bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pain matters for central sensitization: sensory and psychological parameters in patients with fibromyalgia syndrome
Authors: Rehm Stefanie , Sachau Juliane , Hellriegel Jana , Forstenpointner Julia , Børsting Jacobsen Henrik , Harten Pontus , Gierthmühlen Janne , Baron Ralf 
Published: March 2021

Abstract

Introduction:
Patients suffering from fibromyalgia syndrome (FMS) are heterogenous. They often present with sensory abnormalities and comorbidities.

Objectives:
We aimed to answer the following questions: (1) Is there a specific somatosensory profile in our patient cohort? (2) Can we detect subgroups characterized by a specific combination of sensory and psychological features? and (3) Do psychological parameters influence sensory signs?

Methods:
In 87 patients with FMS quantitative sensory testing was performed on the hand and evaluated in combination with questionnaire results regarding pain, psychological comorbidities, sleep, and functionality.

Results:
Patients presented different somatosensory patterns, but no specific subgroups regarding sensory signs and psychological features were detected. Hypersensitivity for noxious mechanical and thermal stimuli and hyposensitivity for nonnoxious mechanical stimuli were the most prominent features. Thirty-one percent of patients showed signs of central sensitization as indicated by abnormally increased pinprick hyperalgesia or dynamic mechanical allodynia. Central sensitization was associated with higher pain intensities (P < 0.001). Only a small influence of psychiatric comorbidities on mechanical pain sensitivity (P = 0.044) and vibration detection (P = 0.028) was found, which was partly associated with high pain intensities. A small subgroup of patients (11.4%) demonstrated thermal hyposensitivity (loss of small-fiber function).

Conclusion:
Patients with FMS showed various somatosensory abnormalities. These were not significantly influenced by psychological comorbidities. Signs for central sensitization were detected in about one-third of patients and associated with higher pain intensities. This supports the notion of central sensitization being a major pathophysiological mechanism in FMS, whereas small-fiber loss may be less important.
Factors associated with maternal tetanus vaccination in Myanmar: An analysis of Demographic and Health Survey data
Authors: Tun Zaw Myo , Ring Zau , Tam Clarence C 
Published: March 2021

AbstractBackgroundTetanus toxoid vaccination is a life-saving maternal and child health intervention. Understanding gaps in maternal vaccination coverage is key to informing progress towards universal health coverage. We assessed maternal tetanus vaccination coverage in Myanmar and investigated factors associated with being unvaccinated.MethodWe analysed 2015-16 Demographic and Health Survey data including women aged 15-49 years with at least one childbirth in the last five years. The outcome was self-reported receipt of tetanus vaccine at least once during the last pregnancy. We used logistic regression models to assess factors associated with being unvaccinated.ResultsOverall maternal tetanus vaccination coverage was 85.7%. Sub-national coverage was lowest in the predominantly ethnic minority states of Shan, Kayin, and Chin at 69.6%, 77.4%, and 79.9%, respectively. Factors associated with a lack of vaccination were: not receiving antenatal care (odds ratio (OR): 18.99, 95% confidence interval (CI): 14.21, 25.39); receiving antenatal care at home (OR: 2.05, 95% CI: 1.46, 2.88), private and non-governmental organization clinics (OR: 2.88, 95% CI: 1.81, 4.58, compared to public facilities); and not wanting to go to a health facility alone (OR: 1.53, 95% CI: 1.14, 2.06). Higher educational attainment was associated with lower odds of being unvaccinated (OR: 0.48, 95% CI: 0.32, 0.70 for secondary relative to no education).InterpretationWe identified regional, structural, and individual differences in maternal tetanus vaccination coverage. Achieving universal coverage of maternal tetanus vaccination will largely depend on the ability to provide accessible antenatal care to most women who do not currently receive it.
OsbZIP62/OsFD7, a functional ortholog of Flowering Locus D (FD), regulates floral transition and panicle development in rice
Authors: Kaur Amarjot , Nijhawan Aashima , Yadav Mahesh , Khurana Jitendra P. 
Published: March 2021

