bluuebunny/crossref_metadata_2025_split huggingface dataset:
De-novo transcriptome assembly and analysis of lettuce plants grown under red, blue or white light
Authors: Kumar Vinod , Sugumaran Krishnakumar , Al-Roumi Amwaj , Shajan Anisha 
Published: December 2022

AbstractLettuce (Lactuca sativa) is grown in various parts of the world for use as a leafy vegetable. Although the use of light-emitting diode (LED) in controlled plant production systems has been successfully used to enhance nutritional quality and plant growth efficiently, the molecular basis of lettuce’s response to varying light spectra is not studied. Using next-generation sequencing, we have analyzed the transcriptomes of leaf lettuce (Lactuca sativa var. ‘New Red Fire’) grown hydroponically in a modular agricultural production system under three different types of LED lighting: red, blue, and white light. Illumina HiSeq sequencing platform was used to generate paired-end sequence reads (58 Gb raw and 54 Gb clean data) of the transcriptome of lettuce leaves exposed to varying light spectra. The de novo assembled final transcriptome contained 74,096 transcripts. Around 53% and 39% of the assembled transcripts matched to the UniProt and RefSeq RNA sequences, respectively. The validation of the differentially expressed transcripts using RT-qPCR showed complete agreement with RNA-Seq data for 27 transcripts. A comparison of the blue versus red light treatments showed the highest number of significantly differentially expressed transcripts. Among the transcripts significantly up-regulated in blue-light-exposed leaves compared to white-light-exposed leaves, ~ 26% were involved in the ‘response to stress’. Among the transcripts significantly upregulated under red light compared to white light, ~ 6% were associated with ‘nucleosome assembly’ and other processes, such as ‘oxidation–reduction process’ and ‘response to water deprivation’ were significantly enriched. Thus, the result from the current study provides deeper insights into differential gene expression patterns and associated functional aspects under varying light qualities.
Coumarin biosynthesis genes are required after foliar pathogen infection for the creation of a microbial soil-borne legacy that primes plants for SA-dependent defenses
Authors: Vismans Gilles , van Bentum Sietske , Spooren Jelle , Song Yang , Goossens Pim , Valls Josep , Snoek Basten L. , Thiombiano Benjamin , Schilder Mario , Dong Lemeng , Bouwmeester Harro J. , Pétriacq Pierre , Pieterse Corné M. J. , Bakker Peter A. H. M. , Berendsen Roeland L. 
Published: December 2022

AbstractPlants deposit photosynthetically-fixed carbon in the rhizosphere, the thin soil layer directly around the root, thereby creating a hospitable environment for microbes. To manage the inhabitants of this nutrient-rich environment, plant roots exude and dynamically adjust microbe-attracting and -repelling compounds to stimulate specific members of the microbiome. Previously, we demonstrated that foliar infection of Arabidopsis thaliana by the biotrophic downy mildew pathogen Hyaloperonospora arabidopsidis (Hpa) leads to a disease-induced modification of the rhizosphere microbiome. Soil conditioned with Hpa-infected plants provided enhanced protection against foliar downy mildew infection in a subsequent population of plants, a phenomenon dubbed the soil-borne legacy (SBL). Here, we show that for the creation of the SBL, plant-produced coumarins play a prominent role as coumarin-deficient myb72 and f6’h1 mutants were defective in creating a Hpa-induced SBL. Root exudation profiles changed significantly in Col-0 upon foliar Hpa infection, and this was accompanied by a compositional shift in the root microbiome that was significantly different from microbial shifts occurring on roots of Hpa-infected coumarin-deficient mutants. Our data further show that the Hpa-induced SBL primes Col-0 plants growing in SBL-conditioned soil for salicylic acid (SA)-dependent defenses. The SA-signaling mutants sid2 and npr1 were unresponsive to the Hpa-induced SBL, suggesting that the protective effect of the Hpa-induced shift in the root microbiome results from an induced systemic resistance that requires SA-signaling in the plant.
Current distribution monitoring enables quench and damage detection in superconducting fusion magnets
Authors: Teyber Reed , Weiss Jeremy , Marchevsky Maxim , Prestemon Soren , van der Laan Danko 
Published: December 2022

