bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptome analyses shed light on carotenoid production and plastid development in melon fruit
Authors: Chayut Noam , Yuan Hui , Saar Yuval , Zheng Yi , Sun Tianhu , Zhou Xuesong , Hermanns Anna , Oren Elad , Faigenboim Adi , Hui Maixia , Fei Zhangjun , Mazourek Michael , Burger Joseph , Tadmor Yaakov , Li Li 
Published: May 2021

AbstractCarotenoids, such as β-carotene, accumulate in chromoplasts of various fleshy fruits, awarding them with colors, aromas, and nutrients. The Orange (CmOr) gene controls β-carotene accumulation in melon fruit by posttranslationally enhancing carotenogenesis and repressing β-carotene turnover in chromoplasts. Carotenoid isomerase (CRTISO) isomerizes yellow prolycopene into red lycopene, a prerequisite for further metabolism into β-carotene. We comparatively analyzed the developing fruit transcriptomes of orange-colored melon and its two isogenic EMS-induced mutants, low-β (Cmor) and yofi (Cmcrtiso). The Cmor mutation in low-β caused a major transcriptomic change in the mature fruit. In contrast, the Cmcrtiso mutation in yofi significantly changed the transcriptome only in early fruit developmental stages. These findings indicate that melon fruit transcriptome is primarily altered by changes in carotenoid metabolic flux and plastid conversion, but minimally by carotenoid composition in the ripe fruit. Clustering of the differentially expressed genes into functional groups revealed an association between fruit carotenoid metabolic flux with the maintenance of the photosynthetic apparatus in fruit chloroplasts. Moreover, large numbers of thylakoid localized photosynthetic genes were differentially expressed in low-β. CmOR family proteins were found to physically interact with light-harvesting chlorophyll a–b binding proteins, suggesting a new role of CmOR for chloroplast maintenance in melon fruit. This study brings more insights into the cellular and metabolic processes associated with fruit carotenoid accumulation in melon fruit and reveals a new maintenance mechanism of the photosynthetic apparatus for plastid development.
Learning a genome-wide score of human–mouse conservation at the functional genomics level
Authors: Kwon Soo Bin , Ernst Jason 
Published: May 2021

AbstractIdentifying genomic regions with functional genomic properties that are conserved between human and mouse is an important challenge in the context of mouse model studies. To address this, we develop a method to learn a score of evidence of conservation at the functional genomics level by integrating information from a compendium of epigenomic, transcription factor binding, and transcriptomic data from human and mouse. The method, Learning Evidence of Conservation from Integrated Functional genomic annotations (LECIF), trains neural networks to generate this score for the human and mouse genomes. The resulting LECIF score highlights human and mouse regions with shared functional genomic properties and captures correspondence of biologically similar human and mouse annotations. Analysis with independent datasets shows the score also highlights loci associated with similar phenotypes in both species. LECIF will be a resource for mouse model studies by identifying loci whose functional genomic properties are likely conserved.
Next generation plasma proteome profiling to monitor health and disease
Authors: Zhong Wen , Edfors Fredrik , Gummesson Anders , Bergström Göran , Fagerberg Linn , Uhlén Mathias 
Published: May 2021

AbstractThe need for precision medicine approaches to monitor health and disease makes it important to develop sensitive and accurate assays for proteome profiles in blood. Here, we describe an approach for plasma profiling based on proximity extension assay combined with next generation sequencing. First, we analyze the variability of plasma profiles between and within healthy individuals in a longitudinal wellness study, including the influence of genetic variations on plasma levels. Second, we follow patients newly diagnosed with type 2 diabetes before and during therapeutic intervention using plasma proteome profiling. The studies show that healthy individuals have a unique and stable proteome profile and indicate that a panel of proteins could potentially be used for early diagnosis of diabetes, including stratification of patients with regards to response to metformin treatment. Although validation in larger cohorts is needed, the analysis demonstrates the usefulness of comprehensive plasma profiling for precision medicine efforts.
Room-temperature intrinsic ferromagnetism in epitaxial CrTe2 ultrathin films
Authors: Zhang Xiaoqian , Lu Qiangsheng , Liu Wenqing , Niu Wei , Sun Jiabao , Cook Jacob , Vaninger Mitchel , Miceli Paul F. , Singh David J. , Lian Shang-Wei , Chang Tay-Rong , He Xiaoqing , Du Jun , He Liang , Zhang Rong , Bian Guang , Xu Yongbing 
Published: May 2021

