bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wonky whales: the evolution of cranial asymmetry in cetaceans
Authors: Coombs Ellen J. , Clavel Julien , Park Travis , Churchill Morgan , Goswami Anjali 
Published: July 2020

AbstractBackgroundUnlike most mammals, toothed whale (Odontoceti) skulls lack symmetry in the nasal and facial (nasofacial) region. This asymmetry is hypothesised to relate to echolocation, which may have evolved in the earliest diverging odontocetes. Early cetaceans (whales, dolphins, and porpoises) such as archaeocetes, namely the protocetids and basilosaurids, have asymmetric rostra, but it is unclear when nasofacial asymmetry evolved during the transition from archaeocetes to modern whales. We used three-dimensional geometric morphometrics and phylogenetic comparative methods to reconstruct the evolution of asymmetry in the skulls of 162 living and extinct cetaceans over 50 million years.ResultsIn archaeocetes, we found asymmetry is prevalent in the rostrum and also in the squamosal, jugal, and orbit, possibly reflecting preservational deformation. Asymmetry in odontocetes is predominant in the nasofacial region. Mysticetes (baleen whales) show symmetry similar to terrestrial artiodactyls such as bovines. The first significant shift in asymmetry occurred in the stem odontocete family Xenorophidae during the Early Oligocene. Further increases in asymmetry occur in the physeteroids in the Late Oligocene, Squalodelphinidae and Platanistidae in the Late Oligocene/Early Miocene, and in the Monodontidae in the Late Miocene/Early Pliocene. Additional episodes of rapid change in odontocete skull asymmetry were found in the Mid-Late Oligocene, a period of rapid evolution and diversification. No high-probability increases or jumps in asymmetry were found in mysticetes or archaeocetes. Unexpectedly, no increases in asymmetry were recovered within the highly asymmetric ziphiids, which may result from the extreme, asymmetric shape of premaxillary crests in these taxa not being captured by landmarks alone.ConclusionsEarly ancestors of living whales had little cranial asymmetry and likely were not able to echolocate. Archaeocetes display high levels of asymmetry in the rostrum, potentially related to directional hearing, which is lost in early neocetes—the taxon including the most recent common ancestor of living cetaceans. Nasofacial asymmetry becomes a significant feature of Odontoceti skulls in the Early Oligocene, reaching its highest levels in extant taxa. Separate evolutionary regimes are reconstructed for odontocetes living in acoustically complex environments, suggesting that these niches impose strong selective pressure on echolocation ability and thus increased cranial asymmetry.
The cost-effectiveness of controlling dengue in Indonesia using wMel Wolbachia released at scale: a modelling study
Authors: Brady Oliver J. , Kharisma Dinar D. , Wilastonegoro Nandyan N. , O’Reilly Kathleen M. , Hendrickx Emilie , Bastos Leonardo S. , Yakob Laith , Shepard Donald S. 
Published: July 2020

Abstract
Background
Release of virus-blocking Wolbachia-infected mosquitoes is an emerging disease control strategy that aims to control dengue and other arboviral infections. Early entomological data and modelling analyses have suggested promising outcomes, and wMel Wolbachia releases are now ongoing or planned in 12 countries. To help inform government, donor, or philanthropist decisions on scale-up beyond single city releases, we assessed this technology’s cost-effectiveness under alternative programmatic options.

Methods
Using costing data from existing Wolbachia releases, previous dynamic model-based estimates of Wolbachia effectiveness, and a spatially explicit model of release and surveillance requirements, we predicted the costs and effectiveness of the ongoing programme in Yogyakarta City and three new hypothetical programmes in Yogyakarta Special Autonomous Region, Jakarta, and Bali.

Results
We predicted Wolbachia to be a highly cost-effective intervention when deployed in high-density urban areas with gross cost-effectiveness below $1500 per DALY averted. When offsets from the health system and societal perspective were included, such programmes even became cost saving over 10-year time horizons with favourable benefit-cost ratios of 1.35 to 3.40. Sequencing Wolbachia releases over 10 years could reduce programme costs by approximately 38% compared to simultaneous releases everywhere, but also delays the benefits. Even if unexpected challenges occurred during deployment, such as emergence of resistance in the medium-term or low effective coverage, Wolbachia would remain a cost-saving intervention.

