bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lung delivery of MSCs expressing anti-cancer protein TRAIL visualised with 89Zr-oxine PET-CT
Authors: Patrick P. Stephen , Kolluri Krishna K. , Zaw Thin May , Edwards Adam , Sage Elizabeth K. , Sanderson Tom , Weil Benjamin D. , Dickson John C. , Lythgoe Mark F. , Lowdell Mark , Janes Sam M. , Kalber Tammy L. 
Published: June 2020

AbstractBackgroundMSCTRAIL is a cell-based therapy consisting of human allogeneic umbilical cord-derived MSCs genetically modified to express the anti-cancer protein TRAIL. Though cell-based therapies are typically designed with a target tissue in mind, delivery is rarely assessed due to a lack of translatable non-invasive imaging approaches. In this preclinical study, we demonstrate89Zr-oxine labelling and PET-CT imaging as a potential clinical solution for non-invasively tracking MSCTRAIL biodistribution. Future implementation of this technique should improve our understanding of MSCTRAIL during its evaluation as a therapy for metastatic lung adenocarcinoma.MethodsMSCTRAIL were radiolabelled with89Zr-oxine and assayed for viability, phenotype, and therapeutic efficacy post-labelling. PET-CT imaging of89Zr-oxine-labelled MSCTRAIL was performed in a mouse model of lung cancer following intravenous injection, and biodistribution was confirmed ex vivo.ResultsMSCTRAIL retained the therapeutic efficacy and MSC phenotype in vitro at labelling amounts up to and above those required for clinical imaging. The effect of89Zr-oxine labelling on cell proliferation rate was amount- and time-dependent. PET-CT imaging showed delivery of MSCTRAIL to the lungs in a mouse model of lung cancer up to 1 week post-injection, validated by in vivo bioluminescence imaging, autoradiography, and fluorescence imaging on tissue sections.Conclusions89Zr-oxine labelling and PET-CT imaging present a potential method of evaluating the biodistribution of new cell therapies in patients, including MSCTRAIL. This offers to improve understanding of cell therapies, including mechanism of action, migration dynamics, and inter-patient variability.
Hermite–Hadamard type inequalities for m-convex and $( \alpha , m)$-convex functions
Authors: Özcan Serap 
Published: June 2020

AbstractIn this paper, some new inequalities of the Hermite–Hadamard type for the classes of functions whose derivatives’ absolute values arem-convex and$( \alpha , m) $(α,m)-convex are obtained. The results obtained in this work extend and improve the corresponding ones in the literature. Some applications to special means of real numbers are also given.
First report of plasmid-mediated colistin resistance mcr-8.1 gene from a clinical Klebsiella pneumoniae isolate from Lebanon
Authors: Salloum Tamara , Panossian Balig , Bitar Ibrahim , Hrabak Jaroslav , Araj George F. , Tokajian Sima 
Published: June 2020

AbstractColistin is considered as a last resort treatment for infections caused by multidrug-resistant Enterobacteriaceae. Plasmid-mediated mobile colistin resistance (mcr) genes contributed to the global spread of colistin resistance. This is the first report of plasmid-mediated colistin resistance mcr-8 gene from a clinical Klebsiella pneumoniae K9 isolate recovered from Lebanon. The isolate was characterized phenotypically and genotypically through both short and long read whole-genome sequencing, plasmid typing and conjugation assays. k9 belonged to sequence type 15 and harbored 31 antimicrobial resistance genes. The mcr-8.1 variant was carried on a novel ~ 300 kb multireplicon plasmid having IncFIA, IncR and IncHI1B. The plasmid was conjugative and carried a plethora of antimicrobial resistance determinants. The introduction of novel mcr variants in Lebanon poses an alarming health concern. Surveillance and screening for colistin resistant Enterobacteriaceae and mcr in livestock, animal farms, imported meat and poultry is highly recommended along with monitoring antibiotic use.
New insights into the associations among feed efficiency, metabolizable efficiency traits and related QTL regions in broiler chickens
Authors: Li Wei , Liu Ranran , Zheng Maiqing , Feng Furong , Liu Dawei , Guo Yuming , Zhao Guiping , Wen Jie 
Published: June 2020

Abstract
Background
Improving the feed efficiency would increase profitability for producers while also reducing the environmental footprint of livestock production. This study was conducted to investigate the relationships among feed efficiency traits and metabolizable efficiency traits in 180 male broilers. Significant loci and genes affecting the metabolizable efficiency traits were explored with an imputation-based genome-wide association study. The traits measured or calculated comprised three growth traits, five feed efficiency related traits, and nine metabolizable efficiency traits.

