bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide studies of PAL genes in sorghum and their responses to aphid infestation
Authors: Pant Shankar , Huang Yinghua 
Published: December 2022

AbstractPhenylalanine ammonia-lyase (PAL, EC 4.3.1.25) plays a crucial role in plant adaptation to biotic and abiotic stresses. However, the current knowledge about PAL proteins in sorghum is essentially lacking. Thus, in this study we aimed to analyze the PAL family genes in sorghum using a genome-wide approach and to explore the role of PAL genes in host plant resistance to aphids via SA-mediated defense signaling. Here, we report gene structural features of 8 PAL (SbPAL) genes in sorghum (Sorghum bicolor), their phylogeny, protein motifs and promoter analysis. Furthermore, we demonstrated that the SbPAL genes were induced by sugarcane aphid (SCA) infestation and SbPAL exhibited differential gene expression in susceptible and resistant genotypes. PAL activity assays further validated upregulated expression of the SbPAL genes in a resistant genotype. In addition, exogenous application of SA reduced plant damage and suppressed aphid population growth and fecundity in susceptible genotype, suggesting that those SbPAL genes act as positive regulator of the SA-mediated defense signaling pathway to combat aphid pests in sorghum. This study provides insights for further examination of the defense role of PAL in sorghum against other pests and pathogens.
Soil chemical attributes in areas under conversion from forest to pasture in southern Brazilian Amazon
Authors: de Lima Alan Ferreira Leite , Campos Milton César Costa , Martins Thalita Silva , Silva Guilherme Abadia , Brito Wildson Benedito Mendes , dos Santos Luís Antônio Coutrim , de Oliveira Ivanildo Amorim , da Cunha José Maurício 
Published: December 2022

AbstractThe south of the Brazilian Amazon is one of the largest cattle-producing regions in Brazil, however, most of the pastures are in low fertility soils. Thus, cattle breeders compensate for the low production of pastures, increasing the size of the areas, generating more deforestation and burning. These practices increase the chemical degradation process of Amazonian soils, making them increasingly infertile when improperly managed. With this, the objective of the work was to evaluate the impacts caused in the chemical attributes of soils, in areas under forest-to-pasture conversion, in the south of the Brazilian Amazon. The study was carried out in the district of União Bandeirantes, in an area of forest and two areas with pastures (brachiaria and mombaça grass). In the field, soil samples were collected at two depths (0.00–0.10 and 0.10–0.20 m), to carry out chemical analyzes. Further, uni, bi and multivariate statistical analyzes were carried out, besides geostatistical analyzes were carried out to study spatial variability and management zones. The conversion of forest to pasture increased the pH and exchangeable bases levels, reducing the availability of exchangeable aluminum and potential acidity, however, it induces losses of phosphorus and organic carbon from the soil. Among the pasture environments, the mombaça grass area presented higher fertility. Greater spatial variability of chemical attributes was observed in the environment with mombaça grass, indicating greater heterogeneity in the distribution of attributes in the area. We attribute this behavior to the higher grazing intensity and the micro-reliefs in the area that direct the flow of water and nutrients.
Comparison of 24-month treatment outcomes between as-needed treatment and switching to treat-and-extend in type 3 macular neovascularization
Authors: Kim Jae Hui , Kim Jong Woo , Kim Chul Gu 
Published: December 2022

AbstractThis study aimed to compare 24-month treatment outcomes between patients with type 3 macular neovascularization (MNV) treated using an as-needed regimen and those who switched to treat-and-extend (TAE). This retrospective study included 32 patients who were initially treated with an as-needed regimen but switched to TAE (TAE group) and 74 patients who were treated with an as-needed regimen throughout the follow-up period (as-needed group). The number of anti-vascular endothelial growth factor (VEGF) injections and degree of change in best-corrected visual acuity (BCVA) over 24 months were compared between the two groups. The incidence of fibrotic scarring, tears of the retinal pigment epithelium (RPE), and subretinal hemorrhage was also evaluated. The number of anti-VEGF injections was higher in the TAE group (mean: 11.7) than in the as-needed group (mean: 6.9;P < 0.001). The BCVA outcome (measured using the mean logarithm of the minimal angle of resolution [logMAR]) was significantly better in the TAE group (mean improvement of logMAR 0.15) than in the as-needed group (mean deterioration of logMAR 0.15). The incidence of fibrotic scarring (6.3% vs. 18.9%), RPE tears (3.1% vs. 6.8%), and subretinal hemorrhage (0% vs. 9.5%) was relatively lower in the TAE group. Treatment outcomes of the TAE group were better than those of the as-needed group, suggesting that switching to the TAE regimen would be a useful approach for patients with type 3 MNV requiring efficient treatment.
Genome-wide association study of the response of patients with diabetic macular edema to intravitreal Anti-VEGF injection
Authors: Hong Eun Hee , Yeom Hoseok , Yu Hyo Seon , Park Jong Eun , Shin Yong Un , Bang So-Young , Cho Heeyoon 
Published: December 2022