AbstractWhile the discovery of two-dimensional (2D) magnets opens the door for fundamental physics and next-generation spintronics, it is technically challenging to achieve the room-temperature ferromagnetic (FM) order in a way compatible with potential device applications. Here, we report the growth and properties of single- and few-layer CrTe2, a van der Waals (vdW) material, on bilayer graphene by molecular beam epitaxy (MBE). Intrinsic ferromagnetism with a Curie temperature (TC) up to 300 K, an atomic magnetic moment of ~0.21 $${\mu }_{{\rm{B}}}$$

μ

B

/Cr and perpendicular magnetic anisotropy (PMA) constant (Ku) of 4.89 × 105 erg/cm3 at room temperature in these few-monolayer films have been unambiguously evidenced by superconducting quantum interference device and X-ray magnetic circular dichroism. This intrinsic ferromagnetism has also been identified by the splitting of majority and minority band dispersions with ~0.2 eV at Г point using angle-resolved photoemission spectroscopy. The FM order is preserved with the film thickness down to a monolayer (TC ~ 200 K), benefiting from the strong PMA and weak interlayer coupling. The successful MBE growth of 2D FM CrTe2 films with room-temperature ferromagnetism opens a new avenue for developing large-scale 2D magnet-based spintronics devices.
Amorphous thin-film oxide power devices operating beyond bulk single-crystal silicon limit
Authors: Tsuruma Yuki , Kawashima Emi , Nagasaki Yoshikazu , Sekiya Takashi , Imamura Gaku , Yoshikawa Genki 
Published: May 2021

AbstractPower devices (PD) are ubiquitous elements of the modern electronics industry that must satisfy the rigorous and diverse demands for robust power conversion systems that are essential for emerging technologies including Internet of Things (IoT), mobile electronics, and wearable devices. However, conventional PDs based on “bulk” and “single-crystal” semiconductors require high temperature (> 1000 °C) fabrication processing and a thick (typically a few tens to 100 μm) drift layer, thereby preventing their applications to compact devices, where PDs must be fabricated on a heat sensitive and flexible substrate. Here we report next-generation PDs based on “thin-films” of “amorphous” oxide semiconductors with the performance exceeding the silicon limit (a theoretical limit for a PD based on bulk single-crystal silicon). The breakthrough was achieved by the creation of an ideal Schottky interface without Fermi-level pinning at the interface, resulting in low specific on-resistance Ron,sp (< 1 × 10–4 Ω cm2) and high breakdown voltage VBD (~ 100 V). To demonstrate the unprecedented capability of the amorphous thin-film oxide power devices (ATOPs), we successfully fabricated a prototype on a flexible polyimide film, which is not compatible with the fabrication process of bulk single-crystal devices. The ATOP will play a central role in the development of next generation advanced technologies where devices require large area fabrication on flexible substrates and three-dimensional integration.
Development of experimental ground truth and quantification of intracranial aneurysm pulsation in a patient
Authors: Vanrossomme Axel E. , Chodzyński Kamil J. , Eker Omer F. , Boudjeltia Karim Zouaoui 
Published: May 2021

AbstractAneurysm wall motion has been reported to be associated with rupture. However, its quantification with medical imaging is challenging and should be based on experimental ground-truth to avoid misinterpretation of results. In this work a time-resolved CT angiography (4D-CTA) acquisition protocol is proposed to detect the pulsation of intracranial aneurysms with a low radiation dose. To acquire ground-truth data, the accuracy of volume pulsation detection and quantification in a silicone phantom was assessed by applying pressure sinusoidal waves of increasing amplitudes. These experiments were carried out using a test bench that could reproduce pulsatile waveforms similar to those inside the internal carotid arteries of human subjects. 4D-CTA acquisition parameters (mAs, kVp) were then selected to achieve reliable pulsation detection and quantification with the lowest radiation dose achievable. The resulting acquisition protocol was then used to image an anterior communicating artery aneurysm in a human subject. Data reveals that in a simplified in vitro setting 4D-CTA allows for an effective and reproducible method to detect and quantify aneurysm volume pulsation with an inferior limit as low as 3 mm3 and a background noise of 0.5–1 mm3. Aneurysm pulsation can be detected in vivo with a radiation dose approximating 1 mSv.
GABA enhancement by simple carbohydrates in yoghurt fermented using novel, self-cloned Lactobacillus plantarum Taj-Apis362 and metabolomics profiling
Authors: Hussin Farah Salina , Chay Shyan Yea , Hussin Anis Shobirin Meor , Wan Ibadullah Wan Zunairah , Muhialdin Belal J. , Abd Ghani Mohd Syahmi , Saari Nazamid 
Published: May 2021