AbstractFusion magnets made from high temperature superconducting ReBCO CORC® cables are typically protected with quench detection systems that use voltage or temperature measurements to trigger current extraction processes. Although small coils with low inductances have been demonstrated, magnet protection remains a challenge and magnets are typically operated with little knowledge of the intrinsic performance parameters. We propose a protection framework based on current distribution monitoring in fusion cables with limited inter-cable current sharing. By employing inverse Biot-Savart techniques to distributed Hall probe arrays around CORC® Cable-In-Conduit-Conductor (CICC) terminations, individual cable currents are recreated and used to extract the parameters of a predictive model. These parameters are shown to be of value for detecting conductor damage and defining safe magnet operating limits. The trained model is then used to predict cable current distributions in real-time, and departures between predictions and inverse Biot-Savart recreated current distributions are used to generate quench triggers. The methodology shows promise for quality control, operational planning and real-time quench detection in bundled CORC® cables for compact fusion reactors.
Investigation of anticoagulant rodenticide resistance induced by Vkorc1 mutations in rodents in Lebanon
Authors: Rached Antoine , Abi Rizk Georges , Mahamat Ali Barka , Khoury Graziella El , El Hage Jeanne , Harran Elena , Lattard Virginie 
Published: December 2022

AbstractAnticoagulant rodenticides (AR) remain the most effective chemical substances used to control rodents in order to limit their agricultural and public health damage in both rural and urban environments. The emergence of genetically based resistance to AR worldwide has threatened effective rodent control. This study gives a first overview of the distribution and frequency of single nucleotide polymorphism in the vitamin K epoxide reductase subcomponent 1 (Vkorc1) gene in rodents in Lebanon. In the Mus genus, we detected two missense mutations Leu128Ser and Tyr139Cys, that confer resistance to anticoagulant rodenticides in house mice and a new missense mutation Ala72Val in the Mus macedonicus species, not previously described. In the Rattus genus, we found one missense mutation Leu90Ile in the roof rat and one missense mutation Ser149Ile in the Norway rat. This is the first study to demonstrate potential resistance to AR in Lebanese rodents and therefore it provides data to pest control practitioners to choose the most suitable AR to control rodents in order to keep their efficacy.
The projected burden of non-communicable diseases attributable to overweight in Brazil from 2021 to 2030
Authors: Nilson Eduardo A. F. , Gianicchi Beatriz , Ferrari Gerson , Rezende Leandro F. M. 
Published: December 2022

AbstractAlthough studies have quantified the current burden of diseases attributable to overweight and obesity in Brazil, none have estimated its burden in the future. The study aimed to estimate the potential impact of different scenarios of changes in the prevalence of overweight on non-communicable diseases (NCD) in the Brazilian adult population until 2030. We developed a multistate life table model including 11 body mass index (BMI) related diseases to estimate attributable NCDs cases and deaths under the following scenarios of changes in overweight over a 10-year simulation: (1) the continuity of the current trajectory of BMI increases, (2) reducing the rate of increase by half, (3) stopping future BMI increases, and (4) the reduction of the prevalence of overweight by 6.7%. In Brazil, if the current trends of BMI increase are maintained from 2021 to 2030, approximately 5.26 million incident cases and 808.6 thousand deaths from NCDs may occur due to overweight. If the annual increase in overweight was reduced by half until 2030, 1.1% of new NCD cases and 0.2% of deaths could be prevented (respectively, 29,600 cases and 1900 deaths). Alternatively, if the current prevalence of overweight is maintained, as set as a national goal in Brazil until 2030, the incident NCD cases and the deaths could be reduced by respectively 3.3% (92,900) and 1.5% (12,100) compared to continuation of current trends. If the prevalence of overweight is reduced by 6.7% until 2030, 6.5% (182,200) of NCD cases and 4.2% (33,900) of deaths could be prevented. The epidemiologic burden of overweight in Brazil tends to increase if bold policy interventions are not adopted in Brazil.
RF energy harvesting schemes for intelligent reflecting surface-aided cognitive radio sensor networks
Authors: Wang Jihong , Yu Hongquan 
Published: December 2022