AbstractDiabetic macular edema (DME), a complication of diabetes mellitus, is a leading cause of adult-onset blindness worldwide. Recently, intravitreal anti-VEGF injection has been used as a first-line treatment. This study analyzed the association between the genetic profile of patients with DME and their response to treatment. Intravitreal anti-VEGF injections were administered monthly for three months to Korean patients diagnosed with DME, who were classified into two groups depending on whether they responded to anti-VEGF therapy or showed recurrence within six months. Peripheral blood samples were used for genetic analyses. Genome-wide association analysis results sowed that the genes DIRC3 on chromosome 2 (rs16857280, p = 1.2 × 10–6), SLCO3A1 on chromosome 15 (rs12899055, p = 2.5 × 10–6), and RAB2A on chromosome 8 (rs2272620, p = 4.6 × 10–6) were associated with treatment response to intravitreal anti-VEGF injection. SLC35F1, TMEM132D, KIAA0368, HPCAL1, IGF2BP3, SPN2S, COL23A1, and CREB5 were also related to treatment response (p < 5.0 × 10–5). Using the KEGG pathway analysis, RAB2A and CREB5 were found to be associated with AMPK signaling related to VEGF (p = 0.018). The identified genetic biomarkers can elucidate the factors affecting patient response to intravitreal anti-VEGF injection and help select appropriate therapeutic strategy.
Subtle primes of in-group and out-group affiliation change votes in a large scale field experiment
Authors: Rubenson Daniel , Dawes Christopher T. 
Published: December 2022

AbstractIdentifying the influence of social identity over how individuals evaluate and interact with others is difficult in observational settings, prompting scholars to utilize laboratory and field experiments. These often take place in highly artificial settings or, if in the field, ask subjects to make evaluations based on little information. Here we conducted a large-scale (N = 405,179) field experiment in a real-world high-information context to test the influence of social identity. We collaborated with a popular football live score app during its poll to determine the world’s best football player for the 2017–2018 season. We randomly informed users of the nationality or team affiliation of players, as opposed to just providing their names, to prime in-group status. As a result of this subtle prime, we find strong evidence of in-group favoritism based on national identity. Priming the national identity of a player increased in-group voting by 3.6% compared to receiving no information about nationality. The effect of the national identity prime is greatest among individuals reporting having a strong national identity. In contrast, we do not find evidence of in-group favoritism based on team identity. Informing individuals of players’ team affiliations had no significant effect compared to not receiving any information and the effect did not vary by strength of team identity. We also find evidence of out-group derogation. Priming that a player who used to play for a user’s favorite team but now plays for a rival team reduces voting for that player by between 6.1 and 6.4%.
Antibiotic treatment and supplemental hemin availability affect the volatile organic compounds produced by P. gingivalis in vitro
Authors: Roslund Kajsa , Uosukainen Moona , Järvik Katriin , Hartonen Kari , Lehto Markku , Pussinen Pirkko , Groop Per-Henrik , Metsälä Markus 
Published: December 2022