Conclusions
Wolbachia releases in high-density urban areas are expected to be highly cost-effective and could potentially be the first cost-saving intervention for dengue. Sites with strong public health infrastructure, fiscal capacity, and community support should be prioritised.
Assessment of thoracic volume changes after the collapse of lateral rib fractures based on chest computed tomography data: computer simulation and a multiple variable linear regression analysis
Authors: Chen Xiao-Kun , Liu Yi-Jun , Guo Fu-Zheng , Deng Jiu-Xu , Xiong Jian , Wang Tian-Bing , Jiang Bao-Guo 
Published: July 2020

Abstract
Background
Chest blunt trauma (CBT) and the resultant rib fractures often lead to thoracic collapse. The purpose of this study was to explore the effect of displacement of the rib fracture and thoracic collapse on the thoracic volume by using normal chest CT data.

Methods
In this retrospective study, seven consecutive normal participants were selected from our hospital between June and July 2018. Normal thoracic models were reconstructed, followed by simulation of lateral fractures through the 4th to 9th ribs under three collapse modes with 1–5 cm of collapse. The thoracic collapse models (n = 630) were reconstructed using 3Dmax 2014. We calculated the thoracic volume and reduction percentage for each thoracic collapse model. Linear regression-based comparisons of thoracic volume reductions were performed.

Results
In all three collapse modes, the degree of the collapse was linearly correlated with the mean thoracic volume reduction. The reduction percentage in the posterior collapse mode was higher than that in the anterior collapse mode (P < 0.001). The largest volume reductions in the anterior, posterior, and simultaneous collapse models were in the 6th rib fracture model (P < 0.001), 8th rib fracture model (P < 0.001), and 7th rib fracture model (P < 0.001), respectively.

Conclusions
The influences of rib fracture displacement and collapse on the thoracic volume in the 6th through 8th ribs are critical in lateral rib fractures. For patients with 6th to 8th rib fractures and posterior rib collapse, surgical intervention to restore thoracic volume may be more essential.
Report of a de novo c.2605C > T (p.Pro869Ser) change in the MED13L gene and review of the literature for MED13L-related intellectual disability
Authors: Yi Zhi , Zhang Ying , Song Zhenfeng , Pan Hong , Yang Chengqing , Li Fei , Xue Jiao , Qu Zhenghai 
Published: July 2020

Abstract
Background
MED13L-related intellectual disability is a new syndrome that is characterized by intellectual disability (ID), motor developmental delay, speech impairment, hypotonia and facial dysmorphism. Both the MED13L haploinsufficiency mutation and missense mutation were reported to be causative. It has also been reported that patients carrying missense mutations have more frequent epilepsy and show a more severe phenotype.

Case presentation
We report a child with ID, speech impairment, severe motor developmental delay, facial deformity, hypotonia, muscular atrophy, scoliosis, odontoprisis, abnormal electroencephalogram (EEG), and congenital ureteropelvic junction obstruction (UPJO) combined with high ureter attachment. We used whole-exome sequencing (WES) to detect the genetic aberration of the child and found a de novo mutation, c.2605C > T (p.Pro869Ser), in the MED13L gene. Neither of her parents carried the mutation. Additionally, we review the literature and summarize the phenotypes and features of reported missense mutations. After reviewing the literature, approximately 17 missense mutations in 20 patients have been reported thus far. For 18 patients (including our case) whose clinical manifestations were provided, 100% of the patients had ID or developmental delay (DD). A total of 88.9, 83.3 and 66.7% of the patients had speech impairment, delayed milestones and hypotonia, respectively. A total of 83.3% of the patients exhibited craniofacial deformity or other dysmorphic features. Behavioral difficulties and autistic features were observed in 55.6% of the patients. Cardiac anomalies were seen in only 27.8% of the patients. Of these patients, 44.4% had epileptic seizures. Of the 17 mutations, 2 were located in the N-terminal domain, 8 were located in the C-terminal domain, and 1 was located in an α-helical sequence stretch. One of them was located in the MID domain of the MedPIWI module.

