bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome diversity of Chinese indigenous chicken and the selective signatures in Chinese gamecock chicken
Authors: Luo Wei , Luo Chenglong , Wang Meng , Guo Lijin , Chen Xiaolan , Li Zhenhui , Zheng Ming , Folaniyi Bello Semiu , Luo Wen , Shu Dingming , Song Linliang , Fang Meixia , Zhang Xiquan , Qu Hao , Nie Qinghua 
Published: September 2020

AbstractGamecock chickens are one of the earliest recorded birds in China, and have accumulated some unique morphological and behavioral signatures such as large body size, muscularity and aggressive behavior, whereby being excellent breeding materials and a good model for studying bird muscular development and behavior. In this study, we sequenced 126 chicken genomes from 19 populations, including four commercial chicken breeds that are commonly farmed in China, 13 nationwide Chinese typical indigenous chicken breeds (including two Chinese gamecock breeds), one red jungle fowl from Guangxi Province of China and three gamecock chickens from Laos. Combined with 31 published chicken genomes from three populations, a comparative genomics analysis was performed across 157 chickens. We found a severe confounding effect on potential cold adaptation exerted by introgression from commercial chickens into Chinese indigenous chickens, and argued that the genetic introgression from commercial chickens into indigenous chickens should be seriously considered for identifying selection footprint in indigenous chickens. LX gamecock chickens might have played a core role in recent breeding and conservation of other Chinese gamecock chickens. Importantly, AGMO (Alkylglycerol monooxygenase) and CPZ (Carboxypeptidase Z) might be crucial for determining the behavioral pattern of gamecock chickens, while ISPD (Isoprenoid synthase domain containing) might be essential for the muscularity of gamecock chickens. Our results can further the understanding of the evolution of Chinese gamecock chickens, especially the genetic basis of gamecock chickens revealed here was valuable for us to better understand the mechanisms underlying the behavioral pattern and the muscular development in chicken.
Transition delay using biomimetic fish scale arrays
Authors: Muthuramalingam Muthukumar , Puckert Dominik K. , Rist Ulrich , Bruecker Christoph 
Published: September 2020

AbstractAquatic animals have developed effective strategies to reduce their body drag over a long period of time. In this work, the influence of the scales of fish on the laminar-to-turbulent transition in the boundary layer is investigated. Arrays of biomimetic fish scales in typical overlapping arrangements are placed on a flat plate in a low-turbulence laminar water channel. Transition to turbulence is triggered by controlled excitation of a Tollmien–Schlichting (TS) wave. It was found that the TS wave can be attenuated with scales on the plate which generate streamwise streaks. As a consequence, the transition location was substantially delayed in the downstream direction by 55% with respect to the uncontrolled reference case. This corresponds to a theoretical drag reduction of about 27%. We thus hypothesize that fish scales can stabilize the laminar boundary layer and prevent it from early transition, reducing friction drag. This technique can possibly be used for bio-inspired surfaces as a laminar flow control means.
Structure of Pb(Fe2/3W1/3)O3 single crystals with partial cation order
Authors: Ivanov S. A. , Stash A. I. , Riekehr L. , Chen Y.-S. , Ye Z.-G. 
Published: September 2020

AbstractDespite intensive studies on the complex perovskite Pb(Fe2/3W1/3)O3 (PFWO) relaxor, understanding the exact nature of its multifunctional properties has remained a challenge for decades. In this work we report a comprehensive structural study of the PFWO single crystals using a combination of synchrotron X-ray diffraction and high-resolution electron microscopy. The set of {h + ½, k + ½, l + ½} superlattice reflections was observed for the first time based on single-crystal synchrotron X-ray experiments (100–450 K) and transmission electron microscopy investigations, which indicates some kind of B-cation ordering in PFWO which had been thought to be totally disordered. It was found that (1) the crystal structure of PFWO should be described by a partly ordered cubic perovskite (i.e. Fm − 3m), (2) the weak ferromagnetic properties and excess magnetic moment of PFWO can be understood based on non-random distribution of Fe cations between the 4a and 4b sites, and (3) the Pb displacement disorder is present in this material and the cations are probably displaced along the <100> directions. The X-ray diffraction results of this investigation show that partial cation ordering indeed exists in PFWO, which makes it necessary to revisit the generally accepted interpretations of the results obtained up to date. In agreement with X-ray diffraction study the main results of TEM study include: (1) a long range order that can be described with the Fm − 3m symmetry is reliably detected, (2) the coherence length of that long range order is in the order of 1–2 nm and (3) no remarkable chemical inhomogeneity is found in the tested PFWO crystal, excluding the possibility of a compositional ordering arising from substitutional defects in the perovskite structure.
Lifetime risks and health impacts of hemorrhagic and ischemic stroke in South Korea
Authors: Cheon Soyeon , Lee Hyangsook , Won Jiyoon , Jang Bo-Hyoung , Wang Jung-Der 
Published: September 2020