AbstractWe have measured the changes in the production of volatile organic compounds (VOCs) by the oral pathogen Porphyromonasgingivalis, when treated in vitro with the antibiotic amoxicillin. We have also measured the VOC production of P.gingivalis grown in the presence and absence of supplemental hemin. Planktonic bacterial cultures were treated with different amounts of amoxicillin in the lag phase of the bacterial growth. Planktonic bacteria were also cultured with and without supplemental hemin in the culture medium. Concentrations of VOCs were measured with proton-transfer-reaction time-of-flight mass spectrometry (PTR-ToF–MS) and further molecular identification was done with gas chromatography–mass spectrometry (GC–MS) using solid phase microextraction (SPME) for sampling. The cell growth of P.gingivalis in the cultures was estimated with optical density measurements at the wavelength of 600 nm (OD600). We found that the production of methanethiol, hydrogen sulfide and several short- to medium-chain fatty acids was decreased with antibiotic treatment using amoxicillin. Compounds found to increase with the antibiotic treatment were butyric acid and indole. In cultures without supplemental hemin, indole and short- to medium-chain fatty acid production was significantly reduced. Acetic acid production was found to increase when supplemental hemin was not available. Our results suggest that the metabolic effects of both antibiotic treatment and supplemental hemin availability are reflected in the VOCs produced by P.gingivalis and could be used as markers for bacterial cell growth and response to threat. Analysis of these volatiles from human samples, such as the exhaled breath, could be used in the future to rapidly monitor response to antibacterial treatment.
Short term energy consumption forecasting using neural basis expansion analysis for interpretable time series
Authors: Shaikh Abdul Khalique , Nazir Amril , Khan Imran , Shah Abdul Salam 
Published: December 2022

AbstractSmart grids and smart homes are getting people’s attention in the modern era of smart cities. The advancements of smart technologies and smart grids have created challenges related to energy efficiency and production according to the future demand of clients. Machine learning, specifically neural network-based methods, remained successful in energy consumption prediction, but still, there are gaps due to uncertainty in the data and limitations of the algorithms. Research published in the literature has used small datasets and profiles of primarily single users; therefore, models have difficulties when applied to large datasets with profiles of different customers. Thus, a smart grid environment requires a model that handles consumption data from thousands of customers. The proposed model enhances the newly introduced method of Neural Basis Expansion Analysis for interpretable Time Series (N-BEATS) with a big dataset of energy consumption of 169 customers. Further, to validate the results of the proposed model, a performance comparison has been carried out with the Long Short Term Memory (LSTM), Blocked LSTM, Gated Recurrent Units (GRU), Blocked GRU and Temporal Convolutional Network (TCN). The proposed interpretable model improves the prediction accuracy on the big dataset containing energy consumption profiles of multiple customers. Incorporating covariates into the model improved accuracy by learning past and future energy consumption patterns. Based on a large dataset, the proposed model performed better for daily, weekly, and monthly energy consumption predictions. The forecasting accuracy of the N-BEATS interpretable model for 1-day-ahead energy consumption with “day as covariates” remained better than the 1, 2, 3, and 4-week scenarios.
Interplay of membrane crosslinking and curvature induction by annexins
Authors: Mularski Anna , Sønder Stine Lauritzen , Heitmann Anne Sofie Busk , Pandey Mayank Prakash , Khandelia Himanshu , Nylandsted Jesper , Simonsen Adam Cohen 
Published: December 2022

AbstractEfficient plasma membrane repair (PMR) is required to repair damage sustained in the cellular life cycle. The annexin family of proteins, involved in PMR, are activated by Ca2+influx from extracellular media at the site of injury. Mechanistic studies of the annexins have been overwhelmingly performed using a single annexin, despite the recruitment of multiple annexins to membrane damage sites in living cells. Hence, we investigate the effect of the presence of the crosslinking annexins, annexin A1, A2 and A6 (ANXA1, ANXA2 and ANXA6) on the membrane curvature induction of annexin A4 (ANXA4) in model membrane systems. Our data support a mechanistic model of PMR where ANXA4 induced membrane curvature and ANXA6 crosslinking promotes wound closure. The model now can be expanded to include ANXA1 and ANXA2 as specialist free edge membrane crosslinkers that act in concert with ANXA4 induced curvature and ANXA6 crosslinking.
Detection of Parkinson’s disease from EEG signals using discrete wavelet transform, different entropy measures, and machine learning techniques
Authors: Aljalal Majid , Aldosari Saeed A. , Molinas Marta , AlSharabi Khalil , Alturki Fahd A. 
Published: December 2022

