bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial transmission network construction of influenza-like illness using dynamic Bayesian network and vector-autoregressive moving average model
Authors: Qiu Jianqing , Wang Huimin , Hu Lin , Yang Changhong , Zhang Tao 
Published: February 2021

Abstract
Background
Although vaccination is one of the main countermeasures against influenza epidemic, it is highly essential to make informed prevention decisions to guarantee that limited vaccination resources are allocated to the places where they are most needed. Hence, one of the fundamental steps for decision making in influenza prevention is to characterize its spatio-temporal trend, especially on the key problem about how influenza transmits among adjacent places and how much impact the influenza of one place could have on its neighbors. To solve this problem while avoiding too much additional time-consuming work on data collection, this study proposed a new concept of spatio-temporal route as well as its estimation methods to construct the influenza transmission network.

Methods
The influenza-like illness (ILI) data of Sichuan province in 21 cities was collected from 2010 to 2016. A joint pattern based on the dynamic Bayesian network (DBN) model and the vector autoregressive moving average (VARMA) model was utilized to estimate the spatio-temporal routes, which were applied to the two stages of learning process respectively, namely structure learning and parameter learning. In structure learning, the first-order conditional dependencies approximation algorithm was used to generate the DBN, which could visualize the spatio-temporal routes of influenza among adjacent cities and infer which cities have impacts on others in influenza transmission. In parameter learning, the VARMA model was adopted to estimate the strength of these impacts. Finally, all the estimated spatio-temporal routes were put together to form the final influenza transmission network.

Results
The results showed that the period of influenza transmission cycle was longer in Western Sichuan and Chengdu Plain than that in Northeastern Sichuan, and there would be potential spatio-temporal routes of influenza from bordering provinces or municipalities into Sichuan province. Furthermore, this study also pointed out several estimated spatio-temporal routes with relatively high strength of associations, which could serve as clues of hot spot areas detection for influenza surveillance.

Conclusions
This study proposed a new framework for exploring the potentially stable spatio-temporal routes between different places and measuring specific the sizes of transmission effects. It could help making timely and reliable prediction of the spatio-temporal trend of infectious diseases, and further determining the possible key areas of the next epidemic by considering their neighbors’ incidence and the transmission relationships.
Cognitive functioning in Deaf children using Cochlear implants
Authors: Almomani Fidaa , Al-momani Murad O. , Garadat Soha , Alqudah Safa , Kassab Manal , Hamadneh Shereen , Rauterkus Grant , Gans Richard 
Published: February 2021

AbstractBackgroundCognitive abilities like language, memory, reasoning, visualization, and perceptual functioning shape human action and are considered critical to the successful interaction with the environment. Alternatively, hearing loss can disrupt a child’s ability to communicate, and negatively impact cognitive development. Cochlear implants (CI) restore auditory input thereby supporting communication and may enhance cognitive performance. This study compares general cognitive development after cochlear implantation (2017–2019) in two groups of Jordanian children implanted earlier (age:4–6 years,N = 22) and later (7–9 years,N = 16) to the development of randomly selected normal hearing peers (N = 48).DesignVisualization, reasoning, memory, and attention were assessed using the Leiter-R scale at baseline (before implantation), 8 months and 16 months post implantation for children with hearing loss. Same times of testing (baseline, 8 months and 16 months) were used for normal hearing peers.ResultsOver the 16-month period, the cognitive improvement of 4–6-year-old deaf children was greater than that of their normal hearing peers on the scales of visualization (5.62 vs. 4.40), reasoning (2.53 vs. 2.38) and memory (17.19 vs. 11.67). while the improvement of 7–9-year-old was less major than that of their normal hearing peers on all scales.ConclusionsThese results suggest that CI not only enhances communication skills but may improve cognitive functioning in deaf children. However, the extent of this improvement was dependent on age at intervention; current results demonstrated that the children received CI at young ages had better cognitive improvements.
Assessment of assumptions underlying models of prokaryotic pangenome evolution
Authors: Sela Itamar , Wolf Yuri I. , Koonin Eugene V. 
Published: February 2021

Abstract
Background
The genomes of bacteria and archaea evolve by extensive loss and gain of genes which, for any group of related prokaryotic genomes, result in the formation of a pangenome with the universal, asymmetrical U-shaped distribution of gene commonality. However, the evolutionary factors that define the specific shape of this distribution are not thoroughly understood.