AbstractThis study is aimed toward estimating the lifetime risks, life expectancy, expected years of life lost (EYLL), and lifetime costs related to different subtypes of stroke in South Korea. We included 13,994 patients diagnosed with stroke (ICD-10, I60-I63) in the National Health Insurance Service-National Sample Cohort of Korea between 2006 and 2015. Lifetime risks were calculated using the cumulative incidence rate for patients aged 18–84. Lifetime survival data were obtained through the Kaplan–Meier method and extrapolated with a rolling-over extrapolation algorithm. The lifetime costs were estimated by multiplying the average monthly expenditures with the survival probabilities and adding the values over lifetime. The lifetime risks of stroke in Korea have been decreasing consistently over the last decade with the exception of subarachnoid hemorrhage in females, which appears to have slightly increased. The EYLL is higher in hemorrhagic stroke than in ischemic stroke (6–9.7 vs. 4.7). Expected lifetime costs reimbursed by the NHIS would amount to about $71,406 accompanied with $14,921 copayment from the patients for hemorrhagic stroke, and $50,551 and $11,666, respectively, for ischemic stroke. Further studies are warranted to combine survival with quality of life and functional disability to obtain a more detailed outcome assessment of the potential impact of the prevention of stroke.
Mutation of regulatory phosphorylation sites in PFKFB2 worsens renal fibrosis
Authors: Lee Mardiana , Harley Geoff , Katerelos Marina , Gleich Kurt , Sullivan Mitchell A. , Laskowski Adrienne , Coughlan Melinda , Fraser Scott A. , Mount Peter F. , Power David A. 
Published: September 2020

AbstractFatty acid oxidation is the major energy pathway used by the kidney, although glycolysis becomes more important in the low oxygen environment of the medulla. Fatty acid oxidation appears to be reduced in renal fibrosis, and drugs that reverse this improve fibrosis. Expression of glycolytic genes is more variable, but some studies have shown that inhibiting glycolysis reduces renal fibrosis. To address the role of glycolysis in renal fibrosis, we have used a genetic approach. The crucial control point in the rate of glycolysis is 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase. Phosphorylation of the kidney isoform, PFKFB2, on residues Ser468 and Ser485 stimulates glycolysis and is the most important mechanism regulating glycolysis. We generated transgenic mice with inactivating mutations of Ser468 and Ser485 in PFKFB2 (PFKFB2 KI mice). These mutations were associated with a reduced ability to increase glycolysis in primary cultures of renal tubular cells from PFKFB2 KI mice compared to WT cells. This was associated in PFKFB2 KI mice with increased renal fibrosis, which was more severe in the unilaternal ureteric obstruction (UUO) model compared with the folic acid nephropathy (FAN) model. These studies show that phosphorylation of PFKFB2 is important in limiting renal fibrosis after injury, indicating that the ability to regulate and maintain adequate glycolysis in the kidney is crucial for renal homeostasis. The changes were most marked in the UUO model, probably reflecting a greater effect on distal renal tubules and the greater importance of glycolysis in the distal nephron.
An edge-lit volume holographic optical element for an objective turret in a lensless digital holographic microscope
Authors: Yu Yeh-Wei , Sun Ching-Cherng , Hsieh Po-Kai , Huang Yi-Hao , Song Chih-Yuan , Yang Tsung-Hsun 
Published: September 2020

