bluuebunny/crossref_metadata_2025_split huggingface dataset:
A 192 bp ERV fragment insertion in the first intron of porcine TLR6 may act as an enhancer associated with the increased expressions of TLR6 and TLR1
Authors: Wang XiaoYan , Chen Zixuan , Murani Eduard , D’Alessandro Enrico , An Yalong , Chen Cai , Li Kui , Galeano Grazia , Wimmers Klaus , Song Chengyi 
Published: August 2021

Abstract
Background
Toll-like receptors (TLRs) play important roles in building innate immune and inducing adaptive immune responses. Associations of the TLR genes polymorphisms with disease susceptibility, which are the basis of molecular breeding for disease resistant animals, have been reported extensively. Retrotransposon insertion polymorphisms (RIPs), as a new type of molecular markers developed recently, have great potential in population genetics and quantitative trait locus mapping. In this study, bioinformatic prediction combined with PCR-based amplification was employed to screen for RIPs in porcine TLR genes. Their population distribution was examined, and for one RIP the impact on gene activity and phenotype was further evaluated.

Results
Five RIPs, located at the 3' flank of TLR3, 5' flank of TLR5, intron 1 of TLR6, intron 1 of TLR7, and 3' flank of TLR8 respectively, were identified. These RIPs were detected in different breeds with an uneven distribution among them. By using the dual luciferase activity assay a 192 bp endogenous retrovirus (ERV) in the intron 1 of TLR6 was shown to act as an enhancer increasing the activities of TLR6 putative promoter and two mini-promoters. Furthermore, real-time quantitative polymerase chain reaction (qPCR) analysis revealed significant association (p < 0.05) of the ERV insertion with increased mRNA expression of TLR6, the neighboring gene TLR1, and genes downstream in the TLR signaling pathway such as MyD88 (Myeloid differentiation factor 88), Rac1 (Rac family small GTPase 1), TIRAP (TIR domain containing adaptor protein), Tollip (Toll interacting protein) as well as the inflammatory factors IL6 (Interleukin 6), IL8 (Interleukin 8), and TNFα (Tumor necrosis factor alpha) in tissues of 30 day-old piglet. In addition, serum IL6 and TNFα concentrations were also significantly upregulated by the ERV insertion (p < 0.05).

Conclusions
A total of five RIPs were identified in five different TLR loci. The 192 bp ERV insertion in the first intron of TLR6 was associated with higher expression of TLR6, TLR1, and several genes downstream in the signaling cascade. Thus, the ERV insertion may act as an enhancer affecting regulation of the TLR signaling pathways, and can be potentially applied in breeding of disease resistant animals.
2-D DOA estimation method based on coprime array MIMO radar
Authors: Zhang Fei , Zhang Zijing , Jin Aisuo , Ji Chuantang , Wang Yi 
Published: August 2021

AbstractAiming at the problem that traditional direction of arrival (DOA) estimation methods cannot handle multiple sources with high accuracy while increasing the degrees of freedom (DOF), a new method for 2-D DOA estimation based on coprime array MIMO radar (SA-MIMO-CA) is proposed. First of all, in order to ensure the accuracy of multi-source estimation when the number of elements is finite, a new coprime array model based on MIMO (MIMO-CA) is proposed. This method is based on a new MIMO array-based co-prime array model (MIMO-CA), which improves the accuracy of multi-source estimation when the number of array elements is limited, and obtains a larger array aperture with a smaller number of array elements, and improves the estimation accuracy of 2-D DOA. Finally, the effectiveness and reliability of the proposed SM-MIMO-CA method in improving the DOF of array and DOA accuracy are verified by experiments.
Generalized modular fractal spaces and fixed point theorems
Authors: Alihajimohammad Alireza , Saadati Reza 
Published: August 2021

AbstractIn this article, we introduce a new concept of Hausdorff distance through generalized modular metric on nonempty compact subsets and study some topological properties of it. This concept with contraction theory and the iterated function system (IFS) helps us to define a generalized modular fractal space.
Effects of supplemental irrigation on yield, water use efficiency and nitrogen use efficiency of potato grown in mollic Andosols
Authors: Satognon Felix , Owido Seth F. O. , Lelei Joyce J. 
Published: August 2021