Results
We investigate the fit of simple models of genome evolution to the empirically observed gene commonality distributions and genome intersections for 33 groups of closely related bacterial genomes. A model with an infinite external gene pool available for gene acquisition and constant genome size (IGP-CGS model), and two gene turnover rates, one for slow- and the other one for fast-evolving genes, allows two approaches to estimate the parameters for gene content dynamics. One is by fitting the model prediction to the distribution of the number of genes shared by precisely k genomes (gene commonality distribution) and another by analyzing the distribution of the number of genes common for k genome sets (k-cores). Both approaches produce a comparable overall quality of fit, although the former significantly overestimates the number of the universally conserved genes, while the latter overestimates the number of singletons. We further explore the effect of dropping each of the assumptions of the IGP-CGS model on the fit to the gene commonality distributions and show that models with either a finite gene pool or unequal rates of gene loss and gain (greater gene loss rate) eliminate the overestimate of the number of singletons or the core genome size.

Conclusions
We examine the assumptions that are usually adopted for modeling the evolution of the U-shaped gene commonality distributions in prokaryote genomes, namely, those of infinitely many genes and constant genome size. The combined analysis of genome intersections and gene commonality suggests that at least one of these assumptions is invalid. The violation of both these assumptions reflects the limited ability of prokaryotes to gain new genes. This limitation seems to stem, at least partly, from the horizontal gene transfer barrier, i.e., the cost of accommodation of foreign genes by prokaryotes. Further development of models taking into account the complexity of microbial evolution is necessary for an improved understanding of the evolution of prokaryotes.
Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly
Authors: Chakraborty Mahul , Ramaiah Arunachalam , Adolfi Adriana , Halas Paige , Kaduskar Bhagyashree , Ngo Luna Thanh , Jayaprasad Suvratha , Paul Kiran , Whadgar Saurabh , Srinivasan Subhashini , Subramani Suresh , Bier Ethan , James Anthony A. , Emerson J. J. 
Published: February 2021

Abstract
Background
The mosquito Anopheles stephensi is a vector of urban malaria in Asia that recently invaded Africa. Studying the genetic basis of vectorial capacity and engineering genetic interventions are both impeded by limitations of a vector’s genome assembly. The existing assemblies of An. stephensi are draft-quality and contain thousands of sequence gaps, potentially missing genetic elements important for its biology and evolution.

Results
To access previously intractable genomic regions, we generated a reference-grade genome assembly and full transcript annotations that achieve a new standard for reference genomes of disease vectors. Here, we report novel species-specific transposable element (TE) families and insertions in functional genetic elements, demonstrating the widespread role of TEs in genome evolution and phenotypic variation. We discovered 29 previously hidden members of insecticide resistance genes, uncovering new candidate genetic elements for the widespread insecticide resistance observed in An. stephensi. We identified 2.4 Mb of the Y chromosome and seven new male-linked gene candidates, representing the most extensive coverage of the Y chromosome in any mosquito. By tracking full-length mRNA for > 15 days following blood feeding, we discover distinct roles of previously uncharacterized genes in blood metabolism and female reproduction. The Y-linked heterochromatin landscape reveals extensive accumulation of long-terminal repeat retrotransposons throughout the evolution and degeneration of this chromosome. Finally, we identify a novel Y-linked putative transcription factor that is expressed constitutively throughout male development and adulthood, suggesting an important role.