AbstractEnergy harvesting (EH) is a potential solution to enhance the node sustainability and prolong the network lifetime of cognitive radio sensor networks (CRSNs). However, CRSNs nodes can only harvest energy from the direct link with energy sources, and severe path loss results in low energy utilization ratio. To solve the above problem, intelligent reflecting surface (IRS) is introduced, and a shared reflection coefficient matrix-based EH scheme is proposed for IRS-aided CRSNs in this paper. An optimization problem with the objective of maximizing the total amount of energy harvested by all CRSNs nodes is formulated, and by optimally adjusting the IRS reflection coefficient, CRSNs nodes can harvest energy from both the direct link and the cascaded reflection link via IRS, which increases the amount of harvested energy. In addition, a subsurface partition-based EH scheme is proposed to reduce the additional computational complexity brought by increasing IRS elements or CRSNs nodes. Simulation results show that the proposed schemes can both dramatically improve energy utilization ratio, and the subsurface partition-based EH scheme will bring in less than 1 percent performance loss when compared with the other scheme, i.e., reasonable subsurface partition can achieve a balance between harvested energy and computational complexity.
A sputum bioassay for airway eosinophilia using an eosinophil peroxidase aptamer
Authors: Ali M. Monsur , Wolfe Michael G. , Mukherjee Manali , Radford Katherine , Patel Zil , White Dawn , Milojevic Julijana , Capretta Alfredo , Nair Parameswaran , Brennan John D. 
Published: December 2022

AbstractEosinophils are granulocytes that play a significant role in the pathogenesis of asthma and other airway diseases. Directing patient treatment based on the level of eosinophilia has been shown to be extremely effective in reducing exacerbations and therefore has tremendous potential as a routine clinical test. Herein, we describe the in vitro selection and optimization of DNA aptamers that bind to eosinophil peroxidase (EPX), a protein biomarker unique to eosinophils. Fifteen rounds of magnetic bead aptamer selection were performed prior to high throughput DNA sequencing. The top 10 aptamer candidates were assessed for EPX binding using a mobility shift assay. This process identified a lead aptamer candidate termed EAP1-05 with low nanomolar affinity and high specificity for EPX over other common sputum proteins. This aptamer sequence was further optimized through truncation and used to develop an easy-to-use colourimetric pull-down assay that can detect EPX over a concentration range from 1 – 100 nM in processed sputum. Forty-six clinical samples were processed using a new sputum dispersal method, appropriate for a rapid assessment assay, that avoids centrifugation and lengthy processing times. The assay showed 89% sensitivity and 96% specificity to detect eosinophilia (compared to gold standard sputum cytometry), with results being produced in under an hour. This assay could allow for an easy assessment of eosinophil activity in the airway to guide anti-inflammatory therapy for several airway diseases.
Supplementation of Alpha-lipoic acid-loaded nanoliposomes in semen extender improves freezability of buffalo spermatozoa
Authors: Hassan Mahmoud A. E. , Khalil Wael A. , Abdelnour Sameh A. , Aman Reham Mokhtar 
Published: December 2022

AbstractThis research was designed to explore the protective effect of alpha-lipoic acid–loaded nanoliposomes (ALAN) during cryopreservation of buffalo sperm. Buffalo semen was cryopreserved in a tris-citrate egg yolk extender without any supplement (ALAN0, control group) or with ALAN at levels of 25, 50, 75 or 150 µg (ALAN25, ALAN50, ALAN75 and ALAN150, respectively). The ALAN had a size of 171.80 nm and a negative zeta potential (− 43.40 mV). The progressive motility, vitality and membrane integrity significantly improved in all ALAN groups (except ALAN25 for membrane integrity). ALAN150 group exhibited the best values of progressive sperm motility, vitality and membrane integrity after thawing at 37 °C for 30 s or incubated for 2 h at 37 °C and 5% CO2 compared with those in other groups. Both ALAN75 and ALAN150 groups significantly improved the TAC, GR and catalase, while lipid peroxidation and early apoptotic spermatozoa significantly decreased in ALAN150 group followed by ALAN75 group. Collectively, the adding ALAN to buffalo semen freezing extender plays a substantial shielding function against cryodamage by preserving the sperm functional parameters.
Low genetic diversity and predation threaten a rediscovered marine sponge
Authors: Quek Z. B. Randolph , Ng Juat Ying , Jain Sudhanshi S. , Long J. X. Sean , Lim Swee Cheng , Tun Karenne , Huang Danwei 
Published: December 2022