Abstract
Background
Low soil fertility and reduced seasonal rainfall contribute to low potato (Solanum tuberosum L.) yield in Kenya. Nitrogen (N) deficiency is the major problem facing by the smallholder farmers of Kenya due to lack of fallow. Hence an introduction of supplemental irrigation with an adequate application of this nutrient could increase potato yield. The objective of this study was to determine the effects of supplemental irrigation and N-fertilisation on potato tuber yield, water use efficiency (WUE) and nitrogen use efficiency (NUE). The experiment was conducted in Nakuru County, Kenya for two seasons. The experimental soils are classified as mollic Andosols. The treatments comprised two irrigation treatments of full supplemental irrigation (FI) and rainfed production (RF) and four N levels of four N levels of 0 (N0), 60 (N1), 90 (N2) and 130 kg N/ha (N3).

Results
The results showed that total tuber yield, marketable tuber yield and NUE were significantly (P < 0.001) affected by irrigation × N-fertilisation while WUE was only affected (P < 0.001) by N-fertilisation. The highest total tuber yield, 58.28 tonnes/hectare (t/ha), was recorded under FI combined with N3. Treatment FI significantly increased marketable tuber yield by approximately 125.58% in all N treatments compared to RF. The highest NUE of potato (236.44 kg/kg of N) was obtained under FI combined with N3 but not significantly different from the NUE of potato obtained under FI with N2. N-fertilisation N3 produced the highest WUE of 14.24 kg/m3. Significant correlation was obtained between tuber yield and number of tubers/plant (r = 0.75, P < 0.001), NUE (r = 0.95, P < 0.001) and WUE (r = 0.72, P < 0.001).

Conclusion
High potato yield and marketable tuber yield can be achieved in mollic Andosols when water deficits of the growing season are eliminated with supplemental irrigation and an application of 130 kg N/ha.
Application of the analytic hierarchy process in the selection of traditional food criteria in Vojvodina (Serbia)
Authors: Blešić Ivana , Petrović Marko D. , Gajić Tamara , Tretiakova Tatiana , Vujičić Miroslav , Syromiatnikova Julia 
Published: August 2021

AbstractVojvodina Province (Northern Serbia) represents a multicultural area inhabited by around thirty nations and national or ethnic groups with their authentic tradition and culture. The gastronomy of Vojvodina has been forming as a reflection of geographic characteristics—natural conditions and social events in this area. The life numerous nations share on this fertile soil of Vojvodina has initiated mutual impact of various customs, which contributed to the creation of a unique and specific Vojvodina cuisine. In this paper, mixed-method research approach was applied. The application of the analytic hierarchy process (AHP) method was preceded by a survey research on the sample of 289 guests in the restaurants on the territory of Vojvodina. The aim of the research was to define the key motives when choosing a traditional Vojvodina dish. In the second stage, AHP model was used for ranking factors significant for choosing traditional food by 29 experts in the field of hospitality and gastronomy. The result shows that Sensory appeal is the most important criterion for choosing traditional food in restaurants by the experts, followed by Health concern, and Familiarity.
Recurrent acute pancreatitis in a Wilson disease patient: an unusual association
Authors: Kumar Sanjay , Sundaram Sridhar , Darak Harish , Giri Suprabhat , Bhatia Shobna 
Published: August 2021

Abstract
Background
Wilson’s disease is a multisystem disorder with predominant clinical symptoms depending on the site of copper deposition in the body. Hepatic presentation is usually seen in the younger age group. And pancreatitis is rarely associated with Wilson’s disease. To the best of our knowledge, recurrent acute pancreatitis as a presenting manifestation in a WD patient has not been mentioned before in the literature.

Case presentation
We report a 17-year-old boy who presented with recurrent acute pancreatitis and subsequently developed deranged liver enzymes and ascites. Work up for the cause of recurrent acute pancreatitis was normal. Low ceruloplasmin (0.07 mg/dL), high 24-h urinary copper excretion (576 μg/day), and dry copper content in the liver (270 μg/g) clinched the diagnosis of Wilson’s disease. The patient was started on a low-copper diet and D-penicillamine therapy resulting in an improvement in symptoms and no further recurrence of pancreatitis.