Results
The residual feed intake (RFI) showed moderate to high and positive phenotypic correlations with eight other traits measured, including average daily feed intake (ADFI), dry excreta weight (DEW), gross energy excretion (GEE), crude protein excretion (CPE), metabolizable dry matter (MDM), nitrogen corrected apparent metabolizable energy (AMEn), abdominal fat weight (AbF), and percentage of abdominal fat (AbP). Greater correlations were observed between growth traits and the feed conversion ratio (FCR) than RFI. In addition, the RFI, FCR, ADFI, DEW, GEE, CPE, MDM, AMEn, AbF, and AbP were lower in low-RFI birds than high-RFI birds (P < 0.01 or P < 0.05), whereas the coefficients of MDM and MCP of low-RFI birds were greater than those of high-RFI birds (P < 0.01). Five narrow QTLs for metabolizable efficiency traits were detected, including one 82.46-kb region for DEW and GEE on Gallus gallus chromosome (GGA) 26, one 120.13-kb region for MDM and AMEn on GGA1, one 691.25-kb region for the coefficients of MDM and AMEn on GGA5, one region for the coefficients of MDM and MCP on GGA2 (103.45–103.53 Mb), and one 690.50-kb region for the coefficient of MCP on GGA14. Linkage disequilibrium (LD) analysis indicated that the five regions contained high LD blocks, as well as the genes chromosome 26 C6orf106 homolog (C26H6orf106), LOC396098, SH3 and multiple ankyrin repeat domains 2 (SHANK2), ETS homologous factor (EHF), and histamine receptor H3-like (HRH3L), which are known to be involved in the regulation of neurodevelopment, cell proliferation and differentiation, and food intake.

Conclusions
Selection for low RFI significantly decreased chicken feed intake, excreta output, and abdominal fat deposition, and increased nutrient digestibility without changing the weight gain. Five novel QTL regions involved in the control of metabolizable efficiency in chickens were identified. These results, combined through nutritional and genetic approaches, should facilitate novel insights into improving feed efficiency in poultry and other species.
Developing standards for the microbiome field
Authors: Amos Gregory C. A. , Logan Alastair , Anwar Saba , Fritzsche Martin , Mate Ryan , Bleazard Thomas , Rijpkema Sjoerd 
Published: June 2020

Abstract
Background
Effective standardisation of methodologies to analyse the microbiome is essential to the entire microbiome community. Despite the microbiome field being established for over a decade, there are no accredited or certified reference materials available to the wider community. In this study, we describe the development of the first reference reagents produced by the National Institute for Biological Standards and Control (NIBSC) for microbiome analysis by next-generation sequencing. These can act as global working standards and will be evaluated as candidate World Health Organization International Reference Reagents.

Results
We developed the NIBSC DNA reference reagents Gut-Mix-RR and Gut-HiLo-RR and a four-measure framework for evaluation of bioinformatics tool and pipeline bias. Using these reagents and reporting system, we performed an independent evaluation of a variety of bioinformatics tools by analysing shotgun sequencing and 16S rRNA sequencing data generated from the Gut-Mix-RR and Gut-HiLo-RR. We demonstrate that key measures of microbiome health, such as diversity estimates, are largely inflated by the majority of bioinformatics tools. Across all tested tools, biases were present, with a clear trade-off occurring between sensitivity and the relative abundance of false positives in the final dataset. Using commercially available mock communities, we investigated how the composition of reference reagents may impact benchmarking studies. Reporting measures consistently changed when the same bioinformatics tools were used on different community compositions. This was influenced by both community complexity and taxonomy of species present. Both NIBSC reference reagents, which consisted of gut commensal species, proved to be the most challenging for the majority of bioinformatics tools tested. Going forward, we recommend the field uses site-specific reagents of a high complexity to ensure pipeline benchmarking is fit for purpose.