AbstractIn this paper, we propose and demonstrate the use of an edge-lit volume holographic optical element (EL-VHOE) as a reference waveguide to reduce the volume of a lensless digital holographic microscope. Additionally, a hybrid lensless Fourier transform digital holography is applied to make the EL-VHOE function as an objective turret. It used a spherical wave in the object beam of the EL-VHOE, which served as the reference beam of the microscope. Another sheared spherical wave was used to illuminate the sample. The longitudinal position of the spherical reference beam is changeable. It was shown that the tradeoff between resolution and field of view can be adjusted by changing the longitudinal position of the spherical reference beam. The corresponding experimental results matched the simulational and theoretical predictions. A resolution of approximately 3.11 μm was achieved when the object distance was 6 mm and the longitudinal distance of the spherical reference was 10 mm.
A cadaver-based biomechanical model of acetabulum reaming for surgical virtual reality training simulators
Authors: Pelliccia Luigi , Lorenz Mario , Heyde Christoph-E. , Kaluschke Maximilian , Klimant Philipp , Knopp Sebastian , Schleifenbaum Stefan , Rotsch Christian , Weller René , Werner Michael , Zachmann Gabriel , Zajonz Dirk , Hammer Niels 
Published: September 2020

AbstractTotal hip arthroplasty (THA) is a highly successful surgical procedure, but complications remain, including aseptic loosening, early dislocation and misalignment. These may partly be related to lacking training opportunities for novices or those performing THA less frequently. A standardized training setting with realistic haptic feedback for THA does not exist to date. Virtual Reality (VR) may help establish THA training scenarios under standardized settings, morphology and material properties. This work summarizes the development and acquisition of mechanical properties on hip reaming, resulting in a tissue-based material model of the acetabulum for force feedback VR hip reaming simulators. With the given forces and torques occurring during the reaming, Cubic Hermite Spline interpolation seemed the most suitable approach to represent the nonlinear force–displacement behavior of the acetabular tissues over Cubic Splines. Further, Cubic Hermite Splines allowed for a rapid force feedback computation below the 1 ms hallmark. The Cubic Hermite Spline material model was implemented using a three-dimensional-sphere packing model. The resulting forces were delivered via a human–machine-interaction certified KUKA iiwa robotic arm used as a force feedback device. Consequently, this novel approach presents a concept to obtain mechanical data from high-force surgical interventions as baseline data for material models and biomechanical considerations; this will allow THA surgeons to train with a variety of machining hardness levels of acetabula for haptic VR acetabulum reaming.
Combined proteomics and transcriptomics reveal the genetic basis underlying the differentiation of skin appendages and immunity in pangolin
Authors: Li Hui-Ming , Liu Ping , Zhang Xiu-Juan , Li Lin-Miao , Jiang Hai-Ying , Yan Hua , Hou Fang-Hui , Chen Jin-Ping 
Published: September 2020

AbstractPangolin (Mains javanica) is an interesting endangered mammal with special morphological characteristics. Here, we applied proteomics and transcriptomics to explore the differentiation of pangolin skin appendages at two developmental stages and to compare gene expression profiles between abdomen hair and dorsal scale tissues. We identified 4,311 genes and 91 proteins differentially expressed between scale-type and hair-type tissue, of which 6 genes were shared by the transcriptome and proteome. Differentiation altered the abundance of hundreds of proteins and mRNA in the two types of skin appendages, many of which are involved in keratinocyte differentiation, epidermal cell differentiation, and multicellular organism development based on GO enrichment analysis, and FoxO, MAPK, and p53 signalling pathways based on KEGG enrichment analysis. DEGs in scale-type tissues were also significantly enriched in immune-related terms and pathways compared with that in hair-type tissues. Thus, we propose that pangolins have a normal skin innate immune system. Compared with the abdomen, the back skin of pangolins had more genes involved in the regulation of immune function, which may be an adaptive adjustment for the vulnerability of scaly skin to infection and injury. This investigation provides a scientific basis for the study of development and immunity of pangolin skin, which may be helpful in the protection of wild pangolin in China.
Effect of di-(2-ethylhexyl) phthalate (DEHP) on allergic rhinitis
Authors: Zou Qi-Yuan , Hong Su-Ling , Kang Hou-Yong , Ke Xia , Wang Xiao-Qiang , Li Jia , Shen Yang 
Published: September 2020