AbstractWe have characterized a rice bZIP protein coding geneOsbZIP62/OsFD7that expresses preferentially in SAM and during early panicle developmental stages in comparison to other OsFDs characterised till date. Surprisingly, unlike OsFD1, OsFD7 interacts directly and more efficiently with OsFTLs; the interaction is strongest with OsFTL1 followed by Hd3a and RFT1, as confirmed by FLIM-FRET analysis. Also, OsFD7 is phosphorylated at its C-terminal end by OsCDPK41 and OsCDPK49in vitroand this phosphorylated moiety is recognized by OsGF14 proteins.OsFD7RNAi transgenics were late flowering; the transcript levels of some floral meristem identity genes (e.g.OsMADS14,OsMADS15andOsMADS18) were also down-regulated. It was quite interesting to note that these RNAi lines exhibited dense panicle morphology with increase in the number of primary and secondary branches resulting in longer panicles and more seeds probably due to downregulation ofSepallata(SEP) family genes. In comparison to other FD-like proteins characterized thus far from rice, it appears that OsFD7 may have undergone diversification during evolution resulting in the acquisition of newer functions and thus playing dual role in floral transition and panicle development in rice.HighlightOsbZIP62/OsFD7 interacts with major flowering regulators participating in the processes of floral transition as well as panicle and floral organ development.
Sex, age, tissue, and disease patterns of matrisome expression in GTEx transcriptome data
Authors: Nieuwenhuis Tim O. , Rosenberg Avi Z. , McCall Matthew N. , Halushka Marc K. 
Published: March 2021

AbstractThe extracellular matrix (ECM) has historically been explored through proteomic methods. Whether or not global transcriptomics can yield meaningful information on the human matrisome is unknown. Gene expression data from 17,382 samples across 52 tissues, were obtained from the Genotype-Tissue Expression (GTEx) project. Additional datasets were obtained from The Cancer Genome Atlas (TCGA) program and the Gene Expression Omnibus for comparisons. Gene expression levels generally recapitulated proteome-derived matrisome expression patterns. Further, matrisome gene expression properly clustered tissue types, with some matrisome genes including SERPIN family members having tissue-restricted expression patterns. Deeper analyses revealed 388 genes varied by age and 222 varied by sex in at least one tissue, with expression correlating with digitally imaged histologic tissue features. A comparison of TCGA tumor, TCGA adjacent normal and GTEx normal tissues demonstrated robustness of the GTEx samples as a generalized control, while also determining a common primary tumor matrisome. Additionally, GTEx tissues served as a useful non-diseased control in a separate study of idiopathic pulmonary fibrosis matrix changes. Altogether, these findings indicate that the transcriptome, in general, and GTEx in particular, has value in understanding the state of organ ECM.
Hierarchical semantic composition of biosimulation models using bond graphs
Authors: Shahidi Niloofar , Pan Michael , Safaei Soroush , Tran Kenneth , Crampin Edmund J. , Nickerson David P. 
Published: March 2021