Conclusion
The possibility of Wilson’s disease should be considered in young patients with recurrent acute pancreatitis, who have a protracted and obscure disease course.
Relationship of horse temperament with breed, age, sex, and body characteristics: a questionnaire-based study
Authors: Abdel-Azeem Naglaa M. , Emeash H. H. 
Published: August 2021

Abstract
Background
Temperament is an important issue that must be taken into consideration when purchasing horses for leisure, racing, or even work in the fields. Those who work with horses have various opinions about the relationship between a horse’s body characteristics and its temperament, but few scientific papers on this issue have been published. The objective of this study was to clarify the relationships of horse temperament with sex, breed, age, and body characteristics to help purchasers when selecting a horse with the desired temperament. A web-based survey consisting of a 32-item questionnaire was used to clarify the associations of sex, breed, age, and body characteristics with a horse’s temperament. The owners of a total of 112 horses from different countries (Egypt, Jordan, Palestine, and Iraq) were recruited to fill in the questionnaire about their horses.

Results
The results showed statistically significant associations of sex and breed with temperament with 89.7% and 108.3%, respectively (p values < 0.001), while there was no significant association between age and temperament (chi-square p value 0.58). The results also clarified significant associations between body characteristics (color, head and body marks, leg marks, and whorls) and temperament (all chi-square p-values < 0.001).

Conclusion
Purchasers can predict a horse’s temperament from its sex, breed, and body characteristics, including coat color, body and leg marks, and whorls
Mapping subsurface karsts and voids using directional elastic wave packets
Authors: Ding Yinshuai , Hu Hao , Malallah Adel , Fehler Michael C. , Huang Lianjie , Malehmir Alireza , Zheng Yingcai 
Published: August 2021

We have developed a new data-driven algorithm that uses directional elastic wave packets as seismic sources to image subsurface voids (i.e., cavities). Compared to a point source, the advantage of the new approach is that the wave packet illuminates only a small volume of the medium around the raypath to significantly reduce multiple scattering effects in the imaging. We take the difference of traces at identical source-receiver offsets from each of two neighboring source packets. The difference mainly contains the void scattering events but not the direct waves, the layer reflections, refractions, nor layer-related multiples. We use P-to-P and P-to-S scattered waves to locate the voids, and the results using scattered P- and S-waves can cross-validate each other to reduce the possibility of false detections. The directional wave packet can be numerically synthesized using existing shot gathers; therefore, no special physical source is required. We determine our method using data calculated using a boundary element method to model the seismic wavefield in an irregularly layered medium containing several empty voids. We test the robustness of our method using the same data but with 15% root-mean-square random noise added. Furthermore, we compare our method with the reverse time migration imaging method using the same data and find that our method provides superior results that are not dependent on the construction of a velocity model.
Personalized Prediction Model to Risk Stratify Patients With Myelodysplastic Syndromes
Authors: Nazha Aziz , Komrokji Rami , Meggendorfer Manja , Jia Xuefei , Radakovich Nathan , Shreve Jacob , Hilton C. Beau , Nagata Yasunubo , Hamilton Betty K. , Mukherjee Sudipto , Al Ali Najla , Walter Wencke , Hutter Stephan , Padron Eric , Sallman David , Kuzmanovic Teodora , Kerr Cassandra , Adema Vera , Steensma David P. , Dezern Amy , Roboz Gail , Garcia-Manero Guillermo , Erba Harry , Haferlach Claudia , Maciejewski Jaroslaw P. , Haferlach Torsten , Sekeres Mikkael A. 
Published: August 2021