AbstractThis study aimed to enhance natural gamma aminobutyric acid (GABA) production in yoghurt by the addition of simple sugars and commercial prebiotics without the need for pyridoxal 5′-phosphate (PLP) cofactor. The simple sugars induced more GABA production (42.83–58.56 mg/100 g) compared to the prebiotics (34.19–40.51 mg/100 g), with glucose promoting the most GABA production in yoghurt (58.56 mg/100 g) surpassing the control sample with added PLP (48.01 mg/100 g). The yoghurt prepared with glucose also had the highest probiotic count (9.31 log CFU/g). Simulated gastrointestinal digestion of this GABA-rich yoghurt showed a non-significant reduction in GABA content and probiotic viability, demonstrating the resistance towards a highly acidic environment (pH 1.2). Refrigerated storage up to 28 days improved GABA production (83.65 mg/100 g) compared to fresh GABA-rich yoghurt prepared on day 1. In conclusion, the addition of glucose successfully mitigates the over-use of glutamate and omits the use of PLP for increased production of GABA in yoghurt, offering an economical approach to produce a probiotic-rich dairy food with potential anti-hypertensive effects.
8806 Russian patients demonstrate T cell count as better marker of COVID-19 clinical course severity than SARS-CoV-2 viral load
Authors: Sharov Konstantin S. 
Published: May 2021

AbstractThe article presents a comparative analysis of SARS-CoV-2 viral load (VL), T lymphocyte count and respiratory index PaO2:FiO2 ratio as prospective markers of COVID-19 course severity and prognosis. 8806 patients and asymptomatic carriers were investigated in time interval 15 March–19 December 2020. T cell count demonstrated better applicability as a marker of aggravating COVID-19 clinical course and unfavourable disease prognosis than SARS-CoV-2 VL or PaO2:FiO2 ratio taken alone. Using T cell count in clinical practice may provide an opportunity of early prediction of deteriorating a patient’s state.
How detection ranges and usage stops impact digital contact tracing effectiveness for COVID-19
Authors: Pandl Konstantin D. , Thiebes Scott , Schmidt-Kraepelin Manuel , Sunyaev Ali 
Published: May 2021

AbstractTo combat the COVID-19 pandemic, many countries around the globe have adopted digital contact tracing apps. Various technologies exist to trace contacts that are potentially prone to different types of tracing errors. Here, we study the impact of different proximity detection ranges on the effectiveness and efficiency of digital contact tracing apps. Furthermore, we study a usage stop effect induced by a false positive quarantine. Our results reveal that policy makers should adjust digital contact tracing apps to the behavioral characteristics of a society. Based on this, the proximity detection range should at least cover the range of a disease spread, and be much wider in certain cases. The widely used Bluetooth Low Energy protocol may not necessarily be the most effective technology for contact tracing.
Advanced glycation end products as predictors of renal function in youth with type 1 diabetes
Authors: Forbes Josephine M. , Le Bagge Selena , Righi Samuel , Fotheringham Amelia K. , Gallo Linda A. , McCarthy Domenica A. , Leung Sherman , Baskerville Tracey , Nisbett Janelle , Morton Adam , Teasdale Stephanie , D’Silva Neisha , Barrett Helen , Jones Timothy , Couper Jennifer , Donaghue Kim , Isbel Nicole , Johnson David W. , Donnellan Leigh , Deo Permal , Akison Lisa K. , Moritz Karen M. , O’Moore-Sullivan Trisha 
Published: May 2021