AbstractEarly detection of Parkinson’s disease (PD) is very important in clinical diagnosis for preventing disease development. In this study, we present efficient discrete wavelet transform (DWT)-based methods for detecting PD from health control (HC) in two cases, namely, off-and on-medication. First, the EEG signals are preprocessed to remove major artifacts before being decomposed into several EEG sub-bands (approximate and details) using DWT. The features are then extracted from the wavelet packet-derived reconstructed signals using different entropy measures, namely, log energy entropy, Shannon entropy, threshold entropy, sure entropy, and norm entropy. Several machine learning techniques are investigated to classify the resulting PD/HC features. The effects of DWT coefficients and brain regions on classification accuracy are being investigated as well. Two public datasets are used to verify the proposed methods: the SanDiego dataset (31 subjects, 93 min) and the UNM dataset (54 subjects, 54 min). The results are promising and show that four entropy measures: log energy entropy, threshold entropy, sure entropy, and modified-Shannon entropy (TShEn) lead to high classification accuracy, indicating they are good biomarkers for PD detection. With the SanDiego dataset, the classification results of off-medication PD versus HC are 99.89, 99.87, and 99.91 for accuracy, sensitivity, and specificity, respectively, using the combination of DWT + TShEn and KNN classifier. Using the same combination, the results of on-medication PD versus HC are 94.21, 93.33, and 95%. With the UNM dataset, the obtained classification accuracy is around 99.5% in both cases of off-and on-medication PD using DWT + TShEn + SVM and DWT + ThEn + KNN, respectively. The results also demonstrate the importance of all DWT coefficients and that selecting a suitable small number of EEG channels from several brain regions could improve the classification accuracy.
Optimizing nutrient inputs by balancing spring wheat yield and environmental effects in the Hetao Irrigation District of China
Authors: Chen Yuzhen , Zhao Na , Hao Yunfeng , Li Xiaohong , Fan Mingshou , Shi Xiaohua , Jia Liguo 
Published: December 2022

AbstractThe Hetao Irrigation District is the primary spring wheat production region in China. However, overuse and unscientific use of chemical fertilizer have resulted in low nutrient use efficiency and potential risks to the environment. Balanced fertilization (BF), a 29.9–36.4% N fertilizer and 40% P fertilizer, was reduced, while a 72 kg K2O ha−1 K fertilizer was supplied and designed to resolve problems encountered during the field trial from 2019 to 2021. The results showed that the grain yield did not decrease significantly in the BF treatments compared in the local farmer practice (FP) treatment. The nitrogen fertilizer partial productivity (PFPN) and agronomic nitrogen efficiency (NAEN) increased 42.95–52.88% and 44.06–49.24% with BF compared to with the FP, respectively. Moreover, the BF treatments reduced nitrate leaching in the 0–100 cm soil layer and reduced the N surplus (Nsur) to approximately 160 kg N per hectare per year, dramatically reducing the environmental risk. The yield maintenance and nitrogen use efficiency increases were attributed to the lower nitrogen concentrations in the seedlings and the higher apparent N translocation efficiency (TR) from the stems and sheaths after anthesis in the BF treatments than in the FP treatments. Considering the yield, nutrient use efficiency, and environmental and economic benefits comprehensively, the BF1 treatment was considered the optimal fertilization scheme for Hetao spring wheat production.
Transcriptome analysis of a dog model of congestive heart failure shows that collagen-related 2-oxoglutarate-dependent dioxygenases contribute to heart failure
Authors: Isono Takahiro , Matsumoto Takehiro , Suzaki Masafumi , Kubota Shigehisa , Kageyama Susumu , Kawauchi Akihiro , Wada Atuyuki 
Published: December 2022

AbstractFibrosis is an important pathological mechanism in heart failure (HF) and is associated with poor prognosis. We analyzed fibrosis in HF patients using transcriptomic data. Genes differentially expressed between normal control and congestive HF (CHF) dogs included P3H1, P3H2, P3H4, P4HA2, PLOD1 and PLOD3, which belong to the 2-oxoglutarate-dependent dioxygenases (2OGD) superfamily that stabilizes collagen during fibrosis. Quantitative polymerase chain reaction analysis demonstrated 2OGD gene expression was increased in CHF samples compared with normal left ventricle (LV) samples. 2OGD gene expression was repressed in angiotensin converting enzyme inhibitor-treated samples. These genes, activated the hydroxylation of proline or lysin residues of procollagen mediated by 2-oxoglutaric acid and O2, produce succinic acid and CO2. Metabolic analysis demonstrated the concentration of succinic acid was significantly increased in CHF samples compared with normal LV samples. Fibrosis was induced in human cardiac fibroblasts by TGF-ß1 treatment. After treatment, the gene and protein expressions of 2OGD, the concentration of succinic acid, and the oxygen consumption rate were increased compared with no treatment. This is the first study to show that collagen-related 2OGD genes contribute to HF during the induction of fibrosis and might be potential therapeutic targets for fibrosis and HF.
Ancient DNA from Protohistoric Period Cambodia indicates that South Asians admixed with local populations as early as 1st–3rd centuries CE
Authors: Changmai Piya , Pinhasi Ron , Pietrusewsky Michael , Stark Miriam T. , Ikehara-Quebral Rona Michi , Reich David , Flegontov Pavel 
Published: December 2022