PURPOSE Patients with myelodysplastic syndromes (MDS) have a survival that can range from months to decades. Prognostic systems that incorporate advanced analytics of clinical, pathologic, and molecular data have the potential to more accurately and dynamically predict survival in patients receiving various therapies. METHODS A total of 1,471 MDS patients with comprehensively annotated clinical and molecular data were included in a training cohort and analyzed using machine learning techniques. A random survival algorithm was used to build a prognostic model, which was then validated in external cohorts. The accuracy of the proposed model, compared with other established models, was assessed using a concordance (c)index. RESULTS The median age for the training cohort was 71 years. Commonly mutated genes included SF3B1, TET2, and ASXL1. The algorithm identified chromosomal karyotype, platelet, hemoglobin levels, bone marrow blast percentage, age, other clinical variables, seven discrete gene mutations, and mutation number as having prognostic impact on overall and leukemia-free survivals. The model was validated in an independent external cohort of 465 patients, a cohort of patients with MDS treated in a prospective clinical trial, a cohort of patients with paired samples at different time points during the disease course, and a cohort of patients who underwent hematopoietic stem-cell transplantation. CONCLUSION A personalized prediction model on the basis of clinical and genomic data outperformed established prognostic models in MDS. The new model was dynamic, predicting survival and leukemia transformation probabilities at different time points that are unique for a given patient, and can upstage and downstage patients into more appropriate risk categories.
Effects of Dietary Fat and Protein on Glucoregulatory Hormones in Adolescents and Young Adults With Type 1 Diabetes
Authors: Harray Amelia J , Binkowski Sabrina , Keating Barbara L , Horowitz Michael , Standfield Scott , Smith Grant , Paramalingam Nirubasini , Jones Timothy , King Bruce R , Smart Carmel E M , Davis Elizabeth A 
Published: August 2021

AbstractContextDietary fat and protein impact postprandial hyperglycemia in people with type 1 diabetes, but the underlying mechanisms are poorly understood. Glucoregulatory hormones are also known to modulate gastric emptying and may contribute to this effect.ObjectiveInvestigate the effects of fat and protein on glucagon-like peptide (GLP-1), glucagon-dependent insulinotropic polypeptide (GIP) and glucagon secretion.Methods2 crossover euglycemic insulin clamp clinical trials at 2 Australian pediatric diabetes centers. Participants were 12-21 years (n = 21) with type 1 diabetes for ≥1 year. Participants consumed a low-protein (LP) or high-protein (HP) meal in Study 1, and low-protein/low-fat (LPLF) or high-protein/high-fat (HPHF) meal in Study 2, all containing 30 g of carbohydrate. An insulin clamp was used to maintain postprandial euglycemia and plasma glucoregulatory hormones were measured every 30 minutes for 5 hours. Data from both cohorts (n = 11, 10) were analyzed separately. The main outcome measure was area under the curve of GLP-1, GIP, and glucagon.ResultsMeals low in fat and protein had minimal effect on GLP-1, while there was sustained elevation after HP (80.3 ± 16.8 pmol/L) vs LP (56.9 ± 18.6), P = .016, and HPHF (103.0 ± 26.9) vs LPLF (69.5 ± 31.9) meals, P = .002. The prompt rise in GIP after all meals was greater after HP (190.2 ± 35.7 pmol/L) vs LP (152.3 ± 23.3), P = .003, and HPHF (258.6 ± 31.0) vs LPLF (151.7 ± 29.4), P &lt; .001. A rise in glucagon was also seen in response to protein, and HP (292.5 ± 88.1 pg/mL) vs LP (182.8 ± 48.5), P = .010.ConclusionThe impact of fat and protein on postprandial glucose excursions may be mediated by the differential secretion of glucoregulatory hormones. Further studies to better understand these mechanisms may lead to improved personalized postprandial glucose management.
Genome-wide Association Study of Lipid Traits in Youth With Type 2 Diabetes
Authors: Santoro Nicola , Chen Ling , Todd Jennifer , Divers Jasmin , Shah Amy S , Gidding Samuel S , Burke Brian , Haymond Morey , Lange Leslie , Marcovina Santica , Flannick Jason , Caprio Sonia , Florez Jose C , Srinivasan Shylaja 
Published: August 2021

Abstract

Context
Dyslipidemia is highly prevalent in youth with type 2 diabetes (T2D), yet the pathogenic components of dyslipidemia in youth with T2D are poorly understood.

Objective
To evaluate the genetic determinants of lipid traits in youth with T2D through a genome-wide association study.

Design, Participants, and Main Outcome Measures
We genotyped 206 928 variants and imputed 17 642 824 variants in 1076 youth (mean age 15.0 ± 2.48 years) with T2D from the Treatment Options for Type 2 Diabetes in Adolescents and Youth (TODAY) and SEARCH for Diabetes in Youth (SEARCH) studies as part of the Progress in Diabetes Genetics in Youth (ProDiGY) consortium. We performed association testing for triglyceride and low-density lipoprotein cholesterol and high-density lipoprotein cholesterol (HDL-c) concentrations adjusted for the genetic relationship matrix within each substudy followed by meta-analyses for each trait.