Conclusions
If a consensus of acceptable levels of error can be agreed on, widespread adoption of these reference reagents will standardise downstream gut microbiome analyses. We propose to do this through a large open-invite collaborative study for multiple laboratories in 2020.
Application of CRISPR/Cas9 to human-induced pluripotent stem cells: from gene editing to drug discovery
Authors: De Masi Claudia , Spitalieri Paola , Murdocca Michela , Novelli Giuseppe , Sangiuolo Federica 
Published: June 2020

AbstractHuman-induced pluripotent stem cells (hiPSCs) and CRISPR/Cas9 gene editing system represent two instruments of basic and translational research, which both allow to acquire deep insight about the molecular bases of many diseases but also to develop pharmacological research.This review is focused to draw up the latest technique of gene editing applied on hiPSCs, exploiting some of the genetic manipulation directed to the discovery of innovative therapeutic strategies. There are many expediencies provided by the use of hiPSCs, which can represent a disease model clinically relevant and predictive, with a great potential if associated to CRISPR/Cas9 technology, a gene editing tool powered by ease and precision never seen before.Here, we describe the possible applications of CRISPR/Cas9 to hiPSCs: from drug development to drug screening and from gene therapy to the induction of the immunological response to specific virus infection, such as HIV and SARS-Cov-2.
3D scanning, modeling, and printing of Chinese classical garden rockeries: Zhanyuan’s South Rockery
Authors: Dong Qianli , Zhang Qingping , Zhu Lingxi 
Published: June 2020

Abstract
Chinese classical garden rockeries have rich historical and cultural value, as they are a part of China’s cultural heritage. In recent years, while the digital research of rockeries has increased, most of it is limited to a rockery’s digital record. However, other issues have not been thoroughly discussed, such as how to digitally protect a rockery, activate it as an immovable, solid site heritage by digital means, and transform its function. To ensure the effectiveness of rockery data, this paper compares the advantages and disadvantages of digitally mapping the Huanxiu Shanzhuang rockery, which was conducted by the team at an early stage, to a convenient and accurate digital rockery data acquisition scheme that was used for the Zhanyuan South Rockery, as an example of carrying out three-dimensional digital mapping. Furthermore, from the perspective of the sustainable development of cultural heritage, this study attempts to print Chinese classical garden rockeries in three dimensions to realize their physical representation. This paper aims to provide a new way to activate, restore, and protect rockeries.
Performance characteristics of the digital uMI550 PET/CT system according to the NEMA NU2-2018 standard
Authors: Chen Shuguang , Hu Pengcheng , Gu Yushen , Yu Haojun , Shi Hongcheng 
Published: June 2020

Abstract
Background
The aim of this study is to conduct physical performance evaluation on the uMI550 whole-body PET/CT system according to the NEMA NU2-2018 standard.

Methods
According to the NEMA NU2-2018, spatial resolution, sensitivity, scatter fraction, count-rate performance, accuracy of count losses and random corrections, image quality, and timing resolution were evaluated. Spatial resolution was measured by using a 22Na point source. System sensitivity was measured by inserting an 18F line-source in six concentric aluminum sleeves with varying diameters. Scatter fraction, count-rate performance, accuracy of count loss, and timing resolution were all calculated by analyzing dynamically acquired data of an 18F line-source inside a polyethylene cylinder in 20 cm diameter and 70 cm length. Image quality was assessed using a NEMA IEC body phantom with a 4:1 ratio of activity concentration of spheres to the warm background. Additionally, three patient studies were performed, with one brain scan and two whole-body scans, separately. The patient images were evaluated to get a visual first impression of uMI550.

Results
The tangential, radial, and axial spatial resolutions were measured as 2.91 mm, 2.98 mm, and 2.97 mm FWHM, respectively, at 1 cm radial offset. The total system sensitivity to line source at center was 10.24 cps/kBq. A NECR peak was measured as 124.4 kcps at 18.85 kBq/mL. The scatter fraction at NECR peak was 36.65%, and the maximum count-rate error at and below NEC peak was 1.55%. Contrast recovery coefficients were from 46.5 (10 mm) to 83.9% (37 mm). The timing resolution was measured as 372 ps at low count rate.