AbstractAllergic rhinitis (AR) is a common chronic inflammatory disease of the upper respiratory tract. Di(2-ethylhexyl) phthalate (DEHP) is a widely used plasticizer and belongs to environmental endocrine disruptors (EDCs). It can be entered the human body which is harmful to health. The relationship between DEHP and AR is still inconclusive. This study aims to investigate the effect of environmental pollutants DEHP on AR. By examining DEHP metabolites in the urine of AR patients and building an AR model. 24 BALB/c mice were used as the study subjects, and ovalbumin (OVA) and DEHP (3 mg/kg/body) were used for intragastric administration. They were divided into control group, DEHP group, OVA group and OVA + DEHP group. Examination, behavioral scoring, inflammatory factor testing, oxidative stress testing, detection of aryl hydrocarbon receptor (AhR) and signaling pathways CYP1A1 and CYP1B1 related proteins and mRNA. The concentrations of 3 metabolites of DEHP (MEHHP, MEOHP, and MEHP) in urine of AR patients were higher. And HE-staining showed that for the control group, many chronic inflammatory cell infiltration and nasal mucosal destruction were observed in the OVA + DEHP group and were more severe than the OVA group. Allergic symptom scores were obtained from sneezing, scratching, number of scratching, and nose flow. The scores of the OVA group and the OVA + DEHP group were higher than 7 points. Serum ELISA and nasal mucosal oxidative stress tests are more serious in the OVA + DEHP group. The expression of AhR protein and its mRNA was increased in the DEHP group, OVA group and OVA + DEHP group. The OVA + DEHP group was more significant in the OVA group and DEHP group. And the mRNAs of the AhR-related signaling pathways CYP1A1 and CYP1B1 were also more prominent in the OVA + DEHP group. DEHP may aggravate its inflammatory response through the AhR pathway closely related to the environment. When combined with OVA, DEHP can further aggravate the OVA-induced nasal inflammatory response and make the nasal cavity have undergone severe changes, and many inflammatory cells have infiltrated. DEHP has shown an adjuvant effect, and the AhR-related signaling pathways CYP1A1 and CYP1B1 may be critical.
Identification and characterization of SET domain family genes in bread wheat (Triticum aestivum L.)
Authors: Batra Ritu , Gautam Tinku , Pal Sunita , Chaturvedi Deepti , Rakhi  , Jan Irfat , Balyan Harindra Singh , Gupta Pushpendra Kumar 
Published: September 2020

AbstractSET domain genes (SDGs) that are involved in histone methylation have been examined in many plant species, but have never been examined in bread wheat; the histone methylation caused due to SDGs is associated with regulation of gene expression at the transcription level. We identified a total of 166 bread wheat TaSDGs, which carry some interesting features including the occurrence of tandem/interspersed duplications, SSRs (simple sequence repeats), transposable elements, lncRNAs and targets for miRNAs along their lengths and transcription factor binding sites (TFBS) in the promoter regions. Only 130 TaSDGs encoded proteins with complete SET domain, the remaining 36 proteins had truncated SET domain. The TaSDG encoded proteins were classified into six classes (I–V and VII). In silico expression analysis indicated relatively higher expression (FPKM > 20) of eight of the 130 TaSDGs in different tissues, and downregulation of 30 TaSDGs under heat and drought at the seedling stage. qRT-PCR was also conducted to validate the expression of seven genes at the seedling stage in pairs of contrasting genotypes in response to abiotic stresses (water and heat) and biotic stress (leaf rust). These genes were generally downregulated in response to the three stresses examined.
Yersinia pestis strains from Latvia show depletion of the pla virulence gene at the end of the second plague pandemic
Authors: Susat Julian , Bonczarowska Joanna H. , Pētersone-Gordina Elīna , Immel Alexander , Nebel Almut , Gerhards Guntis , Krause-Kyora Ben 
Published: September 2020