Conclusions
We report a new patient with a reported missense mutation, c.2605C > T (p.Pro869Ser), who exhibited some infrequent manifestations except common phenotypes, which may broaden the known clinical spectrum. Additionally, by reviewing the literature, we also found that patients with missense mutations have a higher incidence of seizures, MRI abnormalities, autistic features and cardiac anomalies. They also have more severe ID and hypotonia. Our case further demonstrates that Pro869Ser is a hotspot mutation of the MED13L gene.
Genes adapt to outsmart gene-targeting strategies in mutant mouse strains by skipping exons to reinitiate transcription and translation
Authors: Hosur Vishnu , Low Benjamin E. , Li Daniel , Stafford Grace A. , Kohar Vivek , Shultz Leonard D. , Wiles Michael V. 
Published: July 2020

AbstractBackgroundGene disruption in mouse embryonic stem cells or zygotes is a conventional genetics approach to identify gene function in vivo. However, because different gene disruption strategies use different mechanisms to disrupt genes, the strategies can result in diverse phenotypes in the resulting mouse model. To determine whether different gene disruption strategies affect the phenotype of resulting mutant mice, we characterizedRhbdf1mouse mutant strains generated by three commonly used strategies—definitive-null, targeted knockout (KO)-first, and CRISPR/Cas9.ResultsWe find thatRhbdf1responds differently to distinct KO strategies, for example, by skipping exons and reinitiating translation to potentially yield gain-of-function alleles rather than the expected null or severe hypomorphic alleles. Our analysis also revealed that at least 4% of mice generated using the KO-first strategy show conflicting phenotypes.ConclusionsExon skipping is a widespread phenomenon occurring across the genome. These findings have significant implications for the application of genome editing in both basic research and clinical practice.
Understanding Horizontal Gene Transfer network in human gut microbiota
Authors: Li Chen , Chen Jiaxing , Li Shuai Cheng 
Published: July 2020

Abstract
Background
Horizontal Gene Transfer (HGT) is the process of transferring genetic materials between species. Through sharing genetic materials, microorganisms in the human microbiota form a network. The network can provide insights into understanding the microbiota. Here, we constructed the HGT networks from the gut microbiota sequencing data and performed network analysis to characterize the HGT networks of gut microbiota.

Results
We constructed the HGT network and perform the network analysis to two typical gut microbiota datasets, a 283-sample dataset of Mother-to-Child and a 148-sample dataset of longitudinal inflammatory bowel disease (IBD) metagenome. The results indicated that (1) the HGT networks are scale-free. (2) The networks expand their complexities, sizes, and edge numbers, accompanying the early stage of lives; and microbiota established in children shared high similarity as their mother (p-value = 0.0138), supporting the transmission of microbiota from mother to child. (3) Groups harbor group-specific network edges, and network communities, which can potentially serve as biomarkers. For instances, IBD patient group harbors highly abundant communities of Proteobacteria (p-value = 0.0194) and Actinobacteria (p-value = 0.0316); children host highly abundant communities of Proteobacteria (p-value = 2.8785$$e^{-5}$$

e

-
5

) and Actinobacteria (p-value = 0.0015), and the mothers host highly abundant communities of Firmicutes (p-value = 8.0091$$e^{-7}$$

e

-
7

). IBD patient networks contain more HGT edges in pathogenic genus, including Mycobacterium, Sutterella, and Pseudomonas. Children’s networks contain more edges from Bifidobacterium and Escherichia.

Conclusion
Hence, we proposed the HGT network constructions from the gut microbiota sequencing data. The HGT networks capture the host state and the response of microbiota to the environmental and host changes, and they are essential to understand the human microbiota.
Genetic polymorphisms in vitamin D pathway influence 25(OH)D levels and are associated with atopy and asthma
Authors: Galvão Alana Alcântara , de Araújo Sena Flávia , Andrade Belitardo Emília Maria Medeiros de , de Santana Maria Borges Rabelo , Costa Gustavo Nunes de Oliveira , Cruz Álvaro Augusto , Barreto Maurício Lima , Costa Ryan dos Santos , Alcantara-Neves Neuza Maria , Figueiredo Camila Alexandrina 
Published: July 2020

Abstract
Background
Vitamin D deficiency or insufficiency, has been associated with atopy and lack of asthma control. Our objective was to investigate associations between variants in genes of vitamin D pathway with serum levels of 25-hydroxyvitamin D (25(OH)D), atopy, asthma and asthma severity in teenagers from Northeast Brazil.