Conclusion
NEMA NU-2 2018 testing was performed on the new SiPM-based uMI550 PET/CT system. The uMI550 shows a high-spatial resolution of less than 3 mm and a good timing resolution of 372 ps. It shows clinical significances on improving potentially diagnostic ability on small lesions.
A pilot study of essential tremor: cerebellar GABA+/Glx ratio is correlated with tremor severity
Authors: Tapper Sofie , Göransson Nathanael , Lundberg Peter , Tisell Anders , Zsigmond Peter 
Published: June 2020

Abstract
Objective
Essential tremor is a common movement disorder with an unclear origin. Emerging evidence suggests the role of the cerebellum and the thalamus in tremor pathophysiology. We examined the two main neurotransmitters acting inhibitory (GABA+) and excitatory (Glx) respectively, in the thalamus and cerebellum, in patients diagnosed with severe essential tremor. Furthermore, we also investigated the relationship between determined neurotransmitter concentrations and tremor severity in the essential tremor patients.

Methods
Ten essential tremor patients (prior to deep brain stimulation surgery) and six healthy controls, were scanned using a 3 T MR system. GABA+ and Glx concentrations were measured using magnetic resonance spectroscopy (MRS) performed using single voxel MEGA-PRESS. For the purpose of assessing the tremor severity, the essential tremor rating scale (ETRS) was used in accordance with Fahn, Tolosa, and Marin.

Results
We demonstrated that the cerebellar GABA+/Glx ratio was positively correlated to the ETRS (r = 0.70, p = 0.03) in essential tremor. Cerebellar and thalamic GABA+ and Glx concentrations did not show any significant difference when comparing essential tremor patients with healthy controls, at the group level.

Conclusion
We demonstrated a positive correlation between increasing tremor disability and the ratio of GABA+/ Glx in the cerebellum of essential tremor patients. This highlights the impact of an altered balance of the excitatory and inhibitory neurotransmitters in tremor severity. Rather than a change in GABA+, which was constant, we attribute this finding to an overall decrease of Glx.
Left-sided portal hypertension caused by idiopathic splenic vein stenosis improved by splenectomy: a case report
Authors: Hayashi Hikaru , Shimizu Akira , Motoyama Hiroaki , Kubota Koji , Notake Tsuyoshi , Ikehara Tomohiko , Yasukawa Koya , Kobayashi Akira , Soejima Yuji 
Published: June 2020

Abstract
Background
Splenic vein stenosis and occlusion, which are known causes of left-sided portal hypertension, often occur secondary to trauma, pancreatitis, or invasion or compression by pancreatic tumors. However, few reports have described idiopathic splenic vein stenosis.

Case presentation
A 70-year-old man was referred to our hospital for examination of isolated gastric varices. He had no history of liver disease, pancreatitis, or abdominal trauma. Computed tomography revealed stenosis of almost the entire length of the splenic vein, and development of gastric fundal and short gastric varices. No inflammatory changes or neoplastic lesions of the pancreas were observed in any imaging study. The patient was diagnosed with left-sided portal hypertension caused by idiopathic splenic vein stenosis, and splenectomy was performed. The postoperative course was smooth, and improvement of the gastric varices was shown by upper gastrointestinal endoscopy at 3 months after the operation.

Conclusions
Idiopathic splenic vein stenosis is an extremely rare cause of left-sided portal hypertension. Splenectomy is one of the most effective treatments for left-sided portal hypertension caused by idiopathic splenic vein stenosis.
Development of novel EST microsatellite markers for genetic diversity analysis and correlation analysis of velvet antler growth characteristics in Sika deer
Authors: Jia Boyin , Wang Guiwu , Zheng Junjun , Yang Wanyun , Chang Shuzhuo , Zhang Jiali , Liu Yuan , Li Qining , Ge Chenxia , Chen Guang , Liu Dongdong , Yang Fuhe 
Published: June 2020

Abstract
Background
Sika deer is one of the most popular and valued animals in China. However, few studies have been conducted on the microsatellite of Sika deer, which has hampered the progress of genetic selection breeding. To develop and characterize a set of microsatellites for Sika deer which provide helpful information for protection of Sika deer natural resources and effectively increase the yield and quantity of velvet antler.