AbstractSimulating complex biological and physiological systems and predicting their behaviours under different conditions remains challenging. Breaking systems into smaller and more manageable modules can address this challenge, assisting both model development and simulation. Nevertheless, existing computational models in biology and physiology are often not modular and therefore difficult to assemble into larger models. Even when this is possible, the resulting model may not be useful due to inconsistencies either with the laws of physics or the physiological behaviour of the system. Here, we propose a general methodology for composing models, combining the energy-based bond graph approach with semantics-based annotations. This approach improves model composition and ensures that a composite model is physically plausible. As an example, we demonstrate this approach to automated model composition using a model of human arterial circulation. The major benefit is that modellers can spend more time on understanding the behaviour of complex biological and physiological systems and less time wrangling with model composition.Author summaryBiological and physiological systems usually involve multiple underlying processes, mechanisms, structures, and phenomena, referred to here as sub-systems. Modelling the whole system every time from scratch requires a huge amount of effort. An alternative is to model each sub-system in a modular fashion,i.e., containing meaningful interfaces for connecting to other modules. Such modules are readily combined to produce a whole-system model. For the combined model to be consistent, modules must be described using the same modelling scheme. One way to achieve this is to use energy-based models that are consistent with the conservation laws of physics. Here, we present an approach that achieves this using bond graphs, which allows modules to be combined faster and more efficiently. First, physically plausible modules are generated using a small number of template modules. Then a meaningful interface is added to each module to automate connection. This approach is illustrated by applying this method to an existing model of the circulatory system and verifying the results against the reference model.
Capturing scientific knowledge in computable form
Authors: Wong Jeffrey V. , Franz Max , Siper Metin Can , Fong Dylan , Durupinar Funda , Dallago Christian , Luna Augustin , Giorgi John , Rodchenkov Igor , Babur Özgün , Bachman John A. , Gyori Benjamin M. , Demir Emek , Bader Gary D. , Sander Chris 
Published: March 2021

ABSTRACTTechnological advances in computing provide major opportunities to accelerate scientific discovery. The wide availability of structured knowledge would allow us to take full advantage of these by enabling efficient human-computer interaction. Traditionally, biological knowledge is captured in publications and knowledge bases, however, the information in articles is not directly accessible to computers, and knowledge bases are constrained by finite resources available for manual curation. To accelerate knowledge capture and communication and to keep pace with the rapid growth of scientific reports, we developed the Biofactoid (biofactoid.org) software suite, which crowdsources structured knowledge in articles from authors. Biofactoid is a web-based system that lets scientists draw a network of interactions between genes, their products, and chemical compounds and employs smart-automation to translate user input into a structured language using the expressive power of a formal ontology. The resulting data is shared via public information resources, enabling author-curated knowledge to be appreciated in the context of all existing computable knowledge. Authors of recently published papers across a range of journals have already contributed their pathway information, much of which is novel and extends existing pathway databases into new biological areas. We envision the adoption of Biofactoid for crowdsourced curation by scientists and publishers as part of an ecosystem of tools that accelerate scientific communication and discovery.AvailabilityBiofactoid server athttps://biofactoid.org
Effects of hyperinsulinemia on pancreatic cancer development and the immune microenvironment revealed through single-cell transcriptomics
Authors: Zhang Anni M.Y. , de Winter Twan J.J. , Wang Su , Flibotte Stephane , Zhao Yiwei Bernie , Hu Xiaoke , Li Hong , Schaeffer David F. , Johnson James D. , Kopp Janel L. 
Published: March 2021

AbstractHyperinsulinemia is independently associated with increased risk and mortality of pancreatic cancer. We recently reported that a ∼50% reduction in pancreatic intraepithelial neoplasia (PanIN) pre-cancerous lesions in mice could be achieved with reduced insulin production. However, only female mice remained normoglycemic and only the gene dosage of rodent-specificIns1alleles was tested in our previous model. Moreover, we did not delve into the molecular and cellular mechanisms associated with modulating hyperinsulinemia. Here, we studied PanIN lesion development in both male and femalePtf1aCreER;KrasLSL-G12Dmice lacking the rodent specificIns1gene, and possessing one or two alleles of the wild-typeIns2gene to modulate insulin production. High-fat diet induced hyperinsulinemia was transiently and modestly reduced, without affecting glucose tolerance, in male and female mice with only one allele ofIns2. Genetic reduction of insulin production resulted in mice with a tendency for less PanIN and acinar-to-ductal metaplasia (ADM) lesions. Using single-cell transcriptomics, we found hyperinsulinemia affected multiple cell types in the pancreas, with the most statistically significant effects on local immune cell populations, which were highly represented in our analysis. Specifically, hyperinsulinemia modulated pathways associated with protein translation, MAPK-ERK signaling, and PI3K-AKT signaling, which were changed in epithelial cells and subsets of immune cells. These data suggest a role for the immune microenvironment in hyperinsulinemia-driven PanIN development. Together with our previous work, we propose that mild suppression of insulin levels may be useful in preventing pancreatic cancer by acting on multiple cell types.
Distinct generation of subjective vividness and confidence during naturalistic memory retrieval in angular gyrus
Authors: Zou Futing , Kwok Sze Chai 
Published: March 2021