Results
We identified a novel association between a deletion on chromosome 3 (3:67817380_AT/A_Deletion:RP11-81N13.1) and triglyceride levels at genome-wide level of significance (P = 2.3 × 10−8) with each risk allele increasing triglycerides by 20%. We also identified a genome-wide significant signal at rs247617 (P = 5.1 × 10−9) between HERFUD1 and CETP associated with HDL-c, with carriers of 1 copy of the risk allele having twice higher HDL-c.

Conclusions
Our genetic analyses of lipid traits in youth with T2D have identified 1 novel and 1 previously known locus. Additional studies are needed to further characterize the genetic architecture of dyslipidemia in youth with T2D.
Insights into in vivo adipocyte differentiation through cell-specific labeling in zebrafish
Authors: Lepanto Paola , Levin-Ferreyra Florencia , Koziol Uriel , Malacrida Leonel , Badano José L. 
Published: August 2021

ABSTRACT
White adipose tissue hyperplasia has been shown to be crucial for handling excess energy in healthy ways. Though adipogenesis mechanisms have been underscored in vitro, we lack information on how tissue and systemic factors influence the differentiation of new adipocytes. While this could be studied in zebrafish, adipocyte identification currently relies on neutral lipid labeling, thus precluding access to cells in early stages of differentiation. Here we report the generation and analysis of a zebrafish line with the transgene fabp4a(-2.7):EGFPcaax. In vivo confocal microscopy of the pancreatic and abdominal visceral depots of transgenic larvae, revealed the presence of labeled mature adipocytes as well as immature cells in earlier stages of differentiation. Through co-labeling for blood vessels, we observed a close interaction of differentiating adipocytes with endothelial cells through cell protrusions. Finally, we implemented hyperspectral imaging and spectral phasor analysis in Nile Red-labeled transgenic larvae and revealed the lipid metabolic transition towards neutral lipid accumulation of differentiating adipocytes. Altogether our work presents the characterization of a novel adipocyte-specific label in zebrafish and uncovers previously unknown aspects of in vivo adipogenesis.
This article has an associated First Person interview with the first author of the paper.
Multiview tiling light sheet microscopy for 3D high-resolution live imaging
Authors: Aakhte Mostafa , Müller Hans-Arno J. 
Published: August 2021

ABSTRACT
Light-sheet or selective plane illumination microscopy (SPIM) is ideally suited for in toto imaging of living specimens at high temporal-spatial resolution. In SPIM, the light scattering that occurs during imaging of opaque specimens brings about limitations in terms of resolution and the imaging field of view. To ameliorate this shortcoming, the illumination beam can be engineered into a highly confined light sheet over a large field of view and multi-view imaging can be performed by applying multiple lenses combined with mechanical rotation of the sample. Here, we present a Multiview tiling SPIM (MT-SPIM) that combines the Multi-view SPIM (M-SPIM) with a confined, multi-tiled light sheet. The MT-SPIM provides high-resolution, robust and rotation-free imaging of living specimens. We applied the MT-SPIM to image nuclei and Myosin II from the cellular to subcellular spatial scale in early Drosophila embryogenesis. We show that the MT-SPIM improves the axial-resolution relative to the conventional M-SPIM by a factor of two. We further demonstrate that this axial resolution enhancement improves the automated segmentation of Myosin II distribution and of nuclear volumes and shapes.
Electrically tunable lenses – eliminating mechanical axial movements during high-speed 3D live imaging
Authors: Efstathiou Christoforos , Draviam Viji M. 
Published: August 2021

ABSTRACT
The successful investigation of photosensitive and dynamic biological events, such as those in a proliferating tissue or a dividing cell, requires non-intervening high-speed imaging techniques. Electrically tunable lenses (ETLs) are liquid lenses possessing shape-changing capabilities that enable rapid axial shifts of the focal plane, in turn achieving acquisition speeds within the millisecond regime. These human-eye-inspired liquid lenses can enable fast focusing and have been applied in a variety of cell biology studies. Here, we review the history, opportunities and challenges underpinning the use of cost-effective high-speed ETLs. Although other, more expensive solutions for three-dimensional imaging in the millisecond regime are available, ETLs continue to be a powerful, yet inexpensive, contender for live-cell microscopy.