Conclusion
Collectively, these results and resources underscore the significance of previously hidden genomic elements in the biology of malaria mosquitoes and will accelerate the development of genetic control strategies of malaria transmission.
Socioeconomic inequalities in primary-care and specialist physician visits: a systematic review
Authors: Lueckmann Sara Lena , Hoebel Jens , Roick Julia , Markert Jenny , Spallek Jacob , von dem Knesebeck Olaf , Richter Matthias 
Published: February 2021

Abstract
Background
Utilization of primary-care and specialist physicians seems to be associated differently with socioeconomic status (SES). This review aims to summarize and compare the evidence on socioeconomic inequalities in consulting primary-care or specialist physicians in the general adult population in high-income countries.

Methods
We carried out a systematic search across the most relevant databases (Web of Science, Medline) and included all studies, published since 2004, reporting associations between SES and utilization of primary-care and/or specialist physicians. In total, 57 studies fulfilled the eligibility criteria.

Results
Many studies found socioeconomic inequalities in physician utilization, but inequalities were more pronounced in visiting specialists than primary-care physicians. The results of the studies varied strongly according to the operationalization of utilization, namely whether a physician was visited (probability) or how often a physician was visited (frequency). For probabilities of visiting primary-care physicians predominantly no association with SES was found, but frequencies of visits were higher in the most disadvantaged. The most disadvantaged often had lower probabilities of visiting specialists, but in many studies no link was found between the number of visits and SES.

Conclusion
This systematic review emphasizes that inequalities to the detriment of the most deprived is primarily a problem in the probability of visiting specialist physicians. Healthcare policy should focus first off on effective access to specialist physicians in order to tackle inequalities in healthcare.

PROSPERO registration number
CRD42019123222.
The burden of cycling-related trauma to the orthopaedic and trauma department of a level 1 trauma hospital in Adelaide, South Australia
Authors: Abrahams John M. , Sagar Christopher , Rickman Mark 
Published: February 2021

Abstract
Background
With the fourth largest metropolitan population density, motor vehicle drivers in Adelaide, South Australia, record the most number of motor vehicle insurance claims in Australia. Previous studies have shown a rise in cycling-related emergency department presentations from 2005 to 2010. There is no specific data available specifically related to South Australia. Our institution is the largest level 1 trauma centre in South Australia and Northern Territory and has a local geographic pool of the central metropolitan region of Adelaide.
The aims of this study were to establish the demographics of cycling-related presentations to our institution that involved the admission of a patient under the Orthopaedic and Trauma service. Secondary aims were to investigate whether there were any common variables among these presentations that could be modified to prevent or reduce the morbidity of cycling-related trauma.

Methods
A prospective study was performed at our institution from 1 March 2018 until 31 December 2019 of all inpatient admissions under the Orthopaedics and Trauma department, where the patient was injured as a cyclist. We collated patient-reported information about the accident and their cycling habits.

Results
One hundred and ten patients were included in the study. One hundred and thirty-one injuries were recorded, requiring 89 surgical procedures. Eighty were upper limb injuries (61%), 49 were lower limb (37%), and 2 injuries occurred in either the spine or ribs. The most common reason for the accident was excessive cyclist speed.

Conclusions
The majority of cyclists admitted to our unit with orthopaedic injuries were male patients who assessed themselves as experienced riders, and yet still were involved in accidents that resulted predominantly from episodes of poor judgement. Speed is a common and avoidable factor involved in the presentation of orthopaedic-related trauma to the public system. Involvement of other vehicles was relatively uncommon, as was poor weather; upper limb injuries predominate in this group.
Factors affecting thyroid nodule fine needle aspiration non‐diagnostic rates: a retrospective association study of 1975 thyroid biopsies
Authors: Houdek Devon , Cooke-Hubley Sandra , Puttagunta Lakshmi , Morrish Donald 
Published: February 2021