AbstractOur subjective experience of remembering guides and monitors the reconstruction of past and simulation of the future, which enables us to identify mistakes and adjust our behavior accordingly. However, it remains incompletely understood what underlies the process of subjective mnemonic experience. Here, we combined behavior, repetitive transcranial magnetic stimulation (rTMS), and functional neuroimaging to probe whether vividness and confidence are generated differently during retrieval. We found that preretrieval rTMS targeting the left angular gyrus (AnG) selectively attenuated the vividness efficiency compared to control stimulation while keeping metacognitive efficiency and objective memory accuracy unaffected. Using trial-wise data, we showed that AnG stimulation altered the mediating role of vividness in confidence in the accuracy of memory judgment. Moreover, resting-state functional connectivity of hippocampus and AnG was specifically associated with vividness efficiency, but not metacognitive efficiency across individuals. Together, these results identify the causal involvement of AnG in gauging the vividness, but not the confidence, of memory, thereby suggesting a differentiation account of conscious assessment of memory by functionally and anatomically dissociating the monitoring of vividness from confidence.
Genomic heterogeneity affects the response to Daylight Saving Time
Authors: Tyler Jonathan , Fang Yu , Goldstein Cathy , Forger Daniel , Sen Srijan , Burmeister Margit 
Published: March 2021

ABSTRACTCircadian rhythms drive the timing of many physiological events in the 24-hour day. When individuals undergo an abrupt external shift (e.g., change in work schedule or travel across multiple time zones), circadian rhythms become misaligned with the new time and may take several days to adjust. Chronic circadian misalignment, e.g., as a result of shift work, has been shown to lead to several physical and mental health problems. Despite the serious health implications of circadian misalignment, relatively little is known about how genetic variation affects an individual’s ability to shift to abrupt external changes. Accordingly, we use the one-hour advance from the onset of daylight saving time (DST) as a natural experiment to comprehensively study how individual heterogeneity affects the shift of sleep-wake rhythms in response to an abrupt external time change. We find that individuals genetically predisposed to a morning tendency adjust to the advance in a few days, while genetically predisposed evening-inclined individuals have not shifted. Observing differential effects by genetic disposition after a one-hour advance underscores the importance of heterogeneity in adaptation to external schedule shifts, and these genetic differences may affect how individuals adjust to jet lag or shift work as well.
A Comparative Analysis of Novel Deep Learning and Ensemble Learning Models to Predict the Allergenicity of Food Proteins
Authors: Wang Liyang , Niu Dantong , Zhao Xinjie , Wang Xiaoya , Hao Mengzhen , Che Huilian 
Published: March 2021