AbstractAncient genomic studies have identifiedYersinia pestis(Y. pestis) as the causative agent of the second plague pandemic (fourteenth–eighteenth century) that started with the Black Death (1,347–1,353). Most of theY. pestisstrains investigated from this pandemic have been isolated from western Europe, and not much is known about the diversity and microevolution of this bacterium in eastern European countries. In this study, we investigated human remains excavated from two cemeteries in Riga (Latvia). Historical evidence suggests that the burials were a consequence of plague outbreaks during the seventeenth century. DNA was extracted from teeth of 16 individuals and subjected to shotgun sequencing. Analysis of the metagenomic data revealed the presence ofY. pestissequences in four remains, confirming that the buried individuals were victims of plague. In two samples,Y. pestisDNA coverage was sufficient for genome reconstruction. Subsequent phylogenetic analysis showed that the Riga strains fell within the diversity of the already known post-Black Death genomes. Interestingly, the two Latvian isolates did not cluster together. Moreover, we detected a drop in coverage of the pPCP1 plasmid region containing theplagene. Further analysis indicated the presence of two pPCP1 plasmids, one with and one without theplagene region, and only one bacterial chromosome, indicating that the same bacterium carried two distinct pPCP1 plasmids. In addition, we found the same pattern in the majority of previously published post-Black Death strains, but not in the Black Death strains. Thepla gene is an important virulence factor for the infection of and transmission in humans. Thus, the spread ofpla-depleted strains may, among other causes, have contributed to the disappearance of the second plague pandemic in eighteenth century Europe.
Random fields and apparent exchange bias in the dilute Ising antiferromagnet Fe0.6Zn0.4F2
Authors: Joshi D. C. , Nordblad P. , Mathieu R. 
Published: September 2020

AbstractRandom field induced spontaneous excess moments appear in field cooled single crystals of diluted Ising antiferromagnets. Here we report results from low temperature measurements of field cooled (including zero field) magnetic hysteresis loops parallel and perpendicular to the c-axis of a single crystal of composition Fe0.6Zn0.4F2. We find that weak static ferromagnetic excess moments attained on field cooling give rise to an apparent exchange bias of the magnetic hysteresis loops, whose magnitude is controlled by temperature and the strength and direction of the cooling field. Random field induced temporal excess moments only become observable in cooling fields larger than 1 T applied along the c-axis direction of the Fe0.6Zn0.4F2 single crystal.
Association between regional economic status and renal recovery of dialysis-requiring acute kidney injury among critically ill patients
Authors: Shiao Chih-Chung , Chang Yu-Hsing , Yang Ya-Fei , Lin En-Tzu , Pan Heng-Chih , Chang Chih-Hsiang , Huang Chun-Te , Kao Min-Tsung , Chuang Tzung-Fang , Chen Yung-Chang , Kan Wei-Chih , Kuo Feng-Chi , Chen Te-Chuan , Chen Yung-Ming , Wu Chih-Jen , Liou Hung-Hsiang , Lu Kuo-Cheng , Wu Vin-Cent , Chu Tzong-Shinn , Wu Mai-Szu , Wu Kwan-Dun , Fang Ji-Tseng , Huang Chiu-Ching 
Published: September 2020

AbstractThe association between regional economic status and the probability of renal recovery among patients with dialysis-requiring AKI (AKI-D) is unknown. The nationwide prospective multicenter study enrolled critically ill adult patients with AKI-D in four sampled months (October 2014, along with January, April, and July 2015) in Taiwan. The regional economic status was defined by annual disposable income per capita (ADIPC) of the cities the hospitals located. Among the 1,322 enrolled patients (67.1 ± 15.5 years, 36.2% female), 833 patients (63.1%) died, and 306 (23.1%) experienced renal recovery within 90 days following discharge. We categorized all patients into high (n = 992) and low economic status groups (n = 330) by the best cut-point of ADIPC determined by the generalized additive model plot. By using the Fine and Gray competing risk regression model with mortality as a competing risk factor, we found that the independent association between regional economic status and renal recovery persisted from model 1 (no adjustment), model 2 (adjustment to basic variables), to model 3 (adjustment to basic and clinical variables; subdistribution hazard ratio, 1.422; 95% confidence interval, 1.022–1.977; p = 0.037). In conclusion, high regional economic status was an independent factor for renal recovery among critically ill patients with AKI-D.