AbstractDiscovered in 1819 in the tropical waters off Singapore, the magnificent Neptune’s cup sponge Cliona patera (Hardwicke, 1820) was harvested for museums and collectors until it was presumed extinct worldwide for over a century since 1907. Recently in 2011, seven living individuals were rediscovered in Singapore with six relocated to a marine protected area in an effort to better monitor and protect the population, as well as to enhance external fertilisation success. To determine genetic diversity within the population, we sequenced the complete mitochondrial genomes and nuclear ribosomal DNA of these six individuals and found extremely limited variability in their genes. The low genetic diversity of this rediscovered population is confirmed by comparisons with close relatives of C. patera and could compromise the population’s ability to recover from environmental and anthropogenic pressures associated with the highly urbanised coastlines of Singapore. This lack of resilience is compounded by severe predation which has been shrinking sponge sizes by up to 5.6% every month. Recovery of this highly endangered population may require ex situ approaches and crossbreeding with other populations, which are also rare.
The Qixiangzhan eruption, Changbaishan-Tianchi volcano, China/DPRK: new age constraints and their implications
Authors: Pan Bo , de Silva Shanaka L. , Danišík Martin , Schmitt Axel K. , Miggins Daniel P. 
Published: December 2022

AbstractZircon double dating (ZDD) of comendite lava reveals an eruption age of 7.0 ± 0.9 ka for the Qixiangzhan eruption (QXZ), Changbaishan-Tianchi volcano, China/DPRK. This age is supported by new40Ar/39Ar sanidine experiments and a previous age control from charcoal at the base of the QXZ. The revised age supports correlations with distal ash in Eastern China and Central Japan and establishes a significant (estimated at Volcanic Explosivity Index 5+) eruption that may provide a useful Holocene stratigraphic marker in East Asia. The new age indicates that the QXZ lava does not record a ca. 17 ka Hilina Pali/Tianchi geomagnetic field excursion but rather a heretofore unrecognized younger Holocene excursion at ca. 7–8 ka. Comparison between U–Th zircon crystallization and ZDD as well as40Ar/39Ar sanidine ages indicates a protracted period of accumulation of the QXZ magma that extends from ca. 18 ka to the eruption age. This connotes an eruption that mixed remobilized early formed crystals (antecrysts) from prior stages of magma accumulation with crystals formed near the time of eruption. Based on these results, a recurrence rate of ca. 7–8 ka for the Changbaishan-Tianchi magma system is found over the last two major eruption cycles.
Stacked printed MoS2 and Ag electrodes using electrohydrodynamic jet printing for thin-film transistors
Authors: Can Thi Thu Thuy , Choi Woon-Seop 
Published: December 2022

AbstractTransition metal dichalcogenide-based thin-film transistors (TFTs) have drawn intense research attention, but they suffer from high cost of materials and complex methods. Directly printed transistors have been in the limelight due to low cost and an environmentally friendly technique. An electrohydrodynamic (EHD) jet printing technique was employed to pattern both MoS2 active layer and Ag source and drain (S/D) electrodes. Printed MoS2 lines were patterned on a silicon wafer using a precursor solution and simple annealing, and the patterns were transferred on other SiO2 substrates for TFT fabrication. On top of the patterned MoS2, Ag paste was also patterned for S/D electrodes using EHD jet printing. The printed TFTs had a high on–off current ratio exceeding 105, low subthreshold slope, and better hysteresis behavior after transferring MoS2 patterns. This result could be important for practical TFT applications and could be extended to other 2D materials.
Correlation of TROP-2 expression with clinical–pathological characteristics and outcome in triple-negative breast cancer
Authors: Izci Hava , Punie Kevin , Waumans Lise , Laenen Annouschka , Wildiers Hans , Verdoodt Freija , Desmedt Christine , Ardui Jan , Smeets Ann , Han Sileny N. , Nevelsteen Ines , Neven Patrick , Floris Giuseppe 
Published: December 2022

