bluuebunny/crossref_metadata_2025_split huggingface dataset:
ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements
Authors: Liu Meng , Liu Jialin , Liu Guitian , Wang Hui , Wang Xiaoli , Deng Zixin , He Yongqun , Ou Hong-Yu 
Published: January 2022

AbstractBacterial integrative and conjugative elements (ICEs) are highly modular mobile genetic elements critical to the horizontal transfer of antibiotic resistance and virulence factor genes. To better understand and analyze the ongoing increase of ICEs, we developed an Integrative and Conjugative Element Ontology (ICEO) to represent the gene components, functional modules, and other information of experimentally verified ICEs. ICEO is aligned with the upper-level Basic Formal Ontology and reuses existing reliable ontologies. There are 31,081 terms, including 26,814 classes from 14 ontologies and 4128 ICEO-specific classes, representing the information of 271 known experimentally verified ICEs from 235 bacterial strains in ICEO currently and 311 predicted ICEs of 272 completely sequenced Klebsiella pneumoniae strains. Three ICEO use cases were illustrated to investigate complex joins of ICEs and their harboring antibiotic resistance or virulence factor genes by using SPARQL or DL query. ICEO has been approved as an Open Biomedical Ontology library ontology. It may be dedicated to facilitating systematical ICE knowledge representation, integration, and computer-assisted queries.
Trilled /r/ is associated with roughness, linking sound and touch across spoken languages
Authors: Winter Bodo , Sóskuthy Márton , Perlman Marcus , Dingemanse Mark 
Published: January 2022

AbstractCross-modal integration between sound and texture is important to perception and action. Here we show this has repercussions for the structure of spoken languages. We present a new statistical universal linking speech with the evolutionarily ancient sense of touch. Words that express roughness—the primary perceptual dimension of texture—are highly likely to feature a trilled /r/, the most commonly occurring rhotic consonant. In four studies, we show the pattern to be extremely robust, being the first widespread pattern of iconicity documented not just across a large, diverse sample of the world’s spoken languages, but also across numerous sensory words within languages. Our deep analysis of Indo-European languages and Proto-Indo-European roots indicates remarkable historical stability of the pattern, which appears to date back at least 6000 years.
Motor cortex plasticity response to acute cardiorespiratory exercise and intermittent theta-burst stimulation is attenuated in premanifest and early Huntington’s disease
Authors: Andrews Sophie C. , Curtin Dylan , Coxon James P. , Stout Julie C. 
Published: January 2022

AbstractHuntington’s disease (HD) mouse models suggest that cardiovascular exercise may enhance neuroplasticity and delay disease signs, however, the effects of exercise on neuroplasticity in people with HD are unknown. Using a repeated-measures experimental design, we compared the effects of a single bout of high-intensity exercise, moderate-intensity exercise, or rest, on motor cortex synaptic plasticity in 14 HD CAG-expanded participants (9 premanifest and 5 early manifest) and 20 CAG-healthy control participants, using transcranial magnetic stimulation. Measures of cortico-motor excitability, short-interval intracortical inhibition and intracortical facilitation were obtained before and after a 20-min bout of either high-intensity interval exercise, moderate-intensity continuous exercise, or rest, and again after intermittent theta burst stimulation (iTBS). HD participants showed less inhibition at baseline compared to controls. Whereas the control group showed increased excitability and facilitation following high-intensity exercise and iTBS, the HD group showed no differences in neuroplasticity responses following either exercise intensity or rest, with follow-up Bayesian analyses providing consistent evidence that these effects were absent in the HD group. These findings indicate that exercise-induced synaptic plasticity mechanisms in response to acute exercise may be attenuated in HD, and demonstrate the need for future research to further investigate exercise and plasticity mechanisms in people with HD.
Application of ensemble machine learning algorithms on lifestyle factors and wearables for cardiovascular risk prediction
Authors: Huang Weiting , Ying Tan Wei , Chin Woon Loong Calvin , Baskaran Lohendran , Marcus Ong Eng Hock , Yeo Khung Keong , Kiong Ng See 
Published: January 2022