AbstractIndian cultural influence is remarkable in present-day Mainland Southeast Asia (MSEA), and it may have stimulated early state formation in the region. Various present-day populations in MSEA harbor a low level of South Asian ancestry, but previous studies failed to detect such ancestry in any ancient individual from MSEA. In this study, we discovered a substantial level of South Asian admixture (ca. 40–50%) in a Protohistoric individual from the Vat Komnou cemetery at the Angkor Borei site in Cambodia. The location and direct radiocarbon dating result on the human bone (95% confidence interval is 78–234 calCE) indicate that this individual lived during the early period of Funan, one of the earliest states in MSEA, which shows that the South Asian gene flow to Cambodia started about a millennium earlier than indicated by previous published results of genetic dating relying on present-day populations. Plausible proxies for the South Asian ancestry source in this individual are present-day populations in Southern India, and the individual shares more genetic drift with present-day Cambodians than with most present-day East and Southeast Asian populations.
Green synchronous spectrofluorimetric method for the simultaneous determination of agomelatine and venlafaxine in human plasma at part per billion levels
Authors: Magdy Galal , Belal Fathalla , El-Deen Asmaa Kamal 
Published: December 2022

AbstractA novel sustainable, simple, sensitive, and green spectrofluorimetric method was developed for the concurrent estimation of venlafaxine and agomelatine in pharmaceuticals and biological fluids. The method relies on synchronous fluorescence spectroscopy, where venlafaxine and agomelatine were measured at 276 and 328 nm, respectively, using Δλ of 20 nm. The potential factors affecting the fluorescence intensity were optimized by the one-factor-at-a-time (OFAT) strategy, where synchronous fluorescence intensity was significantly enhanced using a 1% w/v sodium dodecyl sulfate micellar system. The method was fully validated and exhibited excellent linearity (r2 > 0.999 for both drugs) with very low limits of detection (LODs) in the range of 0.14–0.84 ng/mL. Consequently, the proposed approach was efficiently adopted to analyze the co-administered drugs in their pharmaceuticals and in spiked human plasma with excellent % recovery between 97.4 and 102.2%. Finally, the method's greenness was evaluated using different metric tools, including Green Analytical Procedure Index (GAPI) and Analytical GREEnness (AGREE), which proved its excellent greenness.
An intranasal recombinant NDV-BRSV Fopt vaccine is safe and reduces lesion severity in a colostrum-deprived calf model of RSV infection
Authors: Sacco Randy E. , Mena Ignacio , Palmer Mitchell V. , Durbin Russell K. , García-Sastre Adolfo , Durbin Joan E. 
Published: December 2022

AbstractHuman respiratory syncytial virus (HRSV) is a major cause of severe lower respiratory tract disease in infants and the elderly, yet no safe, effective vaccine is commercially available. Closely related bovine RSV (BRSV) causes respiratory disease in young calves, with many similar features to those seen in HRSV. We previously showed that a Newcastle disease virus (NDV)-vectored vaccine expressing the F glycoprotein of HRSV reduced viral loads in lungs of mice and cotton rats and protected from HRSV. However, clinical signs and pathogenesis of disease in laboratory animals following HRSV infection differs from that observed in human infants. Thus, we examined whether a similar vaccine would protect neonatal calves from BRSV infection. Codon-optimized rNDV vaccine (rNDV-BRSV Fopt) was constructed and administered to colostrum-deprived calves. The rNDV-BRSV Fopt vaccine was well-tolerated and there was no evidence of vaccine-enhanced disease in the upper airways or lungs of these calves compared to the non-vaccinated calves. We found two intranasal doses reduces severity of gross and microscopic lesions and decreases viral load in the lungs. Furthermore, serum neutralizing antibodies were generated in vaccinated calves. Finally, reduced lung CXC chemokine levels were observed in vaccinated calves after BRSV challenge. In summary, we have shown that rNDV-BRSV Fopt vaccine is safe in colostrum-deprived calves, and is effective in reducing lung lesions, and decreasing viral load in upper respiratory tract and lungs after challenge.