AbstractTo examine if skin autofluorescence (sAF) differed in early adulthood between individuals with type 1 diabetes and age-matched controls and to ascertain if sAF aligned with risk for kidney disease. Young adults with type 1 diabetes (N = 100; 20.0 ± 2.8 years; M:F 54:46; FBG-11.6 ± 4.9 mmol/mol; diabetes duration 10.7 ± 5.2 years; BMI 24.5(5.3) kg/m2) and healthy controls (N = 299; 20.3 ± 1.8 years; M:F-83:116; FBG 5.2 ± 0.8 mmol/L; BMI 22.5(3.3) kg/m2) were recruited. Skin autofluorescence (sAF) and circulating AGEs were measured. In a subset of both groups, kidney function was estimated by GFRCKD-EPI CysC and uACR, and DKD risk defined by uACR tertiles. Youth with type 1 diabetes had higher sAF and BMI, and were taller than controls. For sAF, 13.6% of variance was explained by diabetes duration, height and BMI (Pmodel = 1.5 × 10–12). In the sub-set examining kidney function, eGFR and sAF were higher in type 1 diabetes versus controls. eGFR and sAF predicted 24.5% of variance in DKD risk (Pmodel = 2.2 × 10–9), which increased with diabetes duration (51%; Pmodel < 2.2 × 10–16) and random blood glucose concentrations (56%; Pmodel < 2.2 × 10–16). HbA1C and circulating fructosamine albumin were higher in individuals with type 1 diabetes at high versus low DKD risk. eGFR was independently associated with DKD risk in all models. Higher eGFR and longer diabetes duration are associated with DKD risk in youth with type 1 diabetes. sAF, circulating AGEs, and urinary AGEs were not independent predictors of DKD risk. Changes in eGFR should be monitored early, in addition to uACR, for determining DKD risk in type 1 diabetes.
Aggressive behaviour is affected by demographic, environmental and behavioural factors in purebred dogs
Authors: Mikkola Salla , Salonen Milla , Puurunen Jenni , Hakanen Emma , Sulkama Sini , Araujo César , Lohi Hannes 
Published: May 2021

AbstractAggressive behaviour is an unwanted and serious problem in pet dogs, negatively influencing canine welfare, management and public acceptance. We aimed to identify demographic and environmental factors associated with aggressive behaviour toward people in Finnish purebred pet dogs. We collected behavioural data from 13,715 dogs with an owner-completed online questionnaire. Here we used a dataset of 9270 dogs which included 1791 dogs with frequent aggressive behaviour toward people and 7479 dogs without aggressive behaviour toward people. We studied the effect of several explanatory variables on aggressive behaviour with multiple logistic regression. Several factors increased the probability of aggressive behaviour toward people: older age, being male, fearfulness, small body size, lack of conspecific company, and being the owner’s first dog. The probability of aggressive behaviour also differed between breeds. These results replicate previous studies and suggest that improvements in the owner education and breeding practices could alleviate aggressive behaviour toward people while genetic studies could reveal associated hereditary factors.
The game changing role of traditional ecological knowledge based Agri amendment systems in nutrient dynamics in the stress prone semi arid tropics
Authors: Sharma Seema B. , Thivakaran G. A. , Thakkar Mahesh G. 
Published: May 2021

AbstractThe major crop nutrients determine the nutritional content and vigor of crops. The deficiency or occurrence below minimal level of any of the nutrients are often seen as a cause of poor growth or complete crop failure. The present study was an attempt to understand the impact of Traditional Ecological Knowledge (TEK) (A1)vis-à-vis conventional chemical intensive (A2)agriculture amendment systems in altering/modifying the nutrient dynamics of the soil with respect to nitrogen (N), phosphorus (P), potassium (K) and sulphur (S), calcium (Ca), magnesium (Mg) levels in the pre, mid and post-harvest phases of crop in six cropping seasons spread across four years. The study area was a geo-ecologically unique terrain of Kachchh, Western India, a typical representative of allied arid and semi-arid tropics that are prone to various natural threats and stressors like drought, salinity and erratic rainfall pattern that affect the agri-management activities. Seasonal amendment data, clearly depicts that TEK based systems were efficient in soil organic carbon (SOC) accrual over seasons, an important trait required in challenging settings of tropical aridisols. The major primary (N, P, K) and secondary (S, Ca, Mg) nutrients were at par or higher than integrated chemical intensive systems. TEK based amendments ensured proper and timely management of nutrients in the soil. This inherent value addition offered by indigenous manure applications is an important step in climate change mitigation measures and overall agricultural sustainability.
A rapid density method for taxi passengers hot spot recognition and visualization based on DBSCAN+
Authors: Huang Zihe , Gao Shangbing , Cai Chuangxin , Zheng Hao , Pan Zhigeng , Li Wenting 
Published: May 2021