AbstractTraditional food allergen identification mainly relies on in vivo and in vitro experiments, which often needs a long period and high cost. The artificial intelligence (AI)-driven rapid food allergen identification method has solved the above mentioned two drawbacks and is becoming an efficient auxiliary tool. Aiming to overcome the limitations of lower accuracy of traditional machine learning models in predicting the allergenicity of food proteins, this work proposed to introduce deep learning model - transformer with self-attention mechanism, ensemble learning models (representative as Light Gradient Boosting Machine (LightGBM) eXtreme Gradient Boosting (XGBoost)) to solve the problem. In order to highlight the superiority of the proposed novel method, the study also selected various commonly used machine learning models as the baseline classifiers. The results of 5-fold cross-validation showed that the AUC of the deep model was the highest (0.9578), which was better than the ensemble learning and baseline algorithms. But the deep model need to be pre-trained, and the training cost is the highest. By comparing the characteristics of the transformer model and boosting models, it can be analyzed that, each model has its own advantage, which provides novel clues and inspiration for the rapid prediction of food allergens in the future.
Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European range
Authors: Portinha Beatriz , Avril Amaury , Bernasconi Christian , Helanterä Heikki , Monaghan Josie , Seifert Bernhard , Sousa Vitor C. , Kulmuni Jonna , Nouhaud Pierre 
Published: March 2021

AbstractThe application of demographic history modeling and inference to the study of divergence between species is becoming a cornerstone of speciation genomics. The demographic history is usually reconstructed by analysing a single population from each species, assuming that the divergence history inferred between these populations represents the actual speciation history. However, this assumption is rarely explicitly tested, and it may not be met when species diverge with gene flow. For instance, secondary contact between two species after a range expansion may be confined into a specific geographic region. In this study, we tested to what extent the divergence history inferred from two heterospecific populations would vary depending on their geographic locations, using mound-building red wood ants. The wood ant speciesFormica polyctenaandF. aquiloniahave contrasting distributions in Europe and naturally hybridize in Finland. We first performed whole-genome resequencing of 20 individuals sampled in multiple populations across both species ranges. We then reconstructed the divergence histories of distinct heterospecific population pairs using a coalescent-based approach. We found that the analysis of these different population pairs always supported a scenario of divergence with gene flow, suggesting that species divergence started in the Pleistocene (ca. 500 kya) and occurred with continuous asymmetrical gene flow fromF. aquiloniatoF. polyctenauntil a recent time, when migration stopped (2-19 kya, depending on the population pair considered). However, we found support for contemporary gene flow in the sympatric population pair from Finland, where hybrids have been described. Overall, our results suggest that divergence histories reconstructed from a few individuals may be reliable and applicable at the species level. Nonetheless, the geographical context of populations chosen to represent their species should be taken into account, as it may affect estimates of migration rates between species when gene flow is heterogeneous across their geographical ranges.
Metapopulation Structure of Diatom-associated Marine Bacteria
Authors: Qu Liping , Feng Xiaoyuan , Chen Yuerong , Li Lingyu , Wang Xiaojun , Hu Zhong , Wang Hui , Luo Haiwei 
Published: March 2021

AbstractMarine bacteria-phytoplankton interaction ultimately shapes ecosystem productivity. The biochemical mechanisms underlying their interactions become increasingly known, yet how these ubiquitous interactions drive bacterial evolution has not been illustrated. Here, we sequenced genomes of 294 bacterial isolates associated with 19 coexisting diatom cells. These bacteria constitute eight genetically monomorphic populations of the globally abundant Roseobacter group. Six of these populations are members ofSulfitobacter, arguably the most prevalent bacteria associated with marine diatoms. A key finding is that populations varying at the intra-specific level have been differentiated and each are either associated with a single diatom host or with multiple hosts not overlapping with those of other populations. These closely related populations further show functional differentiation; they differ in motility phenotype and they harbor distinct types of secretion systems with implication for mediating organismal interactions. This interesting host-dependent population structure is even evident for demes within a genetically monomorphic population but each associated with a distinct diatom cell, as shown by a greater similarity in genome content between isolates from the same host compared to those from different hosts. Importantly, the intra- and inter-population differentiation pattern remains when the analyses are restricted to isolates from intra-specific diatom hosts, ruling out distinct selective pressures and instead suggesting coexisting microalgal cells as physical barriers of bacterial gene flow. Taken together, microalgae-associated bacteria display a unique microscale metapopulation structure, which consists of numerous small populations whose evolution is driven by random genetic drift.