Methods
This is a cross sectional study nested in a cohort population of asthma. 25(OH)D was quantified from 968 of 11–17 years old individuals by ELISA. Asthma diagnosis was obtained by using the ISAAC Phase III questionnaire. Specific IgE was determined by ImmunoCAP; genotyping was performed using the 2.5 HumanOmni Biochip from Illumina. Statistical analyses were performed in PLINK 1.07 and SPSS 22.1.

Results
After quality control, 104 Single Nucleotides Variants (SNVs) in vitamin D pathway genes, typed in 792 individuals, were included in the analysis. The allele A of rs10875694 on VDR was positively associated with atopy (OR = 1.35; 95% CI 1.01–1.81). The allele C of rs9279 on VDR, was negatively associated with asthma risk (OR = 0.66; 95% CI 0.45–0.97), vitamin D insufficiency (OR = 0.78; 95% CI 0.70–0.96) and higher VDR expression. Two variants in VDR were associated with asthma severity, the allele A of rs2189480 (OR = 0.34; 95% CI 0.13–0.89) and the allele G of rs4328262 (OR = 3.18; 95% CI 1.09–9.28). The combination of variants in CYP2R1 and CYP24A1 (GAC, to rs10500804, rs12794714 and rs3886163, respectively) was negatively associated with vitamin D production (β = − 1.24; 95% CI − 2.42 to − 0.06).

Conclusions
Genetic variants in the vitamin D pathway affect vitamin D serum levels and, thus, atopy and asthma.
Exploring heterologous prime-boost vaccination approaches to enhance influenza control in pigs
Authors: Li Chong , Culhane Marie R. , Cheeran Maxim , Galina Pantoja Lucina , Jansen Micah L. , Amodie Deborah , Mellencamp Martha A. , Torremorell Montserrat 
Published: July 2020

AbstractInfluenza A viruses evolve rapidly to escape host immunity. In swine, this viral evolution has resulted in the emergence of multiple H1 and H3 influenza A virus (IAV) lineages in the United States (US) pig populations. The heterologous prime-boost vaccination strategy is a promising way to deal with diverse IAV infection in multiple animal models. However, whether or not this vaccination strategy is applicable to US swine to impart immunity against infection from North American strains of IAV is still unknown. We performed a vaccination-challenge study to evaluate the protective efficacy of using multivalent inactivated vaccine and/or a live attenuated IAV vaccine (LAIV) in pigs following multiple prime-boost vaccination protocols against a simultaneous H1N1 and H3N2 IAV infection. Our data show that pigs in the heterologous prime-boost vaccination group had more favorable outcomes consistent with a better response against virus challenge than non-vaccinated pigs. Additionally, delivering a multivalent heterologous inactivated vaccine boost to pigs following a single LAIV administration was also beneficial. We concluded the heterologous prime boost vaccination strategy may potentiate responses to suboptimal immunogens and holds the potential applicability to control IAV in the North American swine industry. However, more studies are needed to validate the application of this vaccination approach under field conditions.
Radiographic analysis and virtual cleaning of a bioarchaeological remain enclosed in mineral deposits from a limestone cave
Authors: Eppenberger Patrick E. , Čavka Mislav , Radović Siniša , Paar Dalibor , Buzjak Nenad , Ahern James C. M. , Biedermann Philipp , Gruber Philipp , Novak Mario , Janković Ivor 
Published: July 2020

AbstractIn limestone caves, environmental processes often cause alterations of human or animal skeletal remains, complicating classical analytical methods. Exemplary, a proximal femoral skeletal fragment, enclosed by a thick layer of speleothemic calcite deposits, was discovered during the exploration of the Bedara cave in Žumberak, Croatia. An examination without removal of the surrounding mineral deposits, possibly leading to damage of the specimen, was, therefore, desirable.We describe and discuss the applied techniques, including clinical computed tomography, virtual cleaning by a specially developed segmentation protocol using an open-source DICOM viewer, and virtual visualisation and dimensioning using computer-aided design software, so that this “hidden” specimen could be non-invasively examined in great detail. We also report on the circumstances and origin of the find, the results of radiocarbon dating, and its anatomical and taxonomic identification, according to which, the bone fragment belonged to a wild boar (Sus scrofa) from the timeframe of the Middle Eneolithic Retz-Gajary culture in the region (4,781 ± 35 years before present). This study provides a reference for future paleontological and anthropological analyses, seeking to unlock the enormous potential of anatomical studies of comparable skeletal remains that are either petrified or enclosed in speleothemic deposits.
Role of positron-emission tomography/computed tomography (PET/CT) in breast cancer
Authors: Shawky Mohamed , Ali Zeinab Abd Elaziz , Hashem Dina Hamdy , Houseni Mohamed 
Published: July 2020