Results
We conducted a transcriptome survey of Sika deer using next-generation sequencing technology. One hundred eighty-two thousand two hundred ninety-five microsatellite markers were identified in the transcriptome, 170 of 200 loci were successfully amplified across panels of 140 individuals from Shuangyang Sika deer population. And 29 loci were found to be obvious polymorphic. Number of alleles is from 3 to 14. The expected heterozygosity ranged from 0.3087 to 0.7644. The observed heterozygosity ranged from 0 to 0.7698. The polymorphism information content values of those microsatellites varied ranged from 0.2602 to 0.7507. The marker-trait association was tested for 6 important and kernel characteristics of two-branched velvet antler in Shuangyang Sika deer through one-way analysis of variance. The results showed that marker-trait associations were identified with 8 different markers, especially M009 and M027.

Conclusions
This study not only provided a large scale of microsatellites which were valuable for future genetic mapping and trait association in Sika deer, but also offers available information for molecular breeding in Sika deer.
Open up: a survey on open and non-anonymized peer reviewing
Authors: Besançon Lonni , Rönnberg Niklas , Löwgren Jonas , Tennant Jonathan P. , Cooper Matthew 
Published: June 2020

AbstractBackgroundOur aim is to highlight the benefits and limitations of open and non-anonymized peer review. Our argument is based on the literature and on responses to a survey on the reviewing process of alt.chi, a more or less open review track within the so-called Computer Human Interaction (CHI) conference, the predominant conference in the field of human-computer interaction. This track currently is the only implementation of an open peer review process in the field of human-computer interaction while, with the recent increase in interest in open scientific practices, open review is now being considered and used in other fields.MethodsWe ran an online survey with 30 responses from alt.chi authors and reviewers, collecting quantitative data using multiple-choice questions and Likert scales. Qualitative data were collected using open questions.ResultsOur main quantitative result is that respondents are more positive to open and non-anonymous reviewing for alt.chi than for other parts of the CHI conference. The qualitative data specifically highlight the benefits of open and transparent academic discussions. The data and scripts are available onhttps://osf.io/vuw7h/, and the figures and follow-up work onhttp://tiny.cc/OpenReviews.ConclusionWhile the benefits are quite clear and the system is generally well-liked by alt.chi participants, they remain reluctant to see it used in other venues. This concurs with a number of recent studies that suggest a divergence between support for a more open review process and its practical implementation.
Habitat selection in the lesser cuckoo, an avian brood parasite breeding on Jeju Island, Korea
Authors: Yun Seongho , Lee Jin-Won , Yoo Jeong-Chil 
Published: June 2020

AbstractBackgroundDetermining patterns of habitat use is key to understanding of animal ecology. Approximately 1% of bird species use brood parasitism for their breeding strategy, in which they exploit other species’ (hosts) parental care by laying eggs in their nests. Brood parasitism may complicate the habitat requirement of brood parasites because they need habitats that support both their host and their own conditions for breeding. Brood parasitism, through changes in reproductive roles of sex or individual, may further diversify habitat use patterns among individuals. However, patterns of habitat use in avian brood parasites have rarely been characterized. In this study, we categorized the habitat preference of a population of brood parasitic lesser cuckoos (Cuculus poliocephalus) breeding on Jeju Island, Korea. By using compositional analyses together with radio-tracking and land cover data, we determined patterns of habitat use and their sexual and diurnal differences.ResultsWe found that the lesser cuckoo had a relatively large home range and its overall habitat composition (the second-order selection) was similar to those of the study area; open areas such as the field and grassland habitats accounted for 80% of the home range. Nonetheless, their habitat, comprised of 2.54 different habitats per hectare, could be characterized as a mosaic. We also found sexual differences in habitat composition and selection in the core-use area of home ranges (third-order selection). In particular, the forest habitat was preferentially utilized by females, while underutilized by males. However, there was no diurnal change in the pattern of habitat use. Both sexes preferred field habitats at the second-order selection. At the third-order selection, males preferred field habitats followed by grasslands and females preferred grasslands followed by forest habitats.ConclusionsWe suggest that the field and grassland habitats represent the two most important areas for the lesser cuckoo on Jeju Island. Nevertheless, this study shows that habitat preference may differ between sexes, likely due to differences in sex roles, sex-based energy demands, and potential sexual conflict.