AbstractWith the development of city size and vehicle interconnection, visual analysis technology is playing a very important role in the course of city calculation and city perception. A Reasonable visual model can effectively present the feature of city. In order to solve the problem of traditional density algorithm that cluster the large scale data slowly and cannot find cluster centers to adapt taxi track data. The DBSCAN+ (density-based spatial clustering of applications with noise plus) algorithm that can split data and extract maximum density clusters under the large scale data was proposed in the paper. The passenger points should be cleaned from the original point of the passenger trajectory data firstly, and then the massive passenger points are sliced and clustered cyclically. In the clustering process, the cluster centers can be extracted based on maximum density, and finally the clustering results are visualized according to the results. The experimental results show that compared with other popular methods, the proposed method has significant advantages in clustering speed, precision and visualization for large-scale city passenger hotspots. Moreover, it provides important decisions for further urban planning and promotes the traffic efficiency.
PbCSE1 promotes lignification during stone cell development in pear (Pyrus bretschneideri) fruit
Authors: Xu Jiahui , Tao Xingyu , Xie Zhihua , Gong Xin , Qi Kaijie , Zhang Shaoling , Shiratake Katsuhiro , Tao Shutian 
Published: May 2021

AbstractPear [Pyrus bretschneidericv. Dangshan Su] fruit quality is not always satisfactory owing to the presence of stone cells, and lignin is the main component of stone cells in pear fruits. Caffeoyl shikimate esterase (CSE) is a key enzyme in the lignin biosynthesis. AlthoughCSE-like genes have been isolated from a variety of plant species, their orthologs are not characterized in pear. In this study, theCSEgene family (PbCSE) fromP. bretschneideriwas identified. According to the physiological data and quantitative RT-PCR (qRT-PCR),PbCSE1was associated with lignin deposition and stone cell formation. The overexpression ofPbCSE1increased the lignin content in pear fruits. Relative to wild-type (WT)Arabidopsis, the overexpression ofPbCSE1delayed growth, increased the lignin deposition and lignin content in stems. Simultaneously, the expression of lignin biosynthetic genes were also increased in pear fruits andArabidopsis. These results demonstrated thatPbCSE1plays an important role in cell lignification and will provide a potential molecular strategy to improve the quality of pear fruits.
Urbanization pressures alter tree rhizosphere microbiomes
Authors: Rosier Carl L. , Polson Shawn W. , D’Amico Vincent , Kan Jinjun , Trammell Tara L. E. 
Published: May 2021

AbstractThe soil microbial community (SMC) provides critical ecosystem services including organic matter decomposition, soil structural formation, and nutrient cycling. Studies suggest plants, specifically trees, act as soil keystone species controlling SMC structure via multiple mechanisms (e.g., litter chemistry, root exudates, and canopy alteration of precipitation). Tree influence on SMC is shaped by local/regional climate effects on forested environments and the connection of forests to surrounding landscapes (e.g., urbanization). Urban soils offer an ideal analog to assess the influence of environmental conditions versus plant species-specific controls on SMC. We used next generation high throughput sequencing to characterize the SMC of specific tree species (Fagus grandifolia [beech] vs Liriodendron tulipifera [yellow poplar]) across an urban–rural gradient. Results indicate SMC dissimilarity within rural forests suggests the SMC is unique to individual tree species. However, greater urbanization pressure increased SMC similarity between tree species. Relative abundance, species richness, and evenness suggest that increases in similarity within urban forests is not the result of biodiversity loss, but rather due to greater overlap of shared taxa. Evaluation of soil chemistry across the rural–urban gradient indicate pH, Ca+, and organic matter are largely responsible for driving relative abundance of specific SMC members.