Abstract
Background
Breast cancer is the most common cancer type in women and the most common cause of deaths in women worldwide.
FDG-PET/CT was used in the early stage, estimation of the therapeutic response, revelation of recurrent disease, and distal metastasis. However, with the increasing use of FDG PET/CT, sites of accelerated activity have been occasionally found out in unexpected locations which may not correlate with the patient’s clinical history or the expected propagation of the primary malignancy.
The aim of this study is to detect the diagnostic value of PET/CT in breast cancer patients; comparing PET/CT performance with that of contrast-enhanced CT in diagnosis of breast cancer and distant metastasis.

Results
The study included 30 female patients with breast cancer, mean age 53.56 years ± 10.64 (SD), age range 33–73 years. PET/CT detect contralateral breast affection in 2 patients (6.7%), and distant metastasis was seen on PET/CT. Sites of distant metastasis included the bone (n = 12), axillary lymph nodes (n = 11), cervical lymph nodes (n = 6), mediastinal lymph nodes (n = 12), abdominal lymph nodes (n = 8), liver (n = 5), lung (n = 11), and other visceral sites metastasis (n = 9). PET/CT detected breast lesions with a sensitivity of 100% and specificity of 95.4%. In contrast, the sensitivity and specificity of CT alone were 81.2% and 90.4%, respectively.

Conclusion
PET/CT has superiority over CT alone in revelation of breast lesions and distant metastases.
Preserving postharvest storage quality of fresh-cut cactus pears by using different bio-materials
Authors: Kahramanoğlu İbrahim , Usanmaz Serhat , Okatan Volkan , Wan Chunpeng 
Published: July 2020

Abstract

Background

Cactus pear (
Opuntia ficus
-
indica
(L.) Miller) is an important food source for human beings but its consumption and marketability are limited due to the presence of spines and glochids on the fruit surface. Fresh-cut, ready-to-eat cactus pears have higher preference than the whole fruits. However, fresh-cut fruits have tissue wounding and quick deterioration, which decrease the marketability of the products. Therefore, present study was aimed to improve the storage quality of ready-to-eat cactus pears with the application of environmentally friendly bio-materials.

Methods

Fruits of present study were hand collected by a traditional way from a farm located in Yayla village of Northern Cyprus. Fruits were then peeled to prepare fresh-cut prickly pears for further experiments. Fruit peeling was carried out in three steps: (i) slicing off and discarding the both ends of the prickly pears, (ii) making one long vertical slice down the body, and (iii) peeling back the skin by sliping our finger into the slice and preparing a peeled prickly pear without skin. The six treatments of present study are: (1) control—dipping the fruits into distilled water, (2) covering the fruits with
Vitis vinifera
leaves, (3) dipping the fruits into jelly, (4) dipping the fruits into
Aloe vera
gel, (5) dipping the fruits into
Portulaca oleracea
extract and (6) dipping the fruits into cactus gel. Totally 108 fruits (replications) were used for each treatment and 18 fruits from each treatment were selected for quality analysis with 3-days interval (3, 6, 9, 12, 15 and 18 days). Fruits of each treatment (6 from same treatment) were placed into an open plastic box (dimensions: 20 * 13 * 5 cm; material: PET) and was covered with a stretch film (LLDPE, 10 µm) for storage. The fruit boxes were stored at storage rooms adjusted to 5 ± 1 °C and 55 ± 5% relative humidity.

Results

Results showed that, all treatments have varying positive effects on the prevention of weight loss. Among them, the highest positive effect was received from
A. vera
gel treatment (0.98%), and is followed by cactus gel (1.15%),
V. vinifera
leaf (1.39%) and jelly (1.61%) at the end of the experiments (18 days).
A. vera
gel and cactus gel were also found to have highest influence on the prevention of off-odor and decay incidence; and to protect the sensory and visual quality of the ready-to-eat cactus pears.

Conclusions

Results suggested that the postharvest storage duration of ready-to-eat cactus pears might be extended from 9 to 15 days with the use of
Aloe vera
gel or cactus gel.