AbstractLimited data exist regarding the associations between TROP-2 protein expression, clinical–pathological characteristics, and outcome in triple-negative breast cancer (TNBC). TROP-2 expression was determined for patients diagnosed with TNBC between 2000 and 2017 by immunohistochemistry (IHC) (ab227689, Abcam) on whole slide tumor sections, and assessed as continuous and categorical variables (H-score high, 201–300, medium 100–200 and low < 100). We investigated the prognostic value of TROP-2 expression for relapse and survival, associations between TROP-2 expression and baseline patient and tumor characteristics, stromal tumor-infiltrating lymphocytes (sTILs), androgen receptor (AR), standardized mitotic index (SMI) and pathological complete response (pCR, in patients with neoadjuvant chemotherapy) were assessed. We included 685 patients with a median age at diagnosis of 54 years (range 22–90 years). After median follow-up of 9.6 years, 17.5% of patients experienced distant relapse. TROP-2 expression was high, medium and low in 97 (16.5%), 149 (25.3%) and 343 (58.2%) of patients, respectively. The presence of LVI, associated DCIS, nodal involvement, apocrine histology and AR expression were correlated with higher TROP-2 levels. There were no associations between TROP-2 expression and sTILs, time-to-event outcomes, or pCR rate after neoadjuvant chemotherapy. TROP-2 expression is not associated with sTILs level and has no prognostic value in our cohort of stage 1–3 TNBC. However, an association with histotype and AR expression was found, suggesting a histotype specific TROP-2 expression pattern with highest expression in apocrine subtype, warranting further research.
A case study on the bearing characteristics of a bottom uplift pile in a layered foundation
Authors: He Laping , Chen Xuwei , Wang Zhengzhen , Han Yun , Su Tiantao , Dai Guoliang , Zhang Enxiang , Long Zhao 
Published: December 2022

AbstractThe bottom uplift pile, which has been applied in practical projects, has the following advantages: the pile body is not easy to crack, good bearing characteristics, and small displacement of the pile top. Based on the bearing capacity test of foundation piles in the third stage expansion project of Lanzhou Zhongchuan International Airport, the upper part pile of the self-balancing test method was used to simulate the bottom uplift pile, and the anchor piles in the anchor pile method were regarded as normal uplift piles. The bearing characteristics of the bottom uplift pile in a layered foundation were studied by comparing these two kinds of piles. The results show that under the same displacement of the pile top, the ultimate uplift bearing capacity of the bottom uplift pile can be more than twice that of the normal uplift pile because of the fully exerted frictional resistance of the soil at the bottom of the pile, the Poisson effect of the pile body and the avoidance of the influence of pile body deformation on the pile top displacement. The maximum axial force of the bottom uplift pile appears at the bottom of the pile and gradually decreases from the bottom to the top, which is opposite to that of the normal uplift pile. The properties and thickness of the soil layers around the pile have a great influence on the distribution curves of the frictional resistance along the pile length of the two kinds of uplift piles. With changing soil layer conditions, the distribution curve may be a "parabola", a "straight line" or a "double line". The soil property plays a decisive role in the frictional resistance, which may cause softening. The influence of the pile diameter on the ultimate uplift bearing capacity is greater than that of the pile length, while the elastic modulus of the pile has little influence.
The role of valence, dominance, and pitch in perceptions of artificial intelligence (AI) conversational agents’ voices
Authors: Shiramizu Victor Kenji M. , Lee Anthony J. , Altenburg Daria , Feinberg David R. , Jones Benedict C. 
Published: December 2022

AbstractThere is growing concern that artificial intelligence conversational agents (e.g., Siri, Alexa) reinforce voice-based social stereotypes. Because little is known about social perceptions of conversational agents’ voices, we investigated (1) the dimensions that underpin perceptions of these synthetic voices and (2) the role that acoustic parameters play in these perceptions. Study 1 (N = 504) found that perceptions of synthetic voices are underpinned by Valence and Dominance components similar to those previously reported for natural human stimuli and that the Dominance component was strongly and negatively related to voice pitch. Study 2 (N = 160) found that experimentally manipulating pitch in synthetic voices directly influenced dominance-related, but not valence-related, perceptions. Collectively, these results suggest that greater consideration of the role that voice pitch plays in dominance-related perceptions when designing conversational agents may be an effective method for controlling stereotypic perceptions of their voices and the downstream consequences of those perceptions.