AbstractThis study looked at novel data sources for cardiovascular risk prediction including detailed lifestyle questionnaire and continuous blood pressure monitoring, using ensemble machine learning algorithms (MLAs). The reference conventional risk score compared against was the Framingham Risk Score (FRS). The outcome variables were low or high risk based on calcium score 0 or calcium score 100 and above. Ensemble MLAs were built based on naive bayes, random forest and support vector classifier for low risk and generalized linear regression, support vector regressor and stochastic gradient descent regressor for high risk categories. MLAs were trained on 600 Southeast Asians aged 21 to 69 years free of cardiovascular disease. All MLAs outperformed the FRS for low and high-risk categories. MLA based on lifestyle questionnaire only achieved AUC of 0.715 (95% CI 0.681, 0.750) and 0.710 (95% CI 0.653, 0.766) for low and high risk respectively. Combining all groups of risk factors (lifestyle survey questionnaires, clinical blood tests, 24-h ambulatory blood pressure and heart rate monitoring) along with feature selection, prediction of low and high CVD risk groups were further enhanced to 0.791 (95% CI 0.759, 0.822) and 0.790 (95% CI 0.745, 0.836). Besides conventional predictors, self-reported physical activity, average daily heart rate, awake blood pressure variability and percentage time in diastolic hypertension were important contributors to CVD risk classification.
Comparative assessment and novel strategy on methods for imputing proteomics data
Authors: Shen Minjie , Chang Yi-Tan , Wu Chiung-Ting , Parker Sarah J. , Saylor Georgia , Wang Yizhi , Yu Guoqiang , Van Eyk Jennifer E. , Clarke Robert , Herrington David M. , Wang Yue 
Published: January 2022

AbstractMissing values are a major issue in quantitative proteomics analysis. While many methods have been developed for imputing missing values in high-throughput proteomics data, a comparative assessment of imputation accuracy remains inconclusive, mainly because mechanisms contributing to true missing values are complex and existing evaluation methodologies are imperfect. Moreover, few studies have provided an outlook of future methodological development. We first re-evaluate the performance of eight representative methods targeting three typical missing mechanisms. These methods are compared on both simulated and masked missing values embedded within real proteomics datasets, and performance is evaluated using three quantitative measures. We then introduce fused regularization matrix factorization, a low-rank global matrix factorization framework, capable of integrating local similarity derived from additional data types. We also explore a biologically-inspired latent variable modeling strategy—convex analysis of mixtures—for missing value imputation and present preliminary experimental results. While some winners emerged from our comparative assessment, the evaluation is intrinsically imperfect because performance is evaluated indirectly on artificial missing or masked values not authentic missing values. Nevertheless, we show that our fused regularization matrix factorization provides a novel incorporation of external and local information, and the exploratory implementation of convex analysis of mixtures presents a biologically plausible new approach.
Intracellular translocation of HMGB1 is important for Zika virus replication in Huh7 cells
Authors: Chin Kim-Ling , Zainal Nurhafiza , Sam Sing-Sin , Hassandarvish Pouya , Lani Rafidah , AbuBakar Sazaly 
Published: January 2022

AbstractNeonatal microcephaly and adult Guillain–Barré syndrome are severe complications of Zika virus (ZIKV) infection. The robustly induced inflammatory cytokine expressions in ZIKV-infected patients may constitute a hallmark for severe disease. In the present study, the potential role of high mobility group box 1 protein (HMGB1) in ZIKV infection was investigated. HMGB1 protein expression was determined by the enzyme-linked immunosorbent assay (ELISA) and immunoblot assay. HMGB1’s role in ZIKV infection was also explored using treatment with dexamethasone, an immunomodulatory drug, and HMGB1-knockdown (shHMGB1) Huh7 cells. Results showed that the Huh7 cells were highly susceptible to ZIKV infection. The infection was found to induce HMGB1 nuclear-to-cytoplasmic translocation, resulting in a > 99% increase in the cytosolic HMGB1 expression at 72-h post-infection (h.p.i). The extracellular HMGB1 level was elevated in a time- and multiplicity of infection (MOI)-dependent manner. Treatment of the ZIKV-infected cells with dexamethasone (150 µM) reduced HMGB1 extracellular release in a dose-dependent manner, with a maximum reduction of 71 ± 5.84% (P < 0.01). The treatment also reduced virus titers by over 83 ± 0.50% (P < 0.01). The antiviral effects, however, were not observed in the dexamethasone-treated shHMGB1 cells. These results suggest that translocation of HMGB1 occurred during ZIKV infection and inhibition of the translocation by dexamethasone coincided with a reduction in ZIKV replication. These findings highlight the potential of targeting the localization of HMGB1 in affecting ZIKV infection.
Thermal excitation signals in the inhomogeneous warm dense electron gas
Authors: Moldabekov Zhandos A. , Dornheim Tobias , Cangi Attila 
Published: January 2022

AbstractWe investigate the emergence of electronic excitations from the inhomogeneous electronic structure at warm dense matter parameters based on first-principles calculations. The emerging modes are controlled by the imposed perturbation amplitude. They include satellite signals around the standard plasmon feature, transformation of plasmons to optical modes, and double-plasmon modes. These modes exhibit a pronounced dependence on the temperature. This makes them potentially invaluable for the diagnostics of plasma parameters in the warm dense matter regime. We demonstrate that these modes can be probed with present experimental techniques.
The impact of control and mitigation strategies during the second wave of coronavirus infections in Spain and Italy
Authors: De Nadai Marco , Roomp Kristof , Lepri Bruno , Oliver Nuria 
Published: January 2022

AbstractEuropean countries struggled to fight against the second and the third waves of the COVID-19 pandemic, as the Test-Trace-Isolate (TTI) strategy widely adopted over the summer and early fall 2020 failed to contain the spread of the disease effectively. This paper sheds light on the effectiveness of such a strategy in two European countries (Spain and Italy) by analysing data from June to December 2020, collected via a large-scale online citizen survey with 95,251 and 43,393 answers in Spain and Italy, respectively. Our analysis describes several weaknesses in each of the three pillars of the TTI strategy: Test, Trace, and Isolate. We find that 40% of respondents had to wait more than 48 hours to obtain coronavirus tests results, while literature has shown that a delay of more than one day might make tracing all cases inefficient. We also identify limitations in the manual contact tracing capabilities in both countries, as only 29% of respondents in close contact with a confirmed infected individual reported having been contact traced. Moreover, our analysis shows that more than 45% of respondents report being unable to self-isolate if needed. We also analyse the mitigation strategies deployed to contain the second wave of coronavirus. We find that these interventions were particularly effective in Italy, where close contacts were reduced by more than 20% in the general population. Finally, we analyse the participants’ perceptions about the coronavirus risk associated with different daily activities. We observe that they are often gender- and age-dependent, and not aligned with the actual risk identified by the literature. This finding emphasises the importance of deploying public-health communication campaigns to debunk misconceptions about SARS-CoV-2. Overall, our work illustrates the value of online citizen surveys to quickly and efficiently collect large-scale population data to support and evaluate policy decisions to combat the spread of infectious diseases, such as coronavirus.
Cluster analysis integrating age and body temperature for mortality in patients with sepsis: a multicenter retrospective study
Authors: Baek Moon Seong , Kim Jong Ho , Kwon Young Suk 
Published: January 2022

AbstractIt is not clear whether mortality is associated with body temperature (BT) in older sepsis patients. This study aimed to evaluate the mortality rates in sepsis patients according to age and BT and identify the risk factors for mortality. We investigated the clusters using a machine learning method based on a combination of age and BT, and identified the mortality rates according to these clusters. This retrospective multicenter study was conducted at five hospitals in Korea. Data of sepsis patients aged ≥ 18 years who were admitted to the intensive care unit between January 1, 2011 and April 30, 2021 were collected. BT was divided into three groups (hypothermia < 36 °C, normothermia 36‒38 °C, and hyperthermia > 38 °C), and age groups were divided using a 75-year age threshold. Kaplan‒Meier analysis was performed to assess the cumulative mortality over 90 days. A K-means clustering algorithm using age and BT was used to characterize phenotypes. During the study period, 15,574 sepsis patients were enrolled. Overall, 90-day mortality was 20.5%. Kaplan‒Meier survival analyses demonstrated that 90-day mortality rates were 27.4%, 19.6%, and 11.9% in the hypothermia, normothermia, and hyperthermia groups, respectively, in those ≥ 75 years old (Log-rank p < 0.001). Cluster analysis demonstrated three groups: Cluster A (relatively older age and lower BT), Cluster B (relatively younger age and wide range of BT), and Cluster C (relatively higher BT than Cluster A). Kaplan‒Meier curve analysis showed that the 90-day mortality rates of Cluster A was significantly higher than those of Clusters B and C (24.2%, 17.1%, and 17.0%, respectively; Log-rank p < 0.001). The 90-day mortality rate correlated inversely with BT groups among sepsis patients in either age group (< 75 and ≥ 75 years). Clustering analysis revealed that the mortality rate was higher in the cluster of patients with relatively older age and lower BT.
Strong and widespread cycloheximide resistance in Stichococcus-like eukaryotic algal taxa
Authors: Syuhada Nur Hidayu , Merican Faradina , Zaki Syazana , Broady Paul A. , Convey Peter , Muangmai Narongrit 
Published: January 2022

AbstractThis study was initiated following the serendipitous discovery of a unialgal culture of a Stichococcus-like green alga (Chlorophyta) newly isolated from soil collected on Signy Island (maritime Antarctica) in growth medium supplemented with 100 µg/mL cycloheximide (CHX, a widely used antibiotic active against most eukaryotes). In order to test the generality of CHX resistance in taxa originally identified as members of Stichococcus (the detailed taxonomic relationships within this group of algae have been updated since our study took place), six strains were studied: two strains isolated from recent substrate collections from Signy Island (maritime Antarctica) (“Antarctica” 1 and “Antarctica” 2), one isolated from this island about 50 years ago (“Antarctica” 3) and single Arctic (“Arctic”), temperate (“Temperate”) and tropical (“Tropical”) strains. The sensitivity of each strain towards CHX was compared by determining the minimum inhibitory concentration (MIC), and growth rate and lag time when exposed to different CHX concentrations. All strains except “Temperate” were highly resistant to CHX (MIC > 1000 µg/mL), while “Temperate” was resistant to 62.5 µg/mL (a concentration still considerably greater than any previously reported for algae). All highly resistant strains showed no significant differences in growth rate between control and treatment (1000 µg/mL CHX) conditions. Morphological examination suggested that four strains were consistent with the description of the species Stichococcus bacillaris while the remaining two conformed to S. mirabilis. However, based on sequence analyses and the recently available phylogeny, only one strain, “Temperate”, was confirmed to be S. bacillaris, while “Tropical” represents the newly erected genus Tetratostichococcus, “Antarctica 1” Tritostichococcus, and “Antarctica 2”, “Antarctica 3” and “Arctic” Deuterostichococcus. Both phylogenetic and CHX sensitivity analyses suggest that CHX resistance is potentially widespread within this group of algae.
Tumor radioresistance caused by radiation-induced changes of stem-like cell content and sub-lethal damage repair capability
Authors: Fukui Roman , Saga Ryo , Matsuya Yusuke , Tomita Kazuo , Kuwahara Yoshikazu , Ohuchi Kentaro , Sato Tomoaki , Okumura Kazuhiko , Date Hiroyuki , Fukumoto Manabu , Hosokawa Yoichiro 
Published: January 2022

AbstractCancer stem-like cells (CSCs) within solid tumors exhibit radioresistance, leading to recurrence and distant metastasis after radiotherapy. To experimentally study the characteristics of CSCs, radioresistant cell lines were successfully established using fractionated X-ray irradiation. The fundamental characteristics of CSCs in vitro have been previously reported; however, the relationship between CSC and acquired radioresistance remains uncertain. To efficiently study this relationship, we performed both in vitro experiments and theoretical analysis using a cell-killing model. Four types of human oral squamous carcinoma cell lines, non-radioresistant cell lines (SAS and HSC2), and radioresistant cell lines (SAS-R and HSC2-R), were used to measure the surviving fraction after single-dose irradiation, split-dose irradiation, and multi-fractionated irradiation. The SAS-R and HSC2-R cell lines were more positive for one of the CSC marker aldehyde dehydrogenase activity than the corresponding non-radioresistant cell lines. The theoretical model analysis showed that changes in both the experimental-based ALDH (+) fractions and DNA repair efficiency of ALDH (−) fractions (i.e., sub-lethal damage repair) are required to reproduce the measured cell survival data of non-radioresistant and radioresistant cell lines. These results suggest that the enhanced cell recovery in SAS-R and HSC2-R is important when predicting tumor control probability in radiotherapy to require a long dose-delivery time; in other words, intensity-modulated radiation therapy is ideal. This work provides a precise understanding of the mechanism of radioresistance, which is induced after irradiation of cancer cells.
Barriers to Equity in Pediatric Hearing Health Care: A Review of the Evidence
Authors: Kingsbury Sarah , Khvalabov Nicole , Stirn Jonathan , Held Cara , Fleckenstein Stephanie M. , Hendrickson Kristi , Walker Elizabeth A. 
Published: January 2022

Purpose:
We review the evidence regarding barriers to hearing health care for children who are deaf or hard of hearing.

Background:
There are considerable data to suggest that hearing health care disparities constitute a major factor in loss to follow-up or documentation for children going through the Early Hearing Detection and Intervention process. Families are affected by a combination of factors underlying these disparities, resulting in delayed care and suboptimal developmental outcomes for children who are deaf or hard of hearing.

Conclusions:
To address the socioeconomic, cultural, and linguistic inequities seen in the diagnosis and management of childhood hearing loss, pediatric audiologists and speech-language pathologists have a responsibility to provide culturally responsive practice to their individual clients and their families, as well as advocate for substantive changes at the policy level that impact their clients' daily lives.
Without detection: Two‐step clustering features with local–global attention for image captioning
Authors: Li Xuan , Zhang Wenkai , Sun Xian , Gao Xin 
Published: January 2022

AbstractThe current image captioning methods usually integrate an object detection network to obtain image features at the level of objects and other salient regions. However, the detection network needs to be independently pre‐trained on additional data. Thus, mainly due to the demand for extra training data and computing resources, the detection network's utilization will impose higher training costs on the overall captioning model. In this work, the authors propose a local–global attention model based on two‐step clustering features for image captioning. The two‐step clustering features can be obtained at a relatively low cost and have the presentation ability in objects or other salient image regions. To make the model perceive the image better, the authors introduce a novel local–global attention mechanism. The model will analyse the clustering features from local perspectives to global ones at each time step, making the model better understand the image contents. The authors evaluate the proposed method on the MSCOCO test server, achieving BLEU‐4/METEOR/ROUGE‐L scores of 36.8, 27.4, and 57.2, respectively. With the benefit of reducing training costs, the authors' model also achieves closing results compared with the models using detection features.
Occasional paternal inheritance of the germline-restricted chromosome in songbirds
Authors: Pei Yifan , Forstmeier Wolfgang , Ruiz-Ruano Francisco J. , Mueller Jakob C. , Cabrero Josefa , Camacho Juan Pedro M. , Alché Juan D. , Franke Andre , Hoeppner Marc , Börno Stefan , Gessara Ivana , Hertel Moritz , Teltscher Kim , Knief Ulrich , Suh Alexander , Kempenaers Bart 
Published: January 2022

SignificanceMost if not all songbirds possess a germline-restricted chromosome (GRC) which is believed to be exclusively maternally inherited. However, we show that, in the zebra finch, the GRC can also be paternally inherited and that the potential for paternal inheritance may differ between families. We further show that the genetic diversity of the GRC is extremely reduced compared to the high diversity of mitochondrial DNA lineages, suggesting that a single GRC haplotype has spread through the Australian zebra finch population relatively recently via occasional paternal inheritance. Our study therefore suggests that the GRC has the potential to evolve in a selfish manner, which could result in intragenomic conflict.
Pathogenic TNF-α drives peripheral nerve inflammation in an Aire-deficient model of autoimmunity
Authors: Wang Yan , Guo Lily , Yin Xihui , McCarthy Ethan C. , Cheng Mandy I. , Hoang Aline T. , Chen Ho-Chung , Patel Anushi Y. , Allard Trout Denise , Xu Erin , Yakobian Natalie , Hugo Willy , Howard James F. , Sheu Katherine M. , Hoffmann Alexander , Lechner Melissa G. , Su Maureen A. 
Published: January 2022

Significance
GBS and CIDP are autoimmune disorders of the PNS that can be debilitating and even life threatening. Current therapies, which include corticosteroids and intravenous gammaglobulin, have poorly defined mechanisms of action and are ineffective in a fraction of patients. To identify more specific therapeutic targets, we used single-cell RNA sequencing to analyze immune cells in nerves during autoimmune attack. This analysis revealed a previously unappreciated TNFα cell–cell communication pathway that recruits and activates multiple immune cell types. Moreover, we show that TNF-α signaling is an essential feature of PNS autoimmunity, since ablating TNF-α signaling protects against disease. These findings suggest that anti–TNF-α agents, which are already used to treat other inflammatory diseases, should be considered for inflammatory neuropathies.