suggest that humans may rely on a graded, task-sensitive weighting of multiple constraints to generate approximately optimal decision outcomes in both hierarchical and non-hierarchical goal-directed tasks.Author SummaryDifferent problems require the consideration of different information sources, including often useful long-range, future information that may impact our immediate decisions. However, when future information is irrelevant to a key subgoal, it can be desirable to focus on achieving the subgoal first. We suggest that humans rely on appropriately weighting relevant information over irrelevant information to generate decision outcomes in both types of situations. We conducted behavioral experiments and fitted models of decision processes to understand to what extent people considered various task factors in choosing the initial path in different mazes, both when a simple maze occurred alone or was embedded as an initial part in a larger maze. Our results show that people approximate the optimal decision outcomes in both tasks by modulating the weighting of different factors during planning, and that people who made more accurate initial path choices modulated these weightings more successfully than those who made less accurate choices.