AbstractBackgroundThyroid nodules are common in clinical practice, and it is important to distinguish benign nodules, the vast majority, from malignant ones. Non-diagnostic (ND) samples have the potential to delay or mis-diagnose or lead to unnecessary surgeries, and it is important to examine what factors influence the ND rate. Prior literature has suggested that the impact of bedside cytology on ND rate is dependent on the initial adequacy rate, whereby higher ND rates benefit most from bedside cytology. We aim to compare the impact of bedside adequacy review between specialist groups who perform high volume thyroid biopsies with low initial ND rates.MethodsWe reviewed the cytopathology results of 1975 thyroid nodule FNAs performed between January 1, 2017 to December 31, 2017 in a multi-centre Canadian city, and the corresponding histopathology reports of 340 resected nodules. Descriptive variables were used to describe the data along with chi-squared testing and univariate logistic regression.ResultsThe FNA biopsies were performed by three different speciality groups, which differed by procedural volume: radiology performed the most at 1171, pathology performed 655 and surgery performed 103. We could not define the operator for 45 of the nodules. The ND rate was lowest in the speciality groups with highest procedural volume, 3.4 % in pathology and 8.3 % in radiology, compared to 37.9 % in surgery (p < 0.001). Completion of bedside cytology rapid onsite evaluation (ROSE) significantly reduced the ND rate from 16.7 to 4.2 % for all samples (p < 0.001). When ROSE was compared with non-ROSE within a high procedural group (radiology), it further reduced the ND rate from 12.5 to 5.1 % (p < 0.001). Of the 340 resected nodules, 10.7 % (18) were in the ND category, of which 28 % (5/18) of these were found to be malignant (4 papillary carcinoma and 1 lymphoma).ConclusionsThe results from this study demonstrate that thyroid FNAs performed with bedside ROSE can significantly reduce the ND rate compared with non-ROSE, even in experienced groups with low initial ND rates. It is therefore imperative that care providers managing patients with thyroid nodules ensure that thyroid FNAs are referred to specialized individuals/groups who do high volume, and ideally with the use of bedside ROSE, whether provided by a cytotechnologist or a pathologist.
Molecular analyses of triple-negative breast cancer in the young and elderly
Authors: Aine Mattias , Boyaci Ceren , Hartman Johan , Häkkinen Jari , Mitra Shamik , Campos Ana Bosch , Nimeus Emma , Ehinger Anna , Vallon-Christersson Johan , Borg Åke , Staaf Johan 
Published: February 2021

Abstract
Background
Breast cancer in young adults has been implicated with a worse outcome. Analyses of genomic traits associated with age have been heterogenous, likely because of an incomplete accounting for underlying molecular subtypes. We aimed to resolve whether triple-negative breast cancer (TNBC) in younger versus older patients represent similar or different molecular diseases in the context of genetic and transcriptional subtypes and immune cell infiltration.

Patients and methods
In total, 237 patients from a reported population-based south Swedish TNBC cohort profiled by RNA sequencing and whole-genome sequencing (WGS) were included. Patients were binned in 10-year intervals. Complimentary PD-L1 and CD20 immunohistochemistry and estimation of tumor-infiltrating lymphocytes (TILs) were performed. Cases were analyzed for differences in patient outcome, genomic, transcriptional, and immune landscape features versus age at diagnosis. Additionally, 560 public WGS breast cancer profiles were used for validation.

Results
Median age at diagnosis was 62 years (range 26–91). Age was not associated with invasive disease-free survival or overall survival after adjuvant chemotherapy. Among the BRCA1-deficient cases (82/237), 90% were diagnosed before the age of 70 and were predominantly of the basal-like subtype. In the full TNBC cohort, reported associations of patient age with changes in Ki67 expression, PIK3CA mutations, and a luminal androgen receptor subtype were confirmed. Within DNA repair deficiency or gene expression defined molecular subgroups, age-related alterations in, e.g., overall gene expression, immune cell marker gene expression, genetic mutational and rearrangement signatures, amount of copy number alterations, and tumor mutational burden did, however, not appear distinct. Similar non-significant associations for genetic alterations with age were obtained for other breast cancer subgroups in public WGS data. Consistent with age-related immunosenescence, TIL counts decreased linearly with patient age across different genetic TNBC subtypes.

Conclusions
Age-related alterations in TNBC, as well as breast cancer in general, need to be viewed in the context of underlying genomic phenotypes. Based on this notion, age at diagnosis alone does not appear to provide an additional layer of biological complexity above that of proposed genetic and transcriptional phenotypes of TNBC. Consequently, treatment decisions should be less influenced by age and more driven by tumor biology.
CRISPRi screens reveal genes modulating yeast growth in lignocellulose hydrolysate
Authors: Gutmann Friederike , Jann Cosimo , Pereira Filipa , Johansson Andreas , Steinmetz Lars M. , Patil Kiran R. 
Published: February 2021

Abstract
Background
Baker’s yeast is a widely used eukaryotic cell factory, producing a diverse range of compounds including biofuels and fine chemicals. The use of lignocellulose as feedstock offers the opportunity to run these processes in an environmentally sustainable way. However, the required hydrolysis pretreatment of lignocellulosic material releases toxic compounds that hamper yeast growth and consequently productivity.

Results
Here, we employ CRISPR interference in S. cerevisiae to identify genes modulating fermentative growth in plant hydrolysate and in presence of lignocellulosic toxins. We find that at least one-third of hydrolysate-associated gene functions are explained by effects of known toxic compounds, such as the decreased growth of YAP1 or HAA1, or increased growth of DOT6 knock-down strains in hydrolysate.

Conclusion
Our study confirms previously known genetic elements and uncovers new targets towards designing more robust yeast strains for the utilization of lignocellulose hydrolysate as sustainable feedstock, and, more broadly, paves the way for applying CRISPRi screens to improve industrial fermentation processes.
Differences in circulating fatty acid-binding protein 4 concentration in the venous and capillary blood immediately after acute exercise
Authors: Numao Shigeharu , Uchida Ryota , Kurosaki Takashi , Nakagaichi Masaki 
Published: February 2021

Abstract
Background
Circulating fatty acid-binding protein 4 (FABP4) is a marker for various diseases. It would be highly useful to have simple and less invasive techniques for the assessment of FABP4 concentrations in the clinical research setting. The purpose of the present study was to assess the concordance of circulating FABP4 concentrations in venous and capillary blood both at rest and immediately after acute exercise in healthy young males.

Results
Thirty-eight healthy young male adults aged from 19 to 25 years (mean age, 20.8 ± 1.2 years) were recruited. Paired blood samples were taken from the cubital vein (venous) and fingertip (capillary) blood at rest (resting state) and immediately after incremental exercise (exercising state). Blood samples were analyzed to determine the circulating FABP4 concentration using an enzyme-linked immunosorbent assay. Pearson’s correlation coefficients for circulating FABP4 concentrations between venous and capillary blood samples indicated a strong positive correlation in both the resting and exercising state (resting state: r = 0.982, exercising state: r = 0.989, both p < 0.001). The mean FABP4 concentration was similar between venous and capillary blood in the resting state (p = 0.178), whereas it was significantly higher in capillary blood than in venous blood in the exercising state (p < 0.001). Furthermore, Bland–Altman plots showed a non-significant bias (− 0.07 ± 0.61 ng/mL, p = 0.453) in the resting state, whereas a significant bias (− 0.45 ± 0.61 ng/mL, p < 0.001) was observed in the exercising state.

Conclusions
These results indicate that capillary blood sampling can slightly overestimate circulating FABP4 concentrations under a physiologically dynamic state. However, the association between the venous and capillary blood in terms of FABP4 concentration was very strong, suggesting that capillary blood sampling can detect changes in FABP4 concentration in both physiologically